Citrus Sinensis ID: 028679

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-----
Protein Sequence
MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMRKDSPVLEVELDVDEMMKNHKA
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHcEEEEEEEHHHHHHcccHHHHHHHHHHHHHHcccEEEEEEEccccccccccccccEEEEEEEccccccccccccEEEEEccccccccEEEEEEEEcccEEEEcccccccEEEccccEEEEEcccccccccccccccccccccccEEEEEEEEEccccccccccccccccccccccccccccHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHcEEEEEEEHHHcccccccHHHHHHHHHHHHHHccEEEEEEcccccccccccccccEEEEEEEccccccccccccEEEEEcccccccEEEEEEEEEcccEEEccccccccEEEccccEEEEEccccccccccccccccccccHHHEEEEEEEEEEcccccccccccHHHccccccEEEEEEcHHHHHHcccc
Coil and Loop (DISEMBL)
MVSLSTWFRYIANKLEYSVSISwksytrgqindiELRDSVWKYLFQGKLtylygnkgdqmapvmgglGGTLLVrklpaadpkrvsvgdvvvmkdpeksdnYIVRRLAAIEGyemvstdekdepfvldkdecwvladnenmkpkeandsrtfgpvpmrniVGRAIYCLRTavdhgpvqnsndsmrkdspvleVELDVDEMMKNHKA
Flexible Loop (DISEMBL)
MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKlpaadpkrvsvgdvvvmkdpeksdnyiVRRLAAIEGYemvstdekdepfvLDKDECWVLadnenmkpkeandsrtfgpvpMRNIVGRAIYCLRTAVDhgpvqnsndsmrkdspvleveldvdemmknhka
Low Complexity Region (SEG)
MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMRKDSPVLEVELDVDEMMKNHKA
Disordered region (IsUnstruct)
***LSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLA****************GPVPMRNIVGRAIYCLRTAVD*********************************
Disordered Region (DISOPRED)
**SLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDS*RKDSPVLEVELDV*********
Disordered Region (DISEMBL)
MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMRKDSPVLEVELDVDEMMKNHKA
Disordered Region (DISPRO)
**SLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMRKDSPVLEVELDVDEMMKN***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMRKDSPVLEVELDVDEMMKNHKA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	205	2.2.26 [Sep-21-2011]
O74800	157	Mitochondrial inner membr	yes	no	0.565	0.738	0.293	2e-07
Q9CQU8	166	Mitochondrial inner membr	yes	no	0.458	0.566	0.277	0.0001
Q96LU5	166	Mitochondrial inner membr	yes	no	0.458	0.566	0.267	0.0004
Q28I39	167	Mitochondrial inner membr	yes	no	0.458	0.562	0.308	0.0006

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

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/126 (29%), Positives = 58/126 (46%), Gaps = 10/126 (7%)

Query: 40  VWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSD 99
           + +YLFQ ++T      G  M P +   G  +L+ KL     +  SVGDVVV   P  S 
Sbjct: 21  IHEYLFQVQMT-----SGPSMMPTLNSGGEFVLLDKLHGRFARSCSVGDVVVSAKPSDSK 75

Query: 100 NYIVRRLAAIEGYEM-VSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRN 158
            ++ +R+  + G  + V     ++   +     W+  DN       + DSR +GPVPM  
Sbjct: 76  QHVCKRIIGMPGDTIYVDPTSSNKKITIPLGHVWLAGDNI----AHSLDSRNYGPVPMGL 131

Query: 159 IVGRAI 164
           I  + I
Sbjct: 132 IKAKVI 137

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: 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 = 46.2 bits (108), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 7/101 (6%)

Query: 87  GDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKD---EPFVLDKDECWVLADNENMKPK 143
           GD+V+ K P    + I +R+  +EG +++ST   D       +     W+  DN     +
Sbjct: 66  GDIVIAKSPSDPKSNICKRVIGLEGDKILSTSPSDVFKSRSYVPTGHVWLEGDNL----Q 121

Query: 144 EANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMR 184
            + DSR +GP+P   I GR  + +    D G +++S +  R
Sbjct: 122 NSTDSRYYGPIPYGLIRGRIFFKIWPFSDFGFLRDSPNGQR 162

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

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

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

 Score = 44.7 bits (104), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/101 (26%), Positives = 48/101 (47%), Gaps = 7/101 (6%)

Query: 87  GDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKD---EPFVLDKDECWVLADNENMKPK 143
           GD+V+ K P    + I +R+  +EG ++++T   D       +     W+  DN     +
Sbjct: 66  GDIVIAKSPSDPKSNICKRVIGLEGDKILTTSPSDFFKSHSYVPMGHVWLEGDNL----Q 121

Query: 144 EANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMR 184
            + DSR +GP+P   I GR  + +    D G ++ S +  R
Sbjct: 122 NSTDSRCYGPIPYGLIRGRIFFKIWPLSDFGFLRASPNGHR 162

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

 Score = 44.3 bits (103), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 33/107 (30%), Positives = 53/107 (49%), Gaps = 13/107 (12%)

Query: 87  GDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDE----KDEPFVLDKDECWVLADNENMKP 142
           GD++V K P+K    I +R+  +EG ++  +      K   +V  K   W+  DN +   
Sbjct: 66  GDIIVAKSPDKPSVNICKRVIGLEGDKVCMSSPSALLKRHTYV-PKGHVWLEGDNLD--- 121

Query: 143 KEANDSRTFGPVPMRNIVGRAIYCLRT--AVDHGPVQNSNDSMRKDS 187
             + DSR++GPVP   I GR   CLR       GP++ S +   +D+
Sbjct: 122 -NSTDSRSYGPVPYALIRGRI--CLRVWPLESFGPLKESPNGRIQDN 165

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: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	205
224082818	205	predicted protein [Populus trichocarpa]	1.0	1.0	0.785	3e-90
225438115	205	PREDICTED: mitochondrial inner membrane	1.0	1.0	0.775	1e-89
224066245	205	predicted protein [Populus trichocarpa]	1.0	1.0	0.775	1e-89
388510892	205	unknown [Lotus japonicus]	1.0	1.0	0.765	7e-87
297744155	244	unnamed protein product [Vitis vinifera]	1.0	0.840	0.651	4e-84
449462419	205	PREDICTED: mitochondrial inner membrane	1.0	1.0	0.712	1e-83
449462417	211	PREDICTED: mitochondrial inner membrane	1.0	0.971	0.691	8e-82
38344766	206	OSJNBa0068L06.9 [Oryza sativa Japonica G	0.995	0.990	0.707	2e-80
357166900	206	PREDICTED: uncharacterized protein LOC10	0.995	0.990	0.692	3e-80
351724419	204	uncharacterized protein LOC100500100 [Gl	0.995	1.0	0.736	2e-78

>gi|224082818|ref|XP_002306852.1| predicted protein [Populus trichocarpa] gi|222856301|gb|EEE93848.1| predicted protein [Populus trichocarpa]

 Score =  336 bits (862), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 161/205 (78%), Positives = 181/205 (88%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQM 60
           MVS+STWFRYIANKL+YSVS+S+KSY  G IND E+ DSVWK L QGKLT+L+ NKG +M
Sbjct: 1   MVSVSTWFRYIANKLDYSVSLSYKSYKGGLINDKEVVDSVWKNLLQGKLTFLHWNKGQEM 60

Query: 61  APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEK 120
           AP +G  GGTLLVRKLP+ADP RV VGDVV++KDPEKSDN++VRRLAAIEGYEM STDEK
Sbjct: 61  APTIGDQGGTLLVRKLPSADPMRVFVGDVVLLKDPEKSDNFLVRRLAAIEGYEMASTDEK 120

Query: 121 DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 180
           DEPFVLDKDECWVLADNE +K KEANDSR FGP+ M NIVGR IYCL+TAVDHGPVQNS+
Sbjct: 121 DEPFVLDKDECWVLADNEKLKAKEANDSRKFGPISMSNIVGRVIYCLQTAVDHGPVQNSH 180

Query: 181 DSMRKDSPVLEVELDVDEMMKNHKA 205
            S RKDSPVLEVELDV+EM K+HKA
Sbjct: 181 FSSRKDSPVLEVELDVEEMAKHHKA 205

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225438115|ref|XP_002278029.1| PREDICTED: mitochondrial inner membrane protease subunit 1-like [Vitis vinifera]

 Score =  334 bits (856), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 159/205 (77%), Positives = 180/205 (87%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQM 60
           MVSLSTW RYIA+KLEYS+SISWKSY  GQI+D E+ D VWK LFQGKLTYL+ NKG +M
Sbjct: 1   MVSLSTWCRYIAHKLEYSISISWKSYKGGQISDREVGDVVWKNLFQGKLTYLHWNKGGEM 60

Query: 61  APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEK 120
           AP +G  GGTLLVRKLPAADP RV VGDVVV+KDPE+SDNY+VRRLAA+EGYEM STDEK
Sbjct: 61  APTIGEQGGTLLVRKLPAADPTRVFVGDVVVLKDPEESDNYLVRRLAAVEGYEMGSTDEK 120

Query: 121 DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 180
           DEPFVL+KD+CWVL+DNE +KP +ANDSR FGPVPM +IVGR IYCLRTAVDHG VQNS+
Sbjct: 121 DEPFVLEKDQCWVLSDNETLKPTQANDSRIFGPVPMSDIVGRVIYCLRTAVDHGRVQNSH 180

Query: 181 DSMRKDSPVLEVELDVDEMMKNHKA 205
            SMRKD+PVLE+ELDVDEM + HK 
Sbjct: 181 FSMRKDTPVLEIELDVDEMARRHKT 205

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224066245|ref|XP_002302044.1| predicted protein [Populus trichocarpa] gi|222843770|gb|EEE81317.1| predicted protein [Populus trichocarpa]

 Score =  334 bits (856), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 159/205 (77%), Positives = 181/205 (88%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQM 60
           M SLSTW RYIA+K EYS+S+S+KSY  G IN+ E+ D+VWK LFQGKLT+L+ NKG +M
Sbjct: 1   MASLSTWCRYIAHKFEYSLSLSYKSYKGGIINNKEVYDTVWKNLFQGKLTFLHWNKGQEM 60

Query: 61  APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEK 120
           AP +G  GGTLLVRKLP ADP RV VGDVV++KDPEKSDN++VRRLAAIEGYEMVSTDEK
Sbjct: 61  APTIGDQGGTLLVRKLPTADPMRVFVGDVVLLKDPEKSDNFLVRRLAAIEGYEMVSTDEK 120

Query: 121 DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 180
           D+PFVLDKDECWVLADN+ +KPKEANDSRTFG + M NIVGR IYCL+TAVDHGPVQNS+
Sbjct: 121 DDPFVLDKDECWVLADNDKLKPKEANDSRTFGSISMSNIVGRVIYCLQTAVDHGPVQNSH 180

Query: 181 DSMRKDSPVLEVELDVDEMMKNHKA 205
            SMRKDSPVLEVELDV+EM KNHKA
Sbjct: 181 FSMRKDSPVLEVELDVEEMAKNHKA 205

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388510892|gb|AFK43512.1| unknown [Lotus japonicus]

 Score =  325 bits (833), Expect = 7e-87,   Method: Compositional matrix adjust.
 Identities = 157/205 (76%), Positives = 175/205 (85%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQM 60
           MVSLSTWFRYI  KLEYSVS+SWK+Y RGQI + E+RD VWK  FQGKLTYL+ N+G++M
Sbjct: 1   MVSLSTWFRYIGYKLEYSVSLSWKNYKRGQIGEGEVRDLVWKNFFQGKLTYLHWNQGEEM 60

Query: 61  APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEK 120
           AP + G   TLLVRKLP ADP RV VGDVVV+KDP K DNY+VRRLAA+EGYEM STDEK
Sbjct: 61  APTIAGKVATLLVRKLPNADPTRVFVGDVVVLKDPWKPDNYLVRRLAAVEGYEMASTDEK 120

Query: 121 DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 180
           DEPFVL+KD+CWV+A+NE  KPKEANDSRTFGPV M +IVGR IYCLR AVDHG VQNS+
Sbjct: 121 DEPFVLEKDQCWVVAENEKFKPKEANDSRTFGPVQMTDIVGRVIYCLRNAVDHGRVQNSH 180

Query: 181 DSMRKDSPVLEVELDVDEMMKNHKA 205
            SM KDSPVLEVELDVDEM KNHKA
Sbjct: 181 YSMPKDSPVLEVELDVDEMAKNHKA 205

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744155|emb|CBI37125.3| unnamed protein product [Vitis vinifera]

 Score =  316 bits (809), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 159/244 (65%), Positives = 180/244 (73%), Gaps = 39/244 (15%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWK------------------------------------ 24
           MVSLSTW RYIA+KLEYS+SISWK                                    
Sbjct: 1   MVSLSTWCRYIAHKLEYSISISWKDGLRKQIEEKLHFEERLKTDFALMEEALSKRKRGKT 60

Query: 25  ---SYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADP 81
              SY  GQI+D E+ D VWK LFQGKLTYL+ NKG +MAP +G  GGTLLVRKLPAADP
Sbjct: 61  CLWSYKGGQISDREVGDVVWKNLFQGKLTYLHWNKGGEMAPTIGEQGGTLLVRKLPAADP 120

Query: 82  KRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMK 141
            RV VGDVVV+KDPE+SDNY+VRRLAA+EGYEM STDEKDEPFVL+KD+CWVL+DNE +K
Sbjct: 121 TRVFVGDVVVLKDPEESDNYLVRRLAAVEGYEMGSTDEKDEPFVLEKDQCWVLSDNETLK 180

Query: 142 PKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMRKDSPVLEVELDVDEMMK 201
           P +ANDSR FGPVPM +IVGR IYCLRTAVDHG VQNS+ SMRKD+PVLE+ELDVDEM +
Sbjct: 181 PTQANDSRIFGPVPMSDIVGRVIYCLRTAVDHGRVQNSHFSMRKDTPVLEIELDVDEMAR 240

Query: 202 NHKA 205
            HK 
Sbjct: 241 RHKT 244

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462419|ref|XP_004148938.1| PREDICTED: mitochondrial inner membrane protease subunit 1-like isoform 2 [Cucumis sativus] gi|449507880|ref|XP_004163156.1| PREDICTED: mitochondrial inner membrane protease subunit 1-like isoform 2 [Cucumis sativus]

 Score =  314 bits (804), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 146/205 (71%), Positives = 175/205 (85%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQM 60
           M S STW RYIANKLE+SVS+SWK+Y  G+I D E+  +VWK L QGKLTYL+  KG +M
Sbjct: 1   MASFSTWLRYIANKLEFSVSLSWKNYKGGRITDREVGHAVWKNLLQGKLTYLHWIKGQEM 60

Query: 61  APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEK 120
           AP +G  GGTLLVRKLP AD   V +GDVVV+K+PEK +NY+VRRLAA+EG+EM+STDEK
Sbjct: 61  APTVGEAGGTLLVRKLPDADSTSVFIGDVVVVKEPEKPENYLVRRLAAVEGHEMLSTDEK 120

Query: 121 DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 180
           D+PF L+KD+CW+LADNE +KPKEA DSRTFGPV M +IVGRAIYCLR+AVDHGPVQNS+
Sbjct: 121 DQPFTLEKDQCWLLADNEKLKPKEAYDSRTFGPVSMSDIVGRAIYCLRSAVDHGPVQNSD 180

Query: 181 DSMRKDSPVLEVELDVDEMMKNHKA 205
            SM++DSP+LE+ELDVDEM KNHKA
Sbjct: 181 FSMKRDSPILEIELDVDEMAKNHKA 205

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462417|ref|XP_004148937.1| PREDICTED: mitochondrial inner membrane protease subunit 1-like isoform 1 [Cucumis sativus] gi|449507877|ref|XP_004163155.1| PREDICTED: mitochondrial inner membrane protease subunit 1-like isoform 1 [Cucumis sativus]

 Score =  308 bits (789), Expect = 8e-82,   Method: Compositional matrix adjust.
 Identities = 146/211 (69%), Positives = 176/211 (83%), Gaps = 6/211 (2%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQM 60
           M S STW RYIANKLE+SVS+SWK+Y  G+I D E+  +VWK L QGKLTYL+  KG +M
Sbjct: 1   MASFSTWLRYIANKLEFSVSLSWKNYKGGRITDREVGHAVWKNLLQGKLTYLHWIKGQEM 60

Query: 61  APVMGGLGGTLLVRKLPAADP------KRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEM 114
           AP +G  GGTLLVRKLP AD       + V +GDVVV+K+PEK +NY+VRRLAA+EG+EM
Sbjct: 61  APTVGEAGGTLLVRKLPDADSTCFLVHRSVFIGDVVVVKEPEKPENYLVRRLAAVEGHEM 120

Query: 115 VSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHG 174
           +STDEKD+PF L+KD+CW+LADNE +KPKEA DSRTFGPV M +IVGRAIYCLR+AVDHG
Sbjct: 121 LSTDEKDQPFTLEKDQCWLLADNEKLKPKEAYDSRTFGPVSMSDIVGRAIYCLRSAVDHG 180

Query: 175 PVQNSNDSMRKDSPVLEVELDVDEMMKNHKA 205
           PVQNS+ SM++DSP+LE+ELDVDEM KNHKA
Sbjct: 181 PVQNSDFSMKRDSPILEIELDVDEMAKNHKA 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|38344766|emb|CAE01583.2| OSJNBa0068L06.9 [Oryza sativa Japonica Group] gi|116317777|emb|CAH65755.1| OSIGBa0123D13.4 [Oryza sativa Indica Group] gi|125546927|gb|EAY92749.1| hypothetical protein OsI_14504 [Oryza sativa Indica Group] gi|125589074|gb|EAZ29424.1| hypothetical protein OsJ_13497 [Oryza sativa Japonica Group] gi|215697911|dbj|BAG92153.1| unnamed protein product [Oryza sativa Japonica Group] gi|215737534|dbj|BAG96664.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  303 bits (777), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 145/205 (70%), Positives = 170/205 (82%), Gaps = 1/205 (0%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKG-DQ 59
           MVSLSTWFRY A+K EYS+S+SWK Y  GQIN  +L D+VWK  FQGKLTY++ NKG + 
Sbjct: 1   MVSLSTWFRYAAHKFEYSISLSWKKYNVGQINSTQLTDAVWKNFFQGKLTYMHWNKGGEA 60

Query: 60  MAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDE 119
           MAP+    GGTLLVRKL    P +V VGDVV++KDPEKSD+ IVRRLAA+EGYEMVS DE
Sbjct: 61  MAPIESTTGGTLLVRKLVNLSPTQVFVGDVVLLKDPEKSDDLIVRRLAALEGYEMVSNDE 120

Query: 120 KDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNS 179
           KDEPFVLDKD+CWVLADN+++KPKEA DSR FGPVPM +I+GR IY LRTAVDHGPV+NS
Sbjct: 121 KDEPFVLDKDQCWVLADNQSLKPKEARDSRLFGPVPMTDILGRVIYSLRTAVDHGPVENS 180

Query: 180 NDSMRKDSPVLEVELDVDEMMKNHK 204
             +M +DSPVL VELDV+EM KN+K
Sbjct: 181 RMAMNQDSPVLAVELDVEEMAKNNK 205

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357166900|ref|XP_003580907.1| PREDICTED: uncharacterized protein LOC100823230 [Brachypodium distachyon]

 Score =  303 bits (776), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 142/205 (69%), Positives = 170/205 (82%), Gaps = 1/205 (0%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKG-DQ 59
           MVSLSTWFRY A+K EYS+S+SWK Y  GQIN  EL D++WK  FQGKLT+ +  KG + 
Sbjct: 1   MVSLSTWFRYAAHKFEYSISLSWKKYNVGQINSTELTDAIWKSFFQGKLTFAHWTKGGEA 60

Query: 60  MAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDE 119
           MAP++   GGT+LVRKL A  PK+V VGD+V++KDPEKSD+ IVRRLAA+EGYE+VSTDE
Sbjct: 61  MAPIVAATGGTVLVRKLAALTPKQVFVGDIVLLKDPEKSDDLIVRRLAALEGYEIVSTDE 120

Query: 120 KDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNS 179
           KDEPFVLDKD+CWVLA+N+ +K KEA DSR FGPVPM +IVGR IY LRTAVDHGPV NS
Sbjct: 121 KDEPFVLDKDQCWVLAENQVLKAKEARDSRLFGPVPMTDIVGRVIYSLRTAVDHGPVDNS 180

Query: 180 NDSMRKDSPVLEVELDVDEMMKNHK 204
           N +M +DSPVL VELDV+E+ KN+K
Sbjct: 181 NIAMSQDSPVLAVELDVEELAKNNK 205

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724419|ref|NP_001236801.1| uncharacterized protein LOC100500100 [Glycine max] gi|255629149|gb|ACU14919.1| unknown [Glycine max]

 Score =  297 bits (760), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 151/205 (73%), Positives = 172/205 (83%), Gaps = 1/205 (0%)

Query: 1   MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQM 60
           MVSLSTWFRYIA+KLEYS S+SWK+Y  GQI D E+RD VWK  FQGKLTYL+ NKG++M
Sbjct: 1   MVSLSTWFRYIAHKLEYSFSLSWKNYKGGQITDREVRDVVWKNFFQGKLTYLHWNKGEEM 60

Query: 61  APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEK 120
           AP + G   TL VRKLP  DP RV VGDVVV+KDPEK DNY++RRL A+EGYEMVSTDEK
Sbjct: 61  APTIDGKAVTL-VRKLPVVDPTRVFVGDVVVVKDPEKPDNYLLRRLTAVEGYEMVSTDEK 119

Query: 121 DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 180
           DE FVL+KD+CWV+A+NE +K KEA DSRTFGPV M +IVGR IYCLR+AVDHG VQNS 
Sbjct: 120 DEAFVLEKDQCWVVAENEKLKAKEAKDSRTFGPVQMTDIVGRVIYCLRSAVDHGRVQNSY 179

Query: 181 DSMRKDSPVLEVELDVDEMMKNHKA 205
             MRKD+PVLEVELDVDEM K+HKA
Sbjct: 180 FGMRKDTPVLEVELDVDEMAKSHKA 204

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	205
TAIR|locus:2055856	205	AT2G31140 "AT2G31140" [Arabido	1.0	1.0	0.619	3.1e-67
TAIR|locus:2038535	206	AT1G06200 [Arabidopsis thalian	1.0	0.995	0.619	2.8e-66
POMBASE|SPBC2D10.07c	157	SPBC2D10.07c "mitochondrial in	0.565	0.738	0.293	1.2e-08
TAIR|locus:2019357	169	AT1G29960 [Arabidopsis thalian	0.604	0.733	0.291	4.4e-08
TAIR|locus:1006230730	155	AT1G23465 [Arabidopsis thalian	0.546	0.722	0.299	4.4e-08
TAIR|locus:2095249	154	AT3G08980 [Arabidopsis thalian	0.478	0.636	0.336	7.1e-07
TAIR|locus:2203688	168	AT1G53530 [Arabidopsis thalian	0.502	0.613	0.283	1.7e-05
MGI|MGI:1913791	166	Immp1l "IMP1 inner mitochondri	0.458	0.566	0.277	0.00017
UNIPROTKB|F1P533	163	IMMP1L "Uncharacterized protei	0.453	0.570	0.294	0.0003

TAIR|locus:2055856 AT2G31140 "AT2G31140" [Arabidopsis thaliana (taxid:3702)]

 Score = 683 (245.5 bits), Expect = 3.1e-67, P = 3.1e-67
 Identities = 127/205 (61%), Positives = 164/205 (80%)

Query:     1 MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQM 60
             M S+STWFRY+A+KLEYS+++S KS+   +++D EL   + K LF GK+TYL+ +KG +M
Sbjct:     1 MASISTWFRYMAHKLEYSLTLSLKSHRSNKLSDRELIQIICKNLFYGKITYLHSDKGPEM 60

Query:    61 APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEK 120
             +P M     TLL+RK+P A+ + V +GD VV+KDP  SD Y+VRRLAA+EG+EMVS DEK
Sbjct:    61 SPTMTANENTLLIRKIPIANTRFVFIGDAVVLKDPNDSDKYLVRRLAAVEGFEMVSGDEK 120

Query:   121 DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 180
             +EPFVL+K++CWV A+N+ +K KEA DSRTFGPV   +IVGRAIYCLRTAVDHGPV+NS 
Sbjct:   121 EEPFVLEKNQCWVTAENQELKAKEAYDSRTFGPVSTADIVGRAIYCLRTAVDHGPVRNSQ 180

Query:   181 DSMRKDSPVLEVELDVDEMMKNHKA 205
              +M +DSP+L VELDVDEM KNHKA
Sbjct:   181 TAMGQDSPILAVELDVDEMAKNHKA 205

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005774 "vacuolar membrane" evidence=IDA

TAIR|locus:2038535 AT1G06200 [Arabidopsis thaliana (taxid:3702)]

 Score = 674 (242.3 bits), Expect = 2.8e-66, P = 2.8e-66
 Identities = 127/205 (61%), Positives = 164/205 (80%)

Query:     1 MVSLSTWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQM 60
             M S++ + RY+A+KLEYS+++S K +TR +++D EL   V K LF G+++YL+ +KG +M
Sbjct:     1 MASITNYVRYMAHKLEYSLTLSLKKHTREKLSDRELFGVVMKNLFYGRISYLHSDKGKEM 60

Query:    61 APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEK 120
             AP MG    TLLVRKLP  D + + VGD VV+KDP +++ YIVRRLAA+EG EMVS+DEK
Sbjct:    61 APTMGTNESTLLVRKLPVVDTRYIFVGDAVVLKDPNETNKYIVRRLAALEGSEMVSSDEK 120

Query:   121 DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN 180
             DEPFVL+KD+CWV+A+N+ MK KEA DSRTFGP+ M +IVGRAIYCLRTAVDHGPV NS 
Sbjct:   121 DEPFVLEKDQCWVVAENQEMKSKEAYDSRTFGPISMADIVGRAIYCLRTAVDHGPVSNSE 180

Query:   181 DSMRKDSPVLEVELDVDEMMKNHKA 205
              +M +DSP+L VELDVDE+ K HKA
Sbjct:   181 FAMDEDSPILAVELDVDELAKGHKA 205

GO:0005739 "mitochondrion" evidence=ISM

GO:0006508 "proteolysis" evidence=IEA

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

GO:0016020 "membrane" evidence=IEA

POMBASE|SPBC2D10.07c SPBC2D10.07c "mitochondrial inner membrane peptidase complex catalytic subunit (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 130 (50.8 bits), Expect = 1.2e-08, P = 1.2e-08
 Identities = 37/126 (29%), Positives = 58/126 (46%)

Query:    40 VWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSD 99
             + +YLFQ ++T      G  M P +   G  +L+ KL     +  SVGDVVV   P  S 
Sbjct:    21 IHEYLFQVQMT-----SGPSMMPTLNSGGEFVLLDKLHGRFARSCSVGDVVVSAKPSDSK 75

Query:   100 NYIVRRLAAIEGYEM-VSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRN 158
              ++ +R+  + G  + V     ++   +     W+  DN       + DSR +GPVPM  
Sbjct:    76 QHVCKRIIGMPGDTIYVDPTSSNKKITIPLGHVWLAGDNI----AHSLDSRNYGPVPMGL 131

Query:   159 IVGRAI 164
             I  + I
Sbjct:   132 IKAKVI 137

GO:0004222 "metalloendopeptidase activity" evidence=ISS

GO:0005739 "mitochondrion" evidence=IDA

GO:0006508 "proteolysis" evidence=ISM

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

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

GO:0016021 "integral to membrane" evidence=IEA

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

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

 Score = 125 (49.1 bits), Expect = 4.4e-08, P = 4.4e-08
 Identities = 40/137 (29%), Positives = 64/137 (46%)

Query:    45 FQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVR 104
             + G + Y YG     M P +   G  LL  ++     K  S GD+VV++ PE  +   ++
Sbjct:    36 YLGFMAYAYG---PSMTPTLHPSGNVLLAERISKRYQKP-SRGDIVVIRSPENPNKTPIK 91

Query:   105 RLAAIEG---YEMVSTDEKDEP--FVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNI 159
             R+  IEG     ++ + + DE    V+ K   +V  D  +     + DSR FG VP   I
Sbjct:    92 RVIGIEGDCISFVIDSRKSDESQTIVVPKGHVFVQGDYTH----NSRDSRNFGTVPYGLI 147

Query:   160 VGRAIYCLRTAVDHGPV 176
              GR ++ +    D GP+
Sbjct:   148 QGRVLWRVWPFQDFGPL 164

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 = 125 (49.1 bits), Expect = 4.4e-08, P = 4.4e-08
 Identities = 38/127 (29%), Positives = 60/127 (47%)

Query:    45 FQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVR 104
             + G + Y YG     M P +   G  LL  ++     K  S GD+VV++ PE  +   ++
Sbjct:    36 YLGFMAYAYG---PSMIPTLHPSGNMLLAERISKRYQKP-SRGDIVVIRSPENPNKTPIK 91

Query:   105 RLAAIEG------YEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRN 158
             R+  +EG       + V +DE  +  V+ K   +V  D  +     + DSR FGPVP   
Sbjct:    92 RVVGVEGDCISFVIDPVKSDES-QTIVVPKGHVFVQGDYTH----NSRDSRNFGPVPYGL 146

Query:   159 IVGRAIY 165
             I GR ++
Sbjct:   147 IQGRVLW 153

GO:0006508 "proteolysis" evidence=IEA

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

GO:0009507 "chloroplast" evidence=ISM

GO:0016020 "membrane" evidence=IEA

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

 Score = 115 (45.5 bits), Expect = 7.1e-07, P = 7.1e-07
 Identities = 38/113 (33%), Positives = 55/113 (48%)

Query:    56 KGDQMAPVMGG-----LGGTLLVRKLPAADPKRVSVGDVVVMKDPEK-SDNYIVRRLAAI 109
             +GD M+P         L   +LV K    D K  + GDVVV   P    D YI +R+  +
Sbjct:    35 RGDSMSPTFNPQRNSYLDDYVLVDKFCLKDYK-FARGDVVVFSSPTHFGDRYI-KRIVGM 92

Query:   110 EGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGR 162
              G E +S+    +   + +  CWV  DN+      + DSR+FGP+P+  I GR
Sbjct:    93 PG-EWISSSR--DVIRVPEGHCWVEGDNKT----SSLDSRSFGPIPLGLIQGR 138

GO:0005739 "mitochondrion" evidence=ISM

GO:0006508 "proteolysis" evidence=IEA;ISS

GO:0008233 "peptidase activity" evidence=ISS

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

GO:0016020 "membrane" evidence=IEA;ISS

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

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

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

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

 Score = 113 (44.8 bits), Expect = 1.7e-05, P = 1.7e-05
 Identities = 32/113 (28%), Positives = 51/113 (45%)

Query:    57 GDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV- 115
             G  M P +   G  +L   L     K + +GDVV+++ P      + +R+  +EG  +  
Sbjct:    48 GPSMLPTLNLTGDVILAEHLSHRFGK-IGLGDVVLVRSPRDPKRMVTKRILGLEGDRLTF 106

Query:   116 STD----EKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAI 164
             S D    +     ++ K   W+  DN       + DSR FGPVP   I G+A+
Sbjct:   107 SADPLVGDASVSVLVPKGHVWIQGDNLYA----STDSRHFGPVPYSLIEGKAL 155

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

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

 Score = 106 (42.4 bits), Expect = 0.00017, P = 0.00017
 Identities = 28/101 (27%), Positives = 49/101 (48%)

Query:    87 GDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKD---EPFVLDKDECWVLADNENMKPK 143
             GD+V+ K P    + I +R+  +EG +++ST   D       +     W+  DN     +
Sbjct:    66 GDIVIAKSPSDPKSNICKRVIGLEGDKILSTSPSDVFKSRSYVPTGHVWLEGDNL----Q 121

Query:   144 EANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMR 184
              + DSR +GP+P   I GR  + +    D G +++S +  R
Sbjct:   122 NSTDSRYYGPIPYGLIRGRIFFKIWPFSDFGFLRDSPNGQR 162

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

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

 Score = 104 (41.7 bits), Expect = 0.00030, P = 0.00030
 Identities = 30/102 (29%), Positives = 51/102 (50%)

Query:    87 GDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKD----EPFVLDKDECWVLADNENMKP 142
             GD+V++K P    + I +R+  +EG ++ +++  D      FV  K   W+  DN     
Sbjct:    63 GDIVIVKSPTDPKSNICKRVIGLEGDKVCTSNPSDFLKTHSFV-PKGHVWLEGDNL---- 117

Query:   143 KEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSNDSMR 184
             + + DSR +GPVP   I GR  + +    D G ++ S +  R
Sbjct:   118 RNSTDSRCYGPVPYGLIRGRICFKIWPLNDFGFLRASPNGHR 159


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.134   0.399    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      205       205   0.00096  111 3  11 22  0.38    33
                                                     31  0.47    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  9
  No. of states in DFA:  613 (65 KB)
  Total size of DFA:  183 KB (2105 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  17.67u 0.15s 17.82t   Elapsed:  00:00:01
  Total cpu time:  17.67u 0.15s 17.82t   Elapsed:  00:00:01
  Start:  Sat May 11 06:55:49 2013   End:  Sat May 11 06:55:50 2013

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	205
cd06530	85	cd06530, S26_SPase_I, The S26 Type I signal peptid	7e-11
TIGR02227	163	TIGR02227, sigpep_I_bact, signal peptidase I, bact	1e-10
TIGR02754	90	TIGR02754, sod_Ni_protease, nickel-type superoxide	2e-07
cd06462	84	cd06462, Peptidase_S24_S26, The S24, S26 LexA/sign	7e-05

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

 Score = 56.1 bits (136), Expect = 7e-11
 Identities = 32/108 (29%), Positives = 43/108 (39%), Gaps = 28/108 (25%)

Query: 56  KGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV 115
            G  M P +   G  +LV KL     +    GDVVV K P      I++R+         
Sbjct: 6   PGGSMEPTLQP-GDLVLVNKLSY-GFREPKRGDVVVFKSPGDPGKPIIKRVIGY------ 57

Query: 116 STDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRA 163
                           +VL DN N     + DSR +GPVP  +IVG+ 
Sbjct: 58  ----------------FVLGDNRN----NSLDSRYWGPVPEDDIVGKV 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|233790 TIGR02227, sigpep_I_bact, signal peptidase I, bacterial type

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 37/125 (29%)

Query: 71  LLVRKL--PAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEG----------------- 111
           +LV K     +DPKR   GD+VV KDP+ + N  ++R+  + G                 
Sbjct: 40  ILVNKFAYGTSDPKR---GDIVVFKDPDDNKNIYIKRVIGLPGDKVEFRDGKLYINGKKI 96

Query: 112 -----YEMVSTDEKDEPFVLDK------DECWVLADNENMKPKEANDSRTFGPVPMRNIV 160
                      D  +                +VL DN +     + DSR FG VP+ +I+
Sbjct: 97  DEPYLKPNGFLDTSEFNTTDYGPVTVPPGHYFVLGDNRD----NSLDSRYFGFVPIDDII 152

Query: 161 GRAIY 165
           G+  +
Sbjct: 153 GKVSF 157

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

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 29/107 (27%), Positives = 49/107 (45%), Gaps = 23/107 (21%)

Query: 57  GDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVS 116
           G  M+P +   G  ++V        +   +G+VVV++ P +    I++RLAA+       
Sbjct: 5   GVSMSPTLPP-GDRIIVVPWLKIF-RVPPIGNVVVVRHPLQPYGLIIKRLAAV------- 55

Query: 117 TDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRA 163
                     D +  ++L DN    PK + DSR  GPVP   ++G+ 
Sbjct: 56  ----------DDNGLFLLGDN----PKASTDSRQLGPVPRSLLLGKV 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|119396 cd06462, Peptidase_S24_S26, The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families

 Score = 39.9 bits (94), Expect = 7e-05
 Identities = 29/108 (26%), Positives = 41/108 (37%), Gaps = 29/108 (26%)

Query: 56  KGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV 115
           +GD M P +   G  +LV K           GD+VV + P       V+R+  + G    
Sbjct: 6   EGDSMEPTIPD-GDLVLVDKSS----YEPKRGDIVVFRLPG--GELTVKRVIGLPG---- 54

Query: 116 STDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRA 163
                       +   ++L DN N       DSR  GP P  +IVG  
Sbjct: 55  ------------EGHYFLLGDNPNSP-----DSRIDGP-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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	205
TIGR02227	163	sigpep_I_bact signal peptidase I, bacterial type.	100.0
KOG0171	176	consensus Mitochondrial inner membrane protease, s	100.0
KOG1568	174	consensus Mitochondrial inner membrane protease, s	100.0
PRK10861	324	signal peptidase I; Provisional	99.97
TIGR02754	90	sod_Ni_protease nickel-type superoxide dismutase m	99.86
PRK13838	176	conjugal transfer pilin processing protease TraF;	99.86
TIGR02771	171	TraF_Ti conjugative transfer signal peptidase TraF	99.85
PF10502	138	Peptidase_S26: Signal peptidase, peptidase S26 ; I	99.84
PRK13884	178	conjugal transfer peptidase TraF; Provisional	99.83
cd06530	85	S26_SPase_I The S26 Type I signal peptidase (SPase	99.8
TIGR02228	158	sigpep_I_arch signal peptidase I, archaeal type. T	99.61
COG4959	173	TraF Type IV secretory pathway, protease TraF [Pos	99.52
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	99.38
PF00717	70	Peptidase_S24: Peptidase S24-like peptidase classi	99.26
cd06462	84	Peptidase_S24_S26 The S24, S26 LexA/signal peptida	99.19
COG2932	214	Predicted transcriptional regulator [Transcription	98.91
cd06529	81	S24_LexA-like Peptidase S24 LexA-like proteins are	98.88
KOG3342	180	consensus Signal peptidase I [Intracellular traffi	98.79
PRK10276	139	DNA polymerase V subunit UmuD; Provisional	98.73
PRK00215	205	LexA repressor; Validated	98.65
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	98.64
PRK12423	202	LexA repressor; Provisional	98.55
COG1974	201	LexA SOS-response transcriptional repressors (RecA	97.84
PRK00364	95	groES co-chaperonin GroES; Reviewed	81.83

>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type

Probab=100.00  E-value=4.5e-35  Score=237.36  Aligned_cols=130  Identities=28%  Similarity=0.481  Sum_probs=115.2

Q ss_pred             HHHHHHHHHhhceeEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEE
Q 028679           36 LRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV  115 (205)
Q Consensus        36 i~~~~~~~~~~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~  115 (205)
                      +.++++..++..++++.+.|+|+||+|||+ .||+++++|+.+ ...++++||+|+|+.|.+.++.++|||+|+|||+|+
T Consensus         6 ~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~-~Gd~vlv~k~~~-~~~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~   83 (163)
T TIGR02227         6 LIAILLALLIRTFVFFPYKIPGGSMEPTLK-EGDRILVNKFAY-GTSDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVE   83 (163)
T ss_pred             HHHHHHHHHHHhhEEEEEEECCcccccchh-CCCEEEEEEeEc-CCCCCCCCcEEEEecCCCCCceeEEEEEecCCCEEE
Confidence            345666778889999999999999999999 799999999866 247899999999999887788999999999999999


Q ss_pred             ecCCC----------------------------CCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEE
Q 028679          116 STDEK----------------------------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCL  167 (205)
Q Consensus       116 ~~~~~----------------------------~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~  167 (205)
                      ++++.                            ..+.+||+|+|||+|||+.    +|+|||+||+||+++|+|||.+++
T Consensus        84 i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~----~S~DSR~~G~V~~~~I~Gk~~~~~  159 (163)
T TIGR02227        84 FRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRD----NSLDSRYFGFVPIDDIIGKVSFVF  159 (163)
T ss_pred             EECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCC----CCcccCCcCcCCHHHeEEEEEEEE
Confidence            86530                            1236899999999999998    999999999999999999999999


Q ss_pred             ecCC
Q 028679          168 RTAV  171 (205)
Q Consensus       168 ~p~~  171 (205)
                      ||++
T Consensus       160 ~p~~  163 (163)
T TIGR02227       160 YPFD  163 (163)
T ss_pred             CCCC
Confidence            9974

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=3.8e-35  Score=235.48  Aligned_cols=141  Identities=26%  Similarity=0.409  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHhhceeEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceE
Q 028679           35 ELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEM  114 (205)
Q Consensus        35 ~i~~~~~~~~~~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V  114 (205)
                      +++..+|.+++..|+.++..++|.||+||+++.||+++.+|+++ .++++++||||+++.|.++++.+||||+|+|||.|
T Consensus        18 ~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~-~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~v   96 (176)
T KOG0171|consen   18 EIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSY-RFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGDLV   96 (176)
T ss_pred             HHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhH-hhcCCCCCCEEEEeCCCCchhhhhheeeccCCceE
Confidence            35667788999999999999999999999997788888899988 47889999999999999999999999999999988


Q ss_pred             EecCCC----------CCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecCCCCCCccCCC
Q 028679          115 VSTDEK----------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHGPVQNSN  180 (205)
Q Consensus       115 ~~~~~~----------~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~~~~g~~~~~~  180 (205)
                      .+.++.          ..+..||.||+||+|||+.    +|+|||+|||+|.+.|+||+++++||+++++...-+.
T Consensus        97 ~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~----nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~~~~~  168 (176)
T KOG0171|consen   97 EVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRN----NSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGLILHW  168 (176)
T ss_pred             EEecCCcccchhhhhccceeeccCceEEEecCCCC----CcccccccCCCchhheeeeEEEEecCchhcceeeecc
Confidence            776542          2347999999999999999    9999999999999999999999999999998876443

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

Probab=100.00  E-value=6.7e-35  Score=233.66  Aligned_cols=155  Identities=39%  Similarity=0.621  Sum_probs=138.5

Q ss_pred             hHHHHhhccceeEEEEeeecccCCccchHHHHHHHHHHHhhceeEEEEEecCCCcccccccC-----CcEEEEEecCCCC
Q 028679            6 TWFRYIANKLEYSVSISWKSYTRGQINDIELRDSVWKYLFQGKLTYLYGNKGDQMAPVMGGL-----GGTLLVRKLPAAD   80 (205)
Q Consensus         6 ~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~i~~V~g~SM~PTL~~~-----GD~Vlv~k~~~~~   80 (205)
                      .|+++++.+|++++..+.+....-              -|...++.+..|.|.||.||++|.     .|+||+.|+....
T Consensus         1 ~~~~~~~~~~~ksl~~s~~~~v~~--------------t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n   66 (174)
T KOG1568|consen    1 MWRRYIFKVFEKSLTGSLKWHVLL--------------TFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKN   66 (174)
T ss_pred             CHHHHHHHHHHhceeeeeeeheee--------------eeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeecccc
Confidence            489999999999988887764322              255668999999999999999983     3999999997533


Q ss_pred             CCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEE
Q 028679           81 PKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIV  160 (205)
Q Consensus        81 ~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~Ii  160 (205)
                       ..+.+||+|+|..|.++++++||||+|++||+|...+...+.+.||+|||||+|||..    +|+|||.||||+...|.
T Consensus        67 -~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~~k~~~v~vpkghcWVegDn~~----hs~DSntFGPVS~gli~  141 (174)
T KOG1568|consen   67 -RKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTEDEKEEPVVVPKGHCWVEGDNQK----HSYDSNTFGPVSTGLIV  141 (174)
T ss_pred             -ceeccCCEEEEeCCCChhheeeeeeecccccEeccCCCCCCceecCCCcEEEecCCcc----cccccCccCCcchhhee
Confidence             5689999999999999999999999999999999988888999999999999999998    99999999999999999


Q ss_pred             EEEEEEEecCCCCCCccCC
Q 028679          161 GRAIYCLRTAVDHGPVQNS  179 (205)
Q Consensus       161 Gkv~~~~~p~~~~g~~~~~  179 (205)
                      |||++++||+.|++++.++
T Consensus       142 grai~ilwpP~R~~~~~~~  160 (174)
T KOG1568|consen  142 GRAIYILWPPVRWQRLDKE  160 (174)
T ss_pred             eeEEEEEcChHHhhhhccc
Confidence            9999999999999988754

>PRK10861 signal peptidase I; Provisional

Probab=99.97  E-value=7.1e-31  Score=233.15  Aligned_cols=129  Identities=22%  Similarity=0.326  Sum_probs=112.4

Q ss_pred             HHHHHHHhhceeEEEEEecCCCcccccccCCcEEEEEecCCCC-----------CCCCccCeEEEEecCCCCCceEEEEE
Q 028679           38 DSVWKYLFQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAAD-----------PKRVSVGDVVVMKDPEKSDNYIVRRL  106 (205)
Q Consensus        38 ~~~~~~~~~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~-----------~~~~~rGDIVvf~~P~~~~~~~VKRV  106 (205)
                      .++++.++..++++.+.|+|.||+|||. .||+|+++|++|..           ...++|||||+|+.|.+++..+||||
T Consensus        70 ~l~i~~~ir~fv~~~~~Ips~SM~PTL~-~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~~~~~yIKRV  148 (324)
T PRK10861         70 VLAIVLIVRSFIYEPFQIPSGSMMPTLL-IGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPEDPKLDYIKRV  148 (324)
T ss_pred             HHhHHHHHHhhEEEEEEECCCcCcCccc-CCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCCCCCcEEEEe
Confidence            3455567789999999999999999999 79999999998731           25799999999999998888999999


Q ss_pred             EEecCceEEec--------CCC----------------------------------------------------------
Q 028679          107 AAIEGYEMVST--------DEK----------------------------------------------------------  120 (205)
Q Consensus       107 ialpGd~V~~~--------~~~----------------------------------------------------------  120 (205)
                      +|+|||+|+++        |+.                                                          
T Consensus       149 IGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (324)
T PRK10861        149 VGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETKENGIRLSERK  228 (324)
T ss_pred             eecCCcEEEEEeCCCEEEEcCccccccccccccccccccccccccccccccccccccccccccccccccccccccceeEE
Confidence            99999999974        110                                                          


Q ss_pred             ------------------------------CCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecC
Q 028679          121 ------------------------------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA  170 (205)
Q Consensus       121 ------------------------------~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~  170 (205)
                                                    ..+++||+|+||++|||+.    +|+||||||+||.++|+|||.++++++
T Consensus       229 E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~----~S~DSRy~G~Vp~~~i~G~a~~i~~s~  304 (324)
T PRK10861        229 ETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRD----NSADSRYWGFVPEANLVGKATAIWMSF  304 (324)
T ss_pred             EecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCC----CCcccCcccccCHHHcEEEEEEEEEEc
Confidence                                          0123899999999999999    999999999999999999999999997


Q ss_pred             C
Q 028679          171 V  171 (205)
Q Consensus       171 ~  171 (205)
                      .
T Consensus       305 d  305 (324)
T PRK10861        305 E  305 (324)
T ss_pred             C
Confidence            6

>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease

Probab=99.86  E-value=2.6e-21  Score=141.70  Aligned_cols=89  Identities=29%  Similarity=0.561  Sum_probs=77.4

Q ss_pred             EecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEE
Q 028679           54 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWV  133 (205)
Q Consensus        54 ~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~v  133 (205)
                      .|+|+||+|||+ +||+|++++... ....+++||+|+|+.|.+++..++||+++++                 ++++|+
T Consensus         2 ~V~g~SM~P~l~-~GD~vlv~~~~~-~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~-----------------~~~~~l   62 (90)
T TIGR02754         2 KVTGVSMSPTLP-PGDRIIVVPWLK-IFRVPPIGNVVVVRHPLQPYGLIIKRLAAVD-----------------DNGLFL   62 (90)
T ss_pred             EeeCCCccCccC-CCCEEEEEEccc-cCCCCCCCeEEEEecCCCCcceEEEEeeEEc-----------------CCeEEE
Confidence            689999999999 799999998532 1244567999999998866789999999984                 468999


Q ss_pred             EeCCCCCCCCCCCCCCccccccCCCEEEEEEE
Q 028679          134 LADNENMKPKEANDSRTFGPVPMRNIVGRAIY  165 (205)
Q Consensus       134 lGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~  165 (205)
                      +|||+.    .|.|||++|+|+..+|+|+|++
T Consensus        63 ~~dN~~----~~~d~~~~g~v~~~~I~G~v~~   90 (90)
T TIGR02754        63 LGDNPK----ASTDSRQLGPVPRSLLLGKVLW   90 (90)
T ss_pred             eCCCCC----CCCcccccCCCcHHHEEEEEEC
Confidence            999998    8999999999999999999863

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.

>PRK13838 conjugal transfer pilin processing protease TraF; Provisional

Probab=99.86  E-value=2.3e-21  Score=159.37  Aligned_cols=92  Identities=26%  Similarity=0.346  Sum_probs=73.4

Q ss_pred             EEEEecCCCCCCCCccCeEEEEecCCCC-------------------CceEEEEEEEecCceEEecCC------------
Q 028679           71 LLVRKLPAADPKRVSVGDVVVMKDPEKS-------------------DNYIVRRLAAIEGYEMVSTDE------------  119 (205)
Q Consensus        71 Vlv~k~~~~~~~~~~rGDIVvf~~P~~~-------------------~~~~VKRVialpGd~V~~~~~------------  119 (205)
                      +.+.++.+ ...++++||+|+|+.|++.                   ...++|||+|+|||+|++.+.            
T Consensus        39 ig~y~~~~-~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~~v~iNg~~~~~~~  117 (176)
T PRK13838         39 LGLWRIEA-LDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGGSVSIDGRPLPSSS  117 (176)
T ss_pred             EEEEEEec-cCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECCEEEECCEEccccc
Confidence            55555433 2468999999999988643                   135999999999999998631            


Q ss_pred             ------------CCCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEe
Q 028679          120 ------------KDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLR  168 (205)
Q Consensus       120 ------------~~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~  168 (205)
                                  .....+||+|+|||+|||.     +|+||||||+|+.++|+|+|.+++.
T Consensus       118 ~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-----~S~DSRy~G~V~~~~I~G~a~pi~t  173 (176)
T PRK13838        118 VRRRDGEGRPLTPFPGGVVPPGHLFLHSSFA-----GSYDSRYFGPVPASGLLGLARPVLT  173 (176)
T ss_pred             cccccccCCcCCCCCccCcCCCeEEEECCCC-----CCCcccccCcccHHHeEEEEEEEEe
Confidence                        0113479999999999985     7999999999999999999998753

>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF

Probab=99.85  E-value=7.7e-21  Score=155.63  Aligned_cols=102  Identities=22%  Similarity=0.308  Sum_probs=79.9

Q ss_pred             EEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCC-------------------ceEEEEEEEec
Q 028679           50 TYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSD-------------------NYIVRRLAAIE  110 (205)
Q Consensus        50 ~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~-------------------~~~VKRVialp  110 (205)
                      ..+..-.++||-.     |-+. +.+     ..+++|||+|+|+.|+++.                   ..++|||+|+|
T Consensus        24 ~~~~~N~T~S~P~-----g~Y~-~~~-----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglp   92 (171)
T TIGR02771        24 VGARINTTKSLPL-----GLYW-TTS-----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLP   92 (171)
T ss_pred             eeEEEECCCCCcc-----eEEE-eCC-----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeC
Confidence            3444556677664     4444 322     2689999999999886432                   27999999999


Q ss_pred             CceEEecCC-------------------------CCCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEE
Q 028679          111 GYEMVSTDE-------------------------KDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIY  165 (205)
Q Consensus       111 Gd~V~~~~~-------------------------~~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~  165 (205)
                      ||+|+++++                         ...+.+||+| ||++|||+.    +|+||||||+||.++|+|||.+
T Consensus        93 GD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~----~S~DSRy~G~V~~~~IiGk~~p  167 (171)
T TIGR02771        93 GDRVTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSP----TSFDSRYFGPISREQVIGRVKP  167 (171)
T ss_pred             CCEEEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCC----CCCcccccceecHHHeEEEEEE
Confidence            999998653                         0125789999 999999998    9999999999999999999998


Q ss_pred             EE
Q 028679          166 CL  167 (205)
Q Consensus       166 ~~  167 (205)
                      ++
T Consensus       168 l~  169 (171)
T TIGR02771       168 LF  169 (171)
T ss_pred             eE
Confidence            65

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=99.84  E-value=4.4e-22  Score=157.65  Aligned_cols=82  Identities=33%  Similarity=0.520  Sum_probs=32.5

Q ss_pred             CCCccCeEEEEecCCC------------CCceEEEEEEEecCceEEecCC------------------------CCCcee
Q 028679           82 KRVSVGDVVVMKDPEK------------SDNYIVRRLAAIEGYEMVSTDE------------------------KDEPFV  125 (205)
Q Consensus        82 ~~~~rGDIVvf~~P~~------------~~~~~VKRVialpGd~V~~~~~------------------------~~~~~~  125 (205)
                      ..+++||+|+|+.|..            .+..++|||+|+|||+|+++++                        .....+
T Consensus        20 ~~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~   99 (138)
T PF10502_consen   20 DKIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGT   99 (138)
T ss_dssp             ---------------------------------------------------------------------S-T----TEEE
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceE
Confidence            3489999999999873            2358999999999999998753                        013579


Q ss_pred             eeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEE
Q 028679          126 LDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCL  167 (205)
Q Consensus       126 vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~  167 (205)
                      ||+|+|||+|||+.    +|+||||||+|+.++|+|+|.+++
T Consensus       100 vp~g~~~v~gd~~~----~S~DSRy~G~V~~~~I~g~~~pl~  137 (138)
T PF10502_consen  100 VPEGEYFVLGDNRP----NSFDSRYFGPVPRSQIIGKARPLW  137 (138)
T ss_dssp             --TTEEEEE-SBTT----S--SHHHH--EEGGGEEEEEEEEE
T ss_pred             eCCCEEEEecCCCC----CccccCEecccCHHHEEEEEEEEE
Confidence            99999999999998    999999999999999999999886

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.

>PRK13884 conjugal transfer peptidase TraF; Provisional

Probab=99.83  E-value=6.5e-20  Score=151.01  Aligned_cols=103  Identities=19%  Similarity=0.293  Sum_probs=79.2

Q ss_pred             eEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCC-------------------CceEEEEEEEe
Q 028679           49 LTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKS-------------------DNYIVRRLAAI  109 (205)
Q Consensus        49 ~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~-------------------~~~~VKRVial  109 (205)
                      ...+....++||-..+.     .+ ..      .++++||+|+|++|+..                   ..+++|||+|+
T Consensus        28 ~~~~~~N~T~S~P~glY-----~~-~~------~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~   95 (178)
T PRK13884         28 AAGARVNTTKSIPVGLY-----WT-SS------APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAA   95 (178)
T ss_pred             hCcEEEECCCCCcceEE-----EE-eC------CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEee
Confidence            34455555666653333     32 21      47999999999987631                   13799999999


Q ss_pred             cCceEEecCC---------------------C------CCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEE
Q 028679          110 EGYEMVSTDE---------------------K------DEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGR  162 (205)
Q Consensus       110 pGd~V~~~~~---------------------~------~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGk  162 (205)
                      |||+|++.++                     .      ...++||+|+||++|||+.    +|+||||||+|+.++|+|+
T Consensus        96 pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~l~~~~~~~~~lp~g~~fvlgd~~~----~S~DSRYfG~V~~~~I~G~  171 (178)
T PRK13884         96 KGDAVSVTDDGVRVNGELLPLSKPILADGAGRPLPRYQANSYTLGESELLLMSDVSA----TSFDGRYFGPINRSQIKTV  171 (178)
T ss_pred             CCcEEEEECCEEEECCEEccccccccccccCCcccccCCCceEECCCEEEEECCCCC----CCCcccccCcccHHHEEEE
Confidence            9999998653                     0      0124899999999999998    9999999999999999999


Q ss_pred             EEEEE
Q 028679          163 AIYCL  167 (205)
Q Consensus       163 v~~~~  167 (205)
                      +.+++
T Consensus       172 ~~Pl~  176 (178)
T PRK13884        172 IRPVI  176 (178)
T ss_pred             EEEeE
Confidence            99875

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

Probab=99.80  E-value=2.2e-19  Score=129.74  Aligned_cols=84  Identities=38%  Similarity=0.600  Sum_probs=74.7

Q ss_pred             EEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeE
Q 028679           52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC  131 (205)
Q Consensus        52 i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~  131 (205)
                      ++.|.|+||+|++. .||++++++... ....+++||+|+|+.|...+..++|||++                      |
T Consensus         2 ~~~v~g~SM~P~i~-~gd~v~v~~~~~-~~~~~~~GDiv~~~~~~~~~~~~vkRv~~----------------------~   57 (85)
T cd06530           2 PVVVPGGSMEPTLQ-PGDLVLVNKLSY-GFREPKRGDVVVFKSPGDPGKPIIKRVIG----------------------Y   57 (85)
T ss_pred             eeEEcCCCCcCccc-CCCEEEEEEeec-ccCCCCCCCEEEEeCCCCCCCEEEEEEEE----------------------E
Confidence            68899999999999 799999998642 12379999999999987656799999998                      8


Q ss_pred             EEEeCCCCCCCCCCCCCCccccccCCCEEEEE
Q 028679          132 WVLADNENMKPKEANDSRTFGPVPMRNIVGRA  163 (205)
Q Consensus       132 ~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv  163 (205)
                      |+.|||+.    +|.|||+||+++.++|+|++
T Consensus        58 ~~~gDn~~----ns~d~~~~g~~~~~~i~G~~   85 (85)
T cd06530          58 FVLGDNRN----NSLDSRYWGPVPEDDIVGKV   85 (85)
T ss_pred             EEeeCCCC----CCCccCCcCCCcHHHeEEeC
Confidence            99999987    89999999999999999985

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=99.61  E-value=6.1e-15  Score=119.42  Aligned_cols=86  Identities=27%  Similarity=0.402  Sum_probs=69.9

Q ss_pred             EecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEE
Q 028679           54 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWV  133 (205)
Q Consensus        54 ~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~v  133 (205)
                      .|.|+||+||++ .||++++++..   ..++++||+|+|+.|+.+ +.++|||+++.++     +        .+..++.
T Consensus        35 ~V~g~SM~Ptl~-~GD~vlv~~~~---~~~~~~GDIVvf~~~~~~-~~iihRVi~v~~~-----~--------g~~~~~t   96 (158)
T TIGR02228        35 VVLSGSMEPTFN-TGDLILVTGAD---PNDIQVGDVITYKSPGFN-TPVTHRVIEINNS-----G--------GELGFIT   96 (158)
T ss_pred             EEcCCCCcCCcc-CCCEEEEEecc---cCCCCCCCEEEEEECCCC-ccEEEEEEEEECC-----C--------CcEEEEE
Confidence            399999999999 79999999853   368999999999998743 7899999999643     0        1123667


Q ss_pred             EeCCCCCCCCCCCCCCccccccCCCEEEEEEE
Q 028679          134 LADNENMKPKEANDSRTFGPVPMRNIVGRAIY  165 (205)
Q Consensus       134 lGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~  165 (205)
                      .|||+.     ..|   .++|+.++|+|++..
T Consensus        97 kGDnN~-----~~D---~~~v~~~~IiG~v~~  120 (158)
T TIGR02228        97 KGDNNP-----APD---GEPVPSENVIGKYLG  120 (158)
T ss_pred             EecCCC-----CCC---cccCCHHHEEEEEEE
Confidence            799985     556   689999999999984

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=99.52  E-value=7.5e-15  Score=117.32  Aligned_cols=82  Identities=27%  Similarity=0.445  Sum_probs=68.4

Q ss_pred             CCCccCeEEEEecCCC------------CCceEEEEEEEecCceEEecCC-------------------C-----CCcee
Q 028679           82 KRVSVGDVVVMKDPEK------------SDNYIVRRLAAIEGYEMVSTDE-------------------K-----DEPFV  125 (205)
Q Consensus        82 ~~~~rGDIVvf~~P~~------------~~~~~VKRVialpGd~V~~~~~-------------------~-----~~~~~  125 (205)
                      .++.+||+|++++|+.            ...+++|||.|+|||+|++.++                   .     ...-.
T Consensus        52 ~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~  131 (173)
T COG4959          52 APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRY  131 (173)
T ss_pred             CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCce
Confidence            4579999999999884            2357899999999999997542                   0     12235


Q ss_pred             eeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEE
Q 028679          126 LDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCL  167 (205)
Q Consensus       126 vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~  167 (205)
                      +-++++|+++|...    .|+|||||||||.++|+|.+.+++
T Consensus       132 l~~~el~lL~~~~~----~SfDsRYfGpipas~vig~aRPvw  169 (173)
T COG4959         132 LAPSELLLLTDRSS----TSFDSRYFGPIPASQVIGVARPVW  169 (173)
T ss_pred             ecCCeEEEEeccCC----cccccceecccCHHHcceeeeeee
Confidence            88899999999998    899999999999999999998765

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

Probab=99.38  E-value=4e-12  Score=101.39  Aligned_cols=122  Identities=19%  Similarity=0.271  Sum_probs=89.1

Q ss_pred             HHHHHHHh--hceeEEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEE
Q 028679           38 DSVWKYLF--QGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV  115 (205)
Q Consensus        38 ~~~~~~~~--~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~  115 (205)
                      +++++.++  +.++++++.|+|+||+|||+ .||+++++|.++. ...++.++++  ..|......++||+++.+||.|.
T Consensus        17 ~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~-~GD~v~v~k~~~~-~~~~~~~~~~--~~~~~~~~~~~kr~~~~~GD~i~   92 (166)
T COG0681          17 AIILALIIGVRTFVFEPVVVPSGSMEPTLN-VGDRVLVKKFSYG-FGKLKVPDII--VLPAVVEGDLIKRVIGLRGDIVV   92 (166)
T ss_pred             HHHHhheeeeEEEEEEEEEECCCccccccc-cCCEEEEEecccc-ccCCccceee--ecCCCCCcceEEEeccCCCCEEE
Confidence            44444555  68899999999999999999 7999999999873 5567888887  55555677899999999999999


Q ss_pred             ecCCCCC-ceeeeCCeEEEEeCCCCC---CCCCCCCCCccccccCCCEEEEE
Q 028679          116 STDEKDE-PFVLDKDECWVLADNENM---KPKEANDSRTFGPVPMRNIVGRA  163 (205)
Q Consensus       116 ~~~~~~~-~~~vp~g~~~vlGDN~~~---~~~~S~DSR~~GpV~~~~IiGkv  163 (205)
                      ..++... ...+|++..++.++|...   ....+.+++.++.......+.++
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (166)
T COG0681          93 FKDDRLYVVPIIPRVYGLVEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV  144 (166)
T ss_pred             EECCEEEeecccCcchhhhhcccccccccccccccCccccccccccccccce
Confidence            9875322 234455555555443310   00157777878777777777777

>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification

Probab=99.26  E-value=2.5e-11  Score=84.02  Aligned_cols=57  Identities=25%  Similarity=0.365  Sum_probs=46.1

Q ss_pred             EecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEec
Q 028679           54 GNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVST  117 (205)
Q Consensus        54 ~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~  117 (205)
                      +|.|+||+|+|+ +||+|++++.     ..++.||+|+|..+... ..++||+.+.+|+.+.+.
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 7999999985     48999999999986532 489999999999877654

; 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=99.19  E-value=1.5e-10  Score=81.99  Aligned_cols=83  Identities=34%  Similarity=0.547  Sum_probs=63.6

Q ss_pred             EEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeE
Q 028679           52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC  131 (205)
Q Consensus        52 i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~  131 (205)
                      .+.|.|+||+|++. +||++++++..    ..++.||+|++..+.  +..++||+...++                ++++
T Consensus         2 ~~~v~g~SM~P~i~-~gd~v~i~~~~----~~~~~G~iv~~~~~~--~~~~ikrl~~~~~----------------~~~~   58 (84)
T cd06462           2 ALRVEGDSMEPTIP-DGDLVLVDKSS----YEPKRGDIVVFRLPG--GELTVKRVIGLPG----------------EGHY   58 (84)
T ss_pred             eeEEcCCCccCccc-CCCEEEEEecC----CCCcCCEEEEEEcCC--CcEEEEEEEEECC----------------CCEE
Confidence            57899999999999 79999999852    248999999999864  4789999999863                3689


Q ss_pred             EEEeCCCCCCCCCCCCCCccccccCCCEEEEE
Q 028679          132 WVLADNENMKPKEANDSRTFGPVPMRNIVGRA  163 (205)
Q Consensus       132 ~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv  163 (205)
                      ++.+||+     ++.+.+..+. ....++|++
T Consensus        59 ~l~~~N~-----~~~~~~~~~~-~~~~i~g~v   84 (84)
T cd06462          59 FLLGDNP-----NSPDSRIDGP-PELDIVGVV   84 (84)
T ss_pred             EEECCCC-----CCCcccccCC-CHHHEEEeC
Confidence            9999995     3555443332 455666653

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

>COG2932 Predicted transcriptional regulator [Transcription]

Probab=98.91  E-value=1.3e-08  Score=85.58  Aligned_cols=90  Identities=23%  Similarity=0.306  Sum_probs=64.6

Q ss_pred             EEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCe
Q 028679           51 YLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDE  130 (205)
Q Consensus        51 ~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~  130 (205)
                      ....|.|+||+|++. +||.++|+.-     .+..+||.|++..-  .+..+|||+...+|                 |.
T Consensus       124 ~~i~V~GDSMeP~~~-~Gd~ilVd~~-----~~~~~gd~v~v~~~--g~~~~VK~l~~~~~-----------------~~  178 (214)
T COG2932         124 FALRVTGDSMEPTYE-DGDTLLVDPG-----VNTRRGDRVYVETD--GGELYVKKLQREPG-----------------GL  178 (214)
T ss_pred             EEEEEeCCccccccc-CCCEEEECCC-----CceeeCCEEEEEEe--CCeEEEEEEEEecC-----------------Ce
Confidence            678999999999999 7999999974     56778886655542  35789999999854                 57


Q ss_pred             EEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecC
Q 028679          131 CWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA  170 (205)
Q Consensus       131 ~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~  170 (205)
                      +.+..+|+.     ..+...+-.=..=+|+|||++.....
T Consensus       179 ~~l~S~N~~-----~~~~~~~~~~~~v~iIgrVv~~~~~~  213 (214)
T COG2932         179 LRLVSLNPD-----YYPDEIFSEDDDVEIIGRVVWVSRLL  213 (214)
T ss_pred             EEEEeCCCC-----CCcccccCccceEEEEEEEEEEeeec
Confidence            778899986     22222221110135899999887653

>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=98.88  E-value=1.7e-08  Score=71.33  Aligned_cols=62  Identities=29%  Similarity=0.390  Sum_probs=52.1

Q ss_pred             EEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeE
Q 028679           52 LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDEC  131 (205)
Q Consensus        52 i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~  131 (205)
                      .+.|.|+||+|+++ +||.+++++.     ..++.||++++..+.   ..++||+...++                 +.+
T Consensus         2 ~~~v~g~sM~p~i~-~gd~lii~~~-----~~~~~g~i~~~~~~~---~~~ikr~~~~~~-----------------~~~   55 (81)
T cd06529           2 ALRVKGDSMEPTIP-DGDLVLVDPS-----DTPRDGDIVVARLDG---ELTVKRLQRRGG-----------------GRL   55 (81)
T ss_pred             EEEEECCCcCCccC-CCCEEEEcCC-----CCCCCCCEEEEEECC---EEEEEEEEECCC-----------------CcE
Confidence            57899999999999 7999999974     358999999999853   689999998853                 467


Q ss_pred             EEEeCCCC
Q 028679          132 WVLADNEN  139 (205)
Q Consensus       132 ~vlGDN~~  139 (205)
                      ++.++|+.
T Consensus        56 ~L~s~N~~   63 (81)
T cd06529          56 RLISDNPA   63 (81)
T ss_pred             EEEeCCCC
Confidence            78888864

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

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

Probab=98.79  E-value=8.8e-09  Score=82.58  Aligned_cols=91  Identities=23%  Similarity=0.299  Sum_probs=68.5

Q ss_pred             EEEEEecCCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCC
Q 028679           50 TYLYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKD  129 (205)
Q Consensus        50 ~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g  129 (205)
                      -.+..|-+.||+|.++ .||+++....   .....+.||||+|+.+. ...+++|||+.+-+.              .+|
T Consensus        48 SPiVVVLSgSMePaF~-RGDlLfL~N~---~~~p~~vGdivVf~veg-R~IPiVHRviK~he~--------------~~~  108 (180)
T KOG3342|consen   48 SPIVVVLSGSMEPAFH-RGDLLFLTNR---NEDPIRVGDIVVFKVEG-REIPIVHRVIKQHEK--------------SNG  108 (180)
T ss_pred             CCEEEEEcCCcCcccc-cccEEEEecC---CCCcceeccEEEEEECC-ccCchhHHHHHHhcc--------------cCC
Confidence            3588999999999999 8999998854   24678999999999865 357899999998642              334


Q ss_pred             eE--EEEeCCCCCCCCCCCCCCc-c----ccccCCCEEEEEEE
Q 028679          130 EC--WVLADNENMKPKEANDSRT-F----GPVPMRNIVGRAIY  165 (205)
Q Consensus       130 ~~--~vlGDN~~~~~~~S~DSR~-~----GpV~~~~IiGkv~~  165 (205)
                      +.  ..-|||+.      .|-|. |    -...++.|+|+|.-
T Consensus       109 ~~~~LTKGDNN~------~dD~~Ly~~gq~~L~r~~Ivg~~~G  145 (180)
T KOG3342|consen  109 HIKFLTKGDNNA------VDDRGLYAQGQNWLERKDIVGRVRG  145 (180)
T ss_pred             cEEEEecCCCCc------ccchhcccccccceeccceeeEEee
Confidence            44  44499975      45442 1    23778999999864

>PRK10276 DNA polymerase V subunit UmuD; Provisional

Probab=98.73  E-value=1.7e-07  Score=73.98  Aligned_cols=87  Identities=20%  Similarity=0.282  Sum_probs=61.6

Q ss_pred             eEEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeee
Q 028679           49 LTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLD  127 (205)
Q Consensus        49 ~~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp  127 (205)
                      -....+|.|+||. |++. +||++++++-     .+++.||+|++..   .+...+||+...                  
T Consensus        50 ~~f~l~V~GdSM~~~~I~-~GD~liVd~~-----~~~~~Gdivv~~~---~g~~~vKrl~~~------------------  102 (139)
T PRK10276         50 ATYFVKASGDSMIDAGIS-DGDLLIVDSA-----ITASHGDIVIAAV---DGEFTVKKLQLR------------------  102 (139)
T ss_pred             CEEEEEEecCCCCCCCCC-CCCEEEEECC-----CCCCCCCEEEEEE---CCEEEEEEEEEC------------------
Confidence            3567999999998 6899 8999999963     3578899999986   346789998742                  


Q ss_pred             CCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEec
Q 028679          128 KDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT  169 (205)
Q Consensus       128 ~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p  169 (205)
                       +++++..+|+.      +....+-.-..=.|+|+|++++..
T Consensus       103 -~~~~L~s~N~~------y~~i~i~~~~~~~IiG~V~~~~~~  137 (139)
T PRK10276        103 -PTVQLIPMNSA------YSPITISSEDTLDVFGVVTHIVKA  137 (139)
T ss_pred             -CcEEEEcCCCC------CCCEEcCCCCcEEEEEEEEEEEEe
Confidence             24677888875      111111111122799999988764

>PRK00215 LexA repressor; Validated

Probab=98.65  E-value=3.8e-07  Score=75.94  Aligned_cols=89  Identities=21%  Similarity=0.260  Sum_probs=65.1

Q ss_pred             ceeEEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCcee
Q 028679           47 GKLTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFV  125 (205)
Q Consensus        47 ~~~~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~  125 (205)
                      ..-+.+..|.|+||. |++. +||++++++-     ..++.||+|++...   +...+||+.-.                
T Consensus       115 ~~~~~~~~V~GdSM~~~~i~-~Gd~v~v~~~-----~~~~~G~ivv~~~~---~~~~vKrl~~~----------------  169 (205)
T PRK00215        115 PGEDFLLRVRGDSMIDAGIL-DGDLVIVRKQ-----QTARNGQIVVALID---DEATVKRFRRE----------------  169 (205)
T ss_pred             CCCeEEEEEccCCCCCCCcC-CCCEEEEeCC-----CCCCCCCEEEEEEC---CEEEEEEEEEe----------------
Confidence            345678999999995 7999 7999999963     45788999999874   36899999764                


Q ss_pred             eeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEec
Q 028679          126 LDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT  169 (205)
Q Consensus       126 vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p  169 (205)
                        .|.+++..+|+.      ++.....+= .-.|+|+|+..+..
T Consensus       170 --~~~~~L~s~Np~------y~~~~~~~~-~~~IiG~Vv~~~r~  204 (205)
T PRK00215        170 --GGHIRLEPENPA------YEPIIVDPD-RVTIEGKVVGLIRN  204 (205)
T ss_pred             --CCEEEEEcCCCC------CCCEEeCCC-cEEEEEEEEEEEEc
Confidence              246788888885      222211110 35799999987753

>TIGR00498 lexA SOS regulatory protein LexA

Probab=98.64  E-value=4.5e-07  Score=75.10  Aligned_cols=89  Identities=19%  Similarity=0.259  Sum_probs=66.0

Q ss_pred             eeEEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceee
Q 028679           48 KLTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVL  126 (205)
Q Consensus        48 ~~~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~v  126 (205)
                      .-+.++.|.|+||. |++. +||++++++.     ..++.||+|++..   .+...+||+.--                 
T Consensus       109 ~~~f~~~V~GdSM~~~~i~-~Gd~v~v~~~-----~~~~~G~ivvv~~---~~~~~vKrl~~~-----------------  162 (199)
T TIGR00498       109 SAVFLLKVMGDSMVDAGIC-DGDLLIVRSQ-----KDARNGEIVAAMI---DGEVTVKRFYKD-----------------  162 (199)
T ss_pred             CCEEEEEecCCCCCCCCCC-CCCEEEEecC-----CCCCCCCEEEEEE---CCEEEEEEEEEE-----------------
Confidence            34678999999996 5899 7999999863     4788999999998   456899998753                 


Q ss_pred             eCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecC
Q 028679          127 DKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA  170 (205)
Q Consensus       127 p~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~  170 (205)
                       .+.+++..+|+.++      ...... ..=.|+|+|+..++.+
T Consensus       163 -~~~i~L~s~N~~y~------~i~~~~-~~~~IiG~Vv~~~r~~  198 (199)
T TIGR00498       163 -GTKVELKPENPEFD------PIVLNA-EDVTILGKVVGVIRNF  198 (199)
T ss_pred             -CCEEEEEcCCCCCc------CCcCCC-CcEEEEEEEEEEEEec
Confidence             24788889998521      111100 1348999999988754

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

>PRK12423 LexA repressor; Provisional

Probab=98.55  E-value=9.2e-07  Score=73.95  Aligned_cols=87  Identities=22%  Similarity=0.221  Sum_probs=64.1

Q ss_pred             EEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeC
Q 028679           50 TYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDK  128 (205)
Q Consensus        50 ~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~  128 (205)
                      .....|.|+||. |+|. +||+|++++-     ..++.||+|++..   .+...+||+.-..                  
T Consensus       114 ~f~l~V~GdSM~~~~i~-~Gd~viv~~~-----~~~~~Gdivv~~~---~~~~~vKrl~~~~------------------  166 (202)
T PRK12423        114 DYLLQVQGDSMIDDGIL-DGDLVGVHRS-----PEARDGQIVVARL---DGEVTIKRLERSG------------------  166 (202)
T ss_pred             cEEEEEecCcCCCCCcC-CCCEEEEeCC-----CcCCCCCEEEEEE---CCEEEEEEEEEeC------------------
Confidence            357899999997 7999 8999999963     4678899999987   3468899997542                  


Q ss_pred             CeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEec
Q 028679          129 DECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT  169 (205)
Q Consensus       129 g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p  169 (205)
                      +.+++..+|+.      ++...+-+-..-.|+|+|+.+++.
T Consensus       167 ~~~~L~s~N~~------y~~i~~~~~~~~~I~Gvv~g~~r~  201 (202)
T PRK12423        167 DRIRLLPRNPA------YAPIVVAPDQDFAIEGVFCGLIRQ  201 (202)
T ss_pred             CEEEEEcCCCC------CCCEEcCCCCcEEEEEEEEEEEEC
Confidence            46888889875      222222111134799999988764

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

Probab=97.84  E-value=0.00036  Score=58.75  Aligned_cols=89  Identities=19%  Similarity=0.231  Sum_probs=67.5

Q ss_pred             eEEEEEecCCCcc-cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeee
Q 028679           49 LTYLYGNKGDQMA-PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLD  127 (205)
Q Consensus        49 ~~~i~~V~g~SM~-PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp  127 (205)
                      -.++.+|.|+||. +.+. +||.|+|++-     ..++.||+|+....+  ++..+||..--                  
T Consensus       111 ~~f~L~V~GdSM~~~gi~-dGDlvvV~~~-----~~a~~GdiVvA~i~g--~e~TvKrl~~~------------------  164 (201)
T COG1974         111 ATFFLRVSGDSMIDAGIL-DGDLVVVDPT-----EDAENGDIVVALIDG--EEATVKRLYRD------------------  164 (201)
T ss_pred             ceEEEEecCCccccCcCC-CCCEEEEcCC-----CCCCCCCEEEEEcCC--CcEEEEEEEEe------------------
Confidence            5778999999996 4566 8999999974     688999999999865  55789998874                  


Q ss_pred             CCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecC
Q 028679          128 KDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA  170 (205)
Q Consensus       128 ~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~  170 (205)
                      .+++++..-|+.      +.+..+..- .-.|+|+++.++|+.
T Consensus       165 g~~i~L~p~Np~------~~~i~~~~~-~~~I~G~vvgv~r~~  200 (201)
T COG1974         165 GNQILLKPENPA------YPPIPVDAD-SVTILGKVVGVIRDI  200 (201)
T ss_pred             CCEEEEEeCCCC------CCCcccCcc-ceEEEEEEEEEEecC
Confidence            247888888886      222222211 347999999999874

>PRK00364 groES co-chaperonin GroES; Reviewed

Probab=81.83  E-value=12  Score=27.57  Aligned_cols=92  Identities=12%  Similarity=0.172  Sum_probs=49.9

Q ss_pred             cccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEEEeCCCCCCCC
Q 028679           64 MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPK  143 (205)
Q Consensus        64 L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~vlGDN~~~~~~  143 (205)
                      |.|-||+||+.+..   ..+-..|-|++=..  ...+...-+|+|+.-. ....+|...+..+..|..-+..+....  .
T Consensus         3 i~Pl~drVLV~~~~---~e~~T~gGI~Lp~~--a~~k~~~G~VvaVG~G-~~~~~G~~~~~~vk~GD~Vlf~~~~g~--e   74 (95)
T PRK00364          3 LKPLGDRVLVKRLE---EEEKTAGGIVLPDS--AKEKPQEGEVVAVGPG-RRLDNGERVPLDVKVGDKVLFGKYAGT--E   74 (95)
T ss_pred             ceEcCCEEEEEEcc---cCccccceEEcCcc--ccCCcceEEEEEECCC-eECCCCCEeecccCCCCEEEEcCCCCe--E
Confidence            56779999999863   24455666666221  1345667778887421 112233333444555554444443320  0


Q ss_pred             CCCCCCccccccCCCEEEEE
Q 028679          144 EANDSRTFGPVPMRNIVGRA  163 (205)
Q Consensus       144 ~S~DSR~~GpV~~~~IiGkv  163 (205)
                      --+|...|=.++.++|+|++
T Consensus        75 v~~~~~~y~iv~~~DIlavi   94 (95)
T PRK00364         75 VKIDGEEYLILRESDILAIV   94 (95)
T ss_pred             EEECCEEEEEEEHHHEEEEe
Confidence            12344556677777887764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	205
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	100.0
1kca_A	109	Repressor protein CI; gene regulation, DNA-binding	99.41
1umu_A	116	UMUD'; induced mutagenesis, SOS mutagenesis, DNA r	99.29
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	99.08
2hnf_A	133	Repressor protein CI101-229DM-K192A; viral protein	99.0
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	98.92
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	98.8
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	97.06

>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*

Probab=100.00  E-value=1.3e-33  Score=240.92  Aligned_cols=125  Identities=22%  Similarity=0.363  Sum_probs=106.9

Q ss_pred             hhceeEEEEEecCCCcccccccCCcEEEEEecCCC-----------CCCCCccCeEEEEecCCCCCceEEEEEEEecCce
Q 028679           45 FQGKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAA-----------DPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYE  113 (205)
Q Consensus        45 ~~~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~-----------~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~  113 (205)
                      +..|+++++.|+|+||+|||+ .||+|+++|+.|.           ....+++||||+|+.|.+++..+||||+|+|||+
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            356899999999999999999 7999999997541           0257999999999999877889999999999999


Q ss_pred             EEecCC-------------------CC-----------------------------------------------------
Q 028679          114 MVSTDE-------------------KD-----------------------------------------------------  121 (205)
Q Consensus       114 V~~~~~-------------------~~-----------------------------------------------------  121 (205)
                      |++.++                   ..                                                     
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            987654                   00                                                     


Q ss_pred             ------------------------CceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecCCCCC
Q 028679          122 ------------------------EPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHG  174 (205)
Q Consensus       122 ------------------------~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~~~~g  174 (205)
                                              .+++||+|+|||||||+.    +|.|||+||+||.++|+|||.+++||+.+.+
T Consensus       160 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~VP~g~yFvmGDNR~----nS~DSR~~G~Vp~~~IvGka~~i~~s~~~~~  232 (248)
T 1b12_A          160 HRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRD----NSADSRYWGFVPEANLVGRATAIWMSFDKQE  232 (248)
T ss_dssp             EEEEECTTCCCCGGGSCCCTTCCTTEEECCTTEEEEECSBTT----SCCCHHHHCCEEGGGEEEEEEEEEEEBC---
T ss_pred             ceeEecCCccccccchhcccccccccEEeCCCcEEEecCCCc----ccCCCCcccccCHHHeEEEEEEEEEeCCccc
Confidence                                    024899999999999999    9999999999999999999999999988653

>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=99.41  E-value=2e-12  Score=96.93  Aligned_cols=91  Identities=18%  Similarity=0.267  Sum_probs=71.6

Q ss_pred             EEEEEecCCCcc------cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCc
Q 028679           50 TYLYGNKGDQMA------PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEP  123 (205)
Q Consensus        50 ~~i~~V~g~SM~------PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~  123 (205)
                      +....|.|+||+      |+|. +||+|++++.     ..++.||+|++..+.  +..++||+...+             
T Consensus        13 ~f~~~V~GdSM~~~~g~~p~i~-~Gd~v~Vd~~-----~~~~~Gdivv~~~~~--~~~~vKrl~~~~-------------   71 (109)
T 1kca_A           13 AFWLEVEGNSMTAPTGSKPSFP-DGMLILVDPE-----QAVEPGDFCIARLGG--DEFTFKKLIRDS-------------   71 (109)
T ss_dssp             CEEEECCSSTTCCCTTCSSCCC-TTCEEEEETT-----SCCCTTCEEEEECST--TCEEEEEEEEET-------------
T ss_pred             EEEEEEeCcCcCCCCCCCCeeC-CCCEEEEecC-----CcCCCCCEEEEEECC--CeEEEEEEEEeC-------------
Confidence            457899999999      9999 8999999974     468999999999754  468999998743             


Q ss_pred             eeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecCCCCC
Q 028679          124 FVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHG  174 (205)
Q Consensus       124 ~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~~~~g  174 (205)
                           |.+++.+||+..      .....-  ..-+|+|+|++.+||+..||
T Consensus        72 -----~~~~L~s~N~~y------~~~~~~--~~~~IiG~Vv~~~~~~~~~~  109 (109)
T 1kca_A           72 -----GQVFLQPLNPQY------PMIPCN--ESCSVVGKVIASQWPEETFG  109 (109)
T ss_dssp             -----TEEEEECSSTTS------CCEECC--TTCEEEEEEEEEECCGGGGC
T ss_pred             -----CEEEEEECCCCC------CCEEcC--CCcEEEEEEEEEEeCHHHcC
Confidence                 478899999852      111111  34689999999999987765

>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=99.29  E-value=1.7e-11  Score=92.29  Aligned_cols=89  Identities=21%  Similarity=0.297  Sum_probs=65.1

Q ss_pred             eEEEEEecCCCccc-ccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeee
Q 028679           49 LTYLYGNKGDQMAP-VMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLD  127 (205)
Q Consensus        49 ~~~i~~V~g~SM~P-TL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp  127 (205)
                      -+..+.|.|+||+| +|+ +||++++++.     ..++.||+|++..+   +..++||+...                 +
T Consensus        26 ~~~~~~v~GdSM~p~~i~-~Gd~v~vd~~-----~~~~~gdivv~~~~---~~~~vKr~~~~-----------------~   79 (116)
T 1umu_A           26 ATYFVKASGDSMIDGGIS-DGDLLIVDSA-----ITASHGDIVIAAVD---GEFTVKKLQLR-----------------P   79 (116)
T ss_dssp             GEEEEECCSSTTGGGTCC-TTCEEEEETT-----SCCCTTCEEEEEET---TEEEEEEEECS-----------------S
T ss_pred             CEEEEEECCCCcCCCCCC-CCCEEEEEcC-----CCCCCCCEEEEEEC---CEEEEEEEEeC-----------------C
Confidence            35689999999999 899 8999999974     36899999999873   46899999874                 3


Q ss_pred             CCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecCC
Q 028679          128 KDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAV  171 (205)
Q Consensus       128 ~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~~  171 (205)
                        .+++.+||+.      +.......-..-+|+|+|++.++.+.
T Consensus        80 --~~~L~s~N~~------y~~~~i~~~~~~~IiG~Vv~~~r~~r  115 (116)
T 1umu_A           80 --TVQLIPMNSA------YSPITISSEDTLDVFGVVIHVVKAAT  115 (116)
T ss_dssp             --SCEEECSSTT------SCCEECCTTSCEEEEEEEEEEEC---
T ss_pred             --cEEEECCCCC------CCCEEcCCCCeEEEEEEEEEEEEecC
Confidence              5778899975      11111111122479999999887654

>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=99.08  E-value=6.7e-10  Score=90.49  Aligned_cols=88  Identities=26%  Similarity=0.324  Sum_probs=65.0

Q ss_pred             EEEEEecCCCcccc-cccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeC
Q 028679           50 TYLYGNKGDQMAPV-MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDK  128 (205)
Q Consensus        50 ~~i~~V~g~SM~PT-L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~  128 (205)
                      +....|.|+||+|+ |. +||+|++++.     ..++.||+|++..   .+...+||+. .+|                 
T Consensus       110 ~~~~~v~GdSM~p~~i~-~Gd~v~vd~~-----~~~~~G~i~v~~~---~~~~~vKrl~-~~~-----------------  162 (202)
T 1jhf_A          110 DFLLRVSGMSMKDIGIM-DGDLLAVHKT-----QDVRNGQVVVARI---DDEVTVKRLK-KQG-----------------  162 (202)
T ss_dssp             CEEEECCSSTTGGGTCC-TTCEEEEEEC-----SCCCTTSEEEEEE---TTEEEEEEEE-EET-----------------
T ss_pred             EEEEEECCCCCCCCCCC-CCCEEEEecc-----CCcCCCeEEEEEE---CCEEEEEEEE-EeC-----------------
Confidence            46889999999999 99 8999999974     3688999999997   3578999998 444                 


Q ss_pred             CeEEEEeCCCCCCCCCCCCCCcccc-ccCCCEEEEEEEEEecC
Q 028679          129 DECWVLADNENMKPKEANDSRTFGP-VPMRNIVGRAIYCLRTA  170 (205)
Q Consensus       129 g~~~vlGDN~~~~~~~S~DSR~~Gp-V~~~~IiGkv~~~~~p~  170 (205)
                      |.+++.+||+.      +....+.. -..-.|+|+|++.++..
T Consensus       163 ~~~~l~s~N~~------y~~~~~~~~~~~~~IiG~Vv~~~r~~  199 (202)
T 1jhf_A          163 NKVELLPENSE------FKPIVVDLRQQSFTIEGLAVGVIRNG  199 (202)
T ss_dssp             TEEEEECSSTT------CCCEEEETTTSCEEEEEEEEEEEEC-
T ss_pred             CEEEEEECCCC------CCCEEccCCCCceEEEEEEEEEEEcc
Confidence            57788889875      11111110 01235999999988754

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

Probab=99.00  E-value=2.7e-09  Score=82.13  Aligned_cols=83  Identities=17%  Similarity=0.243  Sum_probs=63.4

Q ss_pred             EEEEEecCCCcc------cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCc
Q 028679           50 TYLYGNKGDQMA------PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEP  123 (205)
Q Consensus        50 ~~i~~V~g~SM~------PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~  123 (205)
                      +...+|.|+||+      |+|. +||+|++++.     ..++.||+|++....  +...+||+...+             
T Consensus        44 ~f~~~V~GdSM~~~~g~~p~i~-~Gd~v~vd~~-----~~~~~Gdivv~~~~~--~~~~vKrl~~~~-------------  102 (133)
T 2hnf_A           44 AFWLEVEGNSMTTPTGSKTSFP-DGMLILVDPE-----QAVEPGDFCIARLGG--DEFTFAKLIRDS-------------  102 (133)
T ss_dssp             CEEEECCSSTTCCC---CCCCC-TTCEEEEETT-----SCCCTTSEEEEEETT--TEEEEEEEEEET-------------
T ss_pred             EEEEEEeCCCcCCCcCCCCccC-CCCEEEEccC-----CCCCCCCEEEEEECC--CEEEEEEEEEeC-------------
Confidence            468899999999      9999 8999999974     468899999998743  478999998642             


Q ss_pred             eeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEE
Q 028679          124 FVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYC  166 (205)
Q Consensus       124 ~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~  166 (205)
                           |.+++.+||+..      .....-  ..-+|+|+|++.
T Consensus       103 -----~~~~L~s~N~~y------~~~~~~--~~~~IiG~Vv~~  132 (133)
T 2hnf_A          103 -----GQVFLQPLNPQY------PMIPCN--ESCSVVGKVIAS  132 (133)
T ss_dssp             -----TEEEEECSSTTS------CCEECS--TTEEEEEEEEEE
T ss_pred             -----CeEEEEECCCCC------CCEEcC--CCCEEEEEEEEE
Confidence                 478889999852      111111  345799999864

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

Probab=98.92  E-value=2.3e-09  Score=88.73  Aligned_cols=91  Identities=18%  Similarity=0.269  Sum_probs=68.9

Q ss_pred             EEEEEecCCCcc------cccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCc
Q 028679           50 TYLYGNKGDQMA------PVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEP  123 (205)
Q Consensus        50 ~~i~~V~g~SM~------PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~  123 (205)
                      +....|.|+||+      |+|. +||+|+|++.     ..++.||+|++...  .+...+||+...+             
T Consensus       140 ~~~l~V~GdSM~~~~g~~P~i~-~Gd~v~vd~~-----~~~~~g~ivv~~~~--~~~~~vKrl~~~~-------------  198 (236)
T 3bdn_A          140 AFWLEVEGNSMTAPTGSKPSFP-DGMLILVDPE-----QAVEPGDFCIARLG--GDEFTFKKLIRGS-------------  198 (236)
T ss_dssp             CEEEECCSSSSCCCSSCSSCCC-SSCEEEECCS-----SCCCTTSEEEEEST--TTCCCCEEEECCS-------------
T ss_pred             EEEEEEeCCCcCCCCCCCCcCC-CCCEEEECCC-----CCCCCCcEEEEEEC--CCeEEEEEEEEcC-------------
Confidence            467899999999      9999 7999999874     36889999999872  2467899998643             


Q ss_pred             eeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecCCCCC
Q 028679          124 FVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHG  174 (205)
Q Consensus       124 ~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~~~~g  174 (205)
                           |.+++.+||+.+      ....+-  ..-.|+|+|+..+||...|+
T Consensus       199 -----~~~~L~s~N~~y------~~~~~~--~~~~IiG~Vv~~~~~~~~~~  236 (236)
T 3bdn_A          199 -----GQVFLQPLNPQY------PMIPCN--ESCSVVGKVIASQWPEETFG  236 (236)
T ss_dssp             -----SSCEEECSSTTS------CCBC----CCCEEEEEEEECCCCSSSCC
T ss_pred             -----CcEEEEeCCCCC------CCeecC--CCcEEEEEEEEEEcCHHhcC
Confidence                 456788999752      111110  34579999999999877664

>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=98.80  E-value=5.1e-08  Score=79.34  Aligned_cols=86  Identities=22%  Similarity=0.302  Sum_probs=65.5

Q ss_pred             EEEEEecCCCc-ccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeC
Q 028679           50 TYLYGNKGDQM-APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDK  128 (205)
Q Consensus        50 ~~i~~V~g~SM-~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~  128 (205)
                      +....|.|+|| +|++. +||+|++++.     ..++.||+|++...   +...+||+...                  +
T Consensus       109 ~f~l~v~GdSM~~p~i~-~GD~viv~~~-----~~~~~G~ivv~~~~---~~~~vKr~~~~------------------~  161 (196)
T 3k2z_A          109 HFLLKVKGESMIEEHIC-DGDLVLVRRQ-----DWAQNGDIVAAMVD---GEVTLAKFYQR------------------G  161 (196)
T ss_dssp             EEEEECCSSTTGGGTCC-TTCEEEEEEC-----SCCCTTCEEEEEET---TEEEEEEEEEE------------------T
T ss_pred             EEEEEEeCCCcCCCCCC-CCCEEEEecc-----CcCCCCCEEEEEEC---CcEEEEEEEEE------------------C
Confidence            67899999999 69999 8999999984     46788999999873   47899999753                  3


Q ss_pred             CeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEec
Q 028679          129 DECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRT  169 (205)
Q Consensus       129 g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p  169 (205)
                      |.+++..+|+..      .....- -..-.|+|+|+.+++.
T Consensus       162 ~~~~L~~~N~~y------~~i~i~-~~~~~i~G~Vv~~~r~  195 (196)
T 3k2z_A          162 DTVELRPANREM------SSMFFR-AEKVKILGKVVGVFRK  195 (196)
T ss_dssp             TEEEEECSCTTS------CCEEEE-GGGCEEEEEEEEEEEE
T ss_pred             CEEEEEECCCCC------CCEEec-CCCEEEEEEEEEEEEc
Confidence            578888999751      111110 1234799999998764

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

Probab=97.06  E-value=0.0023  Score=50.56  Aligned_cols=77  Identities=12%  Similarity=0.088  Sum_probs=52.9

Q ss_pred             CCCcccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEEEeC
Q 028679           57 GDQMAPVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLAD  136 (205)
Q Consensus        57 g~SM~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~vlGD  136 (205)
                      +++|...-. +||+|+|++-      .+..|+++++..   .+...+||+.-.+|                 |.+.+..|
T Consensus       112 ~~~~~~v~~-~Gd~v~Vd~~------~~~~g~i~vv~~---~g~~~vKrl~~~~~-----------------~~i~L~s~  164 (189)
T 2fjr_A          112 LTDGMAIRS-EGKIYFVDKQ------ASLSDGLWLVDI---KGAISIRELTKLPG-----------------RKLHVAGG  164 (189)
T ss_dssp             CSSEEEEEE-TTEEEEEETT------CCSCSEEEEEEE---TTEEEEEEEEEETT-----------------TEEEEESS
T ss_pred             CCCeEEEee-CCcEEEEEcC------CccCCCEEEEEe---CCeEEEEEEEECCC-----------------CEEEEEeC
Confidence            455555556 8999999962      366799999987   34789999988754                 45667777


Q ss_pred             CCCCCCCCCCCCCccccccCCCEEEEEEEEEecC
Q 028679          137 NENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTA  170 (205)
Q Consensus       137 N~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~  170 (205)
                      |+.    -..+      ...=.|+|||++.+...
T Consensus       165 N~~----~~i~------~~~i~IiG~Vv~~~r~~  188 (189)
T 2fjr_A          165 KVP----FECG------IDDIKTLGRVVGVYSEV  188 (189)
T ss_dssp             SSC----EEEE------TTSSEEEEEEEEEEEEC
T ss_pred             CCC----eEec------ccceEEEEEEEEEEEec
Confidence            753    1111      12336999999887653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	205
d1b12a_	247	b.87.1.2 (A:) Type 1 signal peptidase {Escherichia	6e-05

>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 = 40.3 bits (93), Expect = 6e-05
 Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 4/47 (8%)

Query: 119 EKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIY 165
           ++   +++   + +++ DN +     + DSR +G VP  N+VGRA  
Sbjct: 180 QQLATWIVPPGQYFMMGDNRD----NSADSRYWGFVPEANLVGRATA 222

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	205
d1b12a_	247	Type 1 signal peptidase {Escherichia coli [TaxId:	100.0
d1f39a_	101	lambda repressor C-terminal domain {Bacteriophage	99.18
d1jhfa2	126	LexA C-terminal domain {Escherichia coli [TaxId: 5	99.03
d1umua_	105	UmuD' {Escherichia coli [TaxId: 562]}	98.77
d1aono_	97	Chaperonin-10 (GroES) {Escherichia coli [TaxId: 56	84.22

>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=3e-33  Score=234.65  Aligned_cols=121  Identities=23%  Similarity=0.370  Sum_probs=106.3

Q ss_pred             ceeEEEEEecCCCcccccccCCcEEEEEecCCC-----------CCCCCccCeEEEEecCCCCCceEEEEEEEecCceEE
Q 028679           47 GKLTYLYGNKGDQMAPVMGGLGGTLLVRKLPAA-----------DPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMV  115 (205)
Q Consensus        47 ~~~~~i~~V~g~SM~PTL~~~GD~Vlv~k~~~~-----------~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~  115 (205)
                      .|+++.+.|+++||+|||. .||+|+|+|++|.           ....+++||+|+|..|.++...++|||+|+|||+|+
T Consensus         2 ~f~~~~f~IPs~SMePTL~-~GD~l~V~K~~Yg~r~P~~~~~~~~~~~~~rgdivvf~~p~~~~~~~ikR~ig~pGD~i~   80 (247)
T d1b12a_           2 SFIYEPFQIPSGSMMPTLL-IGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVT   80 (247)
T ss_dssp             BCCEEEEECCSCTTTTTSC-TTEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTTCTTSEEEEEEEECTTCEEE
T ss_pred             EEEEEEEEeCcccccchhc-cCCEEEEEccccCccCCccCcccccccCcccCceeeecCCCCCCccccccccCCCCCeEE
Confidence            5889999999999999999 7999999998762           123579999999999998888999999999999998


Q ss_pred             ecCC----------------------------------------------------------------------------
Q 028679          116 STDE----------------------------------------------------------------------------  119 (205)
Q Consensus       116 ~~~~----------------------------------------------------------------------------  119 (205)
                      +.+.                                                                            
T Consensus        81 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (247)
T d1b12a_          81 YDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHR  160 (247)
T ss_dssp             EETTTTEEEEETTCCSSCCCCCCCCEEECCCEEEEEEEEEECGGGSCEEEEEEECCTTCCCTTEEEEEEEEEEETTEEEE
T ss_pred             EecccceEEecccccccceeecceeecccccCcccceeeeeeccCceeccceeeccccccccCceEeeeeeeccCCccee
Confidence            6420                                                                            


Q ss_pred             --------------------CCCceeeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecCCC
Q 028679          120 --------------------KDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVD  172 (205)
Q Consensus       120 --------------------~~~~~~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~~~  172 (205)
                                          ...+++||+|+|||||||+.    +|.|||+||+||+++|+|||.+++||+.+
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~Vp~~~yfvmGDNR~----nS~DSR~wG~Vp~~~I~Gka~~i~~p~~~  229 (247)
T d1b12a_         161 ILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRD----NSADSRYWGFVPEANLVGRATAIWMSFDK  229 (247)
T ss_dssp             EEECTTCCCCGGGSCCCTTCCTTEEECCTTEEEEECSBTT----SCCCHHHHCCEEGGGEEEEEEEEEEEBC-
T ss_pred             EEecccchhcccccccCCccccceEEEeCCeEEEecCCCC----CCccccccCcCCHHHeEEEEEEEEEECCC
Confidence                                01246899999999999999    99999999999999999999999999864

>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=99.18  E-value=1.2e-10  Score=84.42  Aligned_cols=90  Identities=18%  Similarity=0.264  Sum_probs=69.0

Q ss_pred             EEEEecCCCc------ccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCce
Q 028679           51 YLYGNKGDQM------APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPF  124 (205)
Q Consensus        51 ~i~~V~g~SM------~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~  124 (205)
                      +..+|.|+||      +|+|. +||+|+|++-     .+++.||+|++....  +...+||+.-.               
T Consensus         6 F~l~V~GdSM~~~~~~ep~i~-~Gd~viVd~~-----~~~~~g~ivva~~~~--~~~~vKr~~~~---------------   62 (101)
T d1f39a_           6 FWLEVEGNSMTAPTGSKPSFP-DGMLILVDPE-----QAVEPGDFCIARLGG--DEFTFKKLIRD---------------   62 (101)
T ss_dssp             EEEECCSSTTCCCTTCSSCCC-TTCEEEEETT-----SCCCTTCEEEEECTT--SCEEEEEEEEE---------------
T ss_pred             EEEEEeCCccCCCcccCCCcC-CCCEEEEEec-----CccCCCCEEEEEECC--CeEEEEEEEEc---------------
Confidence            5678999999      89999 8999999974     578899999988643  35789999754               


Q ss_pred             eeeCCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEecCCCCC
Q 028679          125 VLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLRTAVDHG  174 (205)
Q Consensus       125 ~vp~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~p~~~~g  174 (205)
                         .+++++..+|+..      ......  ..-.|+|+|+..+||-..||
T Consensus        63 ---~~~~~L~s~N~~y------~~i~~~--~~~~IiG~Vv~s~~p~~~~~  101 (101)
T d1f39a_          63 ---SGQVFLQPLNPQY------PMIPCN--ESCSVVGKVIASQWPEETFG  101 (101)
T ss_dssp             ---TTEEEEECSSTTS------CCEECS--TTCEEEEEEEEEECCGGGGC
T ss_pred             ---CCEEEEEECCCCC------CCCcCC--CCcEEEEEEEEEECcHHHCC
Confidence               3578899999862      111111  24589999999999977665

>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=99.03  E-value=8.4e-10  Score=82.79  Aligned_cols=86  Identities=26%  Similarity=0.292  Sum_probs=64.8

Q ss_pred             EEEEEecCCCcccc-cccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeC
Q 028679           50 TYLYGNKGDQMAPV-MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDK  128 (205)
Q Consensus        50 ~~i~~V~g~SM~PT-L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~  128 (205)
                      +...+|.|+||+|+ +. +||++++++-     ..++.||+|++..   .++..+||+.-.+                  
T Consensus        38 ~f~lrV~GdSM~~~~i~-~gd~viv~~~-----~~~~~G~ivv~~~---~ge~~vKrl~~~~------------------   90 (126)
T d1jhfa2          38 DFLLRVSGMSMKDIGIM-DGDLLAVHKT-----QDVRNGQVVVARI---DDEVTVKRLKKQG------------------   90 (126)
T ss_dssp             CEEEECCSSTTGGGTCC-TTCEEEEEEC-----SCCCTTSEEEEEE---TTEEEEEEEEEET------------------
T ss_pred             eEEEEEcCCcccCcccC-CCEEEEEecc-----ccccCCCEEEEEE---CCEEEEEEEEEcC------------------
Confidence            45789999999998 88 8999999974     5789999999998   4578999998643                  


Q ss_pred             CeEEEEeCCCCCCCCCCCCCCcccc-ccCCCEEEEEEEEEe
Q 028679          129 DECWVLADNENMKPKEANDSRTFGP-VPMRNIVGRAIYCLR  168 (205)
Q Consensus       129 g~~~vlGDN~~~~~~~S~DSR~~Gp-V~~~~IiGkv~~~~~  168 (205)
                      |.+++..+|+.      +....+.. =..=.|+|+|+.+++
T Consensus        91 ~~~~L~s~N~~------y~pi~~~~~~~~~~IiG~Vv~vir  125 (126)
T d1jhfa2          91 NKVELLPENSE------FKPIVVDLRQQSFTIEGLAVGVIR  125 (126)
T ss_dssp             TEEEEECSSTT------CCCEEEETTTSCEEEEEEEEEEEE
T ss_pred             CEEEEecCCcC------CCCeEccCCCCcEEEEEEEEEEEC
Confidence            57889999985      11111110 011269999998875

>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=98.77  E-value=2.3e-08  Score=72.84  Aligned_cols=86  Identities=21%  Similarity=0.319  Sum_probs=63.2

Q ss_pred             eEEEEEecCCCc-ccccccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeee
Q 028679           49 LTYLYGNKGDQM-APVMGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLD  127 (205)
Q Consensus        49 ~~~i~~V~g~SM-~PTL~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp  127 (205)
                      -+++.+|.|+|| .|.+. +||++++++.     ..++.||+|++..   .++..+||+..                   
T Consensus        19 ~~f~~rV~GdSM~~~gI~-~GDlliVd~~-----~~~~~g~ivva~i---~ge~~vKrl~~-------------------   70 (105)
T d1umua_          19 ATYFVKASGDSMIDGGIS-DGDLLIVDSA-----ITASHGDIVIAAV---DGEFTVKKLQL-------------------   70 (105)
T ss_dssp             GEEEEECCSSTTGGGTCC-TTCEEEEETT-----SCCCTTCEEEEEE---TTEEEEEEEEC-------------------
T ss_pred             ceEEEEEcCCccccCccC-CCCEEEEEcc-----cccccCcEEEEEE---CCEEEEEEEEE-------------------
Confidence            356899999999 58899 7999999984     5788999999998   45789999742                   


Q ss_pred             CCeEEEEeCCCCCCCCCCCCCCccccccCCCEEEEEEEEEe
Q 028679          128 KDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIYCLR  168 (205)
Q Consensus       128 ~g~~~vlGDN~~~~~~~S~DSR~~GpV~~~~IiGkv~~~~~  168 (205)
                      +|..+++.+|+.      ++.....+-..-.|.|+|+.+++
T Consensus        71 ~~~~~L~~~N~~------y~~i~i~~~~~~~I~GvVv~viR  105 (105)
T d1umua_          71 RPTVQLIPMNSA------YSPITISSEDTLDVFGVVIHVVK  105 (105)
T ss_dssp             SSSCEEECSSTT------SCCEECCTTSCEEEEEEEEEEEC
T ss_pred             CCcEEEECCCCC------CCCEEcCCCCCEEEEEEEEEEEC
Confidence            235677888875      33332222122349999998764

>d1aono_ b.35.1.1 (O:) Chaperonin-10 (GroES) {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: GroES-like
superfamily: GroES-like
family: GroES
domain: Chaperonin-10 (GroES)
species: Escherichia coli [TaxId: 562]

Probab=84.22  E-value=1.7  Score=29.25  Aligned_cols=93  Identities=12%  Similarity=0.164  Sum_probs=53.2

Q ss_pred             cccCCcEEEEEecCCCCCCCCccCeEEEEecCCCCCceEEEEEEEecCceEEecCCCCCceeeeCCeEEEEeCCCCCCCC
Q 028679           64 MGGLGGTLLVRKLPAADPKRVSVGDVVVMKDPEKSDNYIVRRLAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPK  143 (205)
Q Consensus        64 L~~~GD~Vlv~k~~~~~~~~~~rGDIVvf~~P~~~~~~~VKRVialpGd~V~~~~~~~~~~~vp~g~~~vlGDN~~~~~~  143 (205)
                      |+|-||+|||.+..   ..+-..|-|++=..  ...+....+|+++.-. ....++...+..+..|..-+.+++... ..
T Consensus         3 ikPlgdrVLVk~~~---~e~kT~gGIiLp~~--~~~~~~~g~VvavG~g-~~~~~g~~~~~~vk~GD~Vl~~~~~g~-~~   75 (97)
T d1aono_           3 IRPLHDRVIVKRKE---VETKSAGGIVLTGS--AAAKSTRGEVLAVGNG-RILENGEVKPLDVKVGDIVIFNDGYGV-KS   75 (97)
T ss_dssp             EEECTTEEEEEECC---TTCTTTTSSCCCCC--CSCCCCEEEEEEECSB-CCTTSSCCCBCSCCTTCEEEECCCSSC-EE
T ss_pred             ceEcCCEEEEEEcc---cccEecceEEECCc--cccCceeEEEEEEeee-EEccCCcCccccCCCCCEEEEecccCc-eE
Confidence            55679999999863   23444677765221  2234556777777421 112233344455667776666654320 00


Q ss_pred             CCCCCCccccccCCCEEEEE
Q 028679          144 EANDSRTFGPVPMRNIVGRA  163 (205)
Q Consensus       144 ~S~DSR~~GpV~~~~IiGkv  163 (205)
                      ..+|...|=.++.++|+|++
T Consensus        76 ~~~dg~~y~ii~e~dIlavi   95 (97)
T d1aono_          76 EKIDNEEVLIMSESDILAIV   95 (97)
T ss_dssp             EESSSCEEEEEETTTEEEEE
T ss_pred             EEECCEEEEEEEHHHEEEEE
Confidence            23566667688888898875