Citrus Sinensis ID: 023926

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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-------210-------220-------230-------240-------250-------260-------270-----
Protein Sequence
MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPPPNYQPKANYRCNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVFGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQFSGSENLNGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS
Secondary Structure (PSIPRED)
ccEEEEEEEHHHHHHHHHHHHccccccccccccHHHccccccEEEEccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccEEEccccccEEccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEcccccccccccccccccEEEEEEccccccccccccEEEEccccccccccccccccEEEEEEEccccEEEEc
Secondary Structure Prediction (SSPRO)
cEEEEEEEcHHHHHHHHHHHcccEccccccccHHHHcccccccccccccccccccccccccccHHHHHHcHHHHHccccccccHHHHHHHHHHcccccccccHccccccccccccHccHHHHccccccccccccccccccccccccccHHHHHHHHHHHcccccHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEccccEEEEEEEEEcccccccccEEEEcccHHHHHcccccccHEEEEEEcccccEEEEc
Coil and Loop (DISEMBL)
MALRVTVNFSGYVAQNlahsagirfgfsttstrsfheclfrprvfchskktdldpppnyqpkanyrCNTLAAeifgdgacnspILMGLVSLMkstagmpgpsatsmgvfgispfkaasiipflqgskwlpcnepgtvpesdyvdkggttdkiqfsgsenlngvSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSflaeprsipsasmnptldvgDRILAEKVSYffkrpevsdivifrappilqeigfssGDVFIKRIVAtagdcvevs
Flexible Loop (DISEMBL)
MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFchskktdldpppnYQPKANYRCNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVFGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQfsgsenlngVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAeprsipsasmnptlDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS
Low Complexity Region (SEG)
MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPPPNYQPKANYRCNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVFGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQFSGSENLNGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS
Disordered region (IsUnstruct)
************************************ECLFRPRVFCHS*************KANYRCNTLAAEIFGDGACNSPILMGLVSLMKS**********SMGVFGISPFKAASIIPFLQGSKWLPCNEPGT***********************LNGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEP*********PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCV***
Disordered Region (DISOPRED)
*ALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRV*****************************************MGLV************************FKAASIIPFLQGSKWLP*************************************************VCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS
Disordered Region (DISEMBL)
MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPPPNYQPKANYRCNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVFGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQFSGSENLNGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS
Disordered Region (DISPRO)
MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKK**L*PPPNYQPKANYRCNTLAAEIFGDGACNSPILMGLVSLMKST*****P*ATSMGVFGISPFKAASIIPFLQGSKWLPCNEPG***********************************GSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPPPNYQPKANYRCNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVFGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQFSGSENLNGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS
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	275	2.2.26 [Sep-21-2011]
Q9M9Z2	367	Probable thylakoidal proc	yes	no	0.949	0.711	0.512	1e-67
O04348	340	Thylakoidal processing pe	no	no	0.894	0.723	0.530	1e-64
Q8H0W1	291	Chloroplast processing pe	no	no	0.396	0.374	0.550	1e-30
P72660	196	Probable signal peptidase	N/A	no	0.28	0.392	0.532	3e-17
P73157	218	Probable signal peptidase	N/A	no	0.345	0.435	0.412	2e-13
Q51876	203	Signal peptidase I OS=Pho	N/A	no	0.327	0.443	0.377	2e-12
P26844	284	Signal peptidase I OS=Pse	yes	no	0.301	0.292	0.375	4e-09
O33021	289	Probable signal peptidase	yes	no	0.414	0.394	0.284	5e-09
Q10789	294	Signal peptidase I OS=Myc	yes	no	0.323	0.302	0.333	6e-09
O67088	256	Signal peptidase I OS=Aqu	yes	no	0.28	0.300	0.383	1e-08

>sp|Q9M9Z2|TPP2_ARATH Probable thylakoidal processing peptidase 2, chloroplastic OS=Arabidopsis thaliana GN=TPP2 PE=2 SV=1

 Score =  256 bits (653), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 148/289 (51%), Positives = 193/289 (66%), Gaps = 28/289 (9%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDL-DPPP-- 57
           MA+RVT  +S YVA+++A SAG R G  T   RS  E   RPR   H++  D+ D  P  
Sbjct: 1   MAIRVTFTYSSYVARSIASSAGTRVG--TGDVRSCFETWVRPRFCGHNQIPDIVDKSPGS 58

Query: 58  -NYQPKANYRC-------NTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVF 109
             + P +  R        +T+A EI  +G C SP+++G++SLM  T     P  + M   
Sbjct: 59  NTWGPSSGPRARPASSMYSTIAREILEEG-CKSPLVLGMISLMNLTGA---PQFSGMTGL 114

Query: 110 GISPFKAASIIPFLQGSKWLPCNEPGTVP-ESDYVDKGGTT--DKIQFSGSENL-NGVSL 165
           GISPFK +S+IPFL+GSKW+PC+ P T+  +   VD+GG     K++   S+ + NG   
Sbjct: 115 GISPFKTSSVIPFLRGSKWMPCSIPATLSTDIAEVDRGGKVCDPKVKLELSDKVSNG--- 171

Query: 166 QLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILA 225
                  W++KLLN+CS+DAKAAFTA+TVS LF+S LAEP+SIPS SM PTLDVGDR++A
Sbjct: 172 ----GNGWVNKLLNICSEDAKAAFTAVTVSLLFRSALAEPKSIPSTSMLPTLDVGDRVIA 227

Query: 226 EKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
           EKVSYFF++PEVSDIVIF+APPIL E G+S  DVFIKRIVA+ GD VEV
Sbjct: 228 EKVSYFFRKPEVSDIVIFKAPPILVEHGYSCADVFIKRIVASEGDWVEV 276

Cleaves the thylakoid-transfer domain from a chloroplast protein.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 4EC: .EC: 2EC: 1EC: .EC: 8EC: 9

>sp|O04348|TPP1_ARATH Thylakoidal processing peptidase 1, chloroplastic OS=Arabidopsis thaliana GN=TPP1 PE=2 SV=2

 Score =  246 bits (628), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 147/277 (53%), Positives = 185/277 (66%), Gaps = 31/277 (11%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPPPNYQ 60
           MA+R+T  +S +VA+NL    G R G          E L RPR F H  K D D  P  +
Sbjct: 1   MAIRITFTYSTHVARNLV---GTRVGPGGYC----FESLVRPRFFSH--KRDFDRSPRNR 51

Query: 61  PKANYRCNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVFGISPFKAASII 120
           P + Y   ++A E+ G+G+  SP++MGL+S++KST G     +++M V G+S FKA+SII
Sbjct: 52  PASMY--GSIARELIGEGS-QSPLVMGLISILKSTTGH---ESSTMNVLGVSSFKASSII 105

Query: 121 PFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQFSGSENLNGVSLQLKTSGSWLSKLLNV 180
           PFLQGSKW+        P  D VDKGGT         E+ NG S        W++KLL+V
Sbjct: 106 PFLQGSKWI-----KNPPVIDDVDKGGTVCDDD-DDKESRNGGS-------GWVNKLLSV 152

Query: 181 CSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDI 240
           CS+DAKAAFTA+TVS LF+S LAEP+SIPS SM PTLD GDR++AEKVSYFF++PEVSDI
Sbjct: 153 CSEDAKAAFTAVTVSILFRSALAEPKSIPSTSMYPTLDKGDRVMAEKVSYFFRKPEVSDI 212

Query: 241 VIFRAPPIL---QEIGFSSGDVFIKRIVATAGDCVEV 274
           VIF+APPIL    E G+SS DVFIKRIVA+ GD VEV
Sbjct: 213 VIFKAPPILLEYPEYGYSSNDVFIKRIVASEGDWVEV 249

Cleaves the thylakoid-transfer domain from a chloroplast protein.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|Q8H0W1|PLSP1_ARATH Chloroplast processing peptidase OS=Arabidopsis thaliana GN=PLSP1 PE=2 SV=2

 Score =  134 bits (336), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 60/109 (55%), Positives = 81/109 (74%)

Query: 166 QLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILA 225
           +++       + L+  SDDA+  F A+ VS  F+ F+AEPR IPS SM PT DVGDR++A
Sbjct: 96  EVEEKNRLFPEWLDFTSDDAQTVFVAIAVSLAFRYFIAEPRYIPSLSMYPTFDVGDRLVA 155

Query: 226 EKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
           EKVSY+F++P  +DIVIF++PP+LQE+G++  DVFIKRIVA  GD VEV
Sbjct: 156 EKVSYYFRKPCANDIVIFKSPPVLQEVGYTDADVFIKRIVAKEGDLVEV 204

Involved in the maturation of the plastid protein translocation channel. Required for the biogenesis of plastid internal membranes. May also function as a thylakoidal processing peptidase.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|P72660|LEP1_SYNY3 Probable signal peptidase I-1 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=lepB1 PE=3 SV=1

 Score = 89.4 bits (220), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 41/77 (53%), Positives = 54/77 (70%)

Query: 199 KSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGD 258
           + F+AEPR IPS SM PTL+ GDR++ EKVSY F  P+V DI++F  P +LQ  G+  G 
Sbjct: 31  RFFVAEPRYIPSDSMLPTLEQGDRLVVEKVSYHFHPPQVGDIIVFHPPELLQVQGYDLGQ 90

Query: 259 VFIKRIVATAGDCVEVS 275
            FIKR++A  G  VEV+
Sbjct: 91  AFIKRVIALPGQTVEVN 107

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

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|P73157|LEP2_SYNY3 Probable signal peptidase I-2 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=lepB2 PE=3 SV=1

 Score = 76.3 bits (186), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/97 (41%), Positives = 57/97 (58%), Gaps = 2/97 (2%)

Query: 179 NVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVS 238
           N   +  K   TA+ ++   ++F+AE R IPS+SM PTL + DR++ EK+SY  + PE  
Sbjct: 19  NTWLELGKTMVTAVILAIGIRTFVAEARYIPSSSMEPTLQINDRLIIEKISYRLRDPERG 78

Query: 239 DIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS 275
           +IV+F     L+   F   D FIKRI+   GD V VS
Sbjct: 79  EIVVFNPTDALKAKNFH--DAFIKRIIGLPGDEVRVS 113

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

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|Q51876|LEP_PHOLA Signal peptidase I OS=Phormidium laminosum GN=lepB PE=3 SV=1

 Score = 73.2 bits (178), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/90 (37%), Positives = 55/90 (61%)

Query: 186 KAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRA 245
           K    ++ ++   ++F+AE R IPS SM PTL+V DR++ EK+SY F  P   DI++F  
Sbjct: 33  KTIGLSVVLALGIRTFVAEARYIPSESMLPTLEVNDRLIVEKISYHFNPPRRGDIIVFHP 92

Query: 246 PPILQEIGFSSGDVFIKRIVATAGDCVEVS 275
              L++   S  + FIKR++   G+ V+V+
Sbjct: 93  TEALKQQNPSLNEAFIKRVIGLPGETVQVT 122

Phormidium laminosum (taxid: 32059)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|P26844|LEP_PSEFL Signal peptidase I OS=Pseudomonas fluorescens GN=lepB PE=3 SV=1

 Score = 62.0 bits (149), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 39/104 (37%), Positives = 52/104 (50%), Gaps = 21/104 (20%)

Query: 185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVS------ 238
            K+ F  L +  + +SFL EP  IPS SM PTLDVGD IL  K SY  + P +       
Sbjct: 63  GKSFFPVLFIVLVLRSFLVEPFQIPSGSMKPTLDVGDFILVNKFSYGIRLPVIDKKVIEV 122

Query: 239 ------DIVIFRAPPILQEIGFSSGDV-FIKRIVATAGDCVEVS 275
                 D+++FR P        S  +V +IKR+V   GD V  +
Sbjct: 123 GDPQRGDVMVFRYP--------SDPNVNYIKRVVGLPGDVVRYT 158

Pseudomonas fluorescens (taxid: 294)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|O33021|LEP_MYCLE Probable signal peptidase I OS=Mycobacterium leprae (strain TN) GN=lepB PE=3 SV=1

 Score = 62.0 bits (149), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 68/151 (45%), Gaps = 37/151 (24%)

Query: 151 KIQFSGSENLNGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPS 210
           ++  + +E   GVS   K S  W   +L         A  A+ + ++  +F+A P  IPS
Sbjct: 32  EVSETAAEAAIGVSEPKKRSALWEFAIL---------AVIAIGLYYVMLTFVARPYLIPS 82

Query: 211 ASMNPTLD-----VGDRILAEKVSYFFKRPEVSDIVIFRAPP------------------ 247
            SM PTL      VGDRI+ +K++Y F  P+  D+++F+ PP                  
Sbjct: 83  ESMEPTLHGCSGCVGDRIMVDKITYRFSSPQPGDVIVFKGPPSWNTMYKSIRSNNIVLRS 142

Query: 248 ---ILQEIGFSSGDV--FIKRIVATAGDCVE 273
               L  +GF   D    +KR++A  G  V+
Sbjct: 143 VQNALSFVGFVPPDENDLVKRVIAVGGQTVQ 173

Mycobacterium leprae (taxid: 1769)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|Q10789|LEP_MYCTU Signal peptidase I OS=Mycobacterium tuberculosis GN=lepB PE=1 SV=1

 Score = 61.6 bits (148), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 39/117 (33%), Positives = 56/117 (47%), Gaps = 28/117 (23%)

Query: 185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLD-----VGDRILAEKVSYFFKRPEVSD 239
           A  A  A+ + ++  +F+A P  IPS SM PTL      VGDRI+ +K+SY F  P+  D
Sbjct: 69  AVLAVIAVVLYYVMLTFVARPYLIPSESMEPTLHGCSTCVGDRIMVDKLSYRFGSPQPGD 128

Query: 240 IVIFRAPP---------------------ILQEIGFSSGDV--FIKRIVATAGDCVE 273
           +++FR PP                      L  IGF   D    +KR++A  G  V+
Sbjct: 129 VIVFRGPPSWNVGYKSIRSHNVAVRWVQNALSFIGFVPPDENDLVKRVIAVGGQTVQ 185

Mycobacterium tuberculosis (taxid: 1773)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|O67088|LEP_AQUAE Signal peptidase I OS=Aquifex aeolicus (strain VF5) GN=lepB PE=3 SV=1

 Score = 60.5 bits (145), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 47/86 (54%), Gaps = 9/86 (10%)

Query: 189 FTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPI 248
           F  +      + ++A+  +IPSASM PTL VGD IL  K+ Y    P   D+++F+ P  
Sbjct: 9   FLIILAVLFIREYIAQAYTIPSASMEPTLLVGDFILVNKLVYSLSEPMRGDMIVFKYP-- 66

Query: 249 LQEIGFSSGDV-FIKRIVATAGDCVE 273
                  + D+ FIKRI+A  GD VE
Sbjct: 67  ------KNPDIDFIKRIIARGGDTVE 86

Aquifex aeolicus (strain VF5) (taxid: 224324)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

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	275
225458489	368	PREDICTED: probable thylakoidal processi	0.956	0.714	0.594	2e-83
356519126	362	PREDICTED: probable thylakoidal processi	0.941	0.715	0.585	3e-80
356510334	362	PREDICTED: probable thylakoidal processi	0.938	0.712	0.576	3e-80
255538440	831	signal peptidase I, putative [Ricinus co	0.963	0.318	0.550	1e-76
449498740	763	PREDICTED: uncharacterized protein LOC10	0.970	0.349	0.567	3e-75
224136660	362	predicted protein [Populus trichocarpa]	0.923	0.701	0.571	7e-75
357465373	334	Thylakoidal processing peptidase [Medica	0.970	0.799	0.541	2e-74
357465371	375	Thylakoidal processing peptidase [Medica	0.970	0.712	0.541	3e-74
449447223	761	PREDICTED: uncharacterized protein LOC10	0.952	0.344	0.563	1e-72
15222236	367	signal peptidase I [Arabidopsis thaliana	0.949	0.711	0.512	9e-66

>gi|225458489|ref|XP_002284120.1| PREDICTED: probable thylakoidal processing peptidase 2, chloroplastic [Vitis vinifera] gi|147810057|emb|CAN78280.1| hypothetical protein VITISV_021649 [Vitis vinifera]

 Score =  314 bits (805), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 173/291 (59%), Positives = 212/291 (72%), Gaps = 28/291 (9%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPP-PNY 59
           MA+++TV +SGYVAQNLA SAGIR G    + RS HEC  R R FC S+K ++D P P+ 
Sbjct: 1   MAIKLTVTYSGYVAQNLASSAGIRVG----NCRSIHECWVRSRFFCPSQKPEVDSPVPSR 56

Query: 60  QPKANYR-----C---------NTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATS 105
             +A+YR     C         +TLA E+FGD +C +P+++GL+SLMKS+ G+   S +S
Sbjct: 57  AYQADYRRPKANCWAKVSTSAYSTLAGEVFGD-SCRNPLIVGLISLMKSSTGV---SESS 112

Query: 106 MGVFGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQFSGSENLNG-VS 164
           +GVFG+SP KA SI+PFL GSKWLPCNEP      D VDKGGT    Q    E ++  + 
Sbjct: 113 VGVFGVSPLKATSILPFLPGSKWLPCNEPIQGSVGDEVDKGGT----QCCDVEVISKPLD 168

Query: 165 LQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRIL 224
            ++    +WLSKLLN CS+DA+A FTA+TVS LF+S LAEPRSIPSASM PTLDVGDRIL
Sbjct: 169 RKVLERSNWLSKLLNCCSEDARAVFTAVTVSLLFRSPLAEPRSIPSASMYPTLDVGDRIL 228

Query: 225 AEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS 275
           AEKVSY F+ PEVSDIVIF+ PPILQEIG+S+GDVFIKRIVA AGD VEVS
Sbjct: 229 AEKVSYVFRNPEVSDIVIFKVPPILQEIGYSAGDVFIKRIVAKAGDYVEVS 279

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356519126|ref|XP_003528225.1| PREDICTED: probable thylakoidal processing peptidase 2, chloroplastic-like [Glycine max]

 Score =  304 bits (779), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 167/285 (58%), Positives = 202/285 (70%), Gaps = 26/285 (9%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFC-HSKKTDLDPP--- 56
           MA+RVT +FSGYVAQ+LA SAG+R      ++R   EC  R R+F   ++KTDLD     
Sbjct: 1   MAIRVTFSFSGYVAQSLASSAGVR----VANSRCVQECWIRTRLFGGATQKTDLDSSAGG 56

Query: 57  -------PNYQPKANYRCNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVF 109
                  PN   ++ Y  ++LA E  GDG   SPI++GL+S+MKST G+ G SA + G+F
Sbjct: 57  GVRNFARPNCWAQSTY--SSLAGEFLGDGCSKSPIILGLISIMKSTVGVSGSSAAAAGIF 114

Query: 110 GISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQFSGSENLNGVSLQLKT 169
           GISPFK  SIIPFL GSKWLPCNE    P S  VDKGGT   +  + S N   +S     
Sbjct: 115 GISPFKTTSIIPFLPGSKWLPCNESVPDPTSWEVDKGGTRRVVSETES-NFAKIS----- 168

Query: 170 SGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVS 229
              WLS+L+NVCS+DAKAAFTALTVS LFKS LAEPRSIPS+SM PTL+VGDR+L EKVS
Sbjct: 169 ---WLSRLMNVCSEDAKAAFTALTVSLLFKSSLAEPRSIPSSSMYPTLEVGDRVLTEKVS 225

Query: 230 YFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
           +FF++P+VSDIVIF+APP L+E GFSS DVFIKRIVA AGD VEV
Sbjct: 226 FFFRKPDVSDIVIFKAPPWLEEFGFSSSDVFIKRIVAKAGDTVEV 270

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356510334|ref|XP_003523894.1| PREDICTED: probable thylakoidal processing peptidase 2, chloroplastic-like [Glycine max]

 Score =  304 bits (779), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 165/286 (57%), Positives = 202/286 (70%), Gaps = 28/286 (9%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLD------ 54
           MA+RVT +FSGYVAQ+LA SAG+R      ++R   EC  R R+   ++KTDLD      
Sbjct: 1   MAIRVTFSFSGYVAQSLASSAGVR----VANSRCVQECWIRTRLSGATQKTDLDSSAGGV 56

Query: 55  -----PPPNYQPKANYRCNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVF 109
                P PN   ++ Y  +TL  E  GDG C SPI++GL+S+MKSTAG+ G SA + G+F
Sbjct: 57  RNFAGPKPNCWAQSTY--STLTGEFLGDG-CKSPIILGLISIMKSTAGVSGSSAAAAGIF 113

Query: 110 GISPFKAASIIPFLQGSKWLPCNEPGTVPESDY-VDKGGTTDKIQFSGSENLNGVSLQLK 168
           GISPFK  SI+PFL GSKWLPCNE    P + + VDKGGT   +  + S           
Sbjct: 114 GISPFKTTSIVPFLPGSKWLPCNESVPDPTTSWEVDKGGTRRVVSDTESNF--------- 164

Query: 169 TSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKV 228
              SWLS+L+NVCS+DAKAAFTA+TVS LFKS LAEPRSIPS+SM PTL+VGDR+L EKV
Sbjct: 165 AKTSWLSRLMNVCSEDAKAAFTAVTVSLLFKSSLAEPRSIPSSSMYPTLEVGDRVLTEKV 224

Query: 229 SYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
           S+FF++P+VSDIVIF+APP L+E GFSS DVFIKRIVA AGD VEV
Sbjct: 225 SFFFRKPDVSDIVIFKAPPCLEEFGFSSSDVFIKRIVAKAGDTVEV 270

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255538440|ref|XP_002510285.1| signal peptidase I, putative [Ricinus communis] gi|223550986|gb|EEF52472.1| signal peptidase I, putative [Ricinus communis]

 Score =  291 bits (746), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 169/307 (55%), Positives = 206/307 (67%), Gaps = 42/307 (13%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCH--SKKTDLDPPP- 57
           MA+RVT  +SGYVAQ++A  AGIR G    + RS HEC  R R+F    ++  DL+PP  
Sbjct: 1   MAIRVTFTYSGYVAQSIASCAGIRVG----NCRSLHECFVRSRIFASPTNQNVDLEPPAP 56

Query: 58  ---------NYQPKANYRCNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGV 108
                     Y+  +    +T+A EIFG+  C SPI +GL+ LMKSTAG+ G S  S GV
Sbjct: 57  RPSRVFQSGGYRKSSTSLYSTIAGEIFGNN-CKSPIAVGLIELMKSTAGV-GVSG-STGV 113

Query: 109 FGISPFKAASIIPFLQGSKWLPCNEPG---------TVPESDYVDKGGTTDKIQFSGSE- 158
           FGISP KA+SI+P LQGS+WLPCNEP          T   S  VD+GGT   ++   S  
Sbjct: 114 FGISPLKASSILPVLQGSRWLPCNEPSPGQKNNEPSTRQNSSDVDRGGTVKCVKNGSSSS 173

Query: 159 -----------NLNGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRS 207
                       +NG   +L   GSWLS++L+  S+DAKA FTA TV+FLF+S LAEPRS
Sbjct: 174 CCTTATTTVTLEINGN--ELDKGGSWLSRVLSSFSEDAKAIFTAATVNFLFRSALAEPRS 231

Query: 208 IPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT 267
           IPS SM PTLDVGDR+LAEKVS+ F++PEVSDIVIF+APPILQEIG+SSGDVFIKRIVAT
Sbjct: 232 IPSTSMCPTLDVGDRVLAEKVSFIFRQPEVSDIVIFKAPPILQEIGYSSGDVFIKRIVAT 291

Query: 268 AGDCVEV 274
           AGD VEV
Sbjct: 292 AGDIVEV 298

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449498740|ref|XP_004160620.1| PREDICTED: uncharacterized protein LOC101229456 [Cucumis sativus]

 Score =  287 bits (735), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 164/289 (56%), Positives = 199/289 (68%), Gaps = 22/289 (7%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPP---P 57
           MA+RVTV+FSGYVAQNLA SAGIR G    + R+ HEC  R R+F  ++K + DP     
Sbjct: 1   MAIRVTVSFSGYVAQNLASSAGIRVG----NCRAVHECWIRSRLFGSNQKPEFDPSGSVR 56

Query: 58  NYQPK---ANYRC---------NTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATS 105
           NY      +N RC          T+A EI  D +C +PI++GL+SLMKS  G    S  +
Sbjct: 57  NYHSAVLPSNSRCWVKNSASALGTIAGEIV-DESCRNPIVLGLISLMKSAVGTSVSSPMA 115

Query: 106 MGVFGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQFSGSENLNGVSL 165
           MGVFG+S F+A+SIIPFLQGSK +  NE  +    D ++  G  D +   G       S 
Sbjct: 116 MGVFGVSSFEASSIIPFLQGSKTVTGNESVSGSTGDEIESYGVFDCVMDEGMSQPPDPS- 174

Query: 166 QLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILA 225
           +L+ S SW+S+ LN CS+DAKA  TALTVS LF+S LAEPRSIPS+SM PTLDVGDRILA
Sbjct: 175 KLEKS-SWISRFLNNCSEDAKAIATALTVSVLFRSSLAEPRSIPSSSMYPTLDVGDRILA 233

Query: 226 EKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
           EKVSYFF+RP VSDIVIF+APPILQ+IG+ S DVFIKRIVA AGDCVEV
Sbjct: 234 EKVSYFFRRPSVSDIVIFKAPPILQKIGYKSNDVFIKRIVAKAGDCVEV 282

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224136660|ref|XP_002326914.1| predicted protein [Populus trichocarpa] gi|222835229|gb|EEE73664.1| predicted protein [Populus trichocarpa]

 Score =  286 bits (732), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 168/294 (57%), Positives = 197/294 (67%), Gaps = 40/294 (13%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCH------SKKTDLD 54
           MA+RVT +FSGYVAQNL    G+R G    + R  +EC  R R+F        +  +D++
Sbjct: 1   MAIRVTFSFSGYVAQNL----GVRVG----NCRYLNECFIRSRIFASPATTTTTHNSDIE 52

Query: 55  PP--------PNYQPKANYR-----CNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGP 101
           PP             K NY       +T+A EIFGD    S I +GLVSLMKSTAG+   
Sbjct: 53  PPGPRTGTDFRRRNLKRNYSNSAAMYSTMAGEIFGDNCKGSAIAVGLVSLMKSTAGV--- 109

Query: 102 SATSMGVFGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGT-TDKIQFSGSENL 160
           S ++MG  GISPFKA SI+PFLQGS+WLPCNE      S  VD+GGT T K     SE+ 
Sbjct: 110 SCSNMGACGISPFKAVSILPFLQGSRWLPCNEAVLGSRSPEVDRGGTGTVKSVEKVSES- 168

Query: 161 NGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVG 220
                    S SW S++ NVCS+DAKA FTA TVS LF+S LAEPRSIPS+SM+PTLDVG
Sbjct: 169 --------KSRSWFSRVFNVCSEDAKAMFTAATVSLLFRSTLAEPRSIPSSSMSPTLDVG 220

Query: 221 DRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
           DRILAEKVSY F++PEVSDIVIF+APPILQE GFSSGDVFIKRIVA AGD VEV
Sbjct: 221 DRILAEKVSYVFRKPEVSDIVIFKAPPILQEFGFSSGDVFIKRIVAKAGDYVEV 274

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357465373|ref|XP_003602968.1| Thylakoidal processing peptidase [Medicago truncatula] gi|355492016|gb|AES73219.1| Thylakoidal processing peptidase [Medicago truncatula]

 Score =  284 bits (727), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 157/290 (54%), Positives = 201/290 (69%), Gaps = 23/290 (7%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPPPNYQ 60
           MA+RVT +FSGYVAQNL  SAG+R      ++R   EC    R+F  + K DL+    ++
Sbjct: 1   MAIRVTFSFSGYVAQNLVSSAGVR----VANSRCVQECCILSRLFGSNPKPDLERSGGFR 56

Query: 61  PKANYR------------CNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGV 108
            +  Y              +TLA EI  + +CN+PI++GL+S+MKSTA + G ++ +MG 
Sbjct: 57  NRNLYSDFTKPRNSPVSVYSTLAGEILSE-SCNNPIILGLISMMKSTA-ISGSTSAAMGA 114

Query: 109 FGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQ----FSGSENLNGVS 164
            GISPFK +SIIPFLQGSKWLPCNE      +  VDKGGT  + Q     S  E+   ++
Sbjct: 115 MGISPFKTSSIIPFLQGSKWLPCNESVPTATTWEVDKGGTRIQSQPVSVSSDKESRLDLN 174

Query: 165 LQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRIL 224
            +  T+G W+SKLLNVCS+DAKA FTA+TVS LFKSFLAEP+SIPSASM PTL+VGDR+L
Sbjct: 175 QKENTNG-WISKLLNVCSEDAKAVFTAVTVSLLFKSFLAEPKSIPSASMYPTLEVGDRVL 233

Query: 225 AEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
            EK S+FF++P+VSDIVIF+AP  L+  GFSS DVFIKR+VA AGD VEV
Sbjct: 234 TEKFSFFFRKPDVSDIVIFKAPSWLKAYGFSSSDVFIKRVVAKAGDVVEV 283

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357465371|ref|XP_003602967.1| Thylakoidal processing peptidase [Medicago truncatula] gi|355492015|gb|AES73218.1| Thylakoidal processing peptidase [Medicago truncatula]

 Score =  284 bits (726), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 157/290 (54%), Positives = 201/290 (69%), Gaps = 23/290 (7%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPPPNYQ 60
           MA+RVT +FSGYVAQNL  SAG+R      ++R   EC    R+F  + K DL+    ++
Sbjct: 1   MAIRVTFSFSGYVAQNLVSSAGVR----VANSRCVQECCILSRLFGSNPKPDLERSGGFR 56

Query: 61  PKANYR------------CNTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGV 108
            +  Y              +TLA EI  + +CN+PI++GL+S+MKSTA + G ++ +MG 
Sbjct: 57  NRNLYSDFTKPRNSPVSVYSTLAGEILSE-SCNNPIILGLISMMKSTA-ISGSTSAAMGA 114

Query: 109 FGISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQ----FSGSENLNGVS 164
            GISPFK +SIIPFLQGSKWLPCNE      +  VDKGGT  + Q     S  E+   ++
Sbjct: 115 MGISPFKTSSIIPFLQGSKWLPCNESVPTATTWEVDKGGTRIQSQPVSVSSDKESRLDLN 174

Query: 165 LQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRIL 224
            +  T+G W+SKLLNVCS+DAKA FTA+TVS LFKSFLAEP+SIPSASM PTL+VGDR+L
Sbjct: 175 QKENTNG-WISKLLNVCSEDAKAVFTAVTVSLLFKSFLAEPKSIPSASMYPTLEVGDRVL 233

Query: 225 AEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
            EK S+FF++P+VSDIVIF+AP  L+  GFSS DVFIKR+VA AGD VEV
Sbjct: 234 TEKFSFFFRKPDVSDIVIFKAPSWLKAYGFSSSDVFIKRVVAKAGDVVEV 283

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447223|ref|XP_004141368.1| PREDICTED: uncharacterized protein LOC101221060, partial [Cucumis sativus]

 Score =  278 bits (712), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 160/284 (56%), Positives = 194/284 (68%), Gaps = 22/284 (7%)

Query: 6   TVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDLDPP---PNYQPK 62
           TV+FSGYVAQNLA SAGIR G    + R+ HEC  R R+F  ++K + DP     NY   
Sbjct: 1   TVSFSGYVAQNLASSAGIRVG----NCRAVHECWIRSRLFGSNQKPEFDPSGSVRNYHSA 56

Query: 63  ---ANYRC---------NTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVFG 110
              +N RC          T+A EI  D +C +PI++GL+SLMKS  G    S  +MGVFG
Sbjct: 57  VLPSNSRCWVKNSASALGTIAGEIV-DESCRNPIVLGLISLMKSAVGTSVSSPMAMGVFG 115

Query: 111 ISPFKAASIIPFLQGSKWLPCNEPGTVPESDYVDKGGTTDKIQFSGSENLNGVSLQLKTS 170
           +S F+A+SIIPFLQGSK +  NE  +    D ++  G  D +   G       S +L+ S
Sbjct: 116 VSSFEASSIIPFLQGSKTVTGNESVSGSTGDEIESYGVFDCVMDEGMSQPPDPS-KLEKS 174

Query: 171 GSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSY 230
            SW+S+ LN CS+DAKA  TALTVS LF+S LAEPRSIPS+SM PTLDVGDRILAEKVSY
Sbjct: 175 -SWISRFLNNCSEDAKAIATALTVSVLFRSSLAEPRSIPSSSMYPTLDVGDRILAEKVSY 233

Query: 231 FFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
           FF+RP VSDIVIF+APPILQ+IG+ S DVFIKRIVA AGDCVEV
Sbjct: 234 FFRRPSVSDIVIFKAPPILQKIGYKSNDVFIKRIVAKAGDCVEV 277

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15222236|ref|NP_172171.1| signal peptidase I [Arabidopsis thaliana] gi|75312311|sp|Q9M9Z2.1|TPP2_ARATH RecName: Full=Probable thylakoidal processing peptidase 2, chloroplastic; AltName: Full=Signal peptidase I-2; Flags: Precursor gi|7523697|gb|AAF63136.1|AC011001_6 putative signal peptidase [Arabidopsis thaliana] gi|89000987|gb|ABD59083.1| At1g06870 [Arabidopsis thaliana] gi|332189926|gb|AEE28047.1| signal peptidase I [Arabidopsis thaliana]

 Score =  256 bits (653), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 148/289 (51%), Positives = 193/289 (66%), Gaps = 28/289 (9%)

Query: 1   MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFCHSKKTDL-DPPP-- 57
           MA+RVT  +S YVA+++A SAG R G  T   RS  E   RPR   H++  D+ D  P  
Sbjct: 1   MAIRVTFTYSSYVARSIASSAGTRVG--TGDVRSCFETWVRPRFCGHNQIPDIVDKSPGS 58

Query: 58  -NYQPKANYRC-------NTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGVF 109
             + P +  R        +T+A EI  +G C SP+++G++SLM  T     P  + M   
Sbjct: 59  NTWGPSSGPRARPASSMYSTIAREILEEG-CKSPLVLGMISLMNLTGA---PQFSGMTGL 114

Query: 110 GISPFKAASIIPFLQGSKWLPCNEPGTVP-ESDYVDKGGTT--DKIQFSGSENL-NGVSL 165
           GISPFK +S+IPFL+GSKW+PC+ P T+  +   VD+GG     K++   S+ + NG   
Sbjct: 115 GISPFKTSSVIPFLRGSKWMPCSIPATLSTDIAEVDRGGKVCDPKVKLELSDKVSNG--- 171

Query: 166 QLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILA 225
                  W++KLLN+CS+DAKAAFTA+TVS LF+S LAEP+SIPS SM PTLDVGDR++A
Sbjct: 172 ----GNGWVNKLLNICSEDAKAAFTAVTVSLLFRSALAEPKSIPSTSMLPTLDVGDRVIA 227

Query: 226 EKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
           EKVSYFF++PEVSDIVIF+APPIL E G+S  DVFIKRIVA+ GD VEV
Sbjct: 228 EKVSYFFRKPEVSDIVIFKAPPILVEHGYSCADVFIKRIVASEGDWVEV 276

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	275
TAIR|locus:2033108	367	Plsp2A "plastidic type I signa	0.945	0.708	0.520	2.3e-64
TAIR|locus:2064337	340	TPP "thylakoid processing pept	0.643	0.520	0.607	7.2e-52
TAIR|locus:2091717	291	PLSP1 "plastidic type i signal	0.352	0.333	0.618	9.1e-29
UNIPROTKB|Q10789	294	lepB "Signal peptidase I" [Myc	0.258	0.241	0.402	6.7e-08
TIGR_CMR|VC_2462	298	VC_2462 "signal peptidase I" [	0.44	0.406	0.324	2e-06
TIGR_CMR|DET_1192	192	DET_1192 "signal peptidase I"	0.225	0.322	0.417	1.8e-05
TIGR_CMR|CHY_1360	184	CHY_1360 "signal peptidase I"	0.345	0.516	0.304	4.8e-05
TIGR_CMR|SO_1347	305	SO_1347 "signal peptidase I" [	0.32	0.288	0.376	0.00015
TIGR_CMR|SO_2924	220	SO_2924 "signal peptidase I fa	0.294	0.368	0.329	0.00019
UNIPROTKB|P00803	324	lepB [Escherichia coli K-12 (t	0.312	0.265	0.373	0.00029

TAIR|locus:2033108 Plsp2A "plastidic type I signal peptidase 2A" [Arabidopsis thaliana (taxid:3702)]

 Score = 656 (236.0 bits), Expect = 2.3e-64, P = 2.3e-64
 Identities = 151/290 (52%), Positives = 196/290 (67%)

Query:     1 MALRVTVNFSGYVAQNLAHSAGIRFGFSTTSTRSFHECLFRPRVFC-HSKKTDL-DPPPN 58
             MA+RVT  +S YVA+++A SAG R G  T   RS  E   RPR FC H++  D+ D  P 
Sbjct:     1 MAIRVTFTYSSYVARSIASSAGTRVG--TGDVRSCFETWVRPR-FCGHNQIPDIVDKSPG 57

Query:    59 ---YQPKANYRC-------NTLAAEIFGDGACNSPILMGLVSLMKSTAGMPGPSATSMGV 108
                + P +  R        +T+A EI  +G C SP+++G++SLM  T     P  + M  
Sbjct:    58 SNTWGPSSGPRARPASSMYSTIAREILEEG-CKSPLVLGMISLMNLTGA---PQFSGMTG 113

Query:   109 FGISPFKAASIIPFLQGSKWLPCNEPGTVP-ESDYVDKGGTT-D-KIQFSGSENL-NGVS 164
              GISPFK +S+IPFL+GSKW+PC+ P T+  +   VD+GG   D K++   S+ + NG  
Sbjct:   114 LGISPFKTSSVIPFLRGSKWMPCSIPATLSTDIAEVDRGGKVCDPKVKLELSDKVSNG-- 171

Query:   165 LQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRIL 224
                     W++KLLN+CS+DAKAAFTA+TVS LF+S LAEP+SIPS SM PTLDVGDR++
Sbjct:   172 -----GNGWVNKLLNICSEDAKAAFTAVTVSLLFRSALAEPKSIPSTSMLPTLDVGDRVI 226

Query:   225 AEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
             AEKVSYFF++PEVSDIVIF+APPIL E G+S  DVFIKRIVA+ GD VEV
Sbjct:   227 AEKVSYFFRKPEVSDIVIFKAPPILVEHGYSCADVFIKRIVASEGDWVEV 276

GO:0006508 "proteolysis" evidence=IEA;ISS

GO:0008233 "peptidase activity" evidence=ISS

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

GO:0009507 "chloroplast" evidence=ISM

GO:0016020 "membrane" evidence=IEA;ISS

GO:0016021 "integral to membrane" evidence=IEA

TAIR|locus:2064337 TPP "thylakoid processing peptide" [Arabidopsis thaliana (taxid:3702)]

 Score = 538 (194.4 bits), Expect = 7.2e-52, P = 7.2e-52
 Identities = 119/196 (60%), Positives = 145/196 (73%)

Query:    82 SPILMGLVSLMKSTAGMPGPSATSMGVFGISPFKAASIIPFLQGSKWLPCNEPGTVPESD 141
             SP++MGL+S++KST G     +++M V G+S FKA+SIIPFLQGSKW+    P   P  D
Sbjct:    70 SPLVMGLISILKSTTGH---ESSTMNVLGVSSFKASSIIPFLQGSKWI--KNP---PVID 121

Query:   142 YVDKGGTTDKIQFSGSENLNGVSLQLKTSGSWLSKLLNVCSDDAKAAFTALTVSFLFKSF 201
              VDKGGT         E+ NG S        W++KLL+VCS+DAKAAFTA+TVS LF+S 
Sbjct:   122 DVDKGGTVCDDD-DDKESRNGGS-------GWVNKLLSVCSEDAKAAFTAVTVSILFRSA 173

Query:   202 LAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPIL---QEIGFSSGD 258
             LAEP+SIPS SM PTLD GDR++AEKVSYFF++PEVSDIVIF+APPIL    E G+SS D
Sbjct:   174 LAEPKSIPSTSMYPTLDKGDRVMAEKVSYFFRKPEVSDIVIFKAPPILLEYPEYGYSSND 233

Query:   259 VFIKRIVATAGDCVEV 274
             VFIKRIVA+ GD VEV
Sbjct:   234 VFIKRIVASEGDWVEV 249

GO:0006508 "proteolysis" evidence=IEA;ISS

GO:0008233 "peptidase activity" evidence=ISS

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

GO:0009507 "chloroplast" evidence=ISM

GO:0016020 "membrane" evidence=IEA;ISS

GO:0016021 "integral to membrane" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=IDA

GO:0006465 "signal peptide processing" evidence=IDA

GO:0009534 "chloroplast thylakoid" evidence=IDA

TAIR|locus:2091717 PLSP1 "plastidic type i signal peptidase 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 60/97 (61%), Positives = 77/97 (79%)

Query:   178 LNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEV 237
             L+  SDDA+  F A+ VS  F+ F+AEPR IPS SM PT DVGDR++AEKVSY+F++P  
Sbjct:   108 LDFTSDDAQTVFVAIAVSLAFRYFIAEPRYIPSLSMYPTFDVGDRLVAEKVSYYFRKPCA 167

Query:   238 SDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
             +DIVIF++PP+LQE+G++  DVFIKRIVA  GD VEV
Sbjct:   168 NDIVIFKSPPVLQEVGYTDADVFIKRIVAKEGDLVEV 204

GO:0006508 "proteolysis" evidence=IEA;ISS

GO:0008233 "peptidase activity" evidence=ISS;IMP

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

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0016020 "membrane" evidence=ISS

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009526 "plastid envelope" evidence=IDA

GO:0010027 "thylakoid membrane organization" evidence=RCA;IMP

GO:0051604 "protein maturation" evidence=IMP

GO:0006364 "rRNA processing" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

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

GO:0019761 "glucosinolate biosynthetic process" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

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

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

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

UNIPROTKB|Q10789 lepB "Signal peptidase I" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 141 (54.7 bits), Expect = 6.7e-08, Sum P(2) = 6.7e-08
 Identities = 31/77 (40%), Positives = 46/77 (59%)

Query:   185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLD-----VGDRILAEKVSYFFKRPEVSD 239
             A  A  A+ + ++  +F+A P  IPS SM PTL      VGDRI+ +K+SY F  P+  D
Sbjct:    69 AVLAVIAVVLYYVMLTFVARPYLIPSESMEPTLHGCSTCVGDRIMVDKLSYRFGSPQPGD 128

Query:   240 IVIFRAPPILQEIGFSS 256
             +++FR PP    +G+ S
Sbjct:   129 VIVFRGPPSWN-VGYKS 144

GO:0005576 "extracellular region" evidence=IGI

GO:0005887 "integral to plasma membrane" evidence=IDA

GO:0040007 "growth" evidence=IMP

TIGR_CMR|VC_2462 VC_2462 "signal peptidase I" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 133 (51.9 bits), Expect = 2.0e-06, P = 2.0e-06
 Identities = 47/145 (32%), Positives = 68/145 (46%)

Query:   148 TTDKIQFSGSENLNGVSLQLKTSGSWLSKLLNVCS-----DDAKAAFTALTVSFLFKSFL 202
             T +K+ ++         LQ +T     S L  V +     +++ + F  +    + +SF+
Sbjct:    21 TLEKLVWAKKRQQKQAHLQAQTPDMPASALDKVVAQPWWIENSVSIFPVIAFVLVLRSFI 80

Query:   203 AEPRSIPSASMNPTLDVGDRILAEKVSYFFK------------RPEVSDIVIFRAPPILQ 250
              EP  IPS SM PTL VGD IL EK +Y  K            +PE  DIV+F+ P +  
Sbjct:    81 YEPFQIPSGSMMPTLLVGDFILVEKYAYGLKDPVWRTQLVETGKPERGDIVVFKYP-VNP 139

Query:   251 EIGFSSGDVFIKRIVATAGDCVEVS 275
             EI +      IKR+V   GD V  S
Sbjct:   140 EIDY------IKRVVGMPGDTVRYS 158

GO:0006465 "signal peptide processing" evidence=ISS

GO:0009306 "protein secretion" evidence=ISS

TIGR_CMR|DET_1192 DET_1192 "signal peptidase I" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 119 (46.9 bits), Expect = 1.8e-05, P = 1.8e-05
 Identities = 28/67 (41%), Positives = 40/67 (59%)

Query:   208 IPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT 267
             +  +SM+PTL    R+L  K++Y F  P+  DI++F  PP  Q   +S  + FIKRI+  
Sbjct:    42 VDGSSMDPTLKDEQRLLVNKLAYLFGEPQRGDIIVF--PPPEQ---YSYENDFIKRIIGL 96

Query:   268 AGDCVEV 274
              GD VEV
Sbjct:    97 PGDSVEV 103

GO:0009306 "protein secretion" evidence=ISS

TIGR_CMR|CHY_1360 CHY_1360 "signal peptidase I" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 115 (45.5 bits), Expect = 4.8e-05, P = 4.8e-05
 Identities = 32/105 (30%), Positives = 55/105 (52%)

Query:   170 SGSWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVS 229
             S SW +++    S    AA  A+ ++F+ K+F+ +   +P+ SM PT+   DR++  K  
Sbjct:    12 SFSWKNEIKEFIS----AAIWAVILAFIIKTFIFQLTYVPTGSMIPTILPNDRVVVLKFW 67

Query:   230 YFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274
             Y  K  E   IV+F  PP       ++   FIKR++   G+ +E+
Sbjct:    68 YKIKPIERGQIVVFD-PP-----NSANSPPFIKRVIGLPGETLEI 106

GO:0006465 "signal peptide processing" evidence=ISS

GO:0009306 "protein secretion" evidence=ISS

TIGR_CMR|SO_1347 SO_1347 "signal peptidase I" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 117 (46.2 bits), Expect = 0.00015, P = 0.00015
 Identities = 35/93 (37%), Positives = 46/93 (49%)

Query:   183 DDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVI 242
             + A + F  +    + +SF+ EP  IPS SM PTL VGD IL EK SY  K P     +I
Sbjct:    61 ETAHSIFPVIAFVLILRSFIYEPFQIPSGSMMPTLLVGDFILVEKFSYGLKDPVWRTKLI 120

Query:   243 FRAPPILQE-IGFSSGDV----FIKRIVATAGD 270
                 P   + I F   +     +IKR+V   GD
Sbjct:   121 ETGEPKRGDVIVFKYPENPQIDYIKRVVGLPGD 153

GO:0006508 "proteolysis" evidence=ISS

GO:0009306 "protein secretion" evidence=ISS

TIGR_CMR|SO_2924 SO_2924 "signal peptidase I family protein" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 113 (44.8 bits), Expect = 0.00019, P = 0.00019
 Identities = 28/85 (32%), Positives = 49/85 (57%)

Query:   192 LTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQE 251
             +++  +F+S +A+  ++P+ SM PT+  GDRIL  K++Y  + P     ++  A P+  +
Sbjct:    19 ISLMLVFRSAVADWNTVPTGSMLPTIVEGDRILVNKMAYDVRVPFTHIALVKLADPVRGD 78

Query:   252 IG-FSSGDV---FIKRIVATAGDCV 272
             I  F S +     IKR++A  GD V
Sbjct:    79 IVVFDSKNADKRLIKRVIAVPGDTV 103

GO:0006508 "proteolysis" evidence=ISS

GO:0009306 "protein secretion" evidence=ISS

UNIPROTKB|P00803 lepB [Escherichia coli K-12 (taxid:83333)]

 Score = 115 (45.5 bits), Expect = 0.00029, P = 0.00029
 Identities = 34/91 (37%), Positives = 45/91 (49%)

Query:   187 AAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAP 246
             + F  L +  + +SF+ EP  IPS SM PTL +GD IL EK +Y  K P     +I    
Sbjct:    66 SVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGH 125

Query:   247 PILQEIG-FSSGDV----FIKRIVATAGDCV 272
             P   +I  F   +     +IKR V   GD V
Sbjct:   126 PKRGDIVVFKYPEDPKLDYIKRAVGLPGDKV 156

GO:0016485 "protein processing" evidence=IMP

GO:0015643 "toxic substance binding" evidence=IMP

GO:0008233 "peptidase activity" evidence=IEA;IMP;IDA

GO:0006508 "proteolysis" evidence=IEA;IDA;IMP

GO:0016021 "integral to membrane" evidence=IEA;IDA

GO:0005886 "plasma membrane" evidence=IEA;IDA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9M9Z2	TPP2_ARATH	3, ., 4, ., 2, 1, ., 8, 9	0.5121	0.9490	0.7111	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.21	0.921
3rd Layer	3.4.21.89	0.914

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00014743001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (345 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00019235001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (603 aa)	•						•		0.509

---

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	275
TIGR02227	163	TIGR02227, sigpep_I_bact, signal peptidase I, bact	4e-20
cd06530	85	cd06530, S26_SPase_I, The S26 Type I signal peptid	2e-16
PRK10861	324	PRK10861, PRK10861, signal peptidase I; Provisiona	1e-11
COG0681	166	COG0681, LepB, Signal peptidase I [Intracellular t	5e-11
cd06462	84	cd06462, Peptidase_S24_S26, The S24, S26 LexA/sign	2e-08
pfam00717	69	pfam00717, Peptidase_S24, Peptidase S24-like	3e-08

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

 Score = 84.2 bits (209), Expect = 4e-20
 Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 7/89 (7%)

Query: 186 KAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRA 245
            +   A+ ++ L ++F+  P  +P  SM PTL  GDRIL  K +Y    P+  DIV+F+ 
Sbjct: 3   LSLLIAILLALLIRTFVFFPYKVPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKD 62

Query: 246 PPILQEIGFSSGDVFIKRIVATAGDCVEV 274
           P         + +++IKR++   GD VE 
Sbjct: 63  PD-------DNKNIYIKRVIGLPGDKVEF 84

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

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

 Score = 72.2 bits (178), Expect = 2e-16
 Identities = 26/69 (37%), Positives = 37/69 (53%), Gaps = 9/69 (13%)

Query: 204 EPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKR 263
           EP  +P  SM PTL  GD +L  K+SY F+ P+  D+V+F++P          G   IKR
Sbjct: 1   EPVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPG-------DPGKPIIKR 53

Query: 264 IVA--TAGD 270
           ++     GD
Sbjct: 54  VIGYFVLGD 62

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|182787 PRK10861, PRK10861, signal peptidase I; Provisional

 Score = 63.9 bits (156), Expect = 1e-11
 Identities = 37/98 (37%), Positives = 48/98 (48%), Gaps = 23/98 (23%)

Query: 189 FTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFK------------RPE 236
           F  L +  + +SF+ EP  IPS SM PTL +GD IL EK +Y  K             P+
Sbjct: 68  FPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPK 127

Query: 237 VSDIVIFRAP--PILQEIGFSSGDVFIKRIVATAGDCV 272
             DIV+F+ P  P L          +IKR+V   GD V
Sbjct: 128 RGDIVVFKYPEDPKLD---------YIKRVVGLPGDKV 156

Length = 324

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

 Score = 59.6 bits (144), Expect = 5e-11
 Identities = 34/99 (34%), Positives = 47/99 (47%), Gaps = 11/99 (11%)

Query: 172 SWLSKLLNVCSDDAKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYF 231
             L K L + S    A   AL +      F+ EP  +PS SM PTL+VGDR+L +K SY 
Sbjct: 2   KRLLKFLELISSLLIAIILALIIGVRT--FVFEPVVVPSGSMEPTLNVGDRVLVKKFSYG 59

Query: 232 FKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGD 270
           F + +V DI++                  IKR++   GD
Sbjct: 60  FGKLKVPDIIVL---------PAVVEGDLIKRVIGLRGD 89

Length = 166

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 12/63 (19%)

Query: 208 IPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT 267
           +   SM PT+  GD +L +K SY    P+  DIV+FR P          G++ +KR++  
Sbjct: 5   VEGDSMEPTIPDGDLVLVDKSSY---EPKRGDIVVFRLP---------GGELTVKRVIGL 52

Query: 268 AGD 270
            G+
Sbjct: 53  PGE 55

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

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

 Score = 49.1 bits (118), Expect = 3e-08
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 13/68 (19%)

Query: 208 IPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT 267
           +   SM PT+  GD +L +K       P+  DIV+ R             +  +KR++  
Sbjct: 2   VKGDSMEPTIPDGDLLLVDK----TSEPKRGDIVVARLDG---------EEATVKRLIGL 48

Query: 268 AGDCVEVS 275
            GD + + 
Sbjct: 49  PGDIILLP 56

Length = 69

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	275
PRK10861	324	signal peptidase I; Provisional	99.86
TIGR02227	163	sigpep_I_bact signal peptidase I, bacterial type.	99.84
KOG0171	176	consensus Mitochondrial inner membrane protease, s	99.68
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	99.6
TIGR02228	158	sigpep_I_arch signal peptidase I, archaeal type. T	99.45
TIGR02754	90	sod_Ni_protease nickel-type superoxide dismutase m	99.36
KOG1568	174	consensus Mitochondrial inner membrane protease, s	99.31
PF00717	70	Peptidase_S24: Peptidase S24-like peptidase classi	99.29
cd06530	85	S26_SPase_I The S26 Type I signal peptidase (SPase	99.19
cd06462	84	Peptidase_S24_S26 The S24, S26 LexA/signal peptida	98.81
cd06529	81	S24_LexA-like Peptidase S24 LexA-like proteins are	98.77
PRK13838	176	conjugal transfer pilin processing protease TraF;	98.76
TIGR02771	171	TraF_Ti conjugative transfer signal peptidase TraF	98.51
COG2932	214	Predicted transcriptional regulator [Transcription	98.43
PRK00215	205	LexA repressor; Validated	97.93
PRK12423	202	LexA repressor; Provisional	97.84
PRK10276	139	DNA polymerase V subunit UmuD; Provisional	97.82
PRK13884	178	conjugal transfer peptidase TraF; Provisional	97.82
KOG3342	180	consensus Signal peptidase I [Intracellular traffi	97.81
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	97.79
PF10502	138	Peptidase_S26: Signal peptidase, peptidase S26 ; I	97.43
COG1974	201	LexA SOS-response transcriptional repressors (RecA	95.2
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	85.91
COG4959	173	TraF Type IV secretory pathway, protease TraF [Pos	84.73
PF12518	34	DUF3721: Protein of unknown function; InterPro: IP	81.57

>PRK10861 signal peptidase I; Provisional

Probab=99.86  E-value=1.2e-21  Score=185.61  Aligned_cols=84  Identities=40%  Similarity=0.634  Sum_probs=76.6

Q ss_pred             HHHHHHHHHHHHHHHHceeEeEEEcCCCCcccCCCCCEEEEEecccCC------------CCCCCCcEEEEEcCCccccc
Q 023926          185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFF------------KRPEVSDIVIFRAPPILQEI  252 (275)
Q Consensus       185 a~~l~iAviv~llIr~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~~------------~~pkrGDIVVFk~P~~l~~~  252 (275)
                      +..++++++++++++.|+++++.|+|+||+|||++||+|+|+|+.|++            ++|+|||||||+.|.+    
T Consensus        64 ~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~----  139 (324)
T PRK10861         64 GASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPED----  139 (324)
T ss_pred             HHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCC----
Confidence            566788888999999999999999999999999999999999999864            5799999999999873    


Q ss_pred             cCCCCceEEEEEEEeCCCEEEEC
Q 023926          253 GFSSGDVFIKRIVATAGDCVEVS  275 (275)
Q Consensus       253 g~~~~k~~IKRVIGlPGDtVeIk  275 (275)
                         +++.|||||||+|||+|+++
T Consensus       140 ---~~~~yIKRVIGlPGD~I~~~  159 (324)
T PRK10861        140 ---PKLDYIKRVVGLPGDKVTYD  159 (324)
T ss_pred             ---CCCcEEEEeeecCCcEEEEE
Confidence               67899999999999999983

>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type

Probab=99.84  E-value=1.5e-20  Score=160.87  Aligned_cols=84  Identities=36%  Similarity=0.652  Sum_probs=76.8

Q ss_pred             HHHHHHHHHHHHHHHHceeEeEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEE
Q 023926          185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRI  264 (275)
Q Consensus       185 a~~l~iAviv~llIr~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRV  264 (275)
                      +..++++++++++++.|+++++.|+|+||+|||++||+|+++|..|...++++||||+|+.|.+       .++.+||||
T Consensus         2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~-------~~~~~iKRV   74 (163)
T TIGR02227         2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPDD-------NKNIYVKRV   74 (163)
T ss_pred             HHHHHHHHHHHHHHHhhEEEEEEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCCC-------CCceeEEEE
Confidence            5667788888999999999999999999999999999999999988788999999999998752       578999999


Q ss_pred             EEeCCCEEEEC
Q 023926          265 VATAGDCVEVS  275 (275)
Q Consensus       265 IGlPGDtVeIk  275 (275)
                      +|+|||+|+++
T Consensus        75 ig~pGd~v~i~   85 (163)
T TIGR02227        75 IGLPGDKVEFR   85 (163)
T ss_pred             EecCCCEEEEE
Confidence            99999999874

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=99.68  E-value=5.3e-17  Score=141.39  Aligned_cols=74  Identities=46%  Similarity=0.687  Sum_probs=65.3

Q ss_pred             HHHHHHHceeEeEEEcCCCCcccCCC-CCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEE
Q 023926          194 VSFLFKSFLAEPRSIPSASMNPTLDV-GDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCV  272 (275)
Q Consensus       194 v~llIr~fv~~~~~V~G~SMePTL~~-GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtV  272 (275)
                      ++.+...|++++..++|.||+|||++ ||+|+++|++|.++++++||||+++.|.+       .++++||||||+|||.|
T Consensus        24 f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~-------~~~~~cKRIva~eGD~v   96 (176)
T KOG0171|consen   24 FTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPD-------PKEHICKRIVAMEGDLV   96 (176)
T ss_pred             HHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCC-------chhhhhheeeccCCceE
Confidence            34455669999999999999998887 67777799999999999999999999985       78899999999999987


Q ss_pred             EE
Q 023926          273 EV  274 (275)
Q Consensus       273 eI  274 (275)
                      ++
T Consensus        97 ~v   98 (176)
T KOG0171|consen   97 EV   98 (176)
T ss_pred             EE
Confidence            75

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

Probab=99.60  E-value=3.1e-15  Score=124.63  Aligned_cols=85  Identities=35%  Similarity=0.609  Sum_probs=74.2

Q ss_pred             hhhHHHHHHHHHHHHHH--HHceeEeEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCce
Q 023926          182 SDDAKAAFTALTVSFLF--KSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDV  259 (275)
Q Consensus       182 ~~~a~~l~iAviv~llI--r~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~  259 (275)
                      .+++..++.++++++++  +.|+++++.|+|+||+|||+.||+|+++|..|....+..+|++  ..|.       ..+..
T Consensus         8 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~--~~~~-------~~~~~   78 (166)
T COG0681           8 LELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDII--VLPA-------VVEGD   78 (166)
T ss_pred             HHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccccCCEEEEEeccccccCCccceee--ecCC-------CCCcc
Confidence            45577777888888888  8999999999999999999999999999999998889999988  3332       36789


Q ss_pred             EEEEEEEeCCCEEEEC
Q 023926          260 FIKRIVATAGDCVEVS  275 (275)
Q Consensus       260 ~IKRVIGlPGDtVeIk  275 (275)
                      ++||+++++||.|.++
T Consensus        79 ~~kr~~~~~GD~i~~~   94 (166)
T COG0681          79 LIKRVIGLRGDIVVFK   94 (166)
T ss_pred             eEEEeccCCCCEEEEE
Confidence            9999999999999874

>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type

Probab=99.45  E-value=4.7e-13  Score=115.45  Aligned_cols=53  Identities=25%  Similarity=0.463  Sum_probs=46.5

Q ss_pred             EcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCC
Q 023926          208 IPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGD  270 (275)
Q Consensus       208 V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGD  270 (275)
                      |.|+||+|||++||++++++..  ..++++||||+|++|.        .++.++|||+++.++
T Consensus        36 V~g~SM~Ptl~~GD~vlv~~~~--~~~~~~GDIVvf~~~~--------~~~~iihRVi~v~~~   88 (158)
T TIGR02228        36 VLSGSMEPTFNTGDLILVTGAD--PNDIQVGDVITYKSPG--------FNTPVTHRVIEINNS   88 (158)
T ss_pred             EcCCCCcCCccCCCEEEEEecc--cCCCCCCCEEEEEECC--------CCccEEEEEEEEECC
Confidence            9999999999999999999954  3589999999999874        338899999998754

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.

>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease

Probab=99.36  E-value=3.1e-12  Score=98.60  Aligned_cols=61  Identities=30%  Similarity=0.499  Sum_probs=51.4

Q ss_pred             EEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926          207 SIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV  274 (275)
Q Consensus       207 ~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI  274 (275)
                      .|+|+||+|||++||+|+|++.......+++||+|+|+.|..       +++.+|||+++++++.+.+
T Consensus         2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~-------~~~~~vkRv~~~~~~~~~l   62 (90)
T TIGR02754         2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQ-------PYGLIIKRLAAVDDNGLFL   62 (90)
T ss_pred             EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCCC-------CcceEEEEeeEEcCCeEEE
Confidence            689999999999999999998644345567899999998752       4689999999999888765

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.

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

Probab=99.31  E-value=1.4e-12  Score=113.72  Aligned_cols=73  Identities=29%  Similarity=0.417  Sum_probs=63.7

Q ss_pred             HHHHHHHceeEeEEEcCCCCcccCCCC------CEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEe
Q 023926          194 VSFLFKSFLAEPRSIPSASMNPTLDVG------DRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT  267 (275)
Q Consensus       194 v~llIr~fv~~~~~V~G~SMePTL~~G------DrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGl  267 (275)
                      +.+.+...+.....|.|.||+|||+++      |+|+++|+...-+.+.|||||+|++|.+       +++++||||+|+
T Consensus        22 v~~t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~-------p~~~~iKRv~al   94 (174)
T KOG1568|consen   22 VLLTFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPND-------PDKVIIKRVAAL   94 (174)
T ss_pred             eeeeeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCC-------hhheeeeeeecc
Confidence            345566778889999999999999984      9999999975446789999999999984       899999999999


Q ss_pred             CCCEEE
Q 023926          268 AGDCVE  273 (275)
Q Consensus       268 PGDtVe  273 (275)
                      |||++.
T Consensus        95 egd~~~  100 (174)
T KOG1568|consen   95 EGDIMV  100 (174)
T ss_pred             cccEec
Confidence            999974

>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification

Probab=99.29  E-value=8e-12  Score=91.12  Aligned_cols=57  Identities=32%  Similarity=0.591  Sum_probs=46.8

Q ss_pred             EEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEEC
Q 023926          207 SIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS  275 (275)
Q Consensus       207 ~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeIk  275 (275)
                      +|.|+||+|+|++||+|++++..    .++.||+|+|+.+.        .+..+|||+++.+|+.+.+.
T Consensus         1 ~V~GdSM~P~i~~Gd~v~v~~~~----~~~~gdivv~~~~~--------~~~~~iKrv~~~~~~~~~~~   57 (70)
T PF00717_consen    1 RVEGDSMEPTIKDGDIVLVDPSS----EPKDGDIVVVKIDG--------DEELYIKRVVGEPGGIILIS   57 (70)
T ss_dssp             EEESSTTGGTSSTTEEEEEEETS-------TTSEEEEEETT--------EESEEEEEEEEETTEEEEE-
T ss_pred             CeECcCcccCeeCCCEEEEEEcC----CCccCeEEEEEECC--------ceeeEEEEEEEeCCCEEEEe
Confidence            58999999999999999999874    89999999999853        11399999999999998763

; 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 ....

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

Probab=99.19  E-value=7.2e-11  Score=89.63  Aligned_cols=55  Identities=42%  Similarity=0.810  Sum_probs=47.5

Q ss_pred             eEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEE
Q 023926          205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVA  266 (275)
Q Consensus       205 ~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIG  266 (275)
                      .+.|.|+||+|++++||+|++++....+..+++||||+|+.+..       .++.++|||++
T Consensus         2 ~~~v~g~SM~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~-------~~~~~vkRv~~   56 (85)
T cd06530           2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGD-------PGKPIIKRVIG   56 (85)
T ss_pred             eeEEcCCCCcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCCC-------CCCEEEEEEEE
Confidence            57899999999999999999999864445799999999998741       36899999987

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

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

Probab=98.81  E-value=2.4e-08  Score=74.02  Aligned_cols=58  Identities=34%  Similarity=0.619  Sum_probs=49.3

Q ss_pred             eEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCC-CEEEE
Q 023926          205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAG-DCVEV  274 (275)
Q Consensus       205 ~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPG-DtVeI  274 (275)
                      .+.|.|+||+|++.+||.|++++..   ..++.||+|+++.+         .+..+|||+...++ +.+.+
T Consensus         2 ~~~v~g~SM~P~i~~gd~v~i~~~~---~~~~~G~iv~~~~~---------~~~~~ikrl~~~~~~~~~~l   60 (84)
T cd06462           2 ALRVEGDSMEPTIPDGDLVLVDKSS---YEPKRGDIVVFRLP---------GGELTVKRVIGLPGEGHYFL   60 (84)
T ss_pred             eeEEcCCCccCcccCCCEEEEEecC---CCCcCCEEEEEEcC---------CCcEEEEEEEEECCCCEEEE
Confidence            4689999999999999999999864   24899999999973         24899999999997 66654

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

>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=98.77  E-value=2.9e-08  Score=73.72  Aligned_cols=56  Identities=29%  Similarity=0.517  Sum_probs=49.1

Q ss_pred             eEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926          205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV  274 (275)
Q Consensus       205 ~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI  274 (275)
                      .+.|.|+||+|++++||.|++++..    .++.||++++..          +++.+|||+...+++.+.+
T Consensus         2 ~~~v~g~sM~p~i~~gd~lii~~~~----~~~~g~i~~~~~----------~~~~~ikr~~~~~~~~~~L   57 (81)
T cd06529           2 ALRVKGDSMEPTIPDGDLVLVDPSD----TPRDGDIVVARL----------DGELTVKRLQRRGGGRLRL   57 (81)
T ss_pred             EEEEECCCcCCccCCCCEEEEcCCC----CCCCCCEEEEEE----------CCEEEEEEEEECCCCcEEE
Confidence            4689999999999999999999863    599999999997          3488999999999777665

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

>PRK13838 conjugal transfer pilin processing protease TraF; Provisional

Probab=98.76  E-value=4.8e-08  Score=85.76  Aligned_cols=57  Identities=21%  Similarity=0.261  Sum_probs=42.2

Q ss_pred             CCCEEEEEecccCCCCCCCCcEEEEEcCCcccc-----ccC-C------CCceEEEEEEEeCCCEEEEC
Q 023926          219 VGDRILAEKVSYFFKRPEVSDIVIFRAPPILQE-----IGF-S------SGDVFIKRIVATAGDCVEVS  275 (275)
Q Consensus       219 ~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~-----~g~-~------~~k~~IKRVIGlPGDtVeIk  275 (275)
                      +.+.+.+.++.+..+.+++||+|+|+.|...+.     .++ .      ....+||||+|+|||+|+++
T Consensus        35 ~S~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~  103 (176)
T PRK13838         35 PSEPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIG  103 (176)
T ss_pred             CCCEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEEC
Confidence            467888999876668899999999998753210     011 0      12469999999999999975

>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF

Probab=98.51  E-value=5.1e-07  Score=78.88  Aligned_cols=67  Identities=25%  Similarity=0.276  Sum_probs=41.7

Q ss_pred             HceeEeEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCcccc-----ccC-CC------CceEEEEEEEe
Q 023926          200 SFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQE-----IGF-SS------GDVFIKRIVAT  267 (275)
Q Consensus       200 ~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~-----~g~-~~------~k~~IKRVIGl  267 (275)
                      .|......=.++||-..+    +. +.+    .+.++|||||+|+.|.+.+.     .++ ..      ...+||||+|+
T Consensus        21 ~~~~~~~~N~T~S~P~g~----Y~-~~~----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRVigl   91 (171)
T TIGR02771        21 LYCVGARINTTKSLPLGL----YW-TTS----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGL   91 (171)
T ss_pred             cceeeEEEECCCCCcceE----EE-eCC----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEe
Confidence            334334445566665544    33 222    25899999999998753210     011 11      13799999999


Q ss_pred             CCCEEEEC
Q 023926          268 AGDCVEVS  275 (275)
Q Consensus       268 PGDtVeIk  275 (275)
                      |||+|+++
T Consensus        92 pGD~V~i~   99 (171)
T TIGR02771        92 PGDRVTVR   99 (171)
T ss_pred             CCCEEEEE
Confidence            99999974

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.

>COG2932 Predicted transcriptional regulator [Transcription]

Probab=98.43  E-value=5.3e-07  Score=79.89  Aligned_cols=58  Identities=21%  Similarity=0.403  Sum_probs=49.0

Q ss_pred             EeEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926          204 EPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV  274 (275)
Q Consensus       204 ~~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI  274 (275)
                      ....|.|+||+|++++||.|+|+.-    .+..+||.|++..-         .++.||||+...||-.+++
T Consensus       124 ~~i~V~GDSMeP~~~~Gd~ilVd~~----~~~~~gd~v~v~~~---------g~~~~VK~l~~~~~~~~~l  181 (214)
T COG2932         124 FALRVTGDSMEPTYEDGDTLLVDPG----VNTRRGDRVYVETD---------GGELYVKKLQREPGGLLRL  181 (214)
T ss_pred             EEEEEeCCcccccccCCCEEEECCC----CceeeCCEEEEEEe---------CCeEEEEEEEEecCCeEEE
Confidence            3579999999999999999999986    36788997777652         4699999999999988754

>PRK00215 LexA repressor; Validated

Probab=97.93  E-value=4.2e-05  Score=67.07  Aligned_cols=55  Identities=18%  Similarity=0.216  Sum_probs=44.4

Q ss_pred             EeEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEE
Q 023926          204 EPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVE  273 (275)
Q Consensus       204 ~~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVe  273 (275)
                      ..+.|.|+||. |++.+||+|+|++.    ..++.||||++..          +++.+|||+.-. ++.++
T Consensus       119 ~~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivv~~~----------~~~~~vKrl~~~-~~~~~  174 (205)
T PRK00215        119 FLLRVRGDSMIDAGILDGDLVIVRKQ----QTARNGQIVVALI----------DDEATVKRFRRE-GGHIR  174 (205)
T ss_pred             EEEEEccCCCCCCCcCCCCEEEEeCC----CCCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEE
Confidence            45789999995 79999999999974    3678999999986          348899999876 44444

>PRK12423 LexA repressor; Provisional

Probab=97.84  E-value=6.7e-05  Score=66.47  Aligned_cols=55  Identities=25%  Similarity=0.342  Sum_probs=44.4

Q ss_pred             eEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926          205 PRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV  274 (275)
Q Consensus       205 ~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI  274 (275)
                      .+.|.|+||. |+|.+||.|+|++-    ..++.||||++..          +++.+|||+.-. ++.+++
T Consensus       116 ~l~V~GdSM~~~~i~~Gd~viv~~~----~~~~~Gdivv~~~----------~~~~~vKrl~~~-~~~~~L  171 (202)
T PRK12423        116 LLQVQGDSMIDDGILDGDLVGVHRS----PEARDGQIVVARL----------DGEVTIKRLERS-GDRIRL  171 (202)
T ss_pred             EEEEecCcCCCCCcCCCCEEEEeCC----CcCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEEE
Confidence            4799999997 79999999999975    3688999999986          357889998765 455543

>PRK10276 DNA polymerase V subunit UmuD; Provisional

Probab=97.82  E-value=7.8e-05  Score=62.41  Aligned_cols=49  Identities=20%  Similarity=0.286  Sum_probs=41.1

Q ss_pred             eEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEe
Q 023926          205 PRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT  267 (275)
Q Consensus       205 ~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGl  267 (275)
                      .++|.|+||+ |++.+||+|+|++-.    .++.||+|++..          +++..+||+.-.
T Consensus        53 ~l~V~GdSM~~~~I~~GD~liVd~~~----~~~~Gdivv~~~----------~g~~~vKrl~~~  102 (139)
T PRK10276         53 FVKASGDSMIDAGISDGDLLIVDSAI----TASHGDIVIAAV----------DGEFTVKKLQLR  102 (139)
T ss_pred             EEEEecCCCCCCCCCCCCEEEEECCC----CCCCCCEEEEEE----------CCEEEEEEEEEC
Confidence            4799999998 689999999999753    578999999875          457889998864

>PRK13884 conjugal transfer peptidase TraF; Provisional

Probab=97.82  E-value=9.7e-05  Score=64.99  Aligned_cols=43  Identities=33%  Similarity=0.479  Sum_probs=30.5

Q ss_pred             CCCCCCcEEEEEcCCcc-----cccc-----CC--CCceEEEEEEEeCCCEEEEC
Q 023926          233 KRPEVSDIVIFRAPPIL-----QEIG-----FS--SGDVFIKRIVATAGDCVEVS  275 (275)
Q Consensus       233 ~~pkrGDIVVFk~P~~l-----~~~g-----~~--~~k~~IKRVIGlPGDtVeIk  275 (275)
                      ..+++||+|+|..|...     .+.+     +.  ....+||||+|+|||+|+++
T Consensus        49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~  103 (178)
T PRK13884         49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVT  103 (178)
T ss_pred             CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEE
Confidence            46899999999876521     0111     11  12479999999999999874

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

Probab=97.81  E-value=5.1e-05  Score=66.45  Aligned_cols=41  Identities=27%  Similarity=0.378  Sum_probs=33.9

Q ss_pred             eEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCC
Q 023926          205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPP  247 (275)
Q Consensus       205 ~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~  247 (275)
                      .+.|-++||||.++.||.++.....  -...+.||||||+-+.
T Consensus        50 iVVVLSgSMePaF~RGDlLfL~N~~--~~p~~vGdivVf~veg   90 (180)
T KOG3342|consen   50 IVVVLSGSMEPAFHRGDLLFLTNRN--EDPIRVGDIVVFKVEG   90 (180)
T ss_pred             EEEEEcCCcCcccccccEEEEecCC--CCcceeccEEEEEECC
Confidence            4789999999999999999987542  1346889999999864

>TIGR00498 lexA SOS regulatory protein LexA

Probab=97.79  E-value=0.00011  Score=64.13  Aligned_cols=56  Identities=25%  Similarity=0.281  Sum_probs=45.7

Q ss_pred             EeEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926          204 EPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV  274 (275)
Q Consensus       204 ~~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI  274 (275)
                      ..+.|.|+||+ |++.+||+|++++.    ..++.||||++..          +++.+|||+.-. |+.+++
T Consensus       112 f~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~----------~~~~~vKrl~~~-~~~i~L  168 (199)
T TIGR00498       112 FLLKVMGDSMVDAGICDGDLLIVRSQ----KDARNGEIVAAMI----------DGEVTVKRFYKD-GTKVEL  168 (199)
T ss_pred             EEEEecCCCCCCCCCCCCCEEEEecC----CCCCCCCEEEEEE----------CCEEEEEEEEEE-CCEEEE
Confidence            46799999996 68999999999975    4789999999986          467899998765 555544

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.

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

Probab=97.43  E-value=3.2e-05  Score=65.18  Aligned_cols=42  Identities=40%  Similarity=0.712  Sum_probs=0.0

Q ss_pred             CCCCCcEEEEEcCCccc----cccC-CCCceEEEEEEEeCCCEEEEC
Q 023926          234 RPEVSDIVIFRAPPILQ----EIGF-SSGDVFIKRIVATAGDCVEVS  275 (275)
Q Consensus       234 ~pkrGDIVVFk~P~~l~----~~g~-~~~k~~IKRVIGlPGDtVeIk  275 (275)
                      .+++||+|+|..|....    +.++ ..+..+||||+|+|||+|+++
T Consensus        21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~   67 (138)
T PF10502_consen   21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVT   67 (138)
T ss_dssp             -----------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            47999999999886321    1122 346699999999999999874

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.

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

Probab=95.20  E-value=0.098  Score=47.31  Aligned_cols=52  Identities=19%  Similarity=0.217  Sum_probs=41.4

Q ss_pred             EeEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeC
Q 023926          204 EPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATA  268 (275)
Q Consensus       204 ~~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlP  268 (275)
                      ...+|.|+||. +.+.+||.|+|++-    ...+.||||+..-+         .++.-+||..-..
T Consensus       113 f~L~V~GdSM~~~gi~dGDlvvV~~~----~~a~~GdiVvA~i~---------g~e~TvKrl~~~g  165 (201)
T COG1974         113 FFLRVSGDSMIDAGILDGDLVVVDPT----EDAENGDIVVALID---------GEEATVKRLYRDG  165 (201)
T ss_pred             EEEEecCCccccCcCCCCCEEEEcCC----CCCCCCCEEEEEcC---------CCcEEEEEEEEeC
Confidence            45799999996 56777999999986    58899999999873         3457788876544

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

Probab=85.91  E-value=0.9  Score=37.64  Aligned_cols=18  Identities=28%  Similarity=0.517  Sum_probs=15.9

Q ss_pred             CceEEEEEEEeCCCEEEE
Q 023926          257 GDVFIKRIVATAGDCVEV  274 (275)
Q Consensus       257 ~k~~IKRVIGlPGDtVeI  274 (275)
                      ...++||++++|||.+.+
T Consensus       137 ~~~~~~~~~~~~gd~~~~  154 (166)
T COG0681         137 KKDYIKRVIGLPGDNILY  154 (166)
T ss_pred             ccccccceEEeeccceee
Confidence            477999999999999875

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

Probab=84.73  E-value=0.36  Score=42.73  Aligned_cols=40  Identities=25%  Similarity=0.369  Sum_probs=29.9

Q ss_pred             CCCCcEEEEEcCCcc----ccccC-CCCceEEEEEEEeCCCEEEE
Q 023926          235 PEVSDIVIFRAPPIL----QEIGF-SSGDVFIKRIVATAGDCVEV  274 (275)
Q Consensus       235 pkrGDIVVFk~P~~l----~~~g~-~~~k~~IKRVIGlPGDtVeI  274 (275)
                      +.+||+|++..|...    ..-|| ...-..+|||.|+|||+|.+
T Consensus        54 vt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci   98 (173)
T COG4959          54 VTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCI   98 (173)
T ss_pred             cccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEE
Confidence            489999999887631    11233 35667899999999999976

>PF12518 DUF3721: Protein of unknown function; InterPro: IPR022196 This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length

Probab=81.57  E-value=0.61  Score=31.33  Aligned_cols=9  Identities=56%  Similarity=1.782  Sum_probs=7.9

Q ss_pred             cCccccCCC
Q 023926          125 GSKWLPCNE  133 (275)
Q Consensus       125 ~~kwlpc~~  133 (275)
                      +.||+||++
T Consensus        23 g~~WMPC~~   31 (34)
T PF12518_consen   23 GDKWMPCSN   31 (34)
T ss_pred             cCccccCcc
Confidence            689999985

There is a conserved WMPC sequence motif. There are two completely conserved residues (A and C) that may be functionally important.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	275
1kn9_A	249	Crystal Structure Of A Bacterial Signal Peptidase A		7e-07
1t7d_A	250	Crystal Structure Of Escherichia Coli Type I Signal		8e-07
1b12_A	248	Crystal Structure Of Type 1 Signal Peptidase From E		1e-06

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 44/90 (48%), Gaps = 23/90 (25%)
Query: 197 LFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFK------------RPEVSDIVIFR 244
           + +SF+ EP  IPS SM PTL +GD IL EK +Y  K             P+  DIV+F+
Sbjct: 1   MVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFK 60
Query: 245 AP--PILQEIGFSSGDVFIKRIVATAGDCV 272
            P  P L          +IKR V   GD V
Sbjct: 61  YPEDPKLD---------YIKRAVGLPGDKV 81

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 35/91 (38%), Positives = 44/91 (48%), Gaps = 23/91 (25%)
Query: 196 FLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFK------------RPEVSDIVIF 243
            + +SF+ EP  IPS SM PTL +GD IL EK +Y  K             P+  DIV+F
Sbjct: 1   MIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVF 60
Query: 244 RAP--PILQEIGFSSGDVFIKRIVATAGDCV 272
           + P  P L          +IKR V   GD V
Sbjct: 61  KYPEDPKLD---------YIKRAVGLPGDKV 82

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/88 (39%), Positives = 43/88 (48%), Gaps = 23/88 (26%)
Query: 199 KSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFK------------RPEVSDIVIFRAP 246
           +SF+ EP  IPS SM PTL +GD IL EK +Y  K             P+  DIV+F+ P
Sbjct: 2   RSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP 61
Query: 247 --PILQEIGFSSGDVFIKRIVATAGDCV 272
             P L          +IKR V   GD V
Sbjct: 62  EDPKLD---------YIKRAVGLPGDKV 80

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	275
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	3e-17

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

 Score = 77.6 bits (191), Expect = 3e-17
 Identities = 32/88 (36%), Positives = 40/88 (45%), Gaps = 19/88 (21%)

Query: 199 KSFLAEPRSIPSASMNPTLDVGDRILAEKVSY------------FFKRPEVSDIVIFRAP 246
           +SF+ EP  IPS SM PTL +GD IL EK +Y                P+  DIV+F+ P
Sbjct: 2   RSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP 61

Query: 247 PILQEIGFSSGDVFIKRIVATAGDCVEV 274
                        +IKR V   GD V  
Sbjct: 62  E-------DPKLDYIKRAVGLPGDKVTY 82

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	275
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	99.75
1umu_A	116	UMUD'; induced mutagenesis, SOS mutagenesis, DNA r	98.73
1kca_A	109	Repressor protein CI; gene regulation, DNA-binding	98.62
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	98.6
2hnf_A	133	Repressor protein CI101-229DM-K192A; viral protein	98.45
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	98.08
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	98.07
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	94.03

>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=99.75  E-value=1.4e-18  Score=155.61  Aligned_cols=71  Identities=45%  Similarity=0.623  Sum_probs=63.6

Q ss_pred             HHHceeEeEEEcCCCCcccCCCCCEEEEEecccC------------CCCCCCCcEEEEEcCCccccccCCCCceEEEEEE
Q 023926          198 FKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYF------------FKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIV  265 (275)
Q Consensus       198 Ir~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~------------~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVI  265 (275)
                      ++.|+++++.|+|+||+|||++||+|+|+|..|+            ..+|++||||+|+.|.+       .+..||||||
T Consensus         1 ir~fv~~~~~v~g~SM~Ptl~~GD~vlv~k~~yg~r~P~~~~~l~~~~~~~rGDIvvf~~p~~-------~~~~~iKRVi   73 (248)
T 1b12_A            1 VRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPED-------PKLDYIKRAV   73 (248)
T ss_dssp             -CBCCEEEEECCSCTTTTTSCTTEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTTC-------TTSEEEEEEE
T ss_pred             CeEEEEEEEEeccccccccccCCCEEEEEecccCcccccccccccccCCCCCCcEEEEEeCCC-------CCceEEEEEE
Confidence            4789999999999999999999999999999875            36899999999999862       5788999999


Q ss_pred             EeCCCEEEEC
Q 023926          266 ATAGDCVEVS  275 (275)
Q Consensus       266 GlPGDtVeIk  275 (275)
                      |+|||+|+++
T Consensus        74 glpGD~v~i~   83 (248)
T 1b12_A           74 GLPGDKVTYD   83 (248)
T ss_dssp             ECTTCEEEEE
T ss_pred             eeCCCEEEEE
Confidence            9999999874

>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=98.73  E-value=1.6e-08  Score=79.98  Aligned_cols=51  Identities=20%  Similarity=0.251  Sum_probs=44.6

Q ss_pred             EeEEEcCCCCcc-cCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeC
Q 023926          204 EPRSIPSASMNP-TLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATA  268 (275)
Q Consensus       204 ~~~~V~G~SMeP-TL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlP  268 (275)
                      ..+.|.|+||+| +|++||+|++++.    ..++.||||++..          +++.+|||++..+
T Consensus        28 ~~~~v~GdSM~p~~i~~Gd~v~vd~~----~~~~~gdivv~~~----------~~~~~vKr~~~~~   79 (116)
T 1umu_A           28 YFVKASGDSMIDGGISDGDLLIVDSA----ITASHGDIVIAAV----------DGEFTVKKLQLRP   79 (116)
T ss_dssp             EEEECCSSTTGGGTCCTTCEEEEETT----SCCCTTCEEEEEE----------TTEEEEEEEECSS
T ss_pred             EEEEECCCCcCCCCCCCCCEEEEEcC----CCCCCCCEEEEEE----------CCEEEEEEEEeCC
Confidence            467999999999 8999999999986    3689999999987          3588999999865

>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=98.62  E-value=1e-07  Score=75.30  Aligned_cols=53  Identities=23%  Similarity=0.331  Sum_probs=45.4

Q ss_pred             eEEEcCCCCc------ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCC
Q 023926          205 PRSIPSASMN------PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGD  270 (275)
Q Consensus       205 ~~~V~G~SMe------PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGD  270 (275)
                      .+.|.|+||+      |+|++||+|+|++.    ..++.||||++..+         .++.+|||++..+|.
T Consensus        15 ~~~V~GdSM~~~~g~~p~i~~Gd~v~Vd~~----~~~~~Gdivv~~~~---------~~~~~vKrl~~~~~~   73 (109)
T 1kca_A           15 WLEVEGNSMTAPTGSKPSFPDGMLILVDPE----QAVEPGDFCIARLG---------GDEFTFKKLIRDSGQ   73 (109)
T ss_dssp             EEECCSSTTCCCTTCSSCCCTTCEEEEETT----SCCCTTCEEEEECS---------TTCEEEEEEEEETTE
T ss_pred             EEEEeCcCcCCCCCCCCeeCCCCEEEEecC----CcCCCCCEEEEEEC---------CCeEEEEEEEEeCCE
Confidence            5789999999      99999999999985    36999999999863         248899999987543

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

Probab=98.60  E-value=9.2e-08  Score=81.51  Aligned_cols=56  Identities=23%  Similarity=0.319  Sum_probs=48.6

Q ss_pred             EeEEEcCCCCccc-CCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926          204 EPRSIPSASMNPT-LDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV  274 (275)
Q Consensus       204 ~~~~V~G~SMePT-L~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI  274 (275)
                      ..+.|.|+||+|+ |.+||.|+|++.    ..++.||||++..          +++.+|||+. .+|+.+.+
T Consensus       111 ~~~~v~GdSM~p~~i~~Gd~v~vd~~----~~~~~G~i~v~~~----------~~~~~vKrl~-~~~~~~~l  167 (202)
T 1jhf_A          111 FLLRVSGMSMKDIGIMDGDLLAVHKT----QDVRNGQVVVARI----------DDEVTVKRLK-KQGNKVEL  167 (202)
T ss_dssp             EEEECCSSTTGGGTCCTTCEEEEEEC----SCCCTTSEEEEEE----------TTEEEEEEEE-EETTEEEE
T ss_pred             EEEEECCCCCCCCCCCCCCEEEEecc----CCcCCCeEEEEEE----------CCEEEEEEEE-EeCCEEEE
Confidence            3578999999999 999999999985    3689999999986          4689999999 68888765

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

Probab=98.45  E-value=5.1e-07  Score=73.18  Aligned_cols=55  Identities=20%  Similarity=0.229  Sum_probs=46.2

Q ss_pred             eEEEcCCCCc------ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEE
Q 023926          205 PRSIPSASMN------PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVE  273 (275)
Q Consensus       205 ~~~V~G~SMe------PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVe  273 (275)
                      .+.|.|+||+      |+|++||+|+|++.    ..++.||||++...         .++.+|||++-.+| .+.
T Consensus        46 ~~~V~GdSM~~~~g~~p~i~~Gd~v~vd~~----~~~~~Gdivv~~~~---------~~~~~vKrl~~~~~-~~~  106 (133)
T 2hnf_A           46 WLEVEGNSMTTPTGSKTSFPDGMLILVDPE----QAVEPGDFCIARLG---------GDEFTFAKLIRDSG-QVF  106 (133)
T ss_dssp             EEECCSSTTCCC---CCCCCTTCEEEEETT----SCCCTTSEEEEEET---------TTEEEEEEEEEETT-EEE
T ss_pred             EEEEeCCCcCCCcCCCCccCCCCEEEEccC----CCCCCCCEEEEEEC---------CCEEEEEEEEEeCC-eEE
Confidence            5789999999      99999999999985    37899999999863         35899999997654 443

>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=98.08  E-value=1.1e-05  Score=69.01  Aligned_cols=55  Identities=22%  Similarity=0.274  Sum_probs=45.8

Q ss_pred             EeEEEcCCCC-cccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEE
Q 023926          204 EPRSIPSASM-NPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVE  273 (275)
Q Consensus       204 ~~~~V~G~SM-ePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVe  273 (275)
                      ..+.|.|+|| +|++.+||+|+|++.    ..++.||||++..          +++.+|||+.-.+| .+.
T Consensus       110 f~l~v~GdSM~~p~i~~GD~viv~~~----~~~~~G~ivv~~~----------~~~~~vKr~~~~~~-~~~  165 (196)
T 3k2z_A          110 FLLKVKGESMIEEHICDGDLVLVRRQ----DWAQNGDIVAAMV----------DGEVTLAKFYQRGD-TVE  165 (196)
T ss_dssp             EEEECCSSTTGGGTCCTTCEEEEEEC----SCCCTTCEEEEEE----------TTEEEEEEEEEETT-EEE
T ss_pred             EEEEEeCCCcCCCCCCCCCEEEEecc----CcCCCCCEEEEEE----------CCcEEEEEEEEECC-EEE
Confidence            4679999999 699999999999986    3689999999986          35899999987654 443

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

Probab=98.07  E-value=5.1e-06  Score=71.58  Aligned_cols=54  Identities=22%  Similarity=0.310  Sum_probs=45.4

Q ss_pred             eEEEcCCCCc------ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCE
Q 023926          205 PRSIPSASMN------PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDC  271 (275)
Q Consensus       205 ~~~V~G~SMe------PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDt  271 (275)
                      .+.|.|+||+      |+|.+||+|+|++..    .++.||||++...         .++.+|||+.-.+|..
T Consensus       142 ~l~V~GdSM~~~~g~~P~i~~Gd~v~vd~~~----~~~~g~ivv~~~~---------~~~~~vKrl~~~~~~~  201 (236)
T 3bdn_A          142 WLEVEGNSMTAPTGSKPSFPDGMLILVDPEQ----AVEPGDFCIARLG---------GDEFTFKKLIRGSGQV  201 (236)
T ss_dssp             EEECCSSSSCCCSSCSSCCCSSCEEEECCSS----CCCTTSEEEEEST---------TTCCCCEEEECCSSSC
T ss_pred             EEEEeCCCcCCCCCCCCcCCCCCEEEECCCC----CCCCCcEEEEEEC---------CCeEEEEEEEEcCCcE
Confidence            5689999999      999999999999853    6899999999862         3578999998876653

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

Probab=94.03  E-value=0.074  Score=43.88  Aligned_cols=48  Identities=13%  Similarity=0.171  Sum_probs=37.3

Q ss_pred             CCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926          212 SMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV  274 (275)
Q Consensus       212 SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI  274 (275)
                      +|...-.+||.|+|++-     .+..|+|+++..          +++.+|||+.-.||+.+.+
T Consensus       114 ~~~~v~~~Gd~v~Vd~~-----~~~~g~i~vv~~----------~g~~~vKrl~~~~~~~i~L  161 (189)
T 2fjr_A          114 DGMAIRSEGKIYFVDKQ-----ASLSDGLWLVDI----------KGAISIRELTKLPGRKLHV  161 (189)
T ss_dssp             SEEEEEETTEEEEEETT-----CCSCSEEEEEEE----------TTEEEEEEEEEETTTEEEE
T ss_pred             CeEEEeeCCcEEEEEcC-----CccCCCEEEEEe----------CCeEEEEEEEECCCCEEEE
Confidence            33333389999999974     256799999986          4689999999989887765

---

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	275
d1b12a_	247	b.87.1.2 (A:) Type 1 signal peptidase {Escherichia	3e-17

>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 = 76.9 bits (188), Expect = 3e-17
 Identities = 31/81 (38%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 200 SFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSS--- 256
           SF+ EP  IPS SM PTL +GD IL EK +Y  K P     +I    P   +I       
Sbjct: 2   SFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE 61

Query: 257 --GDVFIKRIVATAGDCVEVS 275
                +IKR V   GD V   
Sbjct: 62  DPKLDYIKRAVGLPGDKVTYD 82

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	275
d1b12a_	247	Type 1 signal peptidase {Escherichia coli [TaxId:	99.76
d1jhfa2	126	LexA C-terminal domain {Escherichia coli [TaxId: 5	98.25
d1f39a_	101	lambda repressor C-terminal domain {Bacteriophage	98.23
d1umua_	105	UmuD' {Escherichia coli [TaxId: 562]}	97.9

>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=99.76  E-value=1.7e-19  Score=156.84  Aligned_cols=69  Identities=48%  Similarity=0.670  Sum_probs=63.0

Q ss_pred             HHceeEeEEEcCCCCcccCCCCCEEEEEecccCCCC------------CCCCcEEEEEcCCccccccCCCCceEEEEEEE
Q 023926          199 KSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKR------------PEVSDIVIFRAPPILQEIGFSSGDVFIKRIVA  266 (275)
Q Consensus       199 r~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~~~~------------pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIG  266 (275)
                      |.|+++++.|||+||+|||+.||+|+|+|++|+++.            +++||||+|+.|.+       ....|||||+|
T Consensus         1 R~f~~~~f~IPs~SMePTL~~GD~l~V~K~~Yg~r~P~~~~~~~~~~~~~rgdivvf~~p~~-------~~~~~ikR~ig   73 (247)
T d1b12a_           1 RSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPED-------PKLDYIKRAVG   73 (247)
T ss_dssp             CBCCEEEEECCSCTTTTTSCTTEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTTC-------TTSEEEEEEEE
T ss_pred             CEEEEEEEEeCcccccchhccCCEEEEEccccCccCCccCcccccccCcccCceeeecCCCC-------CCccccccccC
Confidence            579999999999999999999999999999987654            59999999999873       67789999999


Q ss_pred             eCCCEEEE
Q 023926          267 TAGDCVEV  274 (275)
Q Consensus       267 lPGDtVeI  274 (275)
                      +|||+|++
T Consensus        74 ~pGD~i~~   81 (247)
T d1b12a_          74 LPGDKVTY   81 (247)
T ss_dssp             CTTCEEEE
T ss_pred             CCCCeEEE
Confidence            99999986

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

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

Probab=98.25  E-value=1.6e-06  Score=68.24  Aligned_cols=54  Identities=22%  Similarity=0.304  Sum_probs=45.7

Q ss_pred             eEEEcCCCCccc-CCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEE
Q 023926          205 PRSIPSASMNPT-LDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVE  273 (275)
Q Consensus       205 ~~~V~G~SMePT-L~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVe  273 (275)
                      ..+|.|+||+|+ +++||+|++++.    .+++.||||++..          +++.+|||+.-.+ +.+.
T Consensus        40 ~lrV~GdSM~~~~i~~gd~viv~~~----~~~~~G~ivv~~~----------~ge~~vKrl~~~~-~~~~   94 (126)
T d1jhfa2          40 LLRVSGMSMKDIGIMDGDLLAVHKT----QDVRNGQVVVARI----------DDEVTVKRLKKQG-NKVE   94 (126)
T ss_dssp             EEECCSSTTGGGTCCTTCEEEEEEC----SCCCTTSEEEEEE----------TTEEEEEEEEEET-TEEE
T ss_pred             EEEEcCCcccCcccCCCEEEEEecc----ccccCCCEEEEEE----------CCEEEEEEEEEcC-CEEE
Confidence            579999999998 999999999985    4899999999997          4688999998664 4444

>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=98.23  E-value=1.9e-06  Score=65.56  Aligned_cols=53  Identities=23%  Similarity=0.333  Sum_probs=43.6

Q ss_pred             eEEEcCCCC------cccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCC
Q 023926          205 PRSIPSASM------NPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGD  270 (275)
Q Consensus       205 ~~~V~G~SM------ePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGD  270 (275)
                      ..+|.|+||      +|+|.+||+|+|++-    .+++.||+|++...         .++.++||+.-.+|.
T Consensus         7 ~l~V~GdSM~~~~~~ep~i~~Gd~viVd~~----~~~~~g~ivva~~~---------~~~~~vKr~~~~~~~   65 (101)
T d1f39a_           7 WLEVEGNSMTAPTGSKPSFPDGMLILVDPE----QAVEPGDFCIARLG---------GDEFTFKKLIRDSGQ   65 (101)
T ss_dssp             EEECCSSTTCCCTTCSSCCCTTCEEEEETT----SCCCTTCEEEEECT---------TSCEEEEEEEEETTE
T ss_pred             EEEEeCCccCCCcccCCCcCCCCEEEEEec----CccCCCCEEEEEEC---------CCeEEEEEEEEcCCE
Confidence            468999999      899999999999985    47899999988763         356789998766543

>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=97.90  E-value=1.6e-05  Score=61.19  Aligned_cols=48  Identities=21%  Similarity=0.313  Sum_probs=42.1

Q ss_pred             eEEEcCCCC-cccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEE
Q 023926          205 PRSIPSASM-NPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVA  266 (275)
Q Consensus       205 ~~~V~G~SM-ePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIG  266 (275)
                      ..+|.|+|| +|.+.+||.++|+|.    ..++.||||++..          +++.+|||..-
T Consensus        22 ~~rV~GdSM~~~gI~~GDlliVd~~----~~~~~g~ivva~i----------~ge~~vKrl~~   70 (105)
T d1umua_          22 FVKASGDSMIDGGISDGDLLIVDSA----ITASHGDIVIAAV----------DGEFTVKKLQL   70 (105)
T ss_dssp             EEECCSSTTGGGTCCTTCEEEEETT----SCCCTTCEEEEEE----------TTEEEEEEEEC
T ss_pred             EEEEcCCccccCccCCCCEEEEEcc----cccccCcEEEEEE----------CCEEEEEEEEE
Confidence            579999999 588999999999996    4789999999997          46889999864