Citrus Sinensis ID: 031410

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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
Protein Sequence
MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEEEEcccccccccccccEEEEEEccccccccccccEEEEEccccccccEEEEEccccccEEEEcccccccccccEEEccccEEEEccccccccccccccccccccEEEEEEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEcccccccccccccccEEEEEEEEEEccccccccEEEEEccccccccEEEEEEEccccEEEEEccccccccccEEEccccEEEEcccccccccccccccccHHcEEEEEEEEEEEcHHHccccc
Coil and Loop (DISEMBL)
MRRWGLLAKEALTQTLTFARFFCLFHVtnhylwsptlvfgpsmlptlnltgDVILAEYVshrvgrlgpgdivfvrspvdpnkivtkrivgvegdrvtyfkprngdschtvvvpkghvwiqgdnlyasrdsrqfgpvpygliegkaffrqvwppnsfgslg
Flexible Loop (DISEMBL)
MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVgrlgpgdivfvrspvdpnkivtkrivgvegdrvtyfkprngdschtvvvPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKaffrqvwppnsfgslg
Low Complexity Region (SEG)
MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG
Disordered region (IsUnstruct)
***WGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWP********
Disordered Region (DISOPRED)
********KEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG
Disordered Region (DISEMBL)
MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG
Disordered Region (DISPRO)
MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG
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	160	2.2.26 [Sep-21-2011]
Q96LU5	166	Mitochondrial inner membr	yes	no	0.856	0.825	0.414	3e-26
Q9CQU8	166	Mitochondrial inner membr	yes	no	0.943	0.909	0.393	2e-25
Q28I39	167	Mitochondrial inner membr	yes	no	0.856	0.820	0.428	1e-24
O74800	157	Mitochondrial inner membr	yes	no	0.831	0.847	0.384	1e-20
Q6AZD4	183	Mitochondrial inner membr	no	no	0.712	0.622	0.414	4e-15
P28627	190	Mitochondrial inner membr	yes	no	0.812	0.684	0.356	5e-15
P46972	177	Mitochondrial inner membr	no	no	0.893	0.807	0.316	1e-14
Q2KI92	177	Mitochondrial inner membr	yes	no	0.731	0.661	0.380	4e-14
Q96T52	175	Mitochondrial inner membr	no	no	0.731	0.668	0.380	8e-14
Q8BPT6	175	Mitochondrial inner membr	no	no	0.731	0.668	0.380	8e-14

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

 Score =  117 bits (293), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 58/140 (41%), Positives = 85/140 (60%), Gaps = 3/140 (2%)

Query: 20  RFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVD 79
           ++ C+ H    Y+    +  GPSM PT+    D++ AE +S     +  GDIV  +SP D
Sbjct: 18  QYGCIAHCAFEYVGGVVMCSGPSMEPTIQ-NSDIVFAENLSRHFYGIQRGDIVIAKSPSD 76

Query: 80  PNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYG 139
           P   + KR++G+EGD++    P +    H+ V P GHVW++GDNL  S DSR +GP+PYG
Sbjct: 77  PKSNICKRVIGLEGDKILTTSPSDFFKSHSYV-PMGHVWLEGDNLQNSTDSRCYGPIPYG 135

Query: 140 LIEGKAFFRQVWPPNSFGSL 159
           LI G+ FF+ +WP + FG L
Sbjct: 136 LIRGRIFFK-IWPLSDFGFL 154

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: 3EC: .EC: 4EC: .EC: 2EC: 1EC: .EC: -

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

 Score =  114 bits (286), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 89/155 (57%), Gaps = 4/155 (2%)

Query: 5   GLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVG 64
           G+L K       T  ++ C+ H    Y+    +  GPSM PT+    D++ AE +S    
Sbjct: 4   GVLGKAFRLAGYTI-QYGCIAHCAFEYVGGVVMCSGPSMEPTIQ-NSDIVFAENLSRHFY 61

Query: 65  RLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNL 124
            +  GDIV  +SP DP   + KR++G+EGD++    P +     + V P GHVW++GDNL
Sbjct: 62  GIQRGDIVIAKSPSDPKSNICKRVIGLEGDKILSTSPSDVFKSRSYV-PTGHVWLEGDNL 120

Query: 125 YASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
             S DSR +GP+PYGLI G+ FF+ +WP + FG L
Sbjct: 121 QNSTDSRYYGPIPYGLIRGRIFFK-IWPFSDFGFL 154

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|Q28I39|IMP1L_XENTR Mitochondrial inner membrane protease subunit 1 OS=Xenopus tropicalis GN=immp1l PE=2 SV=1

 Score =  111 bits (278), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 60/140 (42%), Positives = 82/140 (58%), Gaps = 3/140 (2%)

Query: 20  RFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVD 79
           ++ C+ H    Y+    +  GPSM PT+    DV+L + +S     +  GDI+  +SP  
Sbjct: 18  QYGCIAHCAFEYIGEVVICSGPSMEPTIR-NYDVLLCDNLSRHFFSIHKGDIIVAKSPDK 76

Query: 80  PNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYG 139
           P+  + KR++G+EGD+V    P      HT V PKGHVW++GDNL  S DSR +GPVPY 
Sbjct: 77  PSVNICKRVIGLEGDKVCMSSPSALLKRHTYV-PKGHVWLEGDNLDNSTDSRSYGPVPYA 135

Query: 140 LIEGKAFFRQVWPPNSFGSL 159
           LI G+   R VWP  SFG L
Sbjct: 136 LIRGRICLR-VWPLESFGPL 154

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 tropicalis (taxid: 8364)

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 = 99.0 bits (245), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 53/138 (38%), Positives = 76/138 (55%), Gaps = 5/138 (3%)

Query: 16  LTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGR-LGPGDIVFV 74
           +   +     H  + YL+   +  GPSM+PTLN  G+ +L + +  R  R    GD+V  
Sbjct: 9   IAVVQIAAFVHQIHEYLFQVQMTSGPSMMPTLNSGGEFVLLDKLHGRFARSCSVGDVVVS 68

Query: 75  RSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFG 134
             P D  + V KRI+G+ GD + Y  P + +    + +P GHVW+ GDN+  S DSR +G
Sbjct: 69  AKPSDSKQHVCKRIIGMPGDTI-YVDPTSSNK--KITIPLGHVWLAGDNIAHSLDSRNYG 125

Query: 135 PVPYGLIEGKAFFRQVWP 152
           PVP GLI+ K   R VWP
Sbjct: 126 PVPMGLIKAKVIAR-VWP 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: -

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

 Score = 80.5 bits (197), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 51/123 (41%), Positives = 70/123 (56%), Gaps = 9/123 (7%)

Query: 38  VFGPSMLPTLNLTG----DVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEG 93
           V G SM P+LN  G    DV+L    S R   +  GDIV V SP +P + + KR++G+EG
Sbjct: 38  VEGASMQPSLNPDGESSPDVVLLNRWSVRNYHVQRGDIVSVLSPKNPQQKIIKRVIGIEG 97

Query: 94  DRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPP 153
           D +     +N      V VP GH+WI+GD+   S DS  FGPV  GL+ G+A    +WPP
Sbjct: 98  DFIKTLGYKN----RYVRVPDGHLWIEGDHHGHSFDSNAFGPVSLGLVHGRA-SHIIWPP 152

Query: 154 NSF 156
           + +
Sbjct: 153 SRW 155

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: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|P28627|IMP1_YEAST Mitochondrial inner membrane protease subunit 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=IMP1 PE=1 SV=3

 Score = 80.1 bits (196), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 52/146 (35%), Positives = 75/146 (51%), Gaps = 16/146 (10%)

Query: 13  TQTLTFA-RFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVI--LAEYVSHRVGRLGPG 69
           ++T ++A R  C  H+ + Y +  T   G SMLPTL+ T D +  L  + + R  ++G  
Sbjct: 10  SKTFSYAIRSLCFLHIIHMYAYEFTETRGESMLPTLSATNDYVHVLKNFQNGRGIKMG-- 67

Query: 70  DIVFVRSPVDPNKIVTKRIVGVEGDRV----TYFKPRNGDSC-------HTVVVPKGHVW 118
           D +    P DPN  + KR+ G+ GD V    +      GD           + VP+GHVW
Sbjct: 68  DCIVALKPTDPNHRICKRVTGMPGDLVLVDPSTIVNYVGDVLVDEERFGTYIKVPEGHVW 127

Query: 119 IQGDNLYASRDSRQFGPVPYGLIEGK 144
           + GDNL  S DSR +  +P GLI GK
Sbjct: 128 VTGDNLSHSLDSRTYNALPMGLIMGK 153

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. IMP1 substrates include nuclear encoded CYB2, mitochondrially encoded COX2, NADH-cytochrome b5 reductase and GUT2.

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

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 = 79.0 bits (193), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 80/161 (49%), Gaps = 18/161 (11%)

Query: 8   AKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYV------SH 61
           +K  L  TL    +  +    N+ +     V G SM PTLN   + +  ++V        
Sbjct: 7   SKRFLRNTLIAISWVPVLLTINNNVVHIAQVKGTSMQPTLNPQTETLATDWVLLWKFGVK 66

Query: 62  RVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVT----YFKPRNGDSCHTVVVPKGHV 117
               L   DI+  ++P +P K+  KR+ G+  D +     Y KP+       V +P+GH+
Sbjct: 67  NPSNLSRDDIILFKAPTNPRKVYCKRVKGLPFDTIDTKFPYPKPQ-------VNLPRGHI 119

Query: 118 WIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGS 158
           W++GDN + S DS  FGP+  GL+ GKA    VWPP+ +G+
Sbjct: 120 WVEGDNYFHSIDSNTFGPISSGLVIGKA-ITIVWPPSRWGT 159

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

 Score = 77.0 bits (188), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 48/126 (38%), Positives = 68/126 (53%), Gaps = 9/126 (7%)

Query: 38  VFGPSMLPTLNLTG----DVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEG 93
           V G SM P+LN  G    DV+L  +   R   +  GDIV + SP +P + + KR++ +EG
Sbjct: 39  VEGASMQPSLNPGGSQSSDVVLLNHWKVRNFEVQRGDIVSLVSPKNPEQKIIKRVIALEG 98

Query: 94  DRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPP 153
           D V     +N      V VP+GH+W++GD+   S DS  FGPV  GL+   A    +WPP
Sbjct: 99  DIVKTMGHKN----RYVKVPRGHIWVEGDHHGHSFDSNSFGPVSLGLLHAHA-THILWPP 153

Query: 154 NSFGSL 159
             +  L
Sbjct: 154 KRWQKL 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. 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 = 76.3 bits (186), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 48/126 (38%), Positives = 68/126 (53%), Gaps = 9/126 (7%)

Query: 38  VFGPSMLPTLNLTG----DVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEG 93
           V G SM P+LN  G    DV+L  +   R   +  GDIV + SP +P + + KR++ +EG
Sbjct: 39  VEGASMQPSLNPGGSQSSDVVLLNHWKVRNFEVHRGDIVSLVSPKNPEQKIIKRVIALEG 98

Query: 94  DRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPP 153
           D V     +N      V VP+GH+W++GD+   S DS  FGPV  GL+   A    +WPP
Sbjct: 99  DIVRTIGHKN----RYVKVPRGHIWVEGDHHGHSFDSNSFGPVSLGLLHAHA-THILWPP 153

Query: 154 NSFGSL 159
             +  L
Sbjct: 154 ERWQKL 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. 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|Q8BPT6|IMP2L_MOUSE Mitochondrial inner membrane protease subunit 2 OS=Mus musculus GN=Immp2l PE=2 SV=1

 Score = 76.3 bits (186), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 48/126 (38%), Positives = 68/126 (53%), Gaps = 9/126 (7%)

Query: 38  VFGPSMLPTLNLTG----DVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEG 93
           V G SM P+LN  G    DV+L  +   R   +  GDIV + SP +P + + KR++ +EG
Sbjct: 39  VEGSSMQPSLNPGGSQSSDVVLLNHWKVRNFEVQRGDIVSLVSPKNPEQKIIKRVIALEG 98

Query: 94  DRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPP 153
           D V     +N      V VP+GH+W++GD+   S DS  FGPV  GL+   A    +WPP
Sbjct: 99  DIVRTIGHKN----RLVKVPRGHMWVEGDHHGHSFDSNSFGPVSLGLLHAHA-THILWPP 153

Query: 154 NSFGSL 159
             +  L
Sbjct: 154 ERWQRL 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. Known to process the nuclear encoded protein DIABLO.

Mus musculus (taxid: 10090)

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	160
449438943	161	PREDICTED: mitochondrial inner membrane	0.987	0.981	0.687	8e-59
224061365	164	predicted protein [Populus trichocarpa]	0.993	0.969	0.652	2e-56
224061361	161	predicted protein [Populus trichocarpa]	0.993	0.987	0.652	2e-56
225461838	167	PREDICTED: mitochondrial inner membrane	0.987	0.946	0.625	2e-54
388519663	166	unknown [Medicago truncatula]	0.987	0.951	0.616	1e-52
30695525	168	peptidase-S24/S26 domain-containing prot	0.987	0.940	0.643	4e-52
297847748	168	signal peptidase I family protein [Arabi	0.987	0.940	0.637	4e-52
255557373	176	mitochondrial inner membrane protease su	0.931	0.846	0.613	5e-50
255562592	158	mitochondrial inner membrane protease su	0.937	0.949	0.582	3e-49
225463444	169	PREDICTED: mitochondrial inner membrane	0.987	0.934	0.587	1e-48

>gi|449438943|ref|XP_004137247.1| PREDICTED: mitochondrial inner membrane protease subunit 1-like [Cucumis sativus] gi|449483132|ref|XP_004156501.1| PREDICTED: mitochondrial inner membrane protease subunit 1-like [Cucumis sativus]

 Score =  231 bits (589), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 110/160 (68%), Positives = 133/160 (83%), Gaps = 2/160 (1%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           M +W  + KEA+ +T+  A+F CL HVTN+Y+ SPTLV+GPSMLPTLNLTGDV+LAE+VS
Sbjct: 1   MGQWRSVVKEAIDRTVIIAKFLCLLHVTNNYICSPTLVYGPSMLPTLNLTGDVLLAEHVS 60

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYF-KPRNGDSCHTVVVPKGHVWI 119
           HRVGR+GPGD+V VRSP +P K++TKRIVGVEGD+V ++  P N +   + VVPKGHVWI
Sbjct: 61  HRVGRVGPGDVVLVRSPRNPRKMLTKRIVGVEGDKVNFYPDPANSNQYQSAVVPKGHVWI 120

Query: 120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
           QGDN+YASRDSR FGPVPYGLIEGKAF R VWPP+ FG L
Sbjct: 121 QGDNVYASRDSRHFGPVPYGLIEGKAFLR-VWPPDCFGRL 159

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224061365|ref|XP_002300443.1| predicted protein [Populus trichocarpa] gi|222847701|gb|EEE85248.1| predicted protein [Populus trichocarpa]

 Score =  223 bits (568), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 105/161 (65%), Positives = 129/161 (80%), Gaps = 2/161 (1%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           M  W  +AKEA +QT   A+F    H+TN+YL SPTLV+GPSMLPTLNLTGDV+L E+VS
Sbjct: 4   MNAWKSIAKEAFSQTCLVAKFLGFLHLTNNYLISPTLVYGPSMLPTLNLTGDVLLVEHVS 63

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYF-KPRNGDSCHTVVVPKGHVWI 119
           HR  ++GPGD+V VRSP+DP K+VTKRIVG+EGD++ +   P   D C TV+VPKGH+WI
Sbjct: 64  HRFQKVGPGDVVLVRSPLDPTKMVTKRIVGMEGDQINFLPDPSITDICRTVMVPKGHIWI 123

Query: 120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG 160
           QGDN+YAS DSR +GPVPYGL++GK FFR VWPP+SFGS G
Sbjct: 124 QGDNMYASCDSRHYGPVPYGLVQGKLFFR-VWPPSSFGSFG 163

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224061361|ref|XP_002300441.1| predicted protein [Populus trichocarpa] gi|222847699|gb|EEE85246.1| predicted protein [Populus trichocarpa]

 Score =  223 bits (567), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 105/161 (65%), Positives = 129/161 (80%), Gaps = 2/161 (1%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           M  W  +AKEA +QT   A+F    H+TN+YL SPTLV+GPSMLPTLNLTGDV+L E+VS
Sbjct: 1   MNAWKSIAKEAFSQTCLVAKFLGFLHLTNNYLISPTLVYGPSMLPTLNLTGDVLLVEHVS 60

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYF-KPRNGDSCHTVVVPKGHVWI 119
           HR  ++GPGD+V VRSP+DP K+VTKRIVG+EGD++ +   P   D C TV+VPKGH+WI
Sbjct: 61  HRFQKVGPGDVVLVRSPLDPTKMVTKRIVGMEGDQINFLPDPSITDICRTVMVPKGHIWI 120

Query: 120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG 160
           QGDN+YAS DSR +GPVPYGL++GK FFR VWPP+SFGS G
Sbjct: 121 QGDNMYASCDSRHYGPVPYGLVQGKLFFR-VWPPSSFGSFG 160

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461838|ref|XP_002283744.1| PREDICTED: mitochondrial inner membrane protease subunit 1 [Vitis vinifera] gi|302142795|emb|CBI20090.3| unnamed protein product [Vitis vinifera]

 Score =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 100/160 (62%), Positives = 127/160 (79%), Gaps = 2/160 (1%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           + +W  LA+EA  +T   A+F C+ HVTN Y+ +PTLV+GPSMLPT NLTGDV+L E ++
Sbjct: 7   LSQWRTLAREAAERTAILAKFLCILHVTNTYICTPTLVYGPSMLPTFNLTGDVLLVENLT 66

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYF-KPRNGDSCHTVVVPKGHVWI 119
            R+G++ PGD+V VRSP +P K V+KRI+G+EGDRVT+   P+N + C +VV+PKGHVWI
Sbjct: 67  VRMGKVRPGDVVLVRSPENPRKTVSKRILGMEGDRVTFMIDPKNSNRCQSVVIPKGHVWI 126

Query: 120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
           QGDN+YAS DSR FGPVPYGLI+GK FFR VWP N FGSL
Sbjct: 127 QGDNIYASHDSRNFGPVPYGLIQGKVFFR-VWPLNGFGSL 165

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388519663|gb|AFK47893.1| unknown [Medicago truncatula]

 Score =  211 bits (536), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 98/159 (61%), Positives = 123/159 (77%), Gaps = 1/159 (0%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           + +W  +AKEAL ++   A+F C  H T +YL SPT  +GPSMLPTLN+ GDV+L E+VS
Sbjct: 7   IAQWKSVAKEALDRSAIIAKFLCYLHFTGNYLCSPTHAYGPSMLPTLNIAGDVVLVEHVS 66

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQ 120
            R+G++G GD+V V+SP++PN+ +TKR+V +EGD VTYF P N +     VVPKGHVWIQ
Sbjct: 67  PRIGKVGHGDLVLVKSPLNPNRNLTKRVVAMEGDTVTYFDPLNSEDSRIAVVPKGHVWIQ 126

Query: 121 GDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
           GDN+YASRDSR FGPVPYGLI GK FFR VWPP+SFG L
Sbjct: 127 GDNVYASRDSRHFGPVPYGLIRGKVFFR-VWPPSSFGRL 164

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30695525|ref|NP_175758.2| peptidase-S24/S26 domain-containing protein [Arabidopsis thaliana] gi|44681348|gb|AAS47614.1| At1g53530 [Arabidopsis thaliana] gi|45773848|gb|AAS76728.1| At1g53530 [Arabidopsis thaliana] gi|110738199|dbj|BAF01030.1| hypothetical protein [Arabidopsis thaliana] gi|332194831|gb|AEE32952.1| peptidase-S24/S26 domain-containing protein [Arabidopsis thaliana]

 Score =  209 bits (531), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 103/160 (64%), Positives = 123/160 (76%), Gaps = 2/160 (1%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           +++W   AKEA       A+F CL HVT+ Y+ S T V GPSMLPTLNLTGDVILAE++S
Sbjct: 9   LKQWRGTAKEAFENVSIVAKFLCLLHVTDRYIISTTHVHGPSMLPTLNLTGDVILAEHLS 68

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTY-FKPRNGDSCHTVVVPKGHVWI 119
           HR G++G GD+V VRSP DP ++VTKRI+G+EGDR+T+   P  GD+  +V+VPKGHVWI
Sbjct: 69  HRFGKIGLGDVVLVRSPRDPKRMVTKRILGLEGDRLTFSADPLVGDASVSVLVPKGHVWI 128

Query: 120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
           QGDNLYAS DSR FGPVPY LIEGKA  R VWPP  FGSL
Sbjct: 129 QGDNLYASTDSRHFGPVPYSLIEGKALLR-VWPPEYFGSL 167

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297847748|ref|XP_002891755.1| signal peptidase I family protein [Arabidopsis lyrata subsp. lyrata] gi|297337597|gb|EFH68014.1| signal peptidase I family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  209 bits (531), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 102/160 (63%), Positives = 123/160 (76%), Gaps = 2/160 (1%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           +++W   AKEA       A+F CL HVT+ Y+ S T V GPSMLPTLNLTGDVILAE++S
Sbjct: 9   LKQWRGTAKEAFENVSIVAKFLCLLHVTDRYIISTTHVHGPSMLPTLNLTGDVILAEHLS 68

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTY-FKPRNGDSCHTVVVPKGHVWI 119
           HR G++G GD+V VRSP DP ++VTKRI+G+EGDR+T+   P  GD+  +V+VPKGHVWI
Sbjct: 69  HRFGKIGLGDVVLVRSPRDPKRMVTKRILGLEGDRLTFSADPLVGDASVSVLVPKGHVWI 128

Query: 120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
           QGDNLYAS DSR FGP+PY LIEGKA  R VWPP  FGSL
Sbjct: 129 QGDNLYASTDSRHFGPIPYSLIEGKALLR-VWPPEYFGSL 167

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255557373|ref|XP_002519717.1| mitochondrial inner membrane protease subunit, putative [Ricinus communis] gi|223541134|gb|EEF42690.1| mitochondrial inner membrane protease subunit, putative [Ricinus communis]

 Score =  202 bits (513), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 92/150 (61%), Positives = 118/150 (78%), Gaps = 1/150 (0%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           + +W   AKEAL Q++  A+F C  HVTN YL +  L +GPSMLPTLNLTGD++LAE +S
Sbjct: 6   LAQWKSFAKEALNQSILVAKFLCFLHVTNTYLCTAALTYGPSMLPTLNLTGDLVLAERIS 65

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTY-FKPRNGDSCHTVVVPKGHVWI 119
            R G++GPGDIV VRSPV+P +IVTKR++GVEGD VTY   P+N D+ +TVVVPKGH+WI
Sbjct: 66  PRFGKVGPGDIVLVRSPVNPKRIVTKRVMGVEGDSVTYVVDPKNSDASNTVVVPKGHIWI 125

Query: 120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQ 149
           +GDN+Y S DSR+FG VPYGL+  K F+R+
Sbjct: 126 EGDNVYDSNDSRKFGAVPYGLLHAKVFWRK 155

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562592|ref|XP_002522302.1| mitochondrial inner membrane protease subunit, putative [Ricinus communis] gi|223538555|gb|EEF40160.1| mitochondrial inner membrane protease subunit, putative [Ricinus communis]

 Score =  199 bits (506), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 88/151 (58%), Positives = 118/151 (78%), Gaps = 1/151 (0%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           + +W   AKEAL Q++  A+F C  HVT+ YL +  L +GPSMLPTLNLTGD++LAE +S
Sbjct: 4   LAQWKSFAKEALNQSILVAKFLCFLHVTDTYLCTAALTYGPSMLPTLNLTGDLVLAERIS 63

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYF-KPRNGDSCHTVVVPKGHVWI 119
            R G++GPGDIV VRSPV+P +IVTKR++G+EGD VTY   P+N D+ +T++VPKGH+WI
Sbjct: 64  PRFGKVGPGDIVLVRSPVNPKRIVTKRVMGIEGDSVTYIVDPKNSDASNTIMVPKGHIWI 123

Query: 120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQV 150
           +GDN+Y S DSR+FG VPYGL+  K F+R +
Sbjct: 124 EGDNVYDSNDSRKFGAVPYGLLHAKVFWRVI 154

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463444|ref|XP_002275543.1| PREDICTED: mitochondrial inner membrane protease subunit 1-like isoform 1 [Vitis vinifera] gi|359483846|ref|XP_003633025.1| PREDICTED: mitochondrial inner membrane protease subunit 1-like isoform 2 [Vitis vinifera]

 Score =  197 bits (501), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 94/160 (58%), Positives = 121/160 (75%), Gaps = 2/160 (1%)

Query: 1   MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
           +++W  + KEAL +    A+F CL HV+N YL +  L  GPSMLPTLNL+GD+ILA+ +S
Sbjct: 6   VKQWSRIVKEALDRAFFTAKFLCLLHVSNTYLCTVALAHGPSMLPTLNLSGDLILADRLS 65

Query: 61  HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTY-FKPRNGDSCHTVVVPKGHVWI 119
            R G++GPGDIV VRSP +P KI+TKR+VG+ GDRVT+   P++   C TVVVP+GHVWI
Sbjct: 66  VRFGKVGPGDIVLVRSPQNPRKIITKRVVGMGGDRVTFSVDPKDSRRCETVVVPEGHVWI 125

Query: 120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
            GDN+YAS DSR FG VPYGL++GK F+R +WPP  FG L
Sbjct: 126 AGDNIYASTDSRNFGAVPYGLLQGKVFWR-IWPPQGFGLL 164

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	160
TAIR|locus:2203688	168	AT1G53530 [Arabidopsis thalian	0.987	0.940	0.643	2.4e-51
TAIR|locus:2019357	169	AT1G29960 [Arabidopsis thalian	0.975	0.923	0.474	2.4e-37
TAIR|locus:1006230730	155	AT1G23465 [Arabidopsis thalian	0.906	0.935	0.479	5.1e-35
UNIPROTKB|F1P533	163	IMMP1L "Uncharacterized protei	0.912	0.895	0.437	3.4e-29
UNIPROTKB|E2QXR0	202	IMMP1L "Uncharacterized protei	0.943	0.747	0.4	1e-27
UNIPROTKB|Q96LU5	166	IMMP1L "Mitochondrial inner me	0.943	0.909	0.4	1.3e-27
UNIPROTKB|F1SGP6	166	IMMP1L "Uncharacterized protei	0.943	0.909	0.406	2.2e-27
MGI|MGI:1913791	166	Immp1l "IMP1 inner mitochondri	0.943	0.909	0.393	5.7e-27
ZFIN|ZDB-GENE-070522-4	189	immp1l "IMP1 inner mitochondri	0.856	0.724	0.414	7.3e-27
RGD|1586505	166	LOC687395 "similar to CG9240-P	0.943	0.909	0.4	1.9e-26

TAIR|locus:2203688 AT1G53530 [Arabidopsis thaliana (taxid:3702)]

 Score = 533 (192.7 bits), Expect = 2.4e-51, P = 2.4e-51
 Identities = 103/160 (64%), Positives = 123/160 (76%)

Query:     1 MRRWGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVS 60
             +++W   AKEA       A+F CL HVT+ Y+ S T V GPSMLPTLNLTGDVILAE++S
Sbjct:     9 LKQWRGTAKEAFENVSIVAKFLCLLHVTDRYIISTTHVHGPSMLPTLNLTGDVILAEHLS 68

Query:    61 HRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFK-PRNGDSCHTVVVPKGHVWI 119
             HR G++G GD+V VRSP DP ++VTKRI+G+EGDR+T+   P  GD+  +V+VPKGHVWI
Sbjct:    69 HRFGKIGLGDVVLVRSPRDPKRMVTKRILGLEGDRLTFSADPLVGDASVSVLVPKGHVWI 128

Query:   120 QGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
             QGDNLYAS DSR FGPVPY LIEGKA  R VWPP  FGSL
Sbjct:   129 QGDNLYASTDSRHFGPVPYSLIEGKALLR-VWPPEYFGSL 167

GO:0005739 "mitochondrion" evidence=ISM

GO:0005886 "plasma membrane" 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:0016021 "integral to membrane" evidence=IEA

TAIR|locus:2019357 AT1G29960 [Arabidopsis thaliana (taxid:3702)]

 Score = 401 (146.2 bits), Expect = 2.4e-37, P = 2.4e-37
 Identities = 75/158 (47%), Positives = 104/158 (65%)

Query:     4 WGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRV 63
             W   ++EA+   +  A+ +C  HVT +YL      +GPSM PTL+ +G+V+LAE +S R 
Sbjct:     9 WNTASREAMKSGVLLAKLYCFLHVTTNYLGFMAYAYGPSMTPTLHPSGNVLLAERISKRY 68

Query:    64 GRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTY-FKPRNGDSCHTVVVPKGHVWIQGD 122
              +   GDIV +RSP +PNK   KR++G+EGD +++    R  D   T+VVPKGHV++QGD
Sbjct:    69 QKPSRGDIVVIRSPENPNKTPIKRVIGIEGDCISFVIDSRKSDESQTIVVPKGHVFVQGD 128

Query:   123 NLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG 160
               + SRDSR FG VPYGLI+G+  +R VWP   FG LG
Sbjct:   129 YTHNSRDSRNFGTVPYGLIQGRVLWR-VWPFQDFGPLG 165

GO:0005886 "plasma membrane" 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:0048445 "carpel morphogenesis" evidence=RCA

TAIR|locus:1006230730 AT1G23465 [Arabidopsis thaliana (taxid:3702)]

 Score = 379 (138.5 bits), Expect = 5.1e-35, P = 5.1e-35
 Identities = 70/146 (47%), Positives = 99/146 (67%)

Query:     4 WGLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRV 63
             W   ++EA+   +  A+ +C  HVT +YL      +GPSM+PTL+ +G+++LAE +S R 
Sbjct:     9 WNTASREAMKSGMFVAKVYCFLHVTTNYLGFMAYAYGPSMIPTLHPSGNMLLAERISKRY 68

Query:    64 GRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTY-FKPRNGDSCHTVVVPKGHVWIQGD 122
              +   GDIV +RSP +PNK   KR+VGVEGD +++   P   D   T+VVPKGHV++QGD
Sbjct:    69 QKPSRGDIVVIRSPENPNKTPIKRVVGVEGDCISFVIDPVKSDESQTIVVPKGHVFVQGD 128

Query:   123 NLYASRDSRQFGPVPYGLIEGKAFFR 148
               + SRDSR FGPVPYGLI+G+  +R
Sbjct:   129 YTHNSRDSRNFGPVPYGLIQGRVLWR 154

GO:0006508 "proteolysis" evidence=IEA

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

GO:0009507 "chloroplast" evidence=ISM

GO:0016020 "membrane" evidence=IEA

UNIPROTKB|F1P533 IMMP1L "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 324 (119.1 bits), Expect = 3.4e-29, P = 3.4e-29
 Identities = 67/153 (43%), Positives = 93/153 (60%)

Query:    11 ALTQTLTF----ARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRL 66
             AL +TL F     ++ C+ H    YL    +  GPSM PT+  + D++ +E +S     +
Sbjct:     2 ALGKTLRFLGYTVQYGCIAHCAFEYLGGIVVCSGPSMEPTIQ-SSDIVFSENLSRHFYSI 60

Query:    67 GPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYA 126
               GDIV V+SP DP   + KR++G+EGD+V    P +    H+ V PKGHVW++GDNL  
Sbjct:    61 RKGDIVIVKSPTDPKSNICKRVIGLEGDKVCTSNPSDFLKTHSFV-PKGHVWLEGDNLRN 119

Query:   127 SRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
             S DSR +GPVPYGLI G+  F+ +WP N FG L
Sbjct:   120 STDSRCYGPVPYGLIRGRICFK-IWPLNDFGFL 151

GO:0006508 "proteolysis" evidence=IEA

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

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

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

UNIPROTKB|E2QXR0 IMMP1L "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 310 (114.2 bits), Expect = 1.0e-27, P = 1.0e-27
 Identities = 62/155 (40%), Positives = 89/155 (57%)

Query:     5 GLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVG 64
             G+L K       T  ++ C+ H    Y+    +  GPSM PT+    D++ AE +S    
Sbjct:    40 GVLGKTFRLVGYTI-QYGCIAHCAFEYVGGVVMCSGPSMEPTIQ-NSDIVFAENLSRHFY 97

Query:    65 RLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNL 124
              +  GDIV  +SP DP   + KR++G+EGD++    P +    H  V P GHVW++GDNL
Sbjct:    98 GIQRGDIVIAKSPSDPKSNICKRVIGLEGDKILTSSPSDFFKSHNYV-PTGHVWLEGDNL 156

Query:   125 YASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
               S DSR +GP+PYGLI G+ FF+ +WP + FG L
Sbjct:   157 QNSTDSRYYGPIPYGLIRGRIFFK-IWPLSDFGFL 190

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

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

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

GO:0006508 "proteolysis" evidence=IEA

UNIPROTKB|Q96LU5 IMMP1L "Mitochondrial inner membrane protease subunit 1" [Homo sapiens (taxid:9606)]

 Score = 309 (113.8 bits), Expect = 1.3e-27, P = 1.3e-27
 Identities = 62/155 (40%), Positives = 90/155 (58%)

Query:     5 GLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVG 64
             G+L K       T  ++ C+ H    Y+    +  GPSM PT+    D++ AE +S    
Sbjct:     4 GVLGKTFRLVGYTI-QYGCIAHCAFEYVGGVVMCSGPSMEPTIQ-NSDIVFAENLSRHFY 61

Query:    65 RLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNL 124
              +  GDIV  +SP DP   + KR++G+EGD++    P +    H+ V P GHVW++GDNL
Sbjct:    62 GIQRGDIVIAKSPSDPKSNICKRVIGLEGDKILTTSPSDFFKSHSYV-PMGHVWLEGDNL 120

Query:   125 YASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
               S DSR +GP+PYGLI G+ FF+ +WP + FG L
Sbjct:   121 QNSTDSRCYGPIPYGLIRGRIFFK-IWPLSDFGFL 154

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

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

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

GO:0006508 "proteolysis" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|F1SGP6 IMMP1L "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 63/155 (40%), Positives = 89/155 (57%)

Query:     5 GLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVG 64
             G+L K       T  ++ C+ H    Y+    +  GPSM PT+    D++ AE +S    
Sbjct:     4 GVLGKTFRLVGYTI-QYGCIAHCAFEYVGGVVMCSGPSMEPTIQ-NPDIVFAENLSRHFY 61

Query:    65 RLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNL 124
              +  GDIV  +SP DP   + KR++G+EGD++    P      H+ V P GHVW++GDNL
Sbjct:    62 SIQRGDIVIAKSPSDPKSNICKRVIGLEGDKILTNSPSGFFKGHSYV-PTGHVWLEGDNL 120

Query:   125 YASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
               S DSR +GPVPYGLI G+ FF+ +WP + FG L
Sbjct:   121 QNSTDSRYYGPVPYGLIRGRIFFK-IWPLSDFGFL 154

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

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

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

GO:0006508 "proteolysis" evidence=IEA

MGI|MGI:1913791 Immp1l "IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 61/155 (39%), Positives = 89/155 (57%)

Query:     5 GLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVG 64
             G+L K       T  ++ C+ H    Y+    +  GPSM PT+    D++ AE +S    
Sbjct:     4 GVLGKAFRLAGYTI-QYGCIAHCAFEYVGGVVMCSGPSMEPTIQ-NSDIVFAENLSRHFY 61

Query:    65 RLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNL 124
              +  GDIV  +SP DP   + KR++G+EGD++    P +     + V P GHVW++GDNL
Sbjct:    62 GIQRGDIVIAKSPSDPKSNICKRVIGLEGDKILSTSPSDVFKSRSYV-PTGHVWLEGDNL 120

Query:   125 YASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
               S DSR +GP+PYGLI G+ FF+ +WP + FG L
Sbjct:   121 QNSTDSRYYGPIPYGLIRGRIFFK-IWPFSDFGFL 154

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

GO:0008233 "peptidase activity" evidence=IEA

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

GO:0016020 "membrane" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

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

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 58/140 (41%), Positives = 85/140 (60%)

Query:    20 RFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVD 79
             ++ C+ H    Y+       GPSM PT+    DV+ +E +S  + R+  GDI+  +SP +
Sbjct:    43 QYGCIAHCAFEYVGEFVSCSGPSMEPTIT-NHDVVFSERISRHLYRIQKGDIIIAKSPSN 101

Query:    80 PNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYG 139
             P   + KR++G+EGD+V    P +    HT V P+GHVW++GDNL  S DSR +GP+PY 
Sbjct:   102 PKMNICKRVIGLEGDKVCTSGPSDIFKTHTYV-PRGHVWLEGDNLRNSTDSRSYGPIPYA 160

Query:   140 LIEGKAFFRQVWPPNSFGSL 159
             LI G+   + +WPP SFG L
Sbjct:   161 LIRGRVCLK-LWPPQSFGVL 179

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

RGD|1586505 LOC687395 "similar to CG9240-PA" [Rattus norvegicus (taxid:10116)]

 Score = 298 (110.0 bits), Expect = 1.9e-26, P = 1.9e-26
 Identities = 62/155 (40%), Positives = 88/155 (56%)

Query:     5 GLLAKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVG 64
             G+L K       T  ++ C+ H    Y+    +  GPSM PT+    D++ AE +S    
Sbjct:     4 GVLGKAFRLAGYTI-QYGCIAHCAFEYVGGVVMCSGPSMEPTIQ-NSDIVFAENLSRHFY 61

Query:    65 RLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNL 124
              +  GDIV  +SP DP   + KR++G+EGD++    P +       V P GHVW++GDNL
Sbjct:    62 GIQRGDIVIAKSPSDPKSSICKRVIGLEGDKILADNPPDIFKSRNYV-PTGHVWLEGDNL 120

Query:   125 YASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSL 159
               S DSR +GPVPYGLI G+ FF+ +WP + FG L
Sbjct:   121 ENSTDSRCYGPVPYGLIRGRIFFK-IWPFSDFGFL 154

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O74800	IMP1_SCHPO	3, ., 4, ., 2, 1, ., -	0.3840	0.8312	0.8471	yes	no
Q96LU5	IMP1L_HUMAN	3, ., 4, ., 2, 1, ., -	0.4142	0.8562	0.8253	yes	no
Q9CQU8	IMP1L_MOUSE	3, ., 4, ., 2, 1, ., -	0.3935	0.9437	0.9096	yes	no
Q28I39	IMP1L_XENTR	3, ., 4, ., 2, 1, ., -	0.4285	0.8562	0.8203	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

Your Input: estExt_Genewise1_v1.C_LG_I5063 hypothetical protein (162 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	160
TIGR02227	163	TIGR02227, sigpep_I_bact, signal peptidase I, bact	2e-26
cd06530	85	cd06530, S26_SPase_I, The S26 Type I signal peptid	2e-22
cd06462	84	cd06462, Peptidase_S24_S26, The S24, S26 LexA/sign	7e-12
TIGR02754	90	TIGR02754, sod_Ni_protease, nickel-type superoxide	1e-11
COG0681	166	COG0681, LepB, Signal peptidase I [Intracellular t	4e-09
PRK10861	324	PRK10861, PRK10861, signal peptidase I; Provisiona	1e-06
pfam10502	138	pfam10502, Peptidase_S26, Signal peptidase, peptid	7e-06
pfam00717	69	pfam00717, Peptidase_S24, Peptidase S24-like	2e-05
PRK10861	324	PRK10861, PRK10861, signal peptidase I; Provisiona	0.001

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

 Score = 97.3 bits (243), Expect = 2e-26
 Identities = 47/148 (31%), Positives = 61/148 (41%), Gaps = 26/148 (17%)

Query: 31  YLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVG 90
           +++ P  V G SM PTL   GD IL    ++       GDIV  + P D   I  KR++G
Sbjct: 18  FVFFPYKVPGGSMEPTLK-EGDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYIKRVIG 76

Query: 91  VEGDRV------------------------TYFKPRNGDSCHTVVVPKGHVWIQGDNLYA 126
           + GD+V                              N      V VP GH ++ GDN   
Sbjct: 77  LPGDKVEFRDGKLYINGKKIDEPYLKPNGFLDTSEFNTTDYGPVTVPPGHYFVLGDNRDN 136

Query: 127 SRDSRQFGPVPYGLIEGKAFFRQVWPPN 154
           S DSR FG VP   I GK  F   +P +
Sbjct: 137 SLDSRYFGFVPIDDIIGKVSFV-FYPFD 163

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 = 84.9 bits (211), Expect = 2e-22
 Identities = 37/112 (33%), Positives = 50/112 (44%), Gaps = 27/112 (24%)

Query: 34  SPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEG 93
            P +V G SM PTL   GD++L   +S+       GD+V  +SP DP K + KR++G   
Sbjct: 1   EPVVVPGGSMEPTLQ-PGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIGY-- 57

Query: 94  DRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKA 145
                                   ++ GDN   S DSR +GPVP   I GK 
Sbjct: 58  ------------------------FVLGDNRNNSLDSRYWGPVPEDDIVGKV 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 = 57.7 bits (140), Expect = 7e-12
 Identities = 34/108 (31%), Positives = 45/108 (41%), Gaps = 28/108 (25%)

Query: 38  VFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVT 97
           V G SM PT+   GD++L   V         GDIV  R P    ++  KR++G+ G    
Sbjct: 5   VEGDSMEPTIP-DGDLVL---VDKSSYEPKRGDIVVFRLPGG--ELTVKRVIGLPG---- 54

Query: 98  YFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKA 145
                           +GH ++ GDN   S DSR  GP P   I G  
Sbjct: 55  ----------------EGHYFLLGDN-PNSPDSRIDGP-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 = 57.5 bits (139), Expect = 1e-11
 Identities = 37/108 (34%), Positives = 49/108 (45%), Gaps = 22/108 (20%)

Query: 38  VFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVT 97
           V G SM PTL   GD I+             G++V VR P+ P  ++ KR+  V+     
Sbjct: 3   VTGVSMSPTLP-PGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVD----- 56

Query: 98  YFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKA 145
                NG            +++ GDN  AS DSRQ GPVP  L+ GK 
Sbjct: 57  ----DNG------------LFLLGDNPKASTDSRQLGPVPRSLLLGKV 88

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

 Score = 52.3 bits (125), Expect = 4e-09
 Identities = 30/117 (25%), Positives = 53/117 (45%), Gaps = 6/117 (5%)

Query: 15  TLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFV 74
           +L  A    L      +++ P +V   SM PTLN  GD +L +  S+  G+L   DI+  
Sbjct: 13  SLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLN-VGDRVLVKKFSYGFGKLKVPDII-- 69

Query: 75  RSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSR 131
             P      + KR++G+ GD V +   ++       ++P+ +  ++ DN     D  
Sbjct: 70  VLPAVVEGDLIKRVIGLRGDIVVF---KDDRLYVVPIIPRVYGLVEKDNGKHLVDVI 123

Length = 166

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

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 28/69 (40%), Positives = 35/69 (50%), Gaps = 13/69 (18%)

Query: 42  SMLPTLNLTGDVILAEYVSH------------RVGRLGPGDIVFVRSPVDPNKIVTKRIV 89
           SM+PTL L GD IL E  ++              G    GDIV  + P DP     KR+V
Sbjct: 91  SMMPTL-LIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPEDPKLDYIKRVV 149

Query: 90  GVEGDRVTY 98
           G+ GD+VTY
Sbjct: 150 GLPGDKVTY 158

Length = 324

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 34/141 (24%), Positives = 50/141 (35%), Gaps = 38/141 (26%)

Query: 46  TLNLTGDVILAEYVSHRVGRLGPGDIVFVRSP------------VDPNKIVTKRIVGVEG 93
             N +  V +  Y    + R   GD+V V  P            +     + KR++ + G
Sbjct: 2   RWNASASVPVGLYRIEPLDRPEVGDLVAVCPPEPAAFFAAERGYLPRGVPLLKRVLALPG 61

Query: 94  DRVTYFK--------------PRNGDS--------CHTVVVPKGHVWIQGDNLYASRDSR 131
            RV                   R+           C   V+P+G +++       S DSR
Sbjct: 62  QRVCIRDGLVTIDGVPVSAALERDRKGRPLPPWQGCR--VLPEGELFLMSVTSPDSFDSR 119

Query: 132 QFGPVPYGLIEGKAFFRQVWP 152
            FGPVP   I G+A  R VW 
Sbjct: 120 YFGPVPASAIIGRA--RPVWT 138

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|216079 pfam00717, Peptidase_S24, Peptidase S24-like

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 7/59 (11%)

Query: 38 VFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRV 96
          V G SM PT+   GD++L +    +      GDIV  R   +   +  KR++G+ GD +
Sbjct: 2  VKGDSMEPTIP-DGDLLLVD----KTSEPKRGDIVVARLDGEEATV--KRLIGLPGDII 53

Length = 69

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 27/64 (42%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 84  VTKRIVGVEG--DRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLI 141
           VT RI+ V G  D+V  +  + G    T VVP G  ++ GDN   S DSR +G VP   +
Sbjct: 234 VTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANL 293

Query: 142 EGKA 145
            GKA
Sbjct: 294 VGKA 297

Length = 324

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	160
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;	99.95
PRK13884	178	conjugal transfer peptidase TraF; Provisional	99.95
TIGR02771	171	TraF_Ti conjugative transfer signal peptidase TraF	99.94
PF10502	138	Peptidase_S26: Signal peptidase, peptidase S26 ; I	99.91
TIGR02754	90	sod_Ni_protease nickel-type superoxide dismutase m	99.9
cd06530	85	S26_SPase_I The S26 Type I signal peptidase (SPase	99.87
TIGR02228	158	sigpep_I_arch signal peptidase I, archaeal type. T	99.82
COG4959	173	TraF Type IV secretory pathway, protease TraF [Pos	99.73
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	99.67
PF00717	70	Peptidase_S24: Peptidase S24-like peptidase classi	99.33
cd06462	84	Peptidase_S24_S26 The S24, S26 LexA/signal peptida	99.27
KOG3342	180	consensus Signal peptidase I [Intracellular traffi	99.11
cd06529	81	S24_LexA-like Peptidase S24 LexA-like proteins are	98.98
COG2932	214	Predicted transcriptional regulator [Transcription	98.97
PRK10276	139	DNA polymerase V subunit UmuD; Provisional	98.57
PRK12423	202	LexA repressor; Provisional	98.51
PRK00215	205	LexA repressor; Validated	98.48
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	98.45
COG1974	201	LexA SOS-response transcriptional repressors (RecA	97.99
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	85.44
PF05257	124	CHAP: CHAP domain; InterPro: IPR007921 The CHAP (c	80.97

>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type

Probab=100.00  E-value=8e-42  Score=249.91  Aligned_cols=138  Identities=34%  Similarity=0.511  Sum_probs=122.1

Q ss_pred             HHHHHHHHHHHHHHhhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCC
Q 031410           15 TLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGD   94 (160)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd   94 (160)
                      +..++++++++++++.|+++.+.|+|+||+|||+ +||++++++..+...++++||+|+|+.|.++++.++|||+|+|||
T Consensus         2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~-~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd   80 (163)
T TIGR02227         2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLK-EGDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGD   80 (163)
T ss_pred             HHHHHHHHHHHHHHHhhEEEEEEECCcccccchh-CCCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeEEEEEecCCC
Confidence            4556667777888999999999999999999999 999999999877678999999999999877788999999999999


Q ss_pred             EEEEecCC----------C---C-----------CCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEe
Q 031410           95 RVTYFKPR----------N---G-----------DSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQV  150 (160)
Q Consensus        95 ~v~~~~~~----------~---~-----------~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~  150 (160)
                      +|+++++.          .   .           ....+.+||+|+|||+|||+++|.||||||+|++++|+|||.++ +
T Consensus        81 ~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk~~~~-~  159 (163)
T TIGR02227        81 KVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFV-F  159 (163)
T ss_pred             EEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEEEEEE-E
Confidence            99998632          0   0           11245789999999999999999999999999999999999999 9


Q ss_pred             cCCC
Q 031410          151 WPPN  154 (160)
Q Consensus       151 ~p~~  154 (160)
                      ||++
T Consensus       160 ~p~~  163 (163)
T TIGR02227       160 YPFD  163 (163)
T ss_pred             CCCC
Confidence            9985

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=7.7e-39  Score=227.84  Aligned_cols=143  Identities=42%  Similarity=0.701  Sum_probs=124.6

Q ss_pred             HHHHHHHHHHHHHHhhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCC
Q 031410           15 TLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGD   94 (160)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd   94 (160)
                      .......+++++....|+.++..++|.||+||+...||+++..+++++++.+++||+|++..|.++++.++|||+|+|||
T Consensus        15 ~~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD   94 (176)
T KOG0171|consen   15 FCSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGD   94 (176)
T ss_pred             hHHHHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhhheeeccCCc
Confidence            33445556777777789999999999999999986677777799999999999999999999999999999999999999


Q ss_pred             EEEEecCCC------CCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCCCCCcc
Q 031410           95 RVTYFKPRN------GDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGS  158 (160)
Q Consensus        95 ~v~~~~~~~------~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~~~~~~  158 (160)
                      -+++.++..      .....+..||+||+||+|||+++|.|||+|||+|...|+||++++ +||.++.+.
T Consensus        95 ~v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r-~Wp~s~~~~  163 (176)
T KOG0171|consen   95 LVEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFR-IWPPSRVSG  163 (176)
T ss_pred             eEEEecCCcccchhhhhccceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEE-ecCchhcce
Confidence            888875432      222356899999999999999999999999999999999999999 999998764

>PRK10861 signal peptidase I; Provisional

Probab=100.00  E-value=8.8e-37  Score=242.51  Aligned_cols=142  Identities=34%  Similarity=0.473  Sum_probs=122.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhceEEeEEEeCCCCccccCCCCcEEEEEecccCC------------CCCCCCcEEEEeeCC
Q 031410           11 ALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRV------------GRLGPGDIVFVRSPV   78 (160)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~------------~~~~~GDiVvf~~p~   78 (160)
                      ++.++..++++++++++++.|+++++.|+|+||+|||. .||+++++|+++..            .+++|||+|+|+.|.
T Consensus        60 ~~~~~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~-~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~  138 (324)
T PRK10861         60 WLETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLL-IGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPE  138 (324)
T ss_pred             HHHHHHHHHHHHhHHHHHHhhEEEEEEECCCcCcCccc-CCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCC
Confidence            56667777778888899999999999999999999999 99999999988642            579999999999999


Q ss_pred             CCCceEEEEEEeeCCCEEEEe--c------CCC-----------------------------------------------
Q 031410           79 DPNKIVTKRIVGVEGDRVTYF--K------PRN-----------------------------------------------  103 (160)
Q Consensus        79 ~~~~~~iKRVv~~~Gd~v~~~--~------~~~-----------------------------------------------  103 (160)
                      +++..+||||+|+|||+|+++  +      +..                                               
T Consensus       139 ~~~~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (324)
T PRK10861        139 DPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETK  218 (324)
T ss_pred             CCCCcEEEEeeecCCcEEEEEeCCCEEEEcCccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            888899999999999999996  2      100                                               


Q ss_pred             ------C-----------------C--------------CcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEE
Q 031410          104 ------G-----------------D--------------SCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAF  146 (160)
Q Consensus       104 ------~-----------------~--------------~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~  146 (160)
                            .                 .              ...+++||+|+||++|||+++|+||||||+||+++|+|+|.
T Consensus       219 ~~~~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G~a~  298 (324)
T PRK10861        219 ENGIRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKAT  298 (324)
T ss_pred             cccccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEEEEE
Confidence                  0                 0              01356899999999999999999999999999999999999


Q ss_pred             EEEecCCC
Q 031410          147 FRQVWPPN  154 (160)
Q Consensus       147 ~~~~~p~~  154 (160)
                      .+ +|+++
T Consensus       299 ~i-~~s~d  305 (324)
T PRK10861        299 AI-WMSFE  305 (324)
T ss_pred             EE-EEEcC
Confidence            98 77765

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

Probab=100.00  E-value=4.2e-34  Score=203.30  Aligned_cols=130  Identities=39%  Similarity=0.690  Sum_probs=114.2

Q ss_pred             HHHhhceEEeEEEeCCCCccccCC-----CCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEec
Q 031410           26 HVTNHYLWSPTLVFGPSMLPTLNL-----TGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFK  100 (160)
Q Consensus        26 ~~~~~~~~~~~~v~g~SM~Ptl~~-----~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~  100 (160)
                      ..+...+.....+.|.||.|+++|     ..|+|++.++.-....+.+||+|+|.+|.++++++||||+|+|||.+...+
T Consensus        24 ~t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~  103 (174)
T KOG1568|consen   24 LTFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTED  103 (174)
T ss_pred             eeeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCChhheeeeeeecccccEeccCC
Confidence            334455678899999999999996     238999999875556689999999999999999999999999999987633


Q ss_pred             CCCCCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCCCCCccCC
Q 031410          101 PRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFGSLG  160 (160)
Q Consensus       101 ~~~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~~~~~~~~  160 (160)
                          .....+.+|+|||||.|||...|+|||.||||+...|+|+|+++ +||+.|++.++
T Consensus       104 ----~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~i-lwpP~R~~~~~  158 (174)
T KOG1568|consen  104 ----EKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYI-LWPPVRWQRLD  158 (174)
T ss_pred             ----CCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEE-EcChHHhhhhc
Confidence                23577899999999999999999999999999999999999999 99999988764

>PRK13838 conjugal transfer pilin processing protease TraF; Provisional

Probab=99.95  E-value=1e-26  Score=171.50  Aligned_cols=96  Identities=27%  Similarity=0.311  Sum_probs=73.7

Q ss_pred             EEEecccCCCCCCCCcEEEEeeCCCC-------------------CceEEEEEEeeCCCEEEEec-----CCC-------
Q 031410           55 LAEYVSHRVGRLGPGDIVFVRSPVDP-------------------NKIVTKRIVGVEGDRVTYFK-----PRN-------  103 (160)
Q Consensus        55 lv~~~~~~~~~~~~GDiVvf~~p~~~-------------------~~~~iKRVv~~~Gd~v~~~~-----~~~-------  103 (160)
                      .+.++.+..+++++||+|+|+.|.+.                   ...++|||+|+|||+|++++     +..       
T Consensus        40 g~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~~~~~  119 (176)
T PRK13838         40 GLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPSSSVR  119 (176)
T ss_pred             EEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEccccccc
Confidence            33444333478999999999987542                   13699999999999999874     110       


Q ss_pred             --------CCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEec
Q 031410          104 --------GDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVW  151 (160)
Q Consensus       104 --------~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~  151 (160)
                              .......+||+|+|||+|||. +|+||||||+|++++|+|+|...|.|
T Consensus       120 ~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-~S~DSRy~G~V~~~~I~G~a~pi~t~  174 (176)
T PRK13838        120 RRDGEGRPLTPFPGGVVPPGHLFLHSSFA-GSYDSRYFGPVPASGLLGLARPVLTF  174 (176)
T ss_pred             cccccCCcCCCCCccCcCCCeEEEECCCC-CCCcccccCcccHHHeEEEEEEEEec
Confidence                    001224579999999999984 89999999999999999999885444

>PRK13884 conjugal transfer peptidase TraF; Provisional

Probab=99.95  E-value=2.9e-26  Score=169.50  Aligned_cols=129  Identities=17%  Similarity=0.156  Sum_probs=89.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCC-------
Q 031410            8 AKEALTQTLTFARFFCLFHVTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDP-------   80 (160)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~-------   80 (160)
                      +|++..+++.+.++++++..+. + +..++++.+...|    .|-+.+. .     ..+++||+|+|+.|+..       
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~N~T~S~P----~glY~~~-~-----~~~~~Gd~V~f~~p~~~~~~~a~~   72 (178)
T PRK13884          5 LKRITAGVAVAGLAALLLAALG-Y-AAGARVNTTKSIP----VGLYWTS-S-----APVEKGAYVLFCPPQRGVFDDAKE   72 (178)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-H-hCcEEEECCCCCc----ceEEEEe-C-----CCCCCCCEEEEeCCchHHHHHHHh
Confidence            4455555444444433333322 2 2444555444434    5666543 2     47999999999977521       


Q ss_pred             ------------CceEEEEEEeeCCCEEEEecCC--------------CC---------CCcceEEccCCcEEEEcCCCC
Q 031410           81 ------------NKIVTKRIVGVEGDRVTYFKPR--------------NG---------DSCHTVVVPKGHVWIQGDNLY  125 (160)
Q Consensus        81 ------------~~~~iKRVv~~~Gd~v~~~~~~--------------~~---------~~~~~~~vp~~~~~v~gdn~~  125 (160)
                                  ..+++|||+|+|||+|+++++.              ..         .....+++|+|+||++|||++
T Consensus        73 rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~l~~~~~~~~~lp~g~~fvlgd~~~  152 (178)
T PRK13884         73 RGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRPLPRYQANSYTLGESELLLMSDVSA  152 (178)
T ss_pred             CCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCcccccCCCceEECCCEEEEECCCCC
Confidence                        1379999999999999998631              00         011235899999999999999


Q ss_pred             CCCCCCcccceeCCCeEEEEEEE
Q 031410          126 ASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       126 ~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                      +|+||||||+|++++|+|++...
T Consensus       153 ~S~DSRYfG~V~~~~I~G~~~Pl  175 (178)
T PRK13884        153 TSFDGRYFGPINRSQIKTVIRPV  175 (178)
T ss_pred             CCCcccccCcccHHHEEEEEEEe
Confidence            99999999999999999999875

>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF

Probab=99.94  E-value=2.9e-26  Score=168.50  Aligned_cols=109  Identities=26%  Similarity=0.305  Sum_probs=81.5

Q ss_pred             hhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCC-------------------ceEEEEEE
Q 031410           29 NHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPN-------------------KIVTKRIV   89 (160)
Q Consensus        29 ~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~-------------------~~~iKRVv   89 (160)
                      ..|........++||-     .|-+. ..+    ..+++|||+|+|+.|.++.                   ..++|||+
T Consensus        20 ~~~~~~~~~N~T~S~P-----~g~Y~-~~~----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRVi   89 (171)
T TIGR02771        20 GLYCVGARINTTKSLP-----LGLYW-TTS----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVL   89 (171)
T ss_pred             hcceeeEEEECCCCCc-----ceEEE-eCC----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEE
Confidence            3344334445556652     45555 322    2589999999999876432                   27999999


Q ss_pred             eeCCCEEEEecCC--------C-------------CCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410           90 GVEGDRVTYFKPR--------N-------------GDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus        90 ~~~Gd~v~~~~~~--------~-------------~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                      |+|||+|+++++.        .             .....+.+||+| ||++|||+++|+||||||+|++++|+||+...
T Consensus        90 glpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl  168 (171)
T TIGR02771        90 GLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPL  168 (171)
T ss_pred             EeCCCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEe
Confidence            9999999998631        0             011236889999 99999999999999999999999999999875

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.

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

Probab=99.91  E-value=1.9e-25  Score=159.10  Aligned_cols=84  Identities=35%  Similarity=0.474  Sum_probs=32.2

Q ss_pred             CCCCCcEEEEeeCCC------------CCceEEEEEEeeCCCEEEEecCC--------------------CCCCcceEEc
Q 031410           65 RLGPGDIVFVRSPVD------------PNKIVTKRIVGVEGDRVTYFKPR--------------------NGDSCHTVVV  112 (160)
Q Consensus        65 ~~~~GDiVvf~~p~~------------~~~~~iKRVv~~~Gd~v~~~~~~--------------------~~~~~~~~~v  112 (160)
                      .+++||+|+|+.|..            .+..++|||+|+|||+|+++++.                    ......+.+|
T Consensus        21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~v  100 (138)
T PF10502_consen   21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGTV  100 (138)
T ss_dssp             --------------------------------------------------------------------S-T----TEEE-
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceEe
Confidence            489999999999862            24589999999999999998642                    0111258999


Q ss_pred             cCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          113 PKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       113 p~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                      |+|+||++|||+.+|+||||||+|++++|+|+|...
T Consensus       101 p~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl  136 (138)
T PF10502_consen  101 PEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPL  136 (138)
T ss_dssp             -TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEE
T ss_pred             CCCEEEEecCCCCCccccCEecccCHHHEEEEEEEE
Confidence            999999999999999999999999999999999884

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.

>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease

Probab=99.90  E-value=2.2e-23  Score=138.23  Aligned_cols=89  Identities=39%  Similarity=0.595  Sum_probs=78.1

Q ss_pred             EEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccCCc
Q 031410           37 LVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGH  116 (160)
Q Consensus        37 ~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~  116 (160)
                      .|.|+||+|+|+ +||++++++.......+++||+|+|+.|.++++.++||++++++                     ++
T Consensus         2 ~V~g~SM~P~l~-~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~---------------------~~   59 (90)
T TIGR02754         2 KVTGVSMSPTLP-PGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDD---------------------NG   59 (90)
T ss_pred             EeeCCCccCccC-CCCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcC---------------------Ce
Confidence            689999999999 99999999854333456789999999987667899999999764                     47


Q ss_pred             EEEEcCCCCCCCCCCcccceeCCCeEEEEEE
Q 031410          117 VWIQGDNLYASRDSRQFGPVPYGLIEGKAFF  147 (160)
Q Consensus       117 ~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~  147 (160)
                      +|++|||+..|.|||++|+|+..+|+|+|+|
T Consensus        60 ~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~   90 (90)
T TIGR02754        60 LFLLGDNPKASTDSRQLGPVPRSLLLGKVLW   90 (90)
T ss_pred             EEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence            9999999999999999999999999999864

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.

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

Probab=99.87  E-value=1.4e-21  Score=128.12  Aligned_cols=84  Identities=44%  Similarity=0.678  Sum_probs=75.5

Q ss_pred             eEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccC
Q 031410           35 PTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPK  114 (160)
Q Consensus        35 ~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~  114 (160)
                      .+.+.|+||+|++. .||++++++......++++||+|+|+.+.+++..++|||++                        
T Consensus         2 ~~~v~g~SM~P~i~-~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~------------------------   56 (85)
T cd06530           2 PVVVPGGSMEPTLQ-PGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG------------------------   56 (85)
T ss_pred             eeEEcCCCCcCccc-CCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE------------------------
Confidence            57899999999999 99999999865433479999999999987556899999997                        


Q ss_pred             CcEEEEcCCCCCCCCCCcccceeCCCeEEEE
Q 031410          115 GHVWIQGDNLYASRDSRQFGPVPYGLIEGKA  145 (160)
Q Consensus       115 ~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v  145 (160)
                        ||+.|||+.+|.|||+||+++.++|+|++
T Consensus        57 --~~~~gDn~~ns~d~~~~g~~~~~~i~G~~   85 (85)
T cd06530          57 --YFVLGDNRNNSLDSRYWGPVPEDDIVGKV   85 (85)
T ss_pred             --EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence              99999999899999999999999999985

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=99.82  E-value=4.1e-19  Score=128.95  Aligned_cols=115  Identities=25%  Similarity=0.270  Sum_probs=84.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhceE---EeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCce
Q 031410            7 LAKEALTQTLTFARFFCLFHVTNHYLW---SPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKI   83 (160)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~   83 (160)
                      +.+.++.+++.+++.++++..+....+   ..+.|.|+||+||++ .||++++++..  ..++++||+|+|+.|+++ ..
T Consensus         2 ~~~~ii~~~~~~~l~~~~~~~l~~~~~~~~p~v~V~g~SM~Ptl~-~GD~vlv~~~~--~~~~~~GDIVvf~~~~~~-~~   77 (158)
T TIGR02228         2 KISNVIYFILIILLVILLLYGLVSKASGPDPVVVVLSGSMEPTFN-TGDLILVTGAD--PNDIQVGDVITYKSPGFN-TP   77 (158)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHheeeccCCCcEEEEcCCCCcCCcc-CCCEEEEEecc--cCCCCCCCEEEEEECCCC-cc
Confidence            355667666666555555544433332   233499999999999 99999999843  358999999999988643 78


Q ss_pred             EEEEEEeeCCCEEEEecCCCCCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEE
Q 031410           84 VTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAF  146 (160)
Q Consensus        84 ~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~  146 (160)
                      ++|||+++.++.                 .+..|++.|||+ ...|   .++|+.++|+|++.
T Consensus        78 iihRVi~v~~~~-----------------g~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~  119 (158)
T TIGR02228        78 VTHRVIEINNSG-----------------GELGFITKGDNN-PAPD---GEPVPSENVIGKYL  119 (158)
T ss_pred             EEEEEEEEECCC-----------------CcEEEEEEecCC-CCCC---cccCCHHHEEEEEE
Confidence            999999987530                 012488889997 4556   68999999999998

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.

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

Probab=99.73  E-value=1.5e-17  Score=117.65  Aligned_cols=107  Identities=24%  Similarity=0.251  Sum_probs=80.6

Q ss_pred             EeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCC------------CCceEEEEEEeeCCCEEEEecC
Q 031410           34 SPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVD------------PNKIVTKRIVGVEGDRVTYFKP  101 (160)
Q Consensus        34 ~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~------------~~~~~iKRVv~~~Gd~v~~~~~  101 (160)
                      ..++++.+...|    -|= .-+.|.+   ..+.+||+|+++.|..            ...+++|||.|+|||+|++.++
T Consensus        30 p~l~~N~S~S~p----lGl-yrv~k~~---~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~  101 (173)
T COG4959          30 PGLRVNASASAP----LGL-YRVSKLS---APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQ  101 (173)
T ss_pred             cceEeccCCCcc----eeE-EEecccC---CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecc
Confidence            456666555555    333 3344432   3569999999999863            3567999999999999999862


Q ss_pred             C--------------------CCCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          102 R--------------------NGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       102 ~--------------------~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                      .                    ......+-.+.++++|+++|..+.|+|||||||||.++|+|.+...
T Consensus       102 ~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPv  168 (173)
T COG4959         102 GIAIDGKPVAASLPVDRVGRALPRWQGCRYLAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPV  168 (173)
T ss_pred             eEEECCEEeeeeccccccCCcCCcccCCceecCCeEEEEeccCCcccccceecccCHHHcceeeeee
Confidence            1                    1112234448899999999999999999999999999999999884

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

Probab=99.67  E-value=6.9e-16  Score=112.33  Aligned_cols=130  Identities=25%  Similarity=0.321  Sum_probs=98.3

Q ss_pred             HHHHHHHHHHHHHHHHHH--hhceEEeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEE
Q 031410           11 ALTQTLTFARFFCLFHVT--NHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRI   88 (160)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRV   88 (160)
                      ...++..++.++++++++  +.++++.+.|+|+||+||++ .||++++++.++...++..+|.+  ..|......++||+
T Consensus         7 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~-~GD~v~v~k~~~~~~~~~~~~~~--~~~~~~~~~~~kr~   83 (166)
T COG0681           7 FLELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLN-VGDRVLVKKFSYGFGKLKVPDII--VLPAVVEGDLIKRV   83 (166)
T ss_pred             HHHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccc-cCCEEEEEeccccccCCccceee--ecCCCCCcceEEEe
Confidence            445555566666666666  89999999999999999999 99999999999888889999998  44555678899999


Q ss_pred             EeeCCCEEEEecCCCCCCcceEEccCCcEEEE-------cCCCCCCCCCCcccceeCCCeEEEEE
Q 031410           89 VGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQ-------GDNLYASRDSRQFGPVPYGLIEGKAF  146 (160)
Q Consensus        89 v~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~-------gdn~~~s~DSR~~G~V~~~~I~G~v~  146 (160)
                      ++++||.+.++++....   ...+|++..++.       .+....+.+++.++.......+.++.
T Consensus        84 ~~~~GD~i~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (166)
T COG0681          84 IGLRGDIVVFKDDRLYV---VPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRVI  145 (166)
T ss_pred             ccCCCCEEEEECCEEEe---ecccCcchhhhhcccccccccccccccCccccccccccccccceE
Confidence            99999999998754211   223444555444       34445677777787777777777773

>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification

Probab=99.33  E-value=1.2e-11  Score=77.62  Aligned_cols=57  Identities=35%  Similarity=0.494  Sum_probs=45.9

Q ss_pred             EEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEe
Q 031410           37 LVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYF   99 (160)
Q Consensus        37 ~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~   99 (160)
                      +|.|+||+|+++ .||++++++.    .+++.||+|++..+.+. ..++||+.+.+|+.+.+.
T Consensus         1 ~V~GdSM~P~i~-~Gd~v~v~~~----~~~~~gdivv~~~~~~~-~~~iKrv~~~~~~~~~~~   57 (70)
T PF00717_consen    1 RVEGDSMEPTIK-DGDIVLVDPS----SEPKDGDIVVVKIDGDE-ELYIKRVVGEPGGIILIS   57 (70)
T ss_dssp             EEESSTTGGTSS-TTEEEEEEET----S---TTSEEEEEETTEE-SEEEEEEEEETTEEEEE-
T ss_pred             CeECcCcccCee-CCCEEEEEEc----CCCccCeEEEEEECCce-eeEEEEEEEeCCCEEEEe
Confidence            589999999999 9999999984    48999999999986532 389999999999877665

; 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 ....

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

Probab=99.27  E-value=5.6e-11  Score=76.76  Aligned_cols=83  Identities=41%  Similarity=0.584  Sum_probs=63.5

Q ss_pred             eEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccC
Q 031410           35 PTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPK  114 (160)
Q Consensus        35 ~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~  114 (160)
                      .+.+.|+||+|++. .||++++++..   ..++.||++++..+.  +..++||+...++                    +
T Consensus         2 ~~~v~g~SM~P~i~-~gd~v~i~~~~---~~~~~G~iv~~~~~~--~~~~ikrl~~~~~--------------------~   55 (84)
T cd06462           2 ALRVEGDSMEPTIP-DGDLVLVDKSS---YEPKRGDIVVFRLPG--GELTVKRVIGLPG--------------------E   55 (84)
T ss_pred             eeEEcCCCccCccc-CCCEEEEEecC---CCCcCCEEEEEEcCC--CcEEEEEEEEECC--------------------C
Confidence            46899999999998 99999999832   248999999999854  4799999999775                    2


Q ss_pred             CcEEEEcCCCCCCCCCCcccceeCCCeEEEE
Q 031410          115 GHVWIQGDNLYASRDSRQFGPVPYGLIEGKA  145 (160)
Q Consensus       115 ~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v  145 (160)
                      +++++.+||+ +..+.+..+. ....++|++
T Consensus        56 ~~~~l~~~N~-~~~~~~~~~~-~~~~i~g~v   84 (84)
T cd06462          56 GHYFLLGDNP-NSPDSRIDGP-PELDIVGVV   84 (84)
T ss_pred             CEEEEECCCC-CCCcccccCC-CHHHEEEeC
Confidence            4889999994 5555544333 456666653

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

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

Probab=99.11  E-value=1e-09  Score=77.98  Aligned_cols=95  Identities=20%  Similarity=0.249  Sum_probs=69.8

Q ss_pred             EeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEcc
Q 031410           34 SPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVP  113 (160)
Q Consensus        34 ~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp  113 (160)
                      ..+.|-++||+|.++ .||.++.....  ....+.||+|+|+.+. .+.+.+|||+.+-+.                .-.
T Consensus        49 PiVVVLSgSMePaF~-RGDlLfL~N~~--~~p~~vGdivVf~veg-R~IPiVHRviK~he~----------------~~~  108 (180)
T KOG3342|consen   49 PIVVVLSGSMEPAFH-RGDLLFLTNRN--EDPIRVGDIVVFKVEG-REIPIVHRVIKQHEK----------------SNG  108 (180)
T ss_pred             CEEEEEcCCcCcccc-cccEEEEecCC--CCcceeccEEEEEECC-ccCchhHHHHHHhcc----------------cCC
Confidence            678899999999999 99999986422  2457999999999864 678899999986541                001


Q ss_pred             CCcEEEEcCCCCCCCCCCc-c----cceeCCCeEEEEEEEEecC
Q 031410          114 KGHVWIQGDNLYASRDSRQ-F----GPVPYGLIEGKAFFRQVWP  152 (160)
Q Consensus       114 ~~~~~v~gdn~~~s~DSR~-~----G~V~~~~I~G~v~~~~~~p  152 (160)
                      +-+++..|||+  ..|.|- |    -...+++|+|+|.-  +.|
T Consensus       109 ~~~~LTKGDNN--~~dD~~Ly~~gq~~L~r~~Ivg~~~G--~~P  148 (180)
T KOG3342|consen  109 HIKFLTKGDNN--AVDDRGLYAQGQNWLERKDIVGRVRG--YLP  148 (180)
T ss_pred             cEEEEecCCCC--cccchhcccccccceeccceeeEEee--ccc
Confidence            12477889995  344442 2    35888999999976  444

>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=98.98  E-value=9.8e-09  Score=65.89  Aligned_cols=52  Identities=33%  Similarity=0.430  Sum_probs=44.6

Q ss_pred             eEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCC
Q 031410           35 PTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGD   94 (160)
Q Consensus        35 ~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd   94 (160)
                      .+.+.|+||+|+++ .||++++++.    ..++.||++++..++   ..++||+...+++
T Consensus         2 ~~~v~g~sM~p~i~-~gd~lii~~~----~~~~~g~i~~~~~~~---~~~ikr~~~~~~~   53 (81)
T cd06529           2 ALRVKGDSMEPTIP-DGDLVLVDPS----DTPRDGDIVVARLDG---ELTVKRLQRRGGG   53 (81)
T ss_pred             EEEEECCCcCCccC-CCCEEEEcCC----CCCCCCCEEEEEECC---EEEEEEEEECCCC
Confidence            36899999999998 9999999873    359999999999843   7899999997754

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=98.97  E-value=7.5e-09  Score=78.70  Aligned_cols=86  Identities=26%  Similarity=0.272  Sum_probs=62.3

Q ss_pred             EeEEEeCCCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEcc
Q 031410           34 SPTLVFGPSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVP  113 (160)
Q Consensus        34 ~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp  113 (160)
                      ...+|.|+||+|++. +||.++|++    .....+||.+++..  ..++.++||+...+|                    
T Consensus       124 ~~i~V~GDSMeP~~~-~Gd~ilVd~----~~~~~~gd~v~v~~--~g~~~~VK~l~~~~~--------------------  176 (214)
T COG2932         124 FALRVTGDSMEPTYE-DGDTLLVDP----GVNTRRGDRVYVET--DGGELYVKKLQREPG--------------------  176 (214)
T ss_pred             EEEEEeCCccccccc-CCCEEEECC----CCceeeCCEEEEEE--eCCeEEEEEEEEecC--------------------
Confidence            457999999999999 999999987    24778899666665  246899999999776                    


Q ss_pred             CCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          114 KGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       114 ~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                       +.+.+.++|+....|- .+..-..=+|+|+|++.
T Consensus       177 -~~~~l~S~N~~~~~~~-~~~~~~~v~iIgrVv~~  209 (214)
T COG2932         177 -GLLRLVSLNPDYYPDE-IFSEDDDVEIIGRVVWV  209 (214)
T ss_pred             -CeEEEEeCCCCCCccc-ccCccceEEEEEEEEEE
Confidence             4566888887443332 22111113589999886

>PRK10276 DNA polymerase V subunit UmuD; Provisional

Probab=98.57  E-value=1.5e-06  Score=61.90  Aligned_cols=83  Identities=16%  Similarity=0.072  Sum_probs=57.8

Q ss_pred             EEeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410           33 WSPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV  111 (160)
Q Consensus        33 ~~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~  111 (160)
                      ....++.|+||. |++. +||++++++-    .+++.||+|++..   .++..+||+.-.                    
T Consensus        51 ~f~l~V~GdSM~~~~I~-~GD~liVd~~----~~~~~Gdivv~~~---~g~~~vKrl~~~--------------------  102 (139)
T PRK10276         51 TYFVKASGDSMIDAGIS-DGDLLIVDSA----ITASHGDIVIAAV---DGEFTVKKLQLR--------------------  102 (139)
T ss_pred             EEEEEEecCCCCCCCCC-CCCEEEEECC----CCCCCCCEEEEEE---CCEEEEEEEEEC--------------------
Confidence            345899999997 6898 9999999872    3678999999986   346789998742                    


Q ss_pred             ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                         +++++..+|+..  .....-.-+.-.|+|+|.+.
T Consensus       103 ---~~~~L~s~N~~y--~~i~i~~~~~~~IiG~V~~~  134 (139)
T PRK10276        103 ---PTVQLIPMNSAY--SPITISSEDTLDVFGVVTHI  134 (139)
T ss_pred             ---CcEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEE
Confidence               146677787532  11111111123699999885

>PRK12423 LexA repressor; Provisional

Probab=98.51  E-value=2.1e-06  Score=64.75  Aligned_cols=83  Identities=20%  Similarity=0.131  Sum_probs=60.2

Q ss_pred             EeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEc
Q 031410           34 SPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVV  112 (160)
Q Consensus        34 ~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~v  112 (160)
                      ....|.|+||. |+|. +||++++++    ..+++.||+|++..   .++..+||+.-..                    
T Consensus       115 f~l~V~GdSM~~~~i~-~Gd~viv~~----~~~~~~Gdivv~~~---~~~~~vKrl~~~~--------------------  166 (202)
T PRK12423        115 YLLQVQGDSMIDDGIL-DGDLVGVHR----SPEARDGQIVVARL---DGEVTIKRLERSG--------------------  166 (202)
T ss_pred             EEEEEecCcCCCCCcC-CCCEEEEeC----CCcCCCCCEEEEEE---CCEEEEEEEEEeC--------------------
Confidence            35799999997 7998 999999987    24788999999987   3468999987643                    


Q ss_pred             cCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          113 PKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       113 p~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                        +.+++..+|+..  +...+-+-..-.|+|++...
T Consensus       167 --~~~~L~s~N~~y--~~i~~~~~~~~~I~Gvv~g~  198 (202)
T PRK12423        167 --DRIRLLPRNPAY--APIVVAPDQDFAIEGVFCGL  198 (202)
T ss_pred             --CEEEEEcCCCCC--CCEEcCCCCcEEEEEEEEEE
Confidence              367788888632  22222221234799999875

>PRK00215 LexA repressor; Validated

Probab=98.48  E-value=3.3e-06  Score=63.64  Aligned_cols=83  Identities=23%  Similarity=0.222  Sum_probs=60.5

Q ss_pred             EEeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410           33 WSPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV  111 (160)
Q Consensus        33 ~~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~  111 (160)
                      ....+|.|+||. |++. +||++++++-    .+++.||+|++...   ++..+||+.-..                   
T Consensus       118 ~~~~~V~GdSM~~~~i~-~Gd~v~v~~~----~~~~~G~ivv~~~~---~~~~vKrl~~~~-------------------  170 (205)
T PRK00215        118 DFLLRVRGDSMIDAGIL-DGDLVIVRKQ----QTARNGQIVVALID---DEATVKRFRREG-------------------  170 (205)
T ss_pred             eEEEEEccCCCCCCCcC-CCCEEEEeCC----CCCCCCCEEEEEEC---CEEEEEEEEEeC-------------------
Confidence            456889999995 7998 9999999872    46789999999873   378999998642                   


Q ss_pred             ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                         |.+++..+|+..  +.....+ ..-.|+|+|...
T Consensus       171 ---~~~~L~s~Np~y--~~~~~~~-~~~~IiG~Vv~~  201 (205)
T PRK00215        171 ---GHIRLEPENPAY--EPIIVDP-DRVTIEGKVVGL  201 (205)
T ss_pred             ---CEEEEEcCCCCC--CCEEeCC-CcEEEEEEEEEE
Confidence               367788888642  2221111 035799999875

>TIGR00498 lexA SOS regulatory protein LexA

Probab=98.45  E-value=4.9e-06  Score=62.43  Aligned_cols=86  Identities=20%  Similarity=0.164  Sum_probs=62.5

Q ss_pred             EEeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410           33 WSPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV  111 (160)
Q Consensus        33 ~~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~  111 (160)
                      ...+++.|+||. |.+. +||++++++.    ..++.||+|++..   .++..+||+.-. |                  
T Consensus       111 ~f~~~V~GdSM~~~~i~-~Gd~v~v~~~----~~~~~G~ivvv~~---~~~~~vKrl~~~-~------------------  163 (199)
T TIGR00498       111 VFLLKVMGDSMVDAGIC-DGDLLIVRSQ----KDARNGEIVAAMI---DGEVTVKRFYKD-G------------------  163 (199)
T ss_pred             EEEEEecCCCCCCCCCC-CCCEEEEecC----CCCCCCCEEEEEE---CCEEEEEEEEEE-C------------------
Confidence            456899999996 5898 9999999862    4889999999997   457899998754 2                  


Q ss_pred             ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecC
Q 031410          112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWP  152 (160)
Q Consensus       112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p  152 (160)
                         +.+++..+|+...  ...... ..-.|+|+|... +..
T Consensus       164 ---~~i~L~s~N~~y~--~i~~~~-~~~~IiG~Vv~~-~r~  197 (199)
T TIGR00498       164 ---TKVELKPENPEFD--PIVLNA-EDVTILGKVVGV-IRN  197 (199)
T ss_pred             ---CEEEEEcCCCCCc--CCcCCC-CcEEEEEEEEEE-EEe
Confidence               3677888886432  111111 135799999887 543

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.

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

Probab=97.99  E-value=0.00016  Score=54.62  Aligned_cols=88  Identities=18%  Similarity=0.113  Sum_probs=65.4

Q ss_pred             EEeEEEeCCCCc-cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410           33 WSPTLVFGPSML-PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV  111 (160)
Q Consensus        33 ~~~~~v~g~SM~-Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~  111 (160)
                      ....+|.|+||. +.+. +||+++|++    ..+.+.||+|+....+  ++.-+||..--.                   
T Consensus       112 ~f~L~V~GdSM~~~gi~-dGDlvvV~~----~~~a~~GdiVvA~i~g--~e~TvKrl~~~g-------------------  165 (201)
T COG1974         112 TFFLRVSGDSMIDAGIL-DGDLVVVDP----TEDAENGDIVVALIDG--EEATVKRLYRDG-------------------  165 (201)
T ss_pred             eEEEEecCCccccCcCC-CCCEEEEcC----CCCCCCCCEEEEEcCC--CcEEEEEEEEeC-------------------
Confidence            345799999995 6776 999999987    4689999999999854  568899987633                   


Q ss_pred             ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCC
Q 031410          112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPP  153 (160)
Q Consensus       112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~  153 (160)
                         +.+++.--|+.  +.+..+..- .-.|+|++... +|+.
T Consensus       166 ---~~i~L~p~Np~--~~~i~~~~~-~~~I~G~vvgv-~r~~  200 (201)
T COG1974         166 ---NQILLKPENPA--YPPIPVDAD-SVTILGKVVGV-IRDI  200 (201)
T ss_pred             ---CEEEEEeCCCC--CCCcccCcc-ceEEEEEEEEE-EecC
Confidence               36778777753  233323222 56799999998 8764

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

Probab=85.44  E-value=1.1  Score=31.84  Aligned_cols=14  Identities=29%  Similarity=0.145  Sum_probs=11.5

Q ss_pred             CCCCCCcEEEEeeC
Q 031410           64 GRLGPGDIVFVRSP   77 (160)
Q Consensus        64 ~~~~~GDiVvf~~p   77 (160)
                      ....+||+|+|+.+
T Consensus        83 ~~~~~GD~i~~~~~   96 (166)
T COG0681          83 VIGLRGDIVVFKDD   96 (166)
T ss_pred             eccCCCCEEEEECC
Confidence            36789999999973

>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family

Probab=80.97  E-value=5.8  Score=27.02  Aligned_cols=37  Identities=24%  Similarity=0.258  Sum_probs=24.2

Q ss_pred             CCCCCCcEEEEeeCCCCCceEEEEEEee-CCCEEEEec
Q 031410           64 GRLGPGDIVFVRSPVDPNKIVTKRIVGV-EGDRVTYFK  100 (160)
Q Consensus        64 ~~~~~GDiVvf~~p~~~~~~~iKRVv~~-~Gd~v~~~~  100 (160)
                      ..|+.||+++|.......--.+--|.++ .+++|.+.+
T Consensus        61 ~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~~i~v~e   98 (124)
T PF05257_consen   61 STPQPGDIVVWDSGSGGGYGHVAIVESVNDGGTITVIE   98 (124)
T ss_dssp             S---TTEEEEEEECTTTTT-EEEEEEEE-TTSEEEEEE
T ss_pred             cccccceEEEeccCCCCCCCeEEEEEEECCCCEEEEEE
Confidence            5899999999964333444577888888 888887754

Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	160
1t7d_A	250	Crystal Structure Of Escherichia Coli Type I Signal		3e-05
1b12_A	248	Crystal Structure Of Type 1 Signal Peptidase From E		5e-05
1kn9_A	249	Crystal Structure Of A Bacterial Signal Peptidase A		5e-05

>pdb|1T7D|A Chain A, Crystal Structure Of Escherichia Coli Type I Signal Peptidase In Complex With A Lipopeptide Inhibitor Length = 250

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 40/84 (47%), Gaps = 13/84 (15%)
Query: 27 VTNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSH------------RVGRLGPGDIVFV 74
          +   +++ P  +   SM+PTL L GD IL E  ++              G    GDIV  
Sbjct: 2  IVRSFIYEPFQIPSGSMMPTL-LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVF 60
Query: 75 RSPVDPNKIVTKRIVGVEGDRVTY 98
          + P DP     KR VG+ GD+VTY
Sbjct: 61 KYPEDPKLDYIKRAVGLPGDKVTY 84

>pdb|1B12|A Chain A, Crystal Structure Of Type 1 Signal Peptidase From Escherichia Coli In Complex With A Beta-Lactam Inhibitor Length = 248

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 39/80 (48%), Gaps = 13/80 (16%)
Query: 31 YLWSPTLVFGPSMLPTLNLTGDVILAEYVSH------------RVGRLGPGDIVFVRSPV 78
          +++ P  +   SM+PTL L GD IL E  ++              G    GDIV  + P 
Sbjct: 4  FIYEPFQIPSGSMMPTL-LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE 62
Query: 79 DPNKIVTKRIVGVEGDRVTY 98
          DP     KR VG+ GD+VTY
Sbjct: 63 DPKLDYIKRAVGLPGDKVTY 82

>pdb|1KN9|A Chain A, Crystal Structure Of A Bacterial Signal Peptidase Apo- Enzyme, Implications For Signal Peptide Binding And The Ser-Lys Dyad Mechanism. Length = 249

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 39/80 (48%), Gaps = 13/80 (16%)
Query: 31 YLWSPTLVFGPSMLPTLNLTGDVILAEYVSH------------RVGRLGPGDIVFVRSPV 78
          +++ P  +   SM+PTL L GD IL E  ++              G    GDIV  + P 
Sbjct: 5  FIYEPFQIPSGSMMPTL-LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE 63
Query: 79 DPNKIVTKRIVGVEGDRVTY 98
          DP     KR VG+ GD+VTY
Sbjct: 64 DPKLDYIKRAVGLPGDKVTY 83

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	160
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	1e-09
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	3e-06

>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 = 54.5 bits (131), Expect = 1e-09
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 80  PNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYG 139
            +       V +  D+V  +  + G    T +VP G  ++ GDN   S DSR +G VP  
Sbjct: 156 GDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEA 215

Query: 140 LIEGKAFFRQVW 151
            + G+A    +W
Sbjct: 216 NLVGRATA--IW 225

>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 = 44.5 bits (105), Expect = 3e-06
 Identities = 30/81 (37%), Positives = 38/81 (46%), Gaps = 19/81 (23%)

Query: 36 TLVFGP------SMLPTLNLTGDVILAE----------YVSHRVGRLGP--GDIVFVRSP 77
          + ++ P      SM+PTL L GD IL E          Y    +    P  GDIV  + P
Sbjct: 3  SFIYEPFQIPSGSMMPTL-LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP 61

Query: 78 VDPNKIVTKRIVGVEGDRVTY 98
           DP     KR VG+ GD+VTY
Sbjct: 62 EDPKLDYIKRAVGLPGDKVTY 82

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	160
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	100.0
1kca_A	109	Repressor protein CI; gene regulation, DNA-binding	99.43
1umu_A	116	UMUD'; induced mutagenesis, SOS mutagenesis, DNA r	99.2
2hnf_A	133	Repressor protein CI101-229DM-K192A; viral protein	99.04
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	98.98
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	98.97
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	98.7
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	97.14
3v2d_O	122	50S ribosomal protein L14; ribosome associated inh	85.67
3r8s_K	122	50S ribosomal protein L14; protein biosynthesis, R	83.77
3bbo_M	121	Ribosomal protein L14; large ribosomal subunit, sp	81.33
1whi_A	122	Ribosomal protein L14; rRNA-binding; 1.50A {Geobac	80.35

>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=1.1e-37  Score=240.70  Aligned_cols=127  Identities=35%  Similarity=0.472  Sum_probs=108.1

Q ss_pred             HhhceEEeEEEeCCCCccccCCCCcEEEEEecccC------------CCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCE
Q 031410           28 TNHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHR------------VGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDR   95 (160)
Q Consensus        28 ~~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~------------~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~   95 (160)
                      ++.|+++++.|.|+||+|||+ .||++++++.++.            ..++++||+|+|+.|.+++..+||||+|+|||+
T Consensus         1 ir~fv~~~~~v~g~SM~Ptl~-~GD~vlv~k~~yg~r~P~~~~~l~~~~~~~rGDIvvf~~p~~~~~~~iKRViglpGD~   79 (248)
T 1b12_A            1 VRSFIYEPFQIPSGSMMPTLL-IGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDK   79 (248)
T ss_dssp             -CBCCEEEEECCSCTTTTTSC-TTEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTTCTTSEEEEEEEECTTCE
T ss_pred             CeEEEEEEEEecccccccccc-CCCEEEEEecccCcccccccccccccCCCCCCcEEEEEeCCCCCceEEEEEEeeCCCE
Confidence            457899999999999999999 9999999997643            258999999999998877889999999999999


Q ss_pred             EEEecC-------------------CCC--------C-------------------------------------------
Q 031410           96 VTYFKP-------------------RNG--------D-------------------------------------------  105 (160)
Q Consensus        96 v~~~~~-------------------~~~--------~-------------------------------------------  105 (160)
                      |+++++                   ...        .                                           
T Consensus        80 v~i~~~~~~l~ING~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ip~~~~~~~~~~~~~~~e~l~~~~  159 (248)
T 1b12_A           80 VTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVT  159 (248)
T ss_dssp             EEEETTTTEEEEETTCCSSCCCCCCCCEEECCCEEEEEEEEEECGGGSCEEEEEEECCTTCCCTTEEEEEEEEEEETTEE
T ss_pred             EEEEcCceEEEECCccccccccccceeeeeeccccccccccccccccccccccccccccccccccchhhhhHHhhhcCcc
Confidence            998754                   100        0                                           


Q ss_pred             ----------------------CcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCCCCC
Q 031410          106 ----------------------SCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSF  156 (160)
Q Consensus       106 ----------------------~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~~~~  156 (160)
                                            ...+++||+|+|||||||+++|.|||+||+||+++|+|||.++ +||+++.
T Consensus       160 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~VP~g~yFvmGDNR~nS~DSR~~G~Vp~~~IvGka~~i-~~s~~~~  231 (248)
T 1b12_A          160 HRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAI-WMSFDKQ  231 (248)
T ss_dssp             EEEEECTTCCCCGGGSCCCTTCCTTEEECCTTEEEEECSBTTSCCCHHHHCCEEGGGEEEEEEEE-EEEBC--
T ss_pred             ceeEecCCccccccchhcccccccccEEeCCCcEEEecCCCcccCCCCcccccCHHHeEEEEEEE-EEeCCcc
Confidence                                  0124689999999999999999999999999999999999999 8776643

>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=99.43  E-value=1.8e-12  Score=87.75  Aligned_cols=90  Identities=26%  Similarity=0.355  Sum_probs=70.7

Q ss_pred             EeEEEeCCCCc------cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCc
Q 031410           34 SPTLVFGPSML------PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSC  107 (160)
Q Consensus        34 ~~~~v~g~SM~------Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~  107 (160)
                      ..++|.|+||+      |+|. +||++++++.    .+++.||+|++..++  ++.++||+...+               
T Consensus        14 f~~~V~GdSM~~~~g~~p~i~-~Gd~v~Vd~~----~~~~~Gdivv~~~~~--~~~~vKrl~~~~---------------   71 (109)
T 1kca_A           14 FWLEVEGNSMTAPTGSKPSFP-DGMLILVDPE----QAVEPGDFCIARLGG--DEFTFKKLIRDS---------------   71 (109)
T ss_dssp             EEEECCSSTTCCCTTCSSCCC-TTCEEEEETT----SCCCTTCEEEEECST--TCEEEEEEEEET---------------
T ss_pred             EEEEEeCcCcCCCCCCCCeeC-CCCEEEEecC----CcCCCCCEEEEEECC--CeEEEEEEEEeC---------------
Confidence            45789999999      9998 9999999873    469999999999743  478999999754               


Q ss_pred             ceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCCCCCc
Q 031410          108 HTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFG  157 (160)
Q Consensus       108 ~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~~~~~  157 (160)
                             |++++.+||+...  .....  ..-+|+|+|.+. +||+..||
T Consensus        72 -------~~~~L~s~N~~y~--~~~~~--~~~~IiG~Vv~~-~~~~~~~~  109 (109)
T 1kca_A           72 -------GQVFLQPLNPQYP--MIPCN--ESCSVVGKVIAS-QWPEETFG  109 (109)
T ss_dssp             -------TEEEEECSSTTSC--CEECC--TTCEEEEEEEEE-ECCGGGGC
T ss_pred             -------CEEEEEECCCCCC--CEEcC--CCcEEEEEEEEE-EeCHHHcC
Confidence                   3788899986322  12111  356799999999 99987775

>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=99.20  E-value=1.4e-10  Score=79.06  Aligned_cols=87  Identities=16%  Similarity=0.085  Sum_probs=62.9

Q ss_pred             EEeEEEeCCCCcc-ccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410           33 WSPTLVFGPSMLP-TLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV  111 (160)
Q Consensus        33 ~~~~~v~g~SM~P-tl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~  111 (160)
                      .....|.|+||+| +++ +||++++++.    .+++.||+|++..+   ++.++||+...+                   
T Consensus        27 ~~~~~v~GdSM~p~~i~-~Gd~v~vd~~----~~~~~gdivv~~~~---~~~~vKr~~~~~-------------------   79 (116)
T 1umu_A           27 TYFVKASGDSMIDGGIS-DGDLLIVDSA----ITASHGDIVIAAVD---GEFTVKKLQLRP-------------------   79 (116)
T ss_dssp             EEEEECCSSTTGGGTCC-TTCEEEEETT----SCCCTTCEEEEEET---TEEEEEEEECSS-------------------
T ss_pred             EEEEEECCCCcCCCCCC-CCCEEEEEcC----CCCCCCCEEEEEEC---CEEEEEEEEeCC-------------------
Confidence            4568999999999 898 9999999873    36899999999973   378999998732                   


Q ss_pred             ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCC
Q 031410          112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPP  153 (160)
Q Consensus       112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~  153 (160)
                          .+++.+||+..  .......-..-+|+|+|.+. +..+
T Consensus        80 ----~~~L~s~N~~y--~~~~i~~~~~~~IiG~Vv~~-~r~~  114 (116)
T 1umu_A           80 ----TVQLIPMNSAY--SPITISSEDTLDVFGVVIHV-VKAA  114 (116)
T ss_dssp             ----SCEEECSSTTS--CCEECCTTSCEEEEEEEEEE-EC--
T ss_pred             ----cEEEECCCCCC--CCEEcCCCCeEEEEEEEEEE-EEec
Confidence                56788888632  12111111234699999997 5544

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

Probab=99.04  E-value=2.2e-09  Score=74.78  Aligned_cols=82  Identities=21%  Similarity=0.199  Sum_probs=62.3

Q ss_pred             EeEEEeCCCCc------cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCc
Q 031410           34 SPTLVFGPSML------PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSC  107 (160)
Q Consensus        34 ~~~~v~g~SM~------Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~  107 (160)
                      ...+|.|+||+      |+|. +||++++++.    .+++.||+|++...+  ++..+||+...+               
T Consensus        45 f~~~V~GdSM~~~~g~~p~i~-~Gd~v~vd~~----~~~~~Gdivv~~~~~--~~~~vKrl~~~~---------------  102 (133)
T 2hnf_A           45 FWLEVEGNSMTTPTGSKTSFP-DGMLILVDPE----QAVEPGDFCIARLGG--DEFTFAKLIRDS---------------  102 (133)
T ss_dssp             EEEECCSSTTCCC---CCCCC-TTCEEEEETT----SCCCTTSEEEEEETT--TEEEEEEEEEET---------------
T ss_pred             EEEEEeCCCcCCCcCCCCccC-CCCEEEEccC----CCCCCCCEEEEEECC--CEEEEEEEEEeC---------------
Confidence            45789999999      9998 9999999973    478999999999743  478999998744               


Q ss_pred             ceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          108 HTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       108 ~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                             |.+++.+||+...  .....  ..-+|+|+|.+.
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                   3677889986321  11111  345799999873

>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=98.98  E-value=5.4e-09  Score=77.38  Aligned_cols=86  Identities=21%  Similarity=0.177  Sum_probs=62.3

Q ss_pred             EeEEEeCCCCccc-cCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEc
Q 031410           34 SPTLVFGPSMLPT-LNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVV  112 (160)
Q Consensus        34 ~~~~v~g~SM~Pt-l~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~v  112 (160)
                      ....|.|+||+|+ +. +||++++++.    .+++.||+|++..   +++..+||+. .+|+                  
T Consensus       111 ~~~~v~GdSM~p~~i~-~Gd~v~vd~~----~~~~~G~i~v~~~---~~~~~vKrl~-~~~~------------------  163 (202)
T 1jhf_A          111 FLLRVSGMSMKDIGIM-DGDLLAVHKT----QDVRNGQVVVARI---DDEVTVKRLK-KQGN------------------  163 (202)
T ss_dssp             EEEECCSSTTGGGTCC-TTCEEEEEEC----SCCCTTSEEEEEE---TTEEEEEEEE-EETT------------------
T ss_pred             EEEEECCCCCCCCCCC-CCCEEEEecc----CCcCCCeEEEEEE---CCEEEEEEEE-EeCC------------------
Confidence            4678999999999 98 9999999873    4689999999997   3478999998 4554                  


Q ss_pred             cCCcEEEEcCCCCCCCCCCccc-ceeCCCeEEEEEEEEecC
Q 031410          113 PKGHVWIQGDNLYASRDSRQFG-PVPYGLIEGKAFFRQVWP  152 (160)
Q Consensus       113 p~~~~~v~gdn~~~s~DSR~~G-~V~~~~I~G~v~~~~~~p  152 (160)
                         .+++.+||+..  ...... .-..-.|+|+|.+. +..
T Consensus       164 ---~~~l~s~N~~y--~~~~~~~~~~~~~IiG~Vv~~-~r~  198 (202)
T 1jhf_A          164 ---KVELLPENSEF--KPIVVDLRQQSFTIEGLAVGV-IRN  198 (202)
T ss_dssp             ---EEEEECSSTTC--CCEEEETTTSCEEEEEEEEEE-EEC
T ss_pred             ---EEEEEECCCCC--CCEEccCCCCceEEEEEEEEE-EEc
Confidence               67778888532  121110 00123599999987 544

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

Probab=98.97  E-value=2.5e-09  Score=80.74  Aligned_cols=90  Identities=26%  Similarity=0.362  Sum_probs=68.4

Q ss_pred             EeEEEeCCCCc------cccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCc
Q 031410           34 SPTLVFGPSML------PTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSC  107 (160)
Q Consensus        34 ~~~~v~g~SM~------Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~  107 (160)
                      ....|.|+||+      |++. +||++++++-    .+++.||+|++..  +.++..+||+...+|              
T Consensus       141 ~~l~V~GdSM~~~~g~~P~i~-~Gd~v~vd~~----~~~~~g~ivv~~~--~~~~~~vKrl~~~~~--------------  199 (236)
T 3bdn_A          141 FWLEVEGNSMTAPTGSKPSFP-DGMLILVDPE----QAVEPGDFCIARL--GGDEFTFKKLIRGSG--------------  199 (236)
T ss_dssp             EEEECCSSSSCCCSSCSSCCC-SSCEEEECCS----SCCCTTSEEEEES--TTTCCCCEEEECCSS--------------
T ss_pred             EEEEEeCCCcCCCCCCCCcCC-CCCEEEECCC----CCCCCCcEEEEEE--CCCeEEEEEEEEcCC--------------
Confidence            35689999999      9998 9999999872    3789999999987  234789999987443              


Q ss_pred             ceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCCCCCc
Q 031410          108 HTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFG  157 (160)
Q Consensus       108 ~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~~~~~  157 (160)
                              .+++.+||+..  .....-  ..-.|+|+|++. .||...|+
T Consensus       200 --------~~~L~s~N~~y--~~~~~~--~~~~IiG~Vv~~-~~~~~~~~  236 (236)
T 3bdn_A          200 --------QVFLQPLNPQY--PMIPCN--ESCSVVGKVIAS-QWPEETFG  236 (236)
T ss_dssp             --------SCEEECSSTTS--CCBC----CCCEEEEEEEEC-CCCSSSCC
T ss_pred             --------cEEEEeCCCCC--CCeecC--CCcEEEEEEEEE-EcCHHhcC
Confidence                    67788888632  222111  345799999999 99988775

>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=98.70  E-value=3e-07  Score=67.76  Aligned_cols=83  Identities=23%  Similarity=0.124  Sum_probs=62.0

Q ss_pred             EEeEEEeCCCC-ccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEE
Q 031410           33 WSPTLVFGPSM-LPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVV  111 (160)
Q Consensus        33 ~~~~~v~g~SM-~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~  111 (160)
                      ....+|.|+|| +|++. +||++++++-    ..++.||+|++...   ++..+||+.-.+                   
T Consensus       109 ~f~l~v~GdSM~~p~i~-~GD~viv~~~----~~~~~G~ivv~~~~---~~~~vKr~~~~~-------------------  161 (196)
T 3k2z_A          109 HFLLKVKGESMIEEHIC-DGDLVLVRRQ----DWAQNGDIVAAMVD---GEVTLAKFYQRG-------------------  161 (196)
T ss_dssp             EEEEECCSSTTGGGTCC-TTCEEEEEEC----SCCCTTCEEEEEET---TEEEEEEEEEET-------------------
T ss_pred             EEEEEEeCCCcCCCCCC-CCCEEEEecc----CcCCCCCEEEEEEC---CcEEEEEEEEEC-------------------
Confidence            45679999999 69998 9999999973    47899999999973   489999997643                   


Q ss_pred             ccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          112 VPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                         |.+++..+|+...  ....- -..-.|+|+|.+.
T Consensus       162 ---~~~~L~~~N~~y~--~i~i~-~~~~~i~G~Vv~~  192 (196)
T 3k2z_A          162 ---DTVELRPANREMS--SMFFR-AEKVKILGKVVGV  192 (196)
T ss_dssp             ---TEEEEECSCTTSC--CEEEE-GGGCEEEEEEEEE
T ss_pred             ---CEEEEEECCCCCC--CEEec-CCCEEEEEEEEEE
Confidence               3678888886321  11111 1234799999886

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

Probab=97.14  E-value=0.0027  Score=45.68  Aligned_cols=72  Identities=10%  Similarity=0.126  Sum_probs=49.3

Q ss_pred             CCCccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEccCCcEEEE
Q 031410           41 PSMLPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVVPKGHVWIQ  120 (160)
Q Consensus        41 ~SM~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~vp~~~~~v~  120 (160)
                      .+|...-. +||++++++   .  .+..|+++++..   .++..+||+.-.+|+                     .+.+.
T Consensus       113 ~~~~~v~~-~Gd~v~Vd~---~--~~~~g~i~vv~~---~g~~~vKrl~~~~~~---------------------~i~L~  162 (189)
T 2fjr_A          113 TDGMAIRS-EGKIYFVDK---Q--ASLSDGLWLVDI---KGAISIRELTKLPGR---------------------KLHVA  162 (189)
T ss_dssp             SSEEEEEE-TTEEEEEET---T--CCSCSEEEEEEE---TTEEEEEEEEEETTT---------------------EEEEE
T ss_pred             CCeEEEee-CCcEEEEEc---C--CccCCCEEEEEe---CCeEEEEEEEECCCC---------------------EEEEE
Confidence            34554344 899999987   2  477899999987   347899999886654                     56677


Q ss_pred             cCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          121 GDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       121 gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                      +||+    + ...-. ..-.|+|+|++.
T Consensus       163 s~N~----~-~~i~~-~~i~IiG~Vv~~  184 (189)
T 2fjr_A          163 GGKV----P-FECGI-DDIKTLGRVVGV  184 (189)
T ss_dssp             SSSS----C-EEEET-TSSEEEEEEEEE
T ss_pred             eCCC----C-eEecc-cceEEEEEEEEE
Confidence            7775    1 11111 334599999886

>3v2d_O 50S ribosomal protein L14; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2j03_O 2jl6_O 2jl8_O 2v47_O 2v49_O 2wdi_O 2wdj_O 2wdl_O 2wdn_O 2wh2_O 2wh4_O 2wrj_O 2wrl_O 2wro_O 2wrr_O 2x9s_O 2x9u_O 2xg0_O 2xg2_O 2xqe_O ...

Probab=85.67  E-value=6.2  Score=26.46  Aligned_cols=85  Identities=26%  Similarity=0.309  Sum_probs=45.0

Q ss_pred             EeEEEeCCCCccccCCCCcEEEEE-ecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEc
Q 031410           34 SPTLVFGPSMLPTLNLTGDVILAE-YVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVV  112 (160)
Q Consensus        34 ~~~~v~g~SM~Ptl~~~Gd~vlv~-~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~v  112 (160)
                      ....+.|.+-...-. -||.+++. +-......+++||++-.-.-...     |-+-...|-.+.+              
T Consensus        20 ~cI~Vlg~~~rr~a~-iGD~IvvsVK~~~p~~~vKkg~v~~AVIVRtk-----k~~rR~dG~~i~F--------------   79 (122)
T 3v2d_O           20 MCIRVLKGSNAKYAT-VGDVIVASVKEAIPRGAVKEGDVVKAVVVRTK-----KEIKRPDGSAIRF--------------   79 (122)
T ss_dssp             EEEEEESTTTCCCBC-TTCEEEEEEEEECSSSSSCTTCEEEEEEEECS-----SCEECTTSCEEEE--------------
T ss_pred             EEEEEeCCCCCcccC-CCCEEEEEEEEcCCCCccccCCEEEEEEEEeC-----CccCCCCCcEEEc--------------
Confidence            445666665555554 67777763 11111234667776422110000     1111223444444              


Q ss_pred             cCCcEEEEcCCCCCCCCCCcccceeCC
Q 031410          113 PKGHVWIQGDNLYASRDSRQFGPVPYG  139 (160)
Q Consensus       113 p~~~~~v~gdn~~~s~DSR~~G~V~~~  139 (160)
                      .+|..-++.++. +..-+|-||||++|
T Consensus        80 ddNa~Vlin~~~-~p~GTrI~GpVarE  105 (122)
T 3v2d_O           80 DDNAAVIINNQL-EPRGTRVFGPVARE  105 (122)
T ss_dssp             SSCEEEEECTTS-CBSSSCBCSCBCTH
T ss_pred             CCcEEEEECCCC-CEeeeEEEccchHH
Confidence            445666666654 78899999999986

>3r8s_K 50S ribosomal protein L14; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3j19_K 3oat_K* 3oas_K* 3ofd_K 3ofc_K 3ofr_K* 3ofz_K* 3og0_K 3ofq_K 3r8t_K 3i1n_K 1p85_I 1p86_I 1vs8_K 1vs6_K 2aw4_K 2awb_K 1vt2_K 2i2v_K 2i2t_K* ...

Probab=83.77  E-value=6.5  Score=26.38  Aligned_cols=87  Identities=22%  Similarity=0.259  Sum_probs=46.0

Q ss_pred             EeEEEeCCCCccccCCCCcEEEEE-ecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEc
Q 031410           34 SPTLVFGPSMLPTLNLTGDVILAE-YVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVV  112 (160)
Q Consensus        34 ~~~~v~g~SM~Ptl~~~Gd~vlv~-~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~v  112 (160)
                      ....+.|.+-...-. -||.+++. +-......+++||++-.-.-..  .   |-+-...|-.+.+              
T Consensus        20 ~cI~Vlgg~~r~~a~-iGD~IvvsVK~~~p~~~vkkg~v~~AVIVRt--k---k~~rR~dG~~i~F--------------   79 (122)
T 3r8s_K           20 MCIKVLGGSHRRYAG-VGDIIKITIKEAIPRGKVKKGDVLKAVVVRT--K---KGVRRPDGSVIRF--------------   79 (122)
T ss_dssp             EEEEECSSSSCCCBC-TTCEEEEEEEEECTTSSSCTTCEEEEEEEEC--S---SCEECTTSCEEEE--------------
T ss_pred             EEEEEeCCCCCCccc-CCCEEEEEEEEcCCCCccccCCEEEEEEEEe--C---CcCCCCCCcEEEc--------------
Confidence            445666665555554 67777763 1111123456677542211000  0   0111223444444              


Q ss_pred             cCCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410          113 PKGHVWIQGDNLYASRDSRQFGPVPYGL  140 (160)
Q Consensus       113 p~~~~~v~gdn~~~s~DSR~~G~V~~~~  140 (160)
                      .+|..-++.++..+..-+|-||||++|.
T Consensus        80 ddNa~Vlin~~~g~p~GTrI~GpVarEl  107 (122)
T 3r8s_K           80 DGNACVLLNNNSEQPIGTRIFGPVTREL  107 (122)
T ss_dssp             SSCEEEEEETTTEEESCSCBCSCCCGGG
T ss_pred             CCceEEEEeCCCCCEeeeEEEccccHHH
Confidence            4456667776634678899999999863

>3bbo_M Ribosomal protein L14; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=81.33  E-value=9.1  Score=25.60  Aligned_cols=27  Identities=19%  Similarity=0.283  Sum_probs=19.7

Q ss_pred             cCCcEEEEcCCCCCCCCCCcccceeCCC
Q 031410          113 PKGHVWIQGDNLYASRDSRQFGPVPYGL  140 (160)
Q Consensus       113 p~~~~~v~gdn~~~s~DSR~~G~V~~~~  140 (160)
                      .+|..-++.++ .+..-+|-||||++|.
T Consensus        80 ddNa~Vlin~~-g~p~GTrI~GPVarEl  106 (121)
T 3bbo_M           80 DDNAAVIIDQE-GNPKGTRIFGAIAREL  106 (121)
T ss_dssp             SSCEEEECCTT-SSCSSSCCCSCCCGGG
T ss_pred             CCceEEEECCC-CCEeEeEEEcCcCHHH
Confidence            44566666655 3788999999999864

>1whi_A Ribosomal protein L14; rRNA-binding; 1.50A {Geobacillus stearothermophilus} SCOP: b.39.1.1 PDB: 1giy_N 1ml5_n* 1c04_D 1yl3_N 2b66_O 2b9n_O 2b9p_O 487d_M

Probab=80.35  E-value=10  Score=25.38  Aligned_cols=27  Identities=30%  Similarity=0.450  Sum_probs=20.2

Q ss_pred             ccCCcEEEEcCCCCCCCCCCcccceeCC
Q 031410          112 VPKGHVWIQGDNLYASRDSRQFGPVPYG  139 (160)
Q Consensus       112 vp~~~~~v~gdn~~~s~DSR~~G~V~~~  139 (160)
                      ..+|..-++.++. +..-+|-||||++|
T Consensus        79 FddNa~Vlin~~g-~p~GTrI~GPVarE  105 (122)
T 1whi_A           79 FDENACVIIRDDK-SPRGTRIFGPVARE  105 (122)
T ss_dssp             CSSCEEEEECTTS-CBSSSCBCSCBCTH
T ss_pred             eCCceEEEECCCC-CEeeeEEEccchHH
Confidence            3455666666664 78889999999976

---

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	160
d1b12a_	247	b.87.1.2 (A:) Type 1 signal peptidase {Escherichia	2e-11
d1b12a_	247	b.87.1.2 (A:) Type 1 signal peptidase {Escherichia	1e-04

>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 = 58.4 bits (140), Expect = 2e-11
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 94  DRVTYFKPRNGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPP 153
           D+V  +  + G    T +VP G  ++ GDN   S DSR +G VP   + G+A        
Sbjct: 169 DQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAI-WMSF 227

Query: 154 NS 155
           + 
Sbjct: 228 DK 229

>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 = 38.8 bits (89), Expect = 1e-04
 Identities = 29/81 (35%), Positives = 40/81 (49%), Gaps = 13/81 (16%)

Query: 31 YLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRV------------GRLGPGDIVFVRSPV 78
          +++ P  +   SM+PTL L GD IL E  ++ +            G    GDIV  + P 
Sbjct: 3  FIYEPFQIPSGSMMPTL-LIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE 61

Query: 79 DPNKIVTKRIVGVEGDRVTYF 99
          DP     KR VG+ GD+VTY 
Sbjct: 62 DPKLDYIKRAVGLPGDKVTYD 82

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	160
d1b12a_	247	Type 1 signal peptidase {Escherichia coli [TaxId:	100.0
d1f39a_	101	lambda repressor C-terminal domain {Bacteriophage	99.21
d1jhfa2	126	LexA C-terminal domain {Escherichia coli [TaxId: 5	98.92
d1umua_	105	UmuD' {Escherichia coli [TaxId: 562]}	98.7

>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-38  Score=243.73  Aligned_cols=124  Identities=36%  Similarity=0.520  Sum_probs=109.4

Q ss_pred             hhceEEeEEEeCCCCccccCCCCcEEEEEecccCC------------CCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEE
Q 031410           29 NHYLWSPTLVFGPSMLPTLNLTGDVILAEYVSHRV------------GRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRV   96 (160)
Q Consensus        29 ~~~~~~~~~v~g~SM~Ptl~~~Gd~vlv~~~~~~~------------~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v   96 (160)
                      +.|+++++.|+++||+|||. .||+++++|++|..            ..+++||+|+|..|.++...++|||+|+|||++
T Consensus         1 R~f~~~~f~IPs~SMePTL~-~GD~l~V~K~~Yg~r~P~~~~~~~~~~~~~rgdivvf~~p~~~~~~~ikR~ig~pGD~i   79 (247)
T d1b12a_           1 RSFIYEPFQIPSGSMMPTLL-IGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKV   79 (247)
T ss_dssp             CBCCEEEEECCSCTTTTTSC-TTEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTTCTTSEEEEEEEECTTCEE
T ss_pred             CEEEEEEEEeCcccccchhc-cCCEEEEEccccCccCCccCcccccccCcccCceeeecCCCCCCccccccccCCCCCeE
Confidence            36899999999999999999 99999999987654            356999999999999888999999999999999


Q ss_pred             EEecCC--------------------------------------------------------------------------
Q 031410           97 TYFKPR--------------------------------------------------------------------------  102 (160)
Q Consensus        97 ~~~~~~--------------------------------------------------------------------------  102 (160)
                      .+.+..                                                                          
T Consensus        80 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (247)
T d1b12a_          80 TYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTH  159 (247)
T ss_dssp             EEETTTTEEEEETTCCSSCCCCCCCCEEECCCEEEEEEEEEECGGGSCEEEEEEECCTTCCCTTEEEEEEEEEEETTEEE
T ss_pred             EEecccceEEecccccccceeecceeecccccCcccceeeeeeccCceeccceeeccccccccCceEeeeeeeccCCcce
Confidence            886310                                                                          


Q ss_pred             ------------------CCCCcceEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCCC
Q 031410          103 ------------------NGDSCHTVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPN  154 (160)
Q Consensus       103 ------------------~~~~~~~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~~  154 (160)
                                        .......++||+|+||||||||++|.|||+||+||+++|+|||.++ +||++
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Vp~~~yfvmGDNR~nS~DSR~wG~Vp~~~I~Gka~~i-~~p~~  228 (247)
T d1b12a_         160 RILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAI-WMSFD  228 (247)
T ss_dssp             EEEECTTCCCCGGGSCCCTTCCTTEEECCTTEEEEECSBTTSCCCHHHHCCEEGGGEEEEEEEE-EEEBC
T ss_pred             eEEecccchhcccccccCCccccceEEEeCCeEEEecCCCCCCccccccCcCCHHHeEEEEEEE-EEECC
Confidence                              0122357899999999999999999999999999999999999999 99965

>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=99.21  E-value=8.4e-11  Score=76.83  Aligned_cols=89  Identities=26%  Similarity=0.369  Sum_probs=68.1

Q ss_pred             eEEEeCCCC------ccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcc
Q 031410           35 PTLVFGPSM------LPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCH  108 (160)
Q Consensus        35 ~~~v~g~SM------~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~  108 (160)
                      ..+|.|+||      +|+++ +||++++++-    .+++.||+|++...  .++..+||+.-.+                
T Consensus         7 ~l~V~GdSM~~~~~~ep~i~-~Gd~viVd~~----~~~~~g~ivva~~~--~~~~~vKr~~~~~----------------   63 (101)
T d1f39a_           7 WLEVEGNSMTAPTGSKPSFP-DGMLILVDPE----QAVEPGDFCIARLG--GDEFTFKKLIRDS----------------   63 (101)
T ss_dssp             EEECCSSTTCCCTTCSSCCC-TTCEEEEETT----SCCCTTCEEEEECT--TSCEEEEEEEEET----------------
T ss_pred             EEEEeCCccCCCcccCCCcC-CCCEEEEEec----CccCCCCEEEEEEC--CCeEEEEEEEEcC----------------
Confidence            468999999      79998 9999999972    57899999988763  3467899998644                


Q ss_pred             eEEccCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEEEecCCCCCc
Q 031410          109 TVVVPKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFRQVWPPNSFG  157 (160)
Q Consensus       109 ~~~vp~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~~~~p~~~~~  157 (160)
                            +++++.++|+..  ......  ..-.|+|+|+.. .||-..||
T Consensus        64 ------~~~~L~s~N~~y--~~i~~~--~~~~IiG~Vv~s-~~p~~~~~  101 (101)
T d1f39a_          64 ------GQVFLQPLNPQY--PMIPCN--ESCSVVGKVIAS-QWPEETFG  101 (101)
T ss_dssp             ------TEEEEECSSTTS--CCEECS--TTCEEEEEEEEE-ECCGGGGC
T ss_pred             ------CEEEEEECCCCC--CCCcCC--CCcEEEEEEEEE-ECcHHHCC
Confidence                  378888898642  222111  245799999999 99988776

>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=98.92  E-value=6.4e-09  Score=70.19  Aligned_cols=83  Identities=20%  Similarity=0.132  Sum_probs=61.6

Q ss_pred             EeEEEeCCCCccc-cCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEc
Q 031410           34 SPTLVFGPSMLPT-LNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVV  112 (160)
Q Consensus        34 ~~~~v~g~SM~Pt-l~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~v  112 (160)
                      ...+|.|+||+|+ +. +||++++++-    .+++.||+|++..   +++..+||+.-.+                    
T Consensus        39 f~lrV~GdSM~~~~i~-~gd~viv~~~----~~~~~G~ivv~~~---~ge~~vKrl~~~~--------------------   90 (126)
T d1jhfa2          39 FLLRVSGMSMKDIGIM-DGDLLAVHKT----QDVRNGQVVVARI---DDEVTVKRLKKQG--------------------   90 (126)
T ss_dssp             EEEECCSSTTGGGTCC-TTCEEEEEEC----SCCCTTSEEEEEE---TTEEEEEEEEEET--------------------
T ss_pred             EEEEEcCCcccCcccC-CCEEEEEecc----ccccCCCEEEEEE---CCEEEEEEEEEcC--------------------
Confidence            4579999999997 88 9999999872    5899999999998   3478999998754                    


Q ss_pred             cCCcEEEEcCCCCCCCCCCccc-ceeCCCeEEEEEEE
Q 031410          113 PKGHVWIQGDNLYASRDSRQFG-PVPYGLIEGKAFFR  148 (160)
Q Consensus       113 p~~~~~v~gdn~~~s~DSR~~G-~V~~~~I~G~v~~~  148 (160)
                        |.+++.++|+..+  ...+. .=..=.|+|+|...
T Consensus        91 --~~~~L~s~N~~y~--pi~~~~~~~~~~IiG~Vv~v  123 (126)
T d1jhfa2          91 --NKVELLPENSEFK--PIVVDLRQQSFTIEGLAVGV  123 (126)
T ss_dssp             --TEEEEECSSTTCC--CEEEETTTSCEEEEEEEEEE
T ss_pred             --CEEEEecCCcCCC--CeEccCCCCcEEEEEEEEEE
Confidence              3788888986432  11110 00112599999886

>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=98.70  E-value=7.4e-08  Score=62.87  Aligned_cols=82  Identities=16%  Similarity=0.078  Sum_probs=59.8

Q ss_pred             EeEEEeCCCC-ccccCCCCcEEEEEecccCCCCCCCCcEEEEeeCCCCCceEEEEEEeeCCCEEEEecCCCCCCcceEEc
Q 031410           34 SPTLVFGPSM-LPTLNLTGDVILAEYVSHRVGRLGPGDIVFVRSPVDPNKIVTKRIVGVEGDRVTYFKPRNGDSCHTVVV  112 (160)
Q Consensus        34 ~~~~v~g~SM-~Ptl~~~Gd~vlv~~~~~~~~~~~~GDiVvf~~p~~~~~~~iKRVv~~~Gd~v~~~~~~~~~~~~~~~v  112 (160)
                      ...+|.|+|| .|.+. +||++++++-    .+++.||+|++..   +++..+||..- .                    
T Consensus        21 f~~rV~GdSM~~~gI~-~GDlliVd~~----~~~~~g~ivva~i---~ge~~vKrl~~-~--------------------   71 (105)
T d1umua_          21 YFVKASGDSMIDGGIS-DGDLLIVDSA----ITASHGDIVIAAV---DGEFTVKKLQL-R--------------------   71 (105)
T ss_dssp             EEEECCSSTTGGGTCC-TTCEEEEETT----SCCCTTCEEEEEE---TTEEEEEEEEC-S--------------------
T ss_pred             EEEEEcCCccccCccC-CCCEEEEEcc----cccccCcEEEEEE---CCEEEEEEEEE-C--------------------
Confidence            4589999999 58898 9999999983    5899999999998   45789999753 2                    


Q ss_pred             cCCcEEEEcCCCCCCCCCCcccceeCCCeEEEEEEE
Q 031410          113 PKGHVWIQGDNLYASRDSRQFGPVPYGLIEGKAFFR  148 (160)
Q Consensus       113 p~~~~~v~gdn~~~s~DSR~~G~V~~~~I~G~v~~~  148 (160)
                        ++.++..+|+.  ++.....+-..-.|.|+|...
T Consensus        72 --~~~~L~~~N~~--y~~i~i~~~~~~~I~GvVv~v  103 (105)
T d1umua_          72 --PTVQLIPMNSA--YSPITISSEDTLDVFGVVIHV  103 (105)
T ss_dssp             --SSCEEECSSTT--SCCEECCTTSCEEEEEEEEEE
T ss_pred             --CcEEEECCCCC--CCCEEcCCCCCEEEEEEEEEE
Confidence              24567778753  333322222233499999875