Citrus Sinensis ID: 029367

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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----
Protein Sequence
MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPSDS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEEcccccccccccccEEEEEEccccccccccccEEEEccccccccccccccEEEEEEEEcccEEEEEccEEEEccEEccccccccccccccccEEcccccEEEEccccccccccccccccccccEEEEEEEEEEccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEccccccccccccccEEEEEEEEEEEcccccccEEEEcccHHHcccccccHHEEEEEEccccEEEEEccEEEEccccccccccccccccccccEEcccccEEEEcccccccccccEEccccHHHEEEEEEEEEcccccc
Coil and Loop (DISEMBL)
msflrpsaLHQFLITCLsvrwmpceswaflrwpgldgsLKILIGLLLwstfseirfipsssmyptlrigDRIIVEKAsyyfrnpsihdivtfrapfqypglgeeDVFIKRIVAkagdlvqvrdgslyvngiaqnedfiaehpkytsdltyvpVGYVYVlgdnrnnsfdshvwgplpvkniagryltrcyrpsds
Flexible Loop (DISEMBL)
msflrpsaLHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRfipsssmyptlrIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAgdlvqvrdgSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNsfdshvwgplpvkniagryltrcyrpsds
Low Complexity Region (SEG)
MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPSDS
Disordered region (IsUnstruct)
*******ALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY*****
Disordered Region (DISOPRED)
***************************AFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPSD*
Disordered Region (DISEMBL)
MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPSDS
Disordered Region (DISPRO)
****RPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPSD*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPSDS
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	194	2.2.26 [Sep-21-2011]
O04348	340	Thylakoidal processing pe	yes	no	0.783	0.447	0.547	4e-43
Q8H0W1	291	Chloroplast processing pe	no	no	0.793	0.529	0.544	6e-42
Q9M9Z2	367	Probable thylakoidal proc	no	no	0.783	0.414	0.545	2e-40
P72660	196	Probable signal peptidase	N/A	no	0.711	0.704	0.478	6e-30
P73157	218	Probable signal peptidase	N/A	no	0.835	0.743	0.412	7e-28
Q51876	203	Signal peptidase I OS=Pho	N/A	no	0.757	0.724	0.431	4e-27
O07560	168	Signal peptidase I V OS=B	yes	no	0.608	0.702	0.354	7e-13
P71013	193	Signal peptidase I T OS=B	no	no	0.711	0.715	0.316	8e-13
Q9I5G7	284	Signal peptidase I OS=Pse	no	no	0.711	0.485	0.298	3e-12
Q10789	294	Signal peptidase I OS=Myc	yes	no	0.701	0.462	0.308	2e-11

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

 Score =  174 bits (440), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 86/157 (54%), Positives = 108/157 (68%), Gaps = 5/157 (3%)

Query: 41  ILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAP---FQ 97
           + + +L  S  +E + IPS+SMYPTL  GDR++ EK SY+FR P + DIV F+AP    +
Sbjct: 164 VTVSILFRSALAEPKSIPSTSMYPTLDKGDRVMAEKVSYFFRKPEVSDIVIFKAPPILLE 223

Query: 98  YP--GLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGY 155
           YP  G    DVFIKRIVA  GD V+VRDG L+VN I Q EDF+ E   Y  +  +VP GY
Sbjct: 224 YPEYGYSSNDVFIKRIVASEGDWVEVRDGKLFVNDIVQEEDFVLEPMSYEMEPMFVPKGY 283

Query: 156 VYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS 192
           V+VLGDNRN SFDSH WGPLP++NI GR + R + PS
Sbjct: 284 VFVLGDNRNKSFDSHNWGPLPIENIVGRSVFRYWPPS 320

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

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

 Score =  170 bits (430), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 85/156 (54%), Positives = 107/156 (68%), Gaps = 2/156 (1%)

Query: 39  LKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAP--F 96
           + I + L      +E R+IPS SMYPT  +GDR++ EK SYYFR P  +DIV F++P   
Sbjct: 120 VAIAVSLAFRYFIAEPRYIPSLSMYPTFDVGDRLVAEKVSYYFRKPCANDIVIFKSPPVL 179

Query: 97  QYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYV 156
           Q  G  + DVFIKRIVAK GDLV+V +G L VNG+A+NE FI E P Y      VP   V
Sbjct: 180 QEVGYTDADVFIKRIVAKEGDLVEVHNGKLMVNGVARNEKFILEPPGYEMTPIRVPENSV 239

Query: 157 YVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS 192
           +V+GDNRNNS+DSHVWGPLP+KNI GR + R + P+
Sbjct: 240 FVMGDNRNNSYDSHVWGPLPLKNIIGRSVFRYWPPN 275

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

 Score =  165 bits (417), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 84/154 (54%), Positives = 102/154 (66%), Gaps = 2/154 (1%)

Query: 41  ILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAP--FQY 98
           + + LL  S  +E + IPS+SM PTL +GDR+I EK SY+FR P + DIV F+AP     
Sbjct: 194 VTVSLLFRSALAEPKSIPSTSMLPTLDVGDRVIAEKVSYFFRKPEVSDIVIFKAPPILVE 253

Query: 99  PGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYV 158
            G    DVFIKRIVA  GD V+V DG L VN   Q EDF+ E   Y  +  +VP GYV+V
Sbjct: 254 HGYSCADVFIKRIVASEGDWVEVCDGKLLVNDTVQAEDFVLEPIDYEMEPMFVPEGYVFV 313

Query: 159 LGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS 192
           LGDNRN SFDSH WGPLP+KNI GR + R + PS
Sbjct: 314 LGDNRNKSFDSHNWGPLPIKNIIGRSVFRYWPPS 347

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

 Score =  130 bits (327), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 67/140 (47%), Positives = 87/140 (62%), Gaps = 2/140 (1%)

Query: 52  SEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAP--FQYPGLGEEDVFIK 109
           +E R+IPS SM PTL  GDR++VEK SY+F  P + DI+ F  P   Q  G      FIK
Sbjct: 35  AEPRYIPSDSMLPTLEQGDRLVVEKVSYHFHPPQVGDIIVFHPPELLQVQGYDLGQAFIK 94

Query: 110 RIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDS 169
           R++A  G  V+V +G +Y +G    E++I E P+Y      VP G V+V+GDNRNNS DS
Sbjct: 95  RVIALPGQTVEVNNGIVYRDGQPLQEEYILEPPQYNLPAVRVPDGQVFVMGDNRNNSNDS 154

Query: 170 HVWGPLPVKNIAGRYLTRCY 189
           HVWG LP +NI G  L R +
Sbjct: 155 HVWGFLPQQNIIGHALFRFF 174

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 =  123 bits (309), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 68/165 (41%), Positives = 93/165 (56%), Gaps = 3/165 (1%)

Query: 23  PCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFR 82
           P  +W  L   G      +++ + + +  +E R+IPSSSM PTL+I DR+I+EK SY  R
Sbjct: 17  PENTWLEL---GKTMVTAVILAIGIRTFVAEARYIPSSSMEPTLQINDRLIIEKISYRLR 73

Query: 83  NPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHP 142
           +P   +IV F            D FIKRI+   GD V+V  G++YVNG   +E++IA  P
Sbjct: 74  DPERGEIVVFNPTDALKAKNFHDAFIKRIIGLPGDEVRVSQGNVYVNGKMLDENYIAAPP 133

Query: 143 KYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTR 187
            Y      VP     VLGDNRNNS+DSH WG +P + + GR   R
Sbjct: 134 AYEYGPVKVPDDQYLVLGDNRNNSYDSHYWGFVPREKLLGRAFVR 178

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 =  120 bits (302), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 66/153 (43%), Positives = 88/153 (57%), Gaps = 6/153 (3%)

Query: 39  LKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRA---- 94
           L +++ L + +  +E R+IPS SM PTL + DR+IVEK SY+F  P   DI+ F      
Sbjct: 37  LSVVLALGIRTFVAEARYIPSESMLPTLEVNDRLIVEKISYHFNPPRRGDIIVFHPTEAL 96

Query: 95  PFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVG 154
             Q P L E   FIKR++   G+ VQV  G + +NG    E++I   P Y      VP  
Sbjct: 97  KQQNPSLNE--AFIKRVIGLPGETVQVTGGRVLINGQPLEENYIQSPPDYQWGPEKVPAD 154

Query: 155 YVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTR 187
              VLGDNRNNS+DSH WG +P +NI GR + R
Sbjct: 155 SFLVLGDNRNNSYDSHFWGYVPRQNIIGRAVVR 187

Phormidium laminosum (taxid: 32059)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|O07560|LEPV_BACSU Signal peptidase I V OS=Bacillus subtilis (strain 168) GN=sipV PE=2 SV=1

 Score = 73.9 bits (180), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 50/141 (35%), Positives = 72/141 (51%), Gaps = 23/141 (16%)

Query: 57  IPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAG 116
           +   SM PT + G+ ++V K S+ F+     DIV F+ P       +  V IKR++   G
Sbjct: 30  VEGVSMNPTFQEGNELLVNKFSHRFKTIHRFDIVLFKGP-------DHKVLIKRVIGLPG 82

Query: 117 DLVQVRDGSLYVNGIAQNEDFIAEHPKYTS------------DLT---YVPVGYVYVLGD 161
           + ++ +D  LYVNG    E F+ +H K  S            D+T    VP G  +V+GD
Sbjct: 83  ETIKYKDDQLYVNGKQVAEPFL-KHLKSVSAGSHVTGDFSLKDVTGTSKVPKGKYFVVGD 141

Query: 162 NRNNSFDSHVWGPLPVKNIAG 182
           NR  SFDS  +GP+  KNI G
Sbjct: 142 NRIYSFDSRHFGPIREKNIVG 162

Bacillus subtilis (strain 168) (taxid: 224308)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|P71013|LEPT_BACSU Signal peptidase I T OS=Bacillus subtilis (strain 168) GN=sipT PE=1 SV=1

 Score = 73.6 bits (179), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 49/155 (31%), Positives = 76/155 (49%), Gaps = 17/155 (10%)

Query: 25  ESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNP 84
           ++  +L W G    + +L+ LL+     E   +  SSMYPTL  G+R+ V K   Y    
Sbjct: 16  KTNTYLEW-GKAIVIAVLLALLIRHFLFEPYLVEGSSMYPTLHDGERLFVNKTVNYIGEL 74

Query: 85  SIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKY 144
              DIV         G   +  ++KR++ K G+ VQ++D +LY+NG    E +++++ K 
Sbjct: 75  KRGDIVIIN------GETSKIHYVKRLIGKPGETVQMKDDTLYINGKKVAEPYLSKNKKE 128

Query: 145 TSDL----------TYVPVGYVYVLGDNRNNSFDS 169
              L            VP G  +V+GDNR NS DS
Sbjct: 129 AEKLGVSLTGDFGPVKVPKGKYFVMGDNRLNSMDS 163

Bacillus subtilis (strain 168) (taxid: 224308)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 8

EC: 9

>sp|Q9I5G7|LEP_PSEAE Signal peptidase I OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=lepB PE=3 SV=1

 Score = 71.6 bits (174), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 58/194 (29%), Positives = 84/194 (43%), Gaps = 56/194 (28%)

Query: 41  ILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFR------------NPSIHD 88
           + I L+L S   E   IPS SM PTL +GD I+V K +Y  R            +P   D
Sbjct: 70  LFIVLVLRSFLVEPFQIPSGSMKPTLEVGDFILVNKFAYGIRLPVLDTKVIPIGDPQRGD 129

Query: 89  IVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ-VRDGSLYVNGIAQNEDFIAEHPKYTSD 147
           ++ FR P + P +     +IKR+V   GD V+  ++  LYVNG    E  + E P     
Sbjct: 130 VMVFRYPSE-PNIN----YIKRVVGLPGDTVRYTKEKRLYVNGELVAEKLVGEEPGTLGS 184

Query: 148 LTY----------------------------VPVGYVYVLGDNRNNSFDSHVW------- 172
           +T                             +P G+ +++GDNR+NS DS  W       
Sbjct: 185 VTLYQEKLGQAEHLIRKEMSRYRIEPDRQWTIPAGHYFMMGDNRDNSNDSRYWNDPKIPK 244

Query: 173 ---GPLPVKNIAGR 183
              G +P +NI G+
Sbjct: 245 DLLGMVPDRNIVGK 258

Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (taxid: 208964)

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 = 69.3 bits (168), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/191 (30%), Positives = 83/191 (43%), Gaps = 55/191 (28%)

Query: 56  FIPSSSMYPTLR-----IGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLG-------- 102
            IPS SM PTL      +GDRI+V+K SY F +P   D++ FR P  +  +G        
Sbjct: 91  LIPSESMEPTLHGCSTCVGDRIMVDKLSYRFGSPQPGDVIVFRGPPSW-NVGYKSIRSHN 149

Query: 103 ------------------EEDVFIKRIVAKAGDLVQVR-DGSLYVNGIAQNEDFI----- 138
                             +E+  +KR++A  G  VQ R D  L VNG    E ++     
Sbjct: 150 VAVRWVQNALSFIGFVPPDENDLVKRVIAVGGQTVQCRSDTGLTVNGRPLKEPYLDPATM 209

Query: 139 ----AEHPKYTSDL--TYVPVGYVYVLGDNRNNSFDSHVWGPL-----------PVKNIA 181
               + +P   S+     VP G V+V+GDNR +S DS    PL           PV N+ 
Sbjct: 210 MADPSIYPCLGSEFGPVTVPPGRVWVMGDNRTHSADSRAHCPLLCTDDPLPGTVPVANVI 269

Query: 182 GRYLTRCYRPS 192
           G+     + PS
Sbjct: 270 GKARLIVWPPS 280

Mycobacterium tuberculosis (taxid: 1773)

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	194
351725865	194	uncharacterized protein LOC100306121 [Gl	0.994	0.994	0.689	1e-74
388519903	193	unknown [Lotus japonicus]	0.994	1.0	0.704	2e-74
388495730	193	unknown [Lotus japonicus]	0.994	1.0	0.699	1e-73
359492389	194	PREDICTED: thylakoidal processing peptid	0.979	0.979	0.663	1e-68
302141777	173	unnamed protein product [Vitis vinifera]	0.871	0.976	0.680	3e-62
449463412	188	PREDICTED: chloroplast processing peptid	0.958	0.989	0.593	7e-62
449524748	183	PREDICTED: chloroplast processing peptid	0.891	0.945	0.597	3e-56
224143200	132	predicted protein [Populus trichocarpa]	0.680	1.0	0.751	5e-53
255558600	171	signal peptidase I, putative [Ricinus co	0.654	0.742	0.742	5e-49
449447223	761	PREDICTED: uncharacterized protein LOC10	0.783	0.199	0.623	7e-47

>gi|351725865|ref|NP_001237875.1| uncharacterized protein LOC100306121 [Glycine max] gi|255627617|gb|ACU14153.1| unknown [Glycine max]

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 133/193 (68%), Positives = 159/193 (82%)

Query: 1   MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSS 60
           MSFLRPSAL+ FLI+  ++RW+ C+SW FLRWPGLDG  ++ + +LLWST SE+RFIPSS
Sbjct: 1   MSFLRPSALYNFLISYPALRWLSCQSWGFLRWPGLDGFFRLFVVVLLWSTLSELRFIPSS 60

Query: 61  SMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ 120
           SMYPTLR+GDRIIVEKASYY R+P+IHDIVTF+ P Q  G   + VFIKRIVAKAGD V+
Sbjct: 61  SMYPTLRVGDRIIVEKASYYIRSPAIHDIVTFKDPTQSSGENTDAVFIKRIVAKAGDTVE 120

Query: 121 VRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNI 180
           V  G+LY+NG+AQ EDFIAE P Y   L +VP G+VYVLGDNRNNS+DSHVWGPLPVKNI
Sbjct: 121 VNHGALYINGVAQQEDFIAEPPAYAMQLAHVPNGHVYVLGDNRNNSYDSHVWGPLPVKNI 180

Query: 181 AGRYLTRCYRPSD 193
            GRY+T  +RP +
Sbjct: 181 VGRYVTCYHRPRN 193

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388519903|gb|AFK48013.1| unknown [Lotus japonicus]

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 136/193 (70%), Positives = 159/193 (82%)

Query: 1   MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSS 60
           MSFLRPSAL+ FLIT  S+RWMPC+S  FLRWPGLDG L++L+  LLWSTFSE+R IPSS
Sbjct: 1   MSFLRPSALYHFLITYSSLRWMPCQSSGFLRWPGLDGFLRLLVVGLLWSTFSELRSIPSS 60

Query: 61  SMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ 120
           SM+PTLR+ DRIIVEKASYYFR+P+IH+IVTFR P Q  G   + VFIKR+VAK GD V+
Sbjct: 61  SMFPTLRVADRIIVEKASYYFRSPAIHEIVTFRDPTQLSGDNPDVVFIKRVVAKEGDTVE 120

Query: 121 VRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNI 180
           V  G LY+NG+AQ EDFIAE P YT   TYVP G+VYVLGDNRNNS+DSHVWGPLPVKNI
Sbjct: 121 VHHGRLYINGVAQEEDFIAEQPAYTVKSTYVPKGHVYVLGDNRNNSYDSHVWGPLPVKNI 180

Query: 181 AGRYLTRCYRPSD 193
            GRY+   +RP++
Sbjct: 181 IGRYVMCFHRPTN 193

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388495730|gb|AFK35931.1| unknown [Lotus japonicus]

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 135/193 (69%), Positives = 158/193 (81%)

Query: 1   MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSS 60
           MSFLRPSAL+ FLIT  S+RWMPC+S  FLRW GLDG L++L+  LLWSTFSE+R IPSS
Sbjct: 1   MSFLRPSALYHFLITYSSLRWMPCQSSGFLRWSGLDGFLRLLVVGLLWSTFSELRSIPSS 60

Query: 61  SMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ 120
           SM+PTLR+ DRIIVEKASYYFR+P+IH+IVTFR P Q  G   + VFIKR+VAK GD V+
Sbjct: 61  SMFPTLRVADRIIVEKASYYFRSPTIHEIVTFRDPTQLSGDNPDVVFIKRVVAKEGDTVE 120

Query: 121 VRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNI 180
           V  G LY+NG+AQ EDFIAE P YT   TYVP G+VYVLGDNRNNS+DSHVWGPLPVKNI
Sbjct: 121 VHHGRLYINGVAQEEDFIAEQPAYTVKSTYVPKGHVYVLGDNRNNSYDSHVWGPLPVKNI 180

Query: 181 AGRYLTRCYRPSD 193
            GRY+   +RP++
Sbjct: 181 IGRYVMCFHRPTN 193

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359492389|ref|XP_003634407.1| PREDICTED: thylakoidal processing peptidase 1, chloroplastic-like [Vitis vinifera]

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 126/190 (66%), Positives = 153/190 (80%)

Query: 1   MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSS 60
           MSFLRPS L+Q L     ++WMPC+SW FLRWPG DG L+ L+ +LLWSTF+EI FI SS
Sbjct: 1   MSFLRPSVLYQLLFMHSWLQWMPCQSWEFLRWPGFDGLLRCLVVVLLWSTFTEISFIRSS 60

Query: 61  SMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ 120
           SMYPTL + DR+++E+ SYYFR P+IH+IVTFRAP + PG  E+++FIKR+VA+AGDLV+
Sbjct: 61  SMYPTLHVQDRVLMERVSYYFRRPAIHEIVTFRAPVRLPGHSEDEIFIKRVVARAGDLVE 120

Query: 121 VRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNI 180
           VRDGSLYVNG  Q EDFI E P Y  DLTYVP  +V+VLGDNRNNS DSH WGPLP+KNI
Sbjct: 121 VRDGSLYVNGDVQTEDFILEQPNYILDLTYVPKDHVFVLGDNRNNSSDSHEWGPLPIKNI 180

Query: 181 AGRYLTRCYR 190
            GR++T  YR
Sbjct: 181 IGRFVTHVYR 190

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302141777|emb|CBI18980.3| unnamed protein product [Vitis vinifera]

 Score =  243 bits (619), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 115/169 (68%), Positives = 139/169 (82%)

Query: 22  MPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYF 81
           MPC+SW FLRWPG DG L+ L+ +LLWSTF+EI FI SSSMYPTL + DR+++E+ SYYF
Sbjct: 1   MPCQSWEFLRWPGFDGLLRCLVVVLLWSTFTEISFIRSSSMYPTLHVQDRVLMERVSYYF 60

Query: 82  RNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEH 141
           R P+IH+IVTFRAP + PG  E+++FIKR+VA+AGDLV+VRDGSLYVNG  Q EDFI E 
Sbjct: 61  RRPAIHEIVTFRAPVRLPGHSEDEIFIKRVVARAGDLVEVRDGSLYVNGDVQTEDFILEQ 120

Query: 142 PKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYR 190
           P Y  DLTYVP  +V+VLGDNRNNS DSH WGPLP+KNI GR++T  YR
Sbjct: 121 PNYILDLTYVPKDHVFVLGDNRNNSSDSHEWGPLPIKNIIGRFVTHVYR 169

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463412|ref|XP_004149428.1| PREDICTED: chloroplast processing peptidase-like [Cucumis sativus]

 Score =  241 bits (616), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 114/192 (59%), Positives = 141/192 (73%), Gaps = 6/192 (3%)

Query: 1   MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSS 60
           M+FLRP   +       S+RWM   SW F RWP  D  L+ L+ L+LWS   EI  IPSS
Sbjct: 1   MTFLRPFLFYS------SLRWMTFHSWGFPRWPSFDAFLRFLVLLILWSMLLEIHSIPSS 54

Query: 61  SMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ 120
           SMYPTLR+GDRI+VE ASY  RNPSI+DI+TFR P Q   L EE++ +KR+VAKAGD V+
Sbjct: 55  SMYPTLRVGDRILVETASYLIRNPSINDIITFRDPTQQSALREENIVVKRVVAKAGDTVE 114

Query: 121 VRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNI 180
           V  G LYVNG+A++E F+ E P YT+  T +P G+VYVLGDNRNNS+DSH+WGPLPVKNI
Sbjct: 115 VCQGCLYVNGVAKDESFLLERPMYTTKSTQIPEGHVYVLGDNRNNSYDSHIWGPLPVKNI 174

Query: 181 AGRYLTRCYRPS 192
            GRYL  C++P+
Sbjct: 175 IGRYLCSCHKPT 186

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449524748|ref|XP_004169383.1| PREDICTED: chloroplast processing peptidase-like [Cucumis sativus]

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 107/179 (59%), Positives = 131/179 (73%), Gaps = 6/179 (3%)

Query: 1   MSFLRPSALHQFLITCLSVRWMPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSS 60
           M+FLRP   +       S+RWM   SW F RWP  D  L+ L+ L+LWS   EI  IPSS
Sbjct: 1   MTFLRPFLFYS------SLRWMTFHSWGFPRWPSFDAFLRFLVLLILWSMLLEIHSIPSS 54

Query: 61  SMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ 120
           SMYPTLR+GDRI+VE ASY  RNPSI+DI+TFR P Q  GL EE++ +KR+VAKAGD V+
Sbjct: 55  SMYPTLRVGDRILVETASYLIRNPSINDIITFRDPTQQSGLREENIVVKRVVAKAGDTVE 114

Query: 121 VRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKN 179
           V  G LYVNG+A++E F+ E P YT+  T +P G+VYVLGDNRNNS+DSH+WGPLPVK 
Sbjct: 115 VCQGCLYVNGVAKDESFLLERPMYTTKSTQIPEGHVYVLGDNRNNSYDSHIWGPLPVKK 173

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224143200|ref|XP_002336006.1| predicted protein [Populus trichocarpa] gi|222838438|gb|EEE76803.1| predicted protein [Populus trichocarpa]

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 100/133 (75%), Positives = 116/133 (87%), Gaps = 1/133 (0%)

Query: 62  MYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQV 121
           MYPTLR+GDRII+EKASYY + P+I+DIVTFRAP Q  G+  EDVFIKR+VAKAGDLVQV
Sbjct: 1   MYPTLRVGDRIIIEKASYYLKVPAINDIVTFRAPKQL-GITGEDVFIKRVVAKAGDLVQV 59

Query: 122 RDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIA 181
             GSLYVNGIAQ EDF+ E P YTS+LTYVP G+VYVLGDNRNNS+DSHVWGPLP+KN+ 
Sbjct: 60  HHGSLYVNGIAQTEDFLVEQPAYTSNLTYVPEGHVYVLGDNRNNSYDSHVWGPLPIKNVI 119

Query: 182 GRYLTRCYRPSDS 194
           GR++T CYRPS+ 
Sbjct: 120 GRFVTCCYRPSNK 132

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255558600|ref|XP_002520325.1| signal peptidase I, putative [Ricinus communis] gi|223540544|gb|EEF42111.1| signal peptidase I, putative [Ricinus communis]

 Score =  199 bits (506), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 95/128 (74%), Positives = 109/128 (85%), Gaps = 1/128 (0%)

Query: 22  MPCESWAFLRWPGLDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYF 81
           MPC+S  FL+WPGLDG L++ +  LLWS   EIRFIPS+SMYPTLRIGDR+IVEKASYYF
Sbjct: 1   MPCQSLGFLKWPGLDGFLRLFVMFLLWSMCLEIRFIPSASMYPTLRIGDRVIVEKASYYF 60

Query: 82  RNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEH 141
           R P+ +DIV FRAP Q PG+ EEDVFIKRIVAKAGDLVQV+ GSLYVNG AQNEDFIA+ 
Sbjct: 61  RAPATNDIVIFRAPKQ-PGIKEEDVFIKRIVAKAGDLVQVQHGSLYVNGKAQNEDFIAQR 119

Query: 142 PKYTSDLT 149
           P YTS++T
Sbjct: 120 PTYTSEIT 127

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  192 bits (487), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 96/154 (62%), Positives = 112/154 (72%), Gaps = 2/154 (1%)

Query: 41  ILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAP--FQY 98
           + + +L  S+ +E R IPSSSMYPTL +GDRI+ EK SY+FR PS+ DIV F+AP   Q 
Sbjct: 195 LTVSVLFRSSLAEPRSIPSSSMYPTLDVGDRILAEKVSYFFRRPSVSDIVIFKAPPILQK 254

Query: 99  PGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYV 158
            G    DVFIKRIVAKAGD V+VRDG L VNG+AQNE FI E   Y  D   VP GYV+V
Sbjct: 255 IGYKSNDVFIKRIVAKAGDCVEVRDGKLLVNGVAQNEKFILEPLSYNMDPVLVPEGYVFV 314

Query: 159 LGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS 192
           LGDNRNNSFDSH WGPLPV+NI GR + R + PS
Sbjct: 315 LGDNRNNSFDSHNWGPLPVENIVGRSVFRYWPPS 348

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	194
TAIR|locus:2064337	340	TPP "thylakoid processing pept	0.783	0.447	0.547	8.4e-42
TAIR|locus:2091717	291	PLSP1 "plastidic type i signal	0.783	0.522	0.551	2.6e-40
TAIR|locus:2033108	367	Plsp2A "plastidic type I signa	0.783	0.414	0.545	9.9e-39
TIGR_CMR|DET_1192	192	DET_1192 "signal peptidase I"	0.711	0.718	0.362	5.3e-17
TIGR_CMR|SO_2924	220	SO_2924 "signal peptidase I fa	0.608	0.536	0.330	8.9e-16
TIGR_CMR|CHY_1360	184	CHY_1360 "signal peptidase I"	0.716	0.755	0.277	2e-15
TIGR_CMR|BA_3977	183	BA_3977 "signal peptidase I S"	0.695	0.737	0.343	1.1e-14
TIGR_CMR|BA_1140	187	BA_1140 "signal peptidase I" [	0.793	0.823	0.327	3e-14
TIGR_CMR|ECH_0690	235	ECH_0690 "signal peptidase I"	0.474	0.391	0.361	1.2e-13
UNIPROTKB|Q47WP4	310	lepB3 "Signal peptidase I" [Co	0.469	0.293	0.37	1.3e-12

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

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 86/157 (54%), Positives = 108/157 (68%)

Query:    41 ILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAP---FQ 97
             + + +L  S  +E + IPS+SMYPTL  GDR++ EK SY+FR P + DIV F+AP    +
Sbjct:   164 VTVSILFRSALAEPKSIPSTSMYPTLDKGDRVMAEKVSYFFRKPEVSDIVIFKAPPILLE 223

Query:    98 YP--GLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGY 155
             YP  G    DVFIKRIVA  GD V+VRDG L+VN I Q EDF+ E   Y  +  +VP GY
Sbjct:   224 YPEYGYSSNDVFIKRIVASEGDWVEVRDGKLFVNDIVQEEDFVLEPMSYEMEPMFVPKGY 283

Query:   156 VYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS 192
             V+VLGDNRN SFDSH WGPLP++NI GR + R + PS
Sbjct:   284 VFVLGDNRNKSFDSHNWGPLPIENIVGRSVFRYWPPS 320

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 = 429 (156.1 bits), Expect = 2.6e-40, P = 2.6e-40
 Identities = 85/154 (55%), Positives = 106/154 (68%)

Query:    41 ILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAP--FQY 98
             I + L      +E R+IPS SMYPT  +GDR++ EK SYYFR P  +DIV F++P   Q 
Sbjct:   122 IAVSLAFRYFIAEPRYIPSLSMYPTFDVGDRLVAEKVSYYFRKPCANDIVIFKSPPVLQE 181

Query:    99 PGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYV 158
              G  + DVFIKRIVAK GDLV+V +G L VNG+A+NE FI E P Y      VP   V+V
Sbjct:   182 VGYTDADVFIKRIVAKEGDLVEVHNGKLMVNGVARNEKFILEPPGYEMTPIRVPENSVFV 241

Query:   159 LGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS 192
             +GDNRNNS+DSHVWGPLP+KNI GR + R + P+
Sbjct:   242 MGDNRNNSYDSHVWGPLPLKNIIGRSVFRYWPPN 275

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

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

 Score = 414 (150.8 bits), Expect = 9.9e-39, P = 9.9e-39
 Identities = 84/154 (54%), Positives = 102/154 (66%)

Query:    41 ILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAP--FQY 98
             + + LL  S  +E + IPS+SM PTL +GDR+I EK SY+FR P + DIV F+AP     
Sbjct:   194 VTVSLLFRSALAEPKSIPSTSMLPTLDVGDRVIAEKVSYFFRKPEVSDIVIFKAPPILVE 253

Query:    99 PGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYV 158
              G    DVFIKRIVA  GD V+V DG L VN   Q EDF+ E   Y  +  +VP GYV+V
Sbjct:   254 HGYSCADVFIKRIVASEGDWVEVCDGKLLVNDTVQAEDFVLEPIDYEMEPMFVPEGYVFV 313

Query:   159 LGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS 192
             LGDNRN SFDSH WGPLP+KNI GR + R + PS
Sbjct:   314 LGDNRNKSFDSHNWGPLPIKNIIGRSVFRYWPPS 347

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

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

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 54/149 (36%), Positives = 84/149 (56%)

Query:    41 ILIGLLLWSTFSEIRF----IPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPF 96
             IL+ L+++   S++      +  SSM PTL+   R++V K +Y F  P   DI+ F  P 
Sbjct:    23 ILVALVIFG-ISKVTLSYSIVDGSSMDPTLKDEQRLLVNKLAYLFGEPQRGDIIVFPPPE 81

Query:    97 QYPGLGEEDVFIKRIVAKAGDLVQVR-DGSLYVNGIAQNEDFIAEHPK-YTSDLTYVPVG 154
             QY     E+ FIKRI+   GD V+V+ DG++Y+N    +E ++  +PK + +   YVP G
Sbjct:    82 QY---SYENDFIKRIIGLPGDSVEVKEDGTVYINDQPLSEPYVV-YPKAFPTTKVYVPEG 137

Query:   155 YVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
               YV+GDNR  S DS     +  ++I G+
Sbjct:   138 QYYVMGDNRVVSLDSRYGFFVAREDIVGK 166

GO:0009306 "protein secretion" evidence=ISS

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

 Score = 141 (54.7 bits), Expect = 8.9e-16, Sum P(2) = 8.9e-16
 Identities = 44/133 (33%), Positives = 65/133 (48%)

Query:    37 GSLKILIGLLLW--STFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIH-DIVTFR 93
             GS  + I L+L   S  ++   +P+ SM PT+  GDRI+V K +Y  R P  H  +V   
Sbjct:    13 GSFLLFISLMLVFRSAVADWNTVPTGSMLPTIVEGDRILVNKMAYDVRVPFTHIALVKLA 72

Query:    94 APFQ-----YPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDL 148
              P +     +     +   IKR++A  GD V +RD  LY+NG     + +A  P+  S  
Sbjct:    73 DPVRGDIVVFDSKNADKRLIKRVIAVPGDTVMMRDNRLYLNG-----EPLAYKPQALSP- 126

Query:   149 TYVPVGYVYVLGD 161
              Y P G V +  D
Sbjct:   127 -YAPAGVVEMQED 138

GO:0006508 "proteolysis" evidence=ISS

GO:0009306 "protein secretion" evidence=ISS

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

 Score = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 40/144 (27%), Positives = 79/144 (54%)

Query:    41 ILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPG 100
             +++  ++ +   ++ ++P+ SM PT+   DR++V K  Y  +      IV F  P   P 
Sbjct:    30 VILAFIIKTFIFQLTYVPTGSMIPTILPNDRVVVLKFWYKIKPIERGQIVVFD-P---PN 85

Query:   101 LGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTY-VPVGYVYVL 159
                   FIKR++   G+ +++++ ++Y+NG    E+++    +      + +P   ++V+
Sbjct:    86 SANSPPFIKRVIGLPGETLEIKNNTVYINGKPLKENYLPAKMEMEPFGPFKIPKDAIFVM 145

Query:   160 GDNRNNSFDSHVWGPLPVKNIAGR 183
             GDNR +S DS  +G +P+KNI GR
Sbjct:   146 GDNRQHSADSRYFGAVPIKNIKGR 169

GO:0006465 "signal peptide processing" evidence=ISS

GO:0009306 "protein secretion" evidence=ISS

TIGR_CMR|BA_3977 BA_3977 "signal peptidase I S" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 187 (70.9 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 54/157 (34%), Positives = 79/157 (50%)

Query:    41 ILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPG 100
             +L G++    F+ I  +   SM  TL   DR+IV K  Y+  +P   DI+ FRA      
Sbjct:    20 VLAGVIRQFFFAPI-LVDGVSMASTLHDRDRMIVNKIGYHIGDPKRFDIIVFRAT----- 73

Query:   101 LGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSD--LTY-------- 150
               E+  +IKRI+   GD ++ R+  LYVNG A  E ++ +  K  +D  LTY        
Sbjct:    74 --EDKDYIKRIIGLPGDEIEYRNDKLYVNGKAYEEPYLDKQKKQIADGPLTYDFTLEEMT 131

Query:   151 ----VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
                 VP G ++VLGDNR  S DS   G + +  + G+
Sbjct:   132 GKKTVPEGQLFVLGDNRRFSKDSRSIGTISMDQVIGK 168

GO:0006508 "proteolysis" evidence=ISS

GO:0009306 "protein secretion" evidence=ISS

TIGR_CMR|BA_1140 BA_1140 "signal peptidase I" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 183 (69.5 bits), Expect = 3.0e-14, P = 3.0e-14
 Identities = 59/180 (32%), Positives = 91/180 (50%)

Query:    30 LRWPGLDGSLKILIGLLLWSTFSEIRF----IPSSSMYPTLRIGDRIIVEKASYYFRNPS 85
             L+  G++    ILIG+LL   F    F    +   SM PTL+ G+ ++V K SY+  + +
Sbjct:     5 LKKEGIEWIRTILIGVLLAVFFRTFFFSTYVVEGKSMMPTLQDGNMLVVNKVSYHVGDLN 64

Query:    86 IHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPK-- 143
               D+V F A        +ED ++KRI+   GD ++ +   LYVNG   +E ++  + K  
Sbjct:    65 RFDVVVFHAN------KKED-YVKRIIGLPGDHIEYKHDKLYVNGQFVDEPYLETYKKEI 117

Query:   144 ----YTSD-----LTY---VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRP 191
                  T D     LT    VP GY++V+GDNR  S+DS  +G +    + G+   R Y P
Sbjct:   118 DGRQLTGDFKLEELTKEKSVPPGYIFVVGDNRLGSWDSRHFGFVKADTVVGKVDLR-YWP 176

GO:0006508 "proteolysis" evidence=ISS

GO:0009306 "protein secretion" evidence=ISS

TIGR_CMR|ECH_0690 ECH_0690 "signal peptidase I" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 121 (47.7 bits), Expect = 1.2e-13, Sum P(2) = 1.2e-13
 Identities = 38/105 (36%), Positives = 52/105 (49%)

Query:    39 LKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIH---DIVTFRAP 95
             L +++ LLL     E   IPS SM  TL +GD I + K SY +   SI     I+  R  
Sbjct:    16 LALVVALLLRVFLFEPFHIPSGSMKSTLLVGDYIFISKYSYGYSKHSIPFSLPIIKGRIF 75

Query:    96 FQYPGLGEEDVF----------IKRIVAKAGDLVQVRDGSLYVNG 130
              + P  G+  VF          IKR++   GD +Q+ DG LY+NG
Sbjct:    76 SKLPKAGDVVVFRPPKEMNLHYIKRVIGVPGDKIQLIDGFLYING 120

GO:0009306 "protein secretion" evidence=ISS

UNIPROTKB|Q47WP4 lepB3 "Signal peptidase I" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 125 (49.1 bits), Expect = 1.3e-12, Sum P(2) = 1.3e-12
 Identities = 37/100 (37%), Positives = 51/100 (51%)

Query:    45 LLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSI-HDIVTFRAP-------F 96
             L+L S   E   IPS SM PTL  GD I+V K +Y  ++P + H  +    P       F
Sbjct:    79 LILRSFLYEPFQIPSGSMMPTLLDGDFILVNKFNYGLKDPVLRHKFIENGLPEHGDVVVF 138

Query:    97 QYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNED 136
             +YP   + D FIKR++   GD +  R+ SLY+    Q  D
Sbjct:   139 KYPQDPKVD-FIKRVIGLPGDRIIYRNKSLYIKRACQESD 177

GO:0009306 "protein secretion" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.21	0.766
3rd Layer	3.4.21.89	0.824

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	194
TIGR02227	163	TIGR02227, sigpep_I_bact, signal peptidase I, bact	4e-39
cd06530	85	cd06530, S26_SPase_I, The S26 Type I signal peptid	1e-24
COG0681	166	COG0681, LepB, Signal peptidase I [Intracellular t	3e-13
cd06462	84	cd06462, Peptidase_S24_S26, The S24, S26 LexA/sign	2e-12
pfam00717	69	pfam00717, Peptidase_S24, Peptidase S24-like	3e-11
PRK10861	324	PRK10861, PRK10861, signal peptidase I; Provisiona	6e-08
pfam10502	138	pfam10502, Peptidase_S26, Signal peptidase, peptid	1e-07
TIGR02771	171	TIGR02771, TraF_Ti, conjugative transfer signal pe	2e-07
TIGR02754	90	TIGR02754, sod_Ni_protease, nickel-type superoxide	2e-06
PRK10861	324	PRK10861, PRK10861, signal peptidase I; Provisiona	1e-05

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

 Score =  131 bits (331), Expect = 4e-39
 Identities = 57/158 (36%), Positives = 86/158 (54%), Gaps = 14/158 (8%)

Query: 41  ILIGLLLWSTF-SEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYP 99
            ++  LL  TF      +P  SM PTL+ GDRI+V K +Y   +P   DIV F+ P    
Sbjct: 8   AILLALLIRTFVFFPYKVPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPDD-- 65

Query: 100 GLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEH-PKYTSDLTY-------V 151
               ++++IKR++   GD V+ RDG LY+NG   +E ++  +    TS+          V
Sbjct: 66  ---NKNIYIKRVIGLPGDKVEFRDGKLYINGKKIDEPYLKPNGFLDTSEFNTTDYGPVTV 122

Query: 152 PVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY 189
           P G+ +VLGDNR+NS DS  +G +P+ +I G+     Y
Sbjct: 123 PPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFVFY 160

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 = 91.5 bits (228), Expect = 1e-24
 Identities = 40/131 (30%), Positives = 53/131 (40%), Gaps = 47/131 (35%)

Query: 53  EIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIV 112
           E   +P  SM PTL+ GD ++V K SY FR P   D+V F++P            IKR++
Sbjct: 1   EPVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGD-----PGKPIIKRVI 55

Query: 113 AKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVW 172
                                                       +VLGDNRNNS DS  W
Sbjct: 56  G------------------------------------------YFVLGDNRNNSLDSRYW 73

Query: 173 GPLPVKNIAGR 183
           GP+P  +I G+
Sbjct: 74  GPVPEDDIVGK 84

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

 Score = 64.2 bits (156), Expect = 3e-13
 Identities = 43/149 (28%), Positives = 61/149 (40%), Gaps = 25/149 (16%)

Query: 41  ILIGLLLWSTFSEIRF------IPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRA 94
           +LI ++L        F      +PS SM PTL +GDR++V+K SY F    + DI+   A
Sbjct: 14  LLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVLPA 73

Query: 95  PFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVG 154
                    E   IKR++   GD+V  +D  LYV             P        V   
Sbjct: 74  VV-------EGDLIKRVIGLRGDIVVFKDDRLYVV------------PIIPRVYGLVEKD 114

Query: 155 YVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
               L D   N+  S V+G +  K+   R
Sbjct: 115 NGKHLVDVIVNANSSRVFGIITKKDYIKR 143

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 = 59.6 bits (145), Expect = 2e-12
 Identities = 33/127 (25%), Positives = 51/127 (40%), Gaps = 48/127 (37%)

Query: 57  IPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAG 116
           +   SM PT+  GD ++V+K+SY  +     DIV FR P         ++ +KR++   G
Sbjct: 5   VEGDSMEPTIPDGDLVLVDKSSYEPKR---GDIVVFRLP-------GGELTVKRVIGLPG 54

Query: 117 DLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLP 176
           +                                    G+ ++LGDN  NS DS + GP P
Sbjct: 55  E------------------------------------GHYFLLGDN-PNSPDSRIDGP-P 76

Query: 177 VKNIAGR 183
             +I G 
Sbjct: 77  ELDIVGV 83

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 = 56.5 bits (137), Expect = 3e-11
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 15/78 (19%)

Query: 57  IPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAG 116
           +   SM PT+  GD ++V+K S   R     DIV  R          E+  +KR++   G
Sbjct: 2   VKGDSMEPTIPDGDLLLVDKTSEPKRG----DIVVARLD-------GEEATVKRLIGLPG 50

Query: 117 DLVQVR----DGSLYVNG 130
           D++ +        +Y+NG
Sbjct: 51  DIILLPSNPEYPPIYING 68

Length = 69

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

 Score = 51.2 bits (123), Expect = 6e-08
 Identities = 31/75 (41%), Positives = 39/75 (52%), Gaps = 17/75 (22%)

Query: 57  IPSSSMYPTLRIGDRIIVEKASYYFRNPSIH------------DIVTFRAPFQYPGLGEE 104
           IPS SM PTL IGD I+VEK +Y  ++P               DIV F+    YP   + 
Sbjct: 87  IPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFK----YPEDPKL 142

Query: 105 DVFIKRIVAKAGDLV 119
           D +IKR+V   GD V
Sbjct: 143 D-YIKRVVGLPGDKV 156

Length = 324

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 28/115 (24%), Positives = 49/115 (42%), Gaps = 15/115 (13%)

Query: 82  RNPSIHDIVTFRAP-------FQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQN 134
             P + D+V    P        +   L      +KR++A  G  V +RDG + ++G+  +
Sbjct: 20  DRPEVGDLVAVCPPEPAAFFAAERGYLPRGVPLLKRVLALPGQRVCIRDGLVTIDGVPVS 79

Query: 135 EDFIAEHPKYTSDLTY------VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
                E  +    L        +P G ++++     +SFDS  +GP+P   I GR
Sbjct: 80  A--ALERDRKGRPLPPWQGCRVLPEGELFLMSVTSPDSFDSRYFGPVPASAIIGR 132

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

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

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 32/160 (20%), Positives = 50/160 (31%), Gaps = 24/160 (15%)

Query: 41  ILIGLLLWSTFSEIRFIPSSSMYP--TLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQY 98
            L GL +   +     I ++   P           VE+  Y    P           F+ 
Sbjct: 12  ALSGLTILGLYCVGARINTTKSLPLGLYWTTSSKPVERGDYVVFCPP------DNPQFEE 65

Query: 99  PGL----------GEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDL 148
                        G     +KR++   GD V VR   + +NG                 L
Sbjct: 66  ARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRPL 125

Query: 149 -----TYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
                  +P G+  V   +   SFDS  +GP+  + + GR
Sbjct: 126 PPFPEGVIPPGFFVVHDTS-PTSFDSRYFGPISREQVIGR 164

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

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

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 39/123 (31%), Positives = 46/123 (37%), Gaps = 42/123 (34%)

Query: 61  SMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ 120
           SM PTL  GDRIIV      FR P I ++V  R P Q  GL      IKR       L  
Sbjct: 7   SMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGL-----IIKR-------LAA 54

Query: 121 VRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNI 180
           V D  L                              ++LGDN   S DS   GP+P   +
Sbjct: 55  VDDNGL------------------------------FLLGDNPKASTDSRQLGPVPRSLL 84

Query: 181 AGR 183
            G+
Sbjct: 85  LGK 87

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

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

 Score = 44.7 bits (106), Expect = 1e-05
 Identities = 16/33 (48%), Positives = 23/33 (69%)

Query: 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
           VP G  +++GDNR+NS DS  WG +P  N+ G+
Sbjct: 264 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGK 296

Length = 324

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	194
TIGR02227	163	sigpep_I_bact signal peptidase I, bacterial type.	100.0
PRK10861	324	signal peptidase I; Provisional	100.0
KOG0171	176	consensus Mitochondrial inner membrane protease, s	100.0
PRK13838	176	conjugal transfer pilin processing protease TraF;	99.97
PRK13884	178	conjugal transfer peptidase TraF; Provisional	99.97
TIGR02771	171	TraF_Ti conjugative transfer signal peptidase TraF	99.97
PF10502	138	Peptidase_S26: Signal peptidase, peptidase S26 ; I	99.96
KOG1568	174	consensus Mitochondrial inner membrane protease, s	99.95
COG4959	173	TraF Type IV secretory pathway, protease TraF [Pos	99.86
TIGR02754	90	sod_Ni_protease nickel-type superoxide dismutase m	99.86
cd06530	85	S26_SPase_I The S26 Type I signal peptidase (SPase	99.82
TIGR02228	158	sigpep_I_arch signal peptidase I, archaeal type. T	99.7
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	99.59
PF00717	70	Peptidase_S24: Peptidase S24-like peptidase classi	99.35
cd06462	84	Peptidase_S24_S26 The S24, S26 LexA/signal peptida	99.17
COG2932	214	Predicted transcriptional regulator [Transcription	98.82
cd06529	81	S24_LexA-like Peptidase S24 LexA-like proteins are	98.74
KOG3342	180	consensus Signal peptidase I [Intracellular traffi	98.74
PRK10276	139	DNA polymerase V subunit UmuD; Provisional	98.53
PRK00215	205	LexA repressor; Validated	98.38
PRK12423	202	LexA repressor; Provisional	98.34
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	98.34
COG1974	201	LexA SOS-response transcriptional repressors (RecA	97.25
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	92.89

>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type

Probab=100.00  E-value=8.8e-44  Score=278.15  Aligned_cols=151  Identities=36%  Similarity=0.590  Sum_probs=133.6

Q ss_pred             HHHHHHHHHHHHHhcceEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCC
Q 029367           37 GSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAG  116 (194)
Q Consensus        37 ~~~~l~~~~li~~~~~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpG  116 (194)
                      .+++++++++++.++++.+.|+|+||+|||++||+++++|..+...++++||+|+|+.|.     ..++.++|||+|+||
T Consensus         5 ~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~-----~~~~~~iKRVig~pG   79 (163)
T TIGR02227         5 LLIAILLALLIRTFVFFPYKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPD-----DNKNIYVKRVIGLPG   79 (163)
T ss_pred             HHHHHHHHHHHHhhEEEEEEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCC-----CCCceeEEEEEecCC
Confidence            344556667888899999999999999999999999999998777899999999999876     356789999999999


Q ss_pred             CeEEEeCCEEEECCEEcccchhccCCC--------CCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEE
Q 029367          117 DLVQVRDGSLYVNGIAQNEDFIAEHPK--------YTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRC  188 (194)
Q Consensus       117 D~V~i~~~~v~vnG~~~~~~~~~~~~~--------~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~  188 (194)
                      |+|++++++++|||+.++++|......        ....+.+||+|+||++|||+++|+||||||+|++++|+|||.+++
T Consensus        80 d~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk~~~~~  159 (163)
T TIGR02227        80 DKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFVF  159 (163)
T ss_pred             CEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEEEEEEE
Confidence            999999999999999999987654311        224467999999999999999999999999999999999999999


Q ss_pred             eCCC
Q 029367          189 YRPS  192 (194)
Q Consensus       189 ~p~~  192 (194)
                      ||.+
T Consensus       160 ~p~~  163 (163)
T TIGR02227       160 YPFD  163 (163)
T ss_pred             CCCC
Confidence            9975

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

>PRK10861 signal peptidase I; Provisional

Probab=100.00  E-value=1.7e-38  Score=270.40  Aligned_cols=151  Identities=33%  Similarity=0.425  Sum_probs=125.9

Q ss_pred             HHHHHHHHHHHHHhcceEEEecCCCcccccCCCCEEEEEeeeecc------------CCCCcceEEEEecCCCCCCCCCC
Q 029367           37 GSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYF------------RNPSIHDIVTFRAPFQYPGLGEE  104 (194)
Q Consensus        37 ~~~~l~~~~li~~~~~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~------------~~~~rGDiVvf~~p~~~~~~~~~  104 (194)
                      .+++++++++++.|+++.+.|+|.||+|||..||+++++|++|..            ++|+|||||+|+.|.     +++
T Consensus        67 ~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~-----~~~  141 (324)
T PRK10861         67 VFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPE-----DPK  141 (324)
T ss_pred             HHHHHhHHHHHHhhEEEEEEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCC-----CCC
Confidence            344556678888999999999999999999999999999998753            578999999999987     367


Q ss_pred             ceEEEEEEEeCCCeEEEe--CCEEEECCEEcccch-----------------hc--------------------------
Q 029367          105 DVFIKRIVAKAGDLVQVR--DGSLYVNGIAQNEDF-----------------IA--------------------------  139 (194)
Q Consensus       105 ~~~vKRVvglpGD~V~i~--~~~v~vnG~~~~~~~-----------------~~--------------------------  139 (194)
                      ..+||||+|+|||+|+++  ++++||||+.+...+                 ..                          
T Consensus       142 ~~yIKRVIGlPGD~I~~~~~~~~l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (324)
T PRK10861        142 LDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETKENG  221 (324)
T ss_pred             CcEEEEeeecCCcEEEEEeCCCEEEEcCcccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            889999999999999997  899999997421110                 00                          


Q ss_pred             ---c---------------CCC-------------CCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEE
Q 029367          140 ---E---------------HPK-------------YTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRC  188 (194)
Q Consensus       140 ---~---------------~~~-------------~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~  188 (194)
                         .               .+.             ....+++||+|+||++|||+++|+||||||+||+++|+|||.++|
T Consensus       222 ~~~~~~~E~l~~~~h~i~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G~a~~i~  301 (324)
T PRK10861        222 IRLSERKETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKATAIW  301 (324)
T ss_pred             ccceeEEEecCCccceeeecCCcccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEEEEEEEE
Confidence               0               000             012467999999999999999999999999999999999999999


Q ss_pred             eCCC
Q 029367          189 YRPS  192 (194)
Q Consensus       189 ~p~~  192 (194)
                      ++.+
T Consensus       302 ~s~d  305 (324)
T PRK10861        302 MSFE  305 (324)
T ss_pred             EEcC
Confidence            9875

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

Probab=100.00  E-value=4.1e-34  Score=218.43  Aligned_cols=144  Identities=42%  Similarity=0.622  Sum_probs=122.3

Q ss_pred             hhHHHHHHHHHHHHHhcceEEEecCCCcccccCCC-CEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367           35 LDGSLKILIGLLLWSTFSEIRFIPSSSMYPTLRIG-DRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA  113 (194)
Q Consensus        35 ~~~~~~l~~~~li~~~~~~~~~V~~~SM~Ptl~~G-d~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg  113 (194)
                      ......+.++.+...++.+....+|.||+||++++ |+++..|+.+.++++++||+|++..|.     .+.+.++|||+|
T Consensus        16 ~~~~~~~~f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~-----~~~~~~cKRIva   90 (176)
T KOG0171|consen   16 CSEIAYAAFTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPP-----DPKEHICKRIVA   90 (176)
T ss_pred             HHHHHHHHHHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCC-----Cchhhhhheeec
Confidence            33444455556666788899999999999988764 566569999999999999999999988     477889999999


Q ss_pred             eCCCeEEEeCCEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCCC
Q 029367          114 KAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPSD  193 (194)
Q Consensus       114 lpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~~  193 (194)
                      +|||.+++.++.+.+|+..  |.+        ..++.||+||+|++|||+++|+|||+|||+|.+.|+||+++++||++.
T Consensus        91 ~eGD~v~v~~~~~~~n~~~--e~~--------~~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~  160 (176)
T KOG0171|consen   91 MEGDLVEVHDGPLVVNDLV--EKF--------STPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSR  160 (176)
T ss_pred             cCCceEEEecCCcccchhh--hhc--------cceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchh
Confidence            9999999988888777543  221        156899999999999999999999999999999999999999999975

>PRK13838 conjugal transfer pilin processing protease TraF; Provisional

Probab=99.97  E-value=3.1e-30  Score=203.59  Aligned_cols=117  Identities=20%  Similarity=0.218  Sum_probs=93.1

Q ss_pred             EEEEEeeeeccCCCCcceEEEEecCCCC--------CCCCC------CceEEEEEEEeCCCeEEEeCCEEEECCEEcccc
Q 029367           71 RIIVEKASYYFRNPSIHDIVTFRAPFQY--------PGLGE------EDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNED  136 (194)
Q Consensus        71 ~vlv~k~~~~~~~~~rGDiVvf~~p~~~--------~~~~~------~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~  136 (194)
                      -+.+.+..+..+++++||+|+|+.|.+.        .++..      ...++|||+|+|||+|++++ +++|||+.++++
T Consensus        38 pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~-~v~iNg~~~~~~  116 (176)
T PRK13838         38 PLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGG-SVSIDGRPLPSS  116 (176)
T ss_pred             EEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECC-EEEECCEEcccc
Confidence            3566666554578999999999987642        11111      24699999999999999985 899999999998


Q ss_pred             hhccCCCC-----CCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367          137 FIAEHPKY-----TSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY  189 (194)
Q Consensus       137 ~~~~~~~~-----~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~  189 (194)
                      |.......     .....+||+|+|||+|||. +|+||||||+|++++|+|+|.++|.
T Consensus       117 ~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~-~S~DSRy~G~V~~~~I~G~a~pi~t  173 (176)
T PRK13838        117 SVRRRDGEGRPLTPFPGGVVPPGHLFLHSSFA-GSYDSRYFGPVPASGLLGLARPVLT  173 (176)
T ss_pred             ccccccccCCcCCCCCccCcCCCeEEEECCCC-CCCcccccCcccHHHeEEEEEEEEe
Confidence            76543221     1234689999999999985 8999999999999999999999875

>PRK13884 conjugal transfer peptidase TraF; Provisional

Probab=99.97  E-value=3.7e-29  Score=197.90  Aligned_cols=128  Identities=21%  Similarity=0.244  Sum_probs=97.0

Q ss_pred             ceEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCC--------CCCC----CCC--ceEEEEEEEeCCC
Q 029367           52 SEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQ--------YPGL----GEE--DVFIKRIVAKAGD  117 (194)
Q Consensus        52 ~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~--------~~~~----~~~--~~~vKRVvglpGD  117 (194)
                      .......++||.    .|=+.+ ..     ..+++||+|+|++|..        +.+.    +++  .+++|||+|+|||
T Consensus        29 ~~~~~N~T~S~P----~glY~~-~~-----~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD   98 (178)
T PRK13884         29 AGARVNTTKSIP----VGLYWT-SS-----APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGD   98 (178)
T ss_pred             CcEEEECCCCCc----ceEEEE-eC-----CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCc
Confidence            344555677764    333333 21     5789999999998773        2222    222  4799999999999


Q ss_pred             eEEEeCCEEEECCEEcccchh--ccC-----CCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367          118 LVQVRDGSLYVNGIAQNEDFI--AEH-----PKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY  189 (194)
Q Consensus       118 ~V~i~~~~v~vnG~~~~~~~~--~~~-----~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~  189 (194)
                      +|+++++.++|||+.+++...  .+.     +......++||+|+||++|||+++|+||||||+|++++|+|+|.++++
T Consensus        99 ~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~Pl~t  177 (178)
T PRK13884         99 AVSVTDDGVRVNGELLPLSKPILADGAGRPLPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRPVIT  177 (178)
T ss_pred             EEEEECCEEEECCEEccccccccccccCCcccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEEeEe
Confidence            999999999999999865432  221     122233469999999999999999999999999999999999999874

>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF

Probab=99.97  E-value=3e-29  Score=197.29  Aligned_cols=127  Identities=24%  Similarity=0.267  Sum_probs=97.6

Q ss_pred             eEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCC--------CCCCCC------ceEEEEEEEeCCCe
Q 029367           53 EIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQY--------PGLGEE------DVFIKRIVAKAGDL  118 (194)
Q Consensus        53 ~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~--------~~~~~~------~~~vKRVvglpGD~  118 (194)
                      ......++||..    |-+. +.+.    ++++|||+|+|+.|.+.        .++..+      ..++|||+|+|||+
T Consensus        25 ~~~~N~T~S~P~----g~Y~-~~~~----~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~   95 (171)
T TIGR02771        25 GARINTTKSLPL----GLYW-TTSS----KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDR   95 (171)
T ss_pred             eEEEECCCCCcc----eEEE-eCCC----CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCE
Confidence            344566777754    4344 3222    68999999999987631        112222      38999999999999


Q ss_pred             EEEeCCEEEECCEEcccchhccCC-----CCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367          119 VQVRDGSLYVNGIAQNEDFIAEHP-----KYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY  189 (194)
Q Consensus       119 V~i~~~~v~vnG~~~~~~~~~~~~-----~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~  189 (194)
                      |+++++.++|||+.+++.+.....     .....+.+||+| ||++|||+++|+||||||+|++++|+|||.++|.
T Consensus        96 V~i~~~~v~INg~~~~~~~~~~~~~~g~~l~~~~~~~vp~g-yf~lgdn~~~S~DSRy~G~V~~~~IiGk~~pl~~  170 (171)
T TIGR02771        96 VTVRADVVAINGQLLPYSKPLATDSSGRPLPPFPEGVIPPG-FFVVHDTSPTSFDSRYFGPISREQVIGRVKPLFT  170 (171)
T ss_pred             EEEECCEEEECCEEcccccccccccCCCccccCCCcEECCC-EEEECCCCCCCCcccccceecHHHeEEEEEEeEe
Confidence            999999999999999876543211     112347899999 9999999999999999999999999999999874

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

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

Probab=99.96  E-value=1.8e-30  Score=197.78  Aligned_cols=108  Identities=37%  Similarity=0.540  Sum_probs=34.4

Q ss_pred             CCCCcceEEEEecCCC-------CCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEcccchhccCCCCC----Cceee
Q 029367           82 RNPSIHDIVTFRAPFQ-------YPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYT----SDLTY  150 (194)
Q Consensus        82 ~~~~rGDiVvf~~p~~-------~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~----~~~~~  150 (194)
                      ..+++||+|+|+.|..       +.+...+..++|||+|+|||+|++++++++|||+.+.+.+..+..+..    ..+.+
T Consensus        20 ~~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~   99 (138)
T PF10502_consen   20 DKIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGT   99 (138)
T ss_dssp             ---------------------------------------------------------------------S-T----TEEE
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceE
Confidence            3489999999999873       334556789999999999999999999999999998887765443322    25789


Q ss_pred             ecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367          151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY  189 (194)
Q Consensus       151 vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~  189 (194)
                      ||+|+||++|||+++|+||||||+|++++|+|||.++|+
T Consensus       100 vp~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~t  138 (138)
T PF10502_consen  100 VPEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLWT  138 (138)
T ss_dssp             --TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEEE
T ss_pred             eCCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEEC
Confidence            999999999999999999999999999999999999985

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.

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

Probab=99.95  E-value=7.7e-28  Score=183.71  Aligned_cols=118  Identities=32%  Similarity=0.497  Sum_probs=103.7

Q ss_pred             hcceEEEecCCCcccccCCC------CEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeC
Q 029367           50 TFSEIRFIPSSSMYPTLRIG------DRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRD  123 (194)
Q Consensus        50 ~~~~~~~V~~~SM~Ptl~~G------d~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~  123 (194)
                      .+.....|.|+||.||++++      |+|++.|+.-....+.+||+|+|..|.     ++++++||||+|+|||++...+
T Consensus        29 rV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~-----~p~~~~iKRv~alegd~~~t~~  103 (174)
T KOG1568|consen   29 RVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPN-----DPDKVIIKRVAALEGDIMVTED  103 (174)
T ss_pred             eEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCC-----ChhheeeeeeecccccEeccCC
Confidence            34566788999999999875      899999987554568999999999998     5899999999999999987632


Q ss_pred             CEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCC
Q 029367          124 GSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS  192 (194)
Q Consensus       124 ~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~  192 (194)
                                          .....+.+|+||+||.|||...|+|||.||||+...|.|||+.++|||.
T Consensus       104 --------------------~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~  152 (174)
T KOG1568|consen  104 --------------------EKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPV  152 (174)
T ss_pred             --------------------CCCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChH
Confidence                                2245678999999999999999999999999999999999999999985

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

Probab=99.86  E-value=1.1e-21  Score=148.64  Aligned_cols=108  Identities=20%  Similarity=0.283  Sum_probs=94.6

Q ss_pred             CCCCcceEEEEecCCC-------CCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEcccchhccCCCCC----Cceee
Q 029367           82 RNPSIHDIVTFRAPFQ-------YPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYT----SDLTY  150 (194)
Q Consensus        82 ~~~~rGDiVvf~~p~~-------~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~~~~~~~~~~~----~~~~~  150 (194)
                      ..+.+||+|++++|..       +.+++...+++|||.|+|||+|++..+.+.|||+.++.....+..+..    .++..
T Consensus        52 ~Pvt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~  131 (173)
T COG4959          52 APVTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRY  131 (173)
T ss_pred             CCcccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCce
Confidence            3459999999999983       667888999999999999999999999999999999877666554443    33456


Q ss_pred             ecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEe
Q 029367          151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCY  189 (194)
Q Consensus       151 vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~  189 (194)
                      +.++++|+|+|..+.||||||||||+.++|+|.+.++|+
T Consensus       132 l~~~el~lL~~~~~~SfDsRYfGpipas~vig~aRPvwt  170 (173)
T COG4959         132 LAPSELLLLTDRSSTSFDSRYFGPIPASQVIGVARPVWT  170 (173)
T ss_pred             ecCCeEEEEeccCCcccccceecccCHHHcceeeeeeec
Confidence            899999999999999999999999999999999999886

>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease

Probab=99.86  E-value=3e-21  Score=136.41  Aligned_cols=89  Identities=38%  Similarity=0.534  Sum_probs=76.2

Q ss_pred             EecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEccc
Q 029367           56 FIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNE  135 (194)
Q Consensus        56 ~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~  135 (194)
                      .|.|+||+|||++||.+++++.......+++||+|+++.|.     .++..++||+++++                    
T Consensus         2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~-----~~~~~~vkRv~~~~--------------------   56 (90)
T TIGR02754         2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPL-----QPYGLIIKRLAAVD--------------------   56 (90)
T ss_pred             EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCC-----CCcceEEEEeeEEc--------------------
Confidence            58999999999999999999854333556789999999875     25689999999863                    


Q ss_pred             chhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEE
Q 029367          136 DFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLT  186 (194)
Q Consensus       136 ~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~  186 (194)
                                       ++++|++|||+..|.|||++|+|+..+|+|||++
T Consensus        57 -----------------~~~~~l~~dN~~~~~d~~~~g~v~~~~I~G~v~~   90 (90)
T TIGR02754        57 -----------------DNGLFLLGDNPKASTDSRQLGPVPRSLLLGKVLW   90 (90)
T ss_pred             -----------------CCeEEEeCCCCCCCCcccccCCCcHHHEEEEEEC
Confidence                             3578999999999999999999999999999964

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

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

Probab=99.82  E-value=5.9e-20  Score=128.26  Aligned_cols=84  Identities=46%  Similarity=0.834  Sum_probs=74.7

Q ss_pred             EEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEc
Q 029367           54 IRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQ  133 (194)
Q Consensus        54 ~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~  133 (194)
                      .+.|.|+||+|++.+||++++++......++++||+|+|+.+..     ++..++|||++                    
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            57899999999999999999998764334799999999999752     46899999996                    


Q ss_pred             ccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEE
Q 029367          134 NEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRY  184 (194)
Q Consensus       134 ~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv  184 (194)
                                            ||+.|||+.+|.|||+||+++.++|+|++
T Consensus        57 ----------------------~~~~gDn~~ns~d~~~~g~~~~~~i~G~~   85 (85)
T cd06530          57 ----------------------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV   85 (85)
T ss_pred             ----------------------EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence                                  89999999899999999999999999985

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

>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type

Probab=99.70  E-value=2.9e-16  Score=122.07  Aligned_cols=85  Identities=29%  Similarity=0.464  Sum_probs=69.1

Q ss_pred             EecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEccc
Q 029367           56 FIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNE  135 (194)
Q Consensus        56 ~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~~~  135 (194)
                      .|.|+||+||+++||.+++++...  .++++||+|+|+.|.      ....++|||+++.++     ++           
T Consensus        35 ~V~g~SM~Ptl~~GD~vlv~~~~~--~~~~~GDIVvf~~~~------~~~~iihRVi~v~~~-----~g-----------   90 (158)
T TIGR02228        35 VVLSGSMEPTFNTGDLILVTGADP--NDIQVGDVITYKSPG------FNTPVTHRVIEINNS-----GG-----------   90 (158)
T ss_pred             EEcCCCCcCCccCCCEEEEEeccc--CCCCCCCEEEEEECC------CCccEEEEEEEEECC-----CC-----------
Confidence            389999999999999999998543  689999999999875      237899999997543     00           


Q ss_pred             chhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEE
Q 029367          136 DFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYL  185 (194)
Q Consensus       136 ~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~  185 (194)
                                       +..|.+.|||+ ...|   .++|+.+||+||+.
T Consensus        91 -----------------~~~~~tkGDnN-~~~D---~~~v~~~~IiG~v~  119 (158)
T TIGR02228        91 -----------------ELGFITKGDNN-PAPD---GEPVPSENVIGKYL  119 (158)
T ss_pred             -----------------cEEEEEEecCC-CCCC---cccCCHHHEEEEEE
Confidence                             12477889997 5556   68999999999997

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

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

Probab=99.59  E-value=1.3e-14  Score=112.44  Aligned_cols=126  Identities=33%  Similarity=0.428  Sum_probs=89.9

Q ss_pred             HHHHHHHH--HHhcceEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCC
Q 029367           40 KILIGLLL--WSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGD  117 (194)
Q Consensus        40 ~l~~~~li--~~~~~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD  117 (194)
                      ++++++++  ..++++.+.|+|+||+||++.||+++++|..+....+..+|++.+  |.     .....++||+++++||
T Consensus        17 ~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~--~~-----~~~~~~~kr~~~~~GD   89 (166)
T COG0681          17 AIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVL--PA-----VVEGDLIKRVIGLRGD   89 (166)
T ss_pred             HHHHhheeeeEEEEEEEEEECCCccccccccCCEEEEEeccccccCCccceeeec--CC-----CCCcceEEEeccCCCC
Confidence            33344444  688899999999999999999999999999988888999998832  32     4678899999999999


Q ss_pred             eEEEeCCEEEECCEEcccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEE
Q 029367          118 LVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRY  184 (194)
Q Consensus       118 ~V~i~~~~v~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv  184 (194)
                      ++.++++..++ +..+++.+..           +..++.++.++....+.+++.++.......+.++
T Consensus        90 ~i~~~~~~~~~-~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (166)
T COG0681          90 IVVFKDDRLYV-VPIIPRVYGL-----------VEKDNGKHLVDVIVNANSSRVFGIITKKDYIKRV  144 (166)
T ss_pred             EEEEECCEEEe-ecccCcchhh-----------hhcccccccccccccccCccccccccccccccce
Confidence            99999999887 3323322211           1111111444555566666766666666666665

>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification

Probab=99.35  E-value=3.2e-12  Score=85.54  Aligned_cols=57  Identities=30%  Similarity=0.579  Sum_probs=47.1

Q ss_pred             EecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEe
Q 029367           56 FIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVR  122 (194)
Q Consensus        56 ~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~  122 (194)
                      +|.|+||+|++++||++++++.    .+++.||+|++..+.      .+..++||+.+.+|+.+.+.
T Consensus         1 ~V~GdSM~P~i~~Gd~v~v~~~----~~~~~gdivv~~~~~------~~~~~iKrv~~~~~~~~~~~   57 (70)
T PF00717_consen    1 RVEGDSMEPTIKDGDIVLVDPS----SEPKDGDIVVVKIDG------DEELYIKRVVGEPGGIILIS   57 (70)
T ss_dssp             EEESSTTGGTSSTTEEEEEEET----S---TTSEEEEEETT------EESEEEEEEEEETTEEEEE-
T ss_pred             CeECcCcccCeeCCCEEEEEEc----CCCccCeEEEEEECC------ceeeEEEEEEEeCCCEEEEe
Confidence            5789999999999999999986    589999999999854      11389999999999999986

; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....

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

Probab=99.17  E-value=3.4e-10  Score=77.71  Aligned_cols=83  Identities=40%  Similarity=0.623  Sum_probs=62.8

Q ss_pred             EEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEEc
Q 029367           54 IRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQ  133 (194)
Q Consensus        54 ~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~~  133 (194)
                      .+.+.|+||+|++.+||.+++++..   ..++.||+|++..+       .+..++||+...++                 
T Consensus         2 ~~~v~g~SM~P~i~~gd~v~i~~~~---~~~~~G~iv~~~~~-------~~~~~ikrl~~~~~-----------------   54 (84)
T cd06462           2 ALRVEGDSMEPTIPDGDLVLVDKSS---YEPKRGDIVVFRLP-------GGELTVKRVIGLPG-----------------   54 (84)
T ss_pred             eeEEcCCCccCcccCCCEEEEEecC---CCCcCCEEEEEEcC-------CCcEEEEEEEEECC-----------------
Confidence            4678999999999999999999863   24899999999984       24899999998654                 


Q ss_pred             ccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEE
Q 029367          134 NEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRY  184 (194)
Q Consensus       134 ~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv  184 (194)
                                         ++++++.+||+ ++.+.+..+. ...+++|++
T Consensus        55 -------------------~~~~~l~~~N~-~~~~~~~~~~-~~~~i~g~v   84 (84)
T cd06462          55 -------------------EGHYFLLGDNP-NSPDSRIDGP-PELDIVGVV   84 (84)
T ss_pred             -------------------CCEEEEECCCC-CCCcccccCC-CHHHEEEeC
Confidence                               25677888884 5555554433 556666653

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

>COG2932 Predicted transcriptional regulator [Transcription]

Probab=98.82  E-value=4.1e-08  Score=79.74  Aligned_cols=56  Identities=23%  Similarity=0.369  Sum_probs=45.3

Q ss_pred             eEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeE
Q 029367           53 EIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLV  119 (194)
Q Consensus        53 ~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V  119 (194)
                      ....|.|+||+|++.+||.++|++-    .+..+||.|++..       ..+..++||+...+|-.+
T Consensus       124 ~~i~V~GDSMeP~~~~Gd~ilVd~~----~~~~~gd~v~v~~-------~g~~~~VK~l~~~~~~~~  179 (214)
T COG2932         124 FALRVTGDSMEPTYEDGDTLLVDPG----VNTRRGDRVYVET-------DGGELYVKKLQREPGGLL  179 (214)
T ss_pred             EEEEEeCCcccccccCCCEEEECCC----CceeeCCEEEEEE-------eCCeEEEEEEEEecCCeE
Confidence            4568999999999999999999886    5678899666665       256899999997666544

>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=98.74  E-value=5.5e-08  Score=66.42  Aligned_cols=56  Identities=27%  Similarity=0.428  Sum_probs=47.1

Q ss_pred             EEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEE
Q 029367           54 IRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQV  121 (194)
Q Consensus        54 ~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i  121 (194)
                      ...+.|+||+|++++||.+++++.    ..++.||++++..+        +..++||+...+++.+.+
T Consensus         2 ~~~v~g~sM~p~i~~gd~lii~~~----~~~~~g~i~~~~~~--------~~~~ikr~~~~~~~~~~L   57 (81)
T cd06529           2 ALRVKGDSMEPTIPDGDLVLVDPS----DTPRDGDIVVARLD--------GELTVKRLQRRGGGRLRL   57 (81)
T ss_pred             EEEEECCCcCCccCCCCEEEEcCC----CCCCCCCEEEEEEC--------CEEEEEEEEECCCCcEEE
Confidence            467899999999999999999986    45999999999983        378999999877655444

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

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

Probab=98.74  E-value=1.6e-08  Score=77.10  Aligned_cols=92  Identities=25%  Similarity=0.333  Sum_probs=65.7

Q ss_pred             eEEEecCCCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEEEECCEE
Q 029367           53 EIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIA  132 (194)
Q Consensus        53 ~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v~vnG~~  132 (194)
                      .+..|-|.||||.++.||.++.....  ....+.||+|+|+.++      ++.++++||+.+-+.    +++        
T Consensus        49 PiVVVLSgSMePaF~RGDlLfL~N~~--~~p~~vGdivVf~veg------R~IPiVHRviK~he~----~~~--------  108 (180)
T KOG3342|consen   49 PIVVVLSGSMEPAFHRGDLLFLTNRN--EDPIRVGDIVVFKVEG------REIPIVHRVIKQHEK----SNG--------  108 (180)
T ss_pred             CEEEEEcCCcCcccccccEEEEecCC--CCcceeccEEEEEECC------ccCchhHHHHHHhcc----cCC--------
Confidence            46788899999999999999987442  2457899999999975      779999999964221    011        


Q ss_pred             cccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCc-c----ccccCCCeeEEEEE
Q 029367          133 QNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHV-W----GPLPVKNIAGRYLT  186 (194)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~-~----G~V~~~~I~Gkv~~  186 (194)
                                          +-.+...|||+  -.|-|- |    -...+++|.|+|.-
T Consensus       109 --------------------~~~~LTKGDNN--~~dD~~Ly~~gq~~L~r~~Ivg~~~G  145 (180)
T KOG3342|consen  109 --------------------HIKFLTKGDNN--AVDDRGLYAQGQNWLERKDIVGRVRG  145 (180)
T ss_pred             --------------------cEEEEecCCCC--cccchhcccccccceeccceeeEEee
Confidence                                11366678884  334442 1    25778999999863

>PRK10276 DNA polymerase V subunit UmuD; Provisional

Probab=98.53  E-value=1.4e-06  Score=66.32  Aligned_cols=49  Identities=24%  Similarity=0.268  Sum_probs=40.5

Q ss_pred             eEEEecCCCcc-cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367           53 EIRFIPSSSMY-PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA  113 (194)
Q Consensus        53 ~~~~V~~~SM~-Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg  113 (194)
                      ...+|.|+||+ |++++||.+++++-    .+++.||+|++..        .+...+||+.-
T Consensus        52 f~l~V~GdSM~~~~I~~GD~liVd~~----~~~~~Gdivv~~~--------~g~~~vKrl~~  101 (139)
T PRK10276         52 YFVKASGDSMIDAGISDGDLLIVDSA----ITASHGDIVIAAV--------DGEFTVKKLQL  101 (139)
T ss_pred             EEEEEecCCCCCCCCCCCCEEEEECC----CCCCCCCEEEEEE--------CCEEEEEEEEE
Confidence            45789999998 68999999999975    4678999999876        34678999874

>PRK00215 LexA repressor; Validated

Probab=98.38  E-value=5.4e-06  Score=66.73  Aligned_cols=50  Identities=22%  Similarity=0.256  Sum_probs=41.6

Q ss_pred             ceEEEecCCCcc-cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367           52 SEIRFIPSSSMY-PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA  113 (194)
Q Consensus        52 ~~~~~V~~~SM~-Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg  113 (194)
                      .....|.|+||. |++.+||++++++.    ..++.||+|++..        .+...+||+.-
T Consensus       118 ~~~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivv~~~--------~~~~~vKrl~~  168 (205)
T PRK00215        118 DFLLRVRGDSMIDAGILDGDLVIVRKQ----QTARNGQIVVALI--------DDEATVKRFRR  168 (205)
T ss_pred             eEEEEEccCCCCCCCcCCCCEEEEeCC----CCCCCCCEEEEEE--------CCEEEEEEEEE
Confidence            456789999995 79999999999874    4678999999987        34789999874

>PRK12423 LexA repressor; Provisional

Probab=98.34  E-value=6.7e-06  Score=66.33  Aligned_cols=49  Identities=24%  Similarity=0.257  Sum_probs=41.1

Q ss_pred             eEEEecCCCcc-cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367           53 EIRFIPSSSMY-PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA  113 (194)
Q Consensus        53 ~~~~V~~~SM~-Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg  113 (194)
                      ....|.|+||. |++.+||+++|++-    ..++.||+|++..        .+...+||+.-
T Consensus       115 f~l~V~GdSM~~~~i~~Gd~viv~~~----~~~~~Gdivv~~~--------~~~~~vKrl~~  164 (202)
T PRK12423        115 YLLQVQGDSMIDDGILDGDLVGVHRS----PEARDGQIVVARL--------DGEVTIKRLER  164 (202)
T ss_pred             EEEEEecCcCCCCCcCCCCEEEEeCC----CcCCCCCEEEEEE--------CCEEEEEEEEE
Confidence            35789999997 79999999999874    5788999999987        34688999874

>TIGR00498 lexA SOS regulatory protein LexA

Probab=98.34  E-value=8.4e-06  Score=65.28  Aligned_cols=50  Identities=22%  Similarity=0.255  Sum_probs=42.0

Q ss_pred             ceEEEecCCCcc-cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367           52 SEIRFIPSSSMY-PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA  113 (194)
Q Consensus        52 ~~~~~V~~~SM~-Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg  113 (194)
                      ...+.|.|+||. |++.+||++++++.    ..++.||+|++..        .+...+||+.-
T Consensus       111 ~f~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~--------~~~~~vKrl~~  161 (199)
T TIGR00498       111 VFLLKVMGDSMVDAGICDGDLLIVRSQ----KDARNGEIVAAMI--------DGEVTVKRFYK  161 (199)
T ss_pred             EEEEEecCCCCCCCCCCCCCEEEEecC----CCCCCCCEEEEEE--------CCEEEEEEEEE
Confidence            457799999996 68999999999865    5789999999987        45789999764

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

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

Probab=97.25  E-value=0.0054  Score=49.55  Aligned_cols=49  Identities=22%  Similarity=0.270  Sum_probs=40.3

Q ss_pred             eEEEecCCCccc-ccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEE
Q 029367           53 EIRFIPSSSMYP-TLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIV  112 (194)
Q Consensus        53 ~~~~V~~~SM~P-tl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVv  112 (194)
                      ...+|.|+||.. .+.+||.++|++.    ...+.||+|+...+       .+..-+||..
T Consensus       113 f~L~V~GdSM~~~gi~dGDlvvV~~~----~~a~~GdiVvA~i~-------g~e~TvKrl~  162 (201)
T COG1974         113 FFLRVSGDSMIDAGILDGDLVVVDPT----EDAENGDIVVALID-------GEEATVKRLY  162 (201)
T ss_pred             EEEEecCCccccCcCCCCCEEEEcCC----CCCCCCCEEEEEcC-------CCcEEEEEEE
Confidence            456899999965 5678999999976    78899999999984       3468899866

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

Probab=92.89  E-value=0.16  Score=38.79  Aligned_cols=29  Identities=31%  Similarity=0.542  Sum_probs=23.6

Q ss_pred             CceEEEEEEEeCCCeEEEeCCEEEECCEE
Q 029367          104 EDVFIKRIVAKAGDLVQVRDGSLYVNGIA  132 (194)
Q Consensus       104 ~~~~vKRVvglpGD~V~i~~~~v~vnG~~  132 (194)
                      ...++||+.++|||.+...+..+.+||+.
T Consensus       137 ~~~~~~~~~~~~gd~~~~~~~~~~~~g~~  165 (166)
T COG0681         137 KKDYIKRVIGLPGDNILYTDDDLPINGKP  165 (166)
T ss_pred             ccccccceEEeeccceeeccCceeecCCC
Confidence            46799999999999999886448787763

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	194
1kn9_A	249	Crystal Structure Of A Bacterial Signal Peptidase A		4e-04
1kn9_A	249	Crystal Structure Of A Bacterial Signal Peptidase A		4e-04
1b12_A	248	Crystal Structure Of Type 1 Signal Peptidase From E		4e-04
1b12_A	248	Crystal Structure Of Type 1 Signal Peptidase From E		4e-04
1t7d_A	250	Crystal Structure Of Escherichia Coli Type I Signal		4e-04
1t7d_A	250	Crystal Structure Of Escherichia Coli Type I Signal		4e-04

>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 = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 38/75 (50%), Gaps = 17/75 (22%)
Query: 57  IPSSSMYPTLRIGDRIIVEKASYYFRNPSIH------------DIVTFRAPFQYPGLGEE 104
           IPS SM PTL IGD I+VEK +Y  ++P               DIV F+ P + P L   
Sbjct: 12  IPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP-EDPKLD-- 68
Query: 105 DVFIKRIVAKAGDLV 119
             +IKR V   GD V
Sbjct: 69  --YIKRAVGLPGDKV 81

>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 = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
           VP G  +++GDNR+NS DS  WG +P  N+ GR
Sbjct: 189 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGR 221

>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 = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 38/75 (50%), Gaps = 17/75 (22%)
Query: 57  IPSSSMYPTLRIGDRIIVEKASYYFRNPSIH------------DIVTFRAPFQYPGLGEE 104
           IPS SM PTL IGD I+VEK +Y  ++P               DIV F+ P + P L   
Sbjct: 11  IPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP-EDPKLD-- 67
Query: 105 DVFIKRIVAKAGDLV 119
             +IKR V   GD V
Sbjct: 68  --YIKRAVGLPGDKV 80

>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 = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
           VP G  +++GDNR+NS DS  WG +P  N+ GR
Sbjct: 188 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGR 220

>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 = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 38/75 (50%), Gaps = 17/75 (22%)
Query: 57  IPSSSMYPTLRIGDRIIVEKASYYFRNPSIH------------DIVTFRAPFQYPGLGEE 104
           IPS SM PTL IGD I+VEK +Y  ++P               DIV F+ P + P L   
Sbjct: 13  IPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYP-EDPKLD-- 69
Query: 105 DVFIKRIVAKAGDLV 119
             +IKR V   GD V
Sbjct: 70  --YIKRAVGLPGDKV 82

>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 = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
           VP G  +++GDNR+NS DS  WG +P  N+ GR
Sbjct: 190 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGR 222

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	194
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	2e-16
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	3e-09

>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 = 73.7 bits (181), Expect = 2e-16
 Identities = 30/94 (31%), Positives = 41/94 (43%), Gaps = 11/94 (11%)

Query: 57  IPSSSMYPTLRIGDRIIVEKASYYFRNPSIHD-IVTFRAP-------FQYPGLGEEDVFI 108
           IPS SM PTL IGD I+VEK +Y  ++P     ++    P       F+YP   + D +I
Sbjct: 11  IPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKLD-YI 69

Query: 109 KRIVAKAGDLVQVR--DGSLYVNGIAQNEDFIAE 140
           KR V   GD V        L +     +      
Sbjct: 70  KRAVGLPGDKVTYDPVSKELTIQPGCSSGQACEN 103

>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 = 53.7 bits (129), Expect = 3e-09
 Identities = 17/33 (51%), Positives = 23/33 (69%)

Query: 151 VPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
           VP G  +++GDNR+NS DS  WG +P  N+ GR
Sbjct: 188 VPPGQYFMMGDNRDNSADSRYWGFVPEANLVGR 220

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	194
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	100.0
1kca_A	109	Repressor protein CI; gene regulation, DNA-binding	99.18
1umu_A	116	UMUD'; induced mutagenesis, SOS mutagenesis, DNA r	99.03
2hnf_A	133	Repressor protein CI101-229DM-K192A; viral protein	98.87
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	98.87
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	98.63
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	98.6
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	95.87
1w4s_A	174	Polybromo, polybromo 1 protein; BAH, bromo-associa	84.56

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

Probab=100.00  E-value=1.8e-39  Score=268.05  Aligned_cols=141  Identities=36%  Similarity=0.467  Sum_probs=119.3

Q ss_pred             HHHhcceEEEecCCCcccccCCCCEEEEEeeeec------------cCCCCcceEEEEecCCCCCCCCCCceEEEEEEEe
Q 029367           47 LWSTFSEIRFIPSSSMYPTLRIGDRIIVEKASYY------------FRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAK  114 (194)
Q Consensus        47 i~~~~~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~------------~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvgl  114 (194)
                      ++.|+++.+.|+|+||+|||+.||+|+|+|..|.            ..++++||||+|+.|.     .++..+||||+|+
T Consensus         1 ir~fv~~~~~v~g~SM~Ptl~~GD~vlv~k~~yg~r~P~~~~~l~~~~~~~rGDIvvf~~p~-----~~~~~~iKRVigl   75 (248)
T 1b12_A            1 VRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE-----DPKLDYIKRAVGL   75 (248)
T ss_dssp             -CBCCEEEEECCSCTTTTTSCTTEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTT-----CTTSEEEEEEEEC
T ss_pred             CeEEEEEEEEeccccccccccCCCEEEEEecccCcccccccccccccCCCCCCcEEEEEeCC-----CCCceEEEEEEee
Confidence            3567899999999999999999999999998764            3689999999999986     3568899999999


Q ss_pred             CCCeEEEeCC--EEEECC-----------EEcccchhcc-----------------------------------------
Q 029367          115 AGDLVQVRDG--SLYVNG-----------IAQNEDFIAE-----------------------------------------  140 (194)
Q Consensus       115 pGD~V~i~~~--~v~vnG-----------~~~~~~~~~~-----------------------------------------  140 (194)
                      |||+|+++++  .+||||           +.+.+++...                                         
T Consensus        76 pGD~v~i~~~~~~l~ING~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ip~~~~~~~~~~~~~~~e~l  155 (248)
T 1b12_A           76 PGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETL  155 (248)
T ss_dssp             TTCEEEEETTTTEEEEETTCCSSCCCCCCCCEEECCCEEEEEEEEEECGGGSCEEEEEEECCTTCCCTTEEEEEEEEEEE
T ss_pred             CCCEEEEEcCceEEEECCccccccccccceeeeeeccccccccccccccccccccccccccccccccccchhhhhHHhhh
Confidence            9999999999  999999           6554321100                                         


Q ss_pred             ---------CCC-------C------CCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCC
Q 029367          141 ---------HPK-------Y------TSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS  192 (194)
Q Consensus       141 ---------~~~-------~------~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~  192 (194)
                               .+.       +      ...+++||+|+|||||||+++|.||||||+||+++|+|||.++|||.+
T Consensus       156 ~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~VP~g~yFvmGDNR~nS~DSR~~G~Vp~~~IvGka~~i~~s~~  229 (248)
T 1b12_A          156 GDVTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFD  229 (248)
T ss_dssp             TTEEEEEEECTTCCCCGGGSCCCTTCCTTEEECCTTEEEEECSBTTSCCCHHHHCCEEGGGEEEEEEEEEEEBC
T ss_pred             cCccceeEecCCccccccchhcccccccccEEeCCCcEEEecCCCcccCCCCcccccCHHHeEEEEEEEEEeCC
Confidence                     011       0      223679999999999999999999999999999999999999999875

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

Probab=99.18  E-value=2.2e-10  Score=82.57  Aligned_cols=87  Identities=15%  Similarity=0.180  Sum_probs=65.7

Q ss_pred             eEEEecCCCcc------cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEE
Q 029367           53 EIRFIPSSSMY------PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSL  126 (194)
Q Consensus        53 ~~~~V~~~SM~------Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v  126 (194)
                      ....|.|+||+      |+|.+||++++++.    .+++.||+|++..+       .+..++||+...            
T Consensus        14 f~~~V~GdSM~~~~g~~p~i~~Gd~v~Vd~~----~~~~~Gdivv~~~~-------~~~~~vKrl~~~------------   70 (109)
T 1kca_A           14 FWLEVEGNSMTAPTGSKPSFPDGMLILVDPE----QAVEPGDFCIARLG-------GDEFTFKKLIRD------------   70 (109)
T ss_dssp             EEEECCSSTTCCCTTCSSCCCTTCEEEEETT----SCCCTTCEEEEECS-------TTCEEEEEEEEE------------
T ss_pred             EEEEEeCcCcCCCCCCCCeeCCCCEEEEecC----CcCCCCCEEEEEEC-------CCeEEEEEEEEe------------
Confidence            46789999999      99999999999985    46899999999873       247899999853            


Q ss_pred             EECCEEcccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCC
Q 029367          127 YVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS  192 (194)
Q Consensus       127 ~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~  192 (194)
                                                .|.+++.++|+..  .....-  ..-+|+|+|+..+||..
T Consensus        71 --------------------------~~~~~L~s~N~~y--~~~~~~--~~~~IiG~Vv~~~~~~~  106 (109)
T 1kca_A           71 --------------------------SGQVFLQPLNPQY--PMIPCN--ESCSVVGKVIASQWPEE  106 (109)
T ss_dssp             --------------------------TTEEEEECSSTTS--CCEECC--TTCEEEEEEEEEECCGG
T ss_pred             --------------------------CCEEEEEECCCCC--CCEEcC--CCcEEEEEEEEEEeCHH
Confidence                                      2456677787621  111111  35689999999999864

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

Probab=99.03  E-value=1.3e-09  Score=79.09  Aligned_cols=50  Identities=24%  Similarity=0.266  Sum_probs=43.3

Q ss_pred             ceEEEecCCCccc-ccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367           52 SEIRFIPSSSMYP-TLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA  113 (194)
Q Consensus        52 ~~~~~V~~~SM~P-tl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg  113 (194)
                      .....|.|+||+| ++++||.+++++.    .+++.||+|++..        ++..++||+..
T Consensus        27 ~~~~~v~GdSM~p~~i~~Gd~v~vd~~----~~~~~gdivv~~~--------~~~~~vKr~~~   77 (116)
T 1umu_A           27 TYFVKASGDSMIDGGISDGDLLIVDSA----ITASHGDIVIAAV--------DGEFTVKKLQL   77 (116)
T ss_dssp             EEEEECCSSTTGGGTCCTTCEEEEETT----SCCCTTCEEEEEE--------TTEEEEEEEEC
T ss_pred             EEEEEECCCCcCCCCCCCCCEEEEEcC----CCCCCCCEEEEEE--------CCEEEEEEEEe
Confidence            3567899999999 8999999999975    4689999999987        34789999986

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

Probab=98.87  E-value=1.3e-08  Score=75.51  Aligned_cols=50  Identities=14%  Similarity=0.140  Sum_probs=43.1

Q ss_pred             eEEEecCCCcc------cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367           53 EIRFIPSSSMY------PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA  113 (194)
Q Consensus        53 ~~~~V~~~SM~------Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg  113 (194)
                      ...+|.|+||+      |++.+||.+++++.    .+++.||+|++..+       .+...+||+..
T Consensus        45 f~~~V~GdSM~~~~g~~p~i~~Gd~v~vd~~----~~~~~Gdivv~~~~-------~~~~~vKrl~~  100 (133)
T 2hnf_A           45 FWLEVEGNSMTTPTGSKTSFPDGMLILVDPE----QAVEPGDFCIARLG-------GDEFTFAKLIR  100 (133)
T ss_dssp             EEEECCSSTTCCC---CCCCCTTCEEEEETT----SCCCTTSEEEEEET-------TTEEEEEEEEE
T ss_pred             EEEEEeCCCcCCCcCCCCccCCCCEEEEccC----CCCCCCCEEEEEEC-------CCEEEEEEEEE
Confidence            46789999999      99999999999985    57899999999873       34789999984

>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=98.87  E-value=2e-08  Score=79.20  Aligned_cols=55  Identities=25%  Similarity=0.352  Sum_probs=45.6

Q ss_pred             eEEEecCCCcccc-cCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEE
Q 029367           53 EIRFIPSSSMYPT-LRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ  120 (194)
Q Consensus        53 ~~~~V~~~SM~Pt-l~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~  120 (194)
                      ....|.|+||+|+ +.+||.+++++.    .+++.||+|++..        .+...+||+. .+|+.+.
T Consensus       111 ~~~~v~GdSM~p~~i~~Gd~v~vd~~----~~~~~G~i~v~~~--------~~~~~vKrl~-~~~~~~~  166 (202)
T 1jhf_A          111 FLLRVSGMSMKDIGIMDGDLLAVHKT----QDVRNGQVVVARI--------DDEVTVKRLK-KQGNKVE  166 (202)
T ss_dssp             EEEECCSSTTGGGTCCTTCEEEEEEC----SCCCTTSEEEEEE--------TTEEEEEEEE-EETTEEE
T ss_pred             EEEEECCCCCCCCCCCCCCEEEEecc----CCcCCCeEEEEEE--------CCEEEEEEEE-EeCCEEE
Confidence            4678999999999 999999999875    4689999999987        3578999998 4555443

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

Probab=98.63  E-value=7.4e-08  Score=77.30  Aligned_cols=87  Identities=15%  Similarity=0.207  Sum_probs=62.8

Q ss_pred             eEEEecCCCcc------cccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEE
Q 029367           53 EIRFIPSSSMY------PTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSL  126 (194)
Q Consensus        53 ~~~~V~~~SM~------Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v  126 (194)
                      ....|.|+||+      |++.+||+++|++.    .+++.||+|++...       .+...+||+...+           
T Consensus       141 ~~l~V~GdSM~~~~g~~P~i~~Gd~v~vd~~----~~~~~g~ivv~~~~-------~~~~~vKrl~~~~-----------  198 (236)
T 3bdn_A          141 FWLEVEGNSMTAPTGSKPSFPDGMLILVDPE----QAVEPGDFCIARLG-------GDEFTFKKLIRGS-----------  198 (236)
T ss_dssp             EEEECCSSSSCCCSSCSSCCCSSCEEEECCS----SCCCTTSEEEEEST-------TTCCCCEEEECCS-----------
T ss_pred             EEEEEeCCCcCCCCCCCCcCCCCCEEEECCC----CCCCCCcEEEEEEC-------CCeEEEEEEEEcC-----------
Confidence            46689999999      99999999999875    47899999999872       3578999998533           


Q ss_pred             EECCEEcccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCC
Q 029367          127 YVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS  192 (194)
Q Consensus       127 ~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~  192 (194)
                                                 |.+++..+|+.  +.....-  ..-+|+|+|+..++|..
T Consensus       199 ---------------------------~~~~L~s~N~~--y~~~~~~--~~~~IiG~Vv~~~~~~~  233 (236)
T 3bdn_A          199 ---------------------------GQVFLQPLNPQ--YPMIPCN--ESCSVVGKVIASQWPEE  233 (236)
T ss_dssp             ---------------------------SSCEEECSSTT--SCCBC----CCCEEEEEEEECCCCSS
T ss_pred             ---------------------------CcEEEEeCCCC--CCCeecC--CCcEEEEEEEEEEcCHH
Confidence                                       33445566652  1111111  34579999999988754

>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=98.60  E-value=4.9e-07  Score=71.12  Aligned_cols=50  Identities=18%  Similarity=0.197  Sum_probs=42.8

Q ss_pred             ceEEEecCCCc-ccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367           52 SEIRFIPSSSM-YPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA  113 (194)
Q Consensus        52 ~~~~~V~~~SM-~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg  113 (194)
                      .....|.|+|| +|++.+||.+++++.    ..++.||+|++..        .+...+||+.-
T Consensus       109 ~f~l~v~GdSM~~p~i~~GD~viv~~~----~~~~~G~ivv~~~--------~~~~~vKr~~~  159 (196)
T 3k2z_A          109 HFLLKVKGESMIEEHICDGDLVLVRRQ----DWAQNGDIVAAMV--------DGEVTLAKFYQ  159 (196)
T ss_dssp             EEEEECCSSTTGGGTCCTTCEEEEEEC----SCCCTTCEEEEEE--------TTEEEEEEEEE
T ss_pred             EEEEEEeCCCcCCCCCCCCCEEEEecc----CcCCCCCEEEEEE--------CCcEEEEEEEE
Confidence            45678999999 699999999999985    5789999999987        35899999864

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

Probab=95.87  E-value=0.052  Score=41.28  Aligned_cols=48  Identities=10%  Similarity=0.120  Sum_probs=31.9

Q ss_pred             CCcccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEE
Q 029367           60 SSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQ  120 (194)
Q Consensus        60 ~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~  120 (194)
                      ++|...-.+||.++|++.     .+..|+++++..        .+...+||+.-.+|+.+.
T Consensus       113 ~~~~~v~~~Gd~v~Vd~~-----~~~~g~i~vv~~--------~g~~~vKrl~~~~~~~i~  160 (189)
T 2fjr_A          113 TDGMAIRSEGKIYFVDKQ-----ASLSDGLWLVDI--------KGAISIRELTKLPGRKLH  160 (189)
T ss_dssp             SSEEEEEETTEEEEEETT-----CCSCSEEEEEEE--------TTEEEEEEEEEETTTEEE
T ss_pred             CCeEEEeeCCcEEEEEcC-----CccCCCEEEEEe--------CCeEEEEEEEECCCCEEE
Confidence            344444478888888763     356688888876        346788888765554443

---

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	194
d1b12a_	247	b.87.1.2 (A:) Type 1 signal peptidase {Escherichia	8e-15
d1b12a_	247	b.87.1.2 (A:) Type 1 signal peptidase {Escherichia	5e-09

>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 = 68.4 bits (166), Expect = 8e-15
 Identities = 31/135 (22%), Positives = 44/135 (32%), Gaps = 7/135 (5%)

Query: 53  EIRFIPSSSMYPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQY-------PGLGEED 105
           E   IPS SM PTL IGD I+VEK +Y  ++P     +      +             + 
Sbjct: 6   EPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPEDPKL 65

Query: 106 VFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNN 165
            +IKR V   GD V     S  +          A         + V           RN 
Sbjct: 66  DYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNG 125

Query: 166 SFDSHVWGPLPVKNI 180
              +  +  +P    
Sbjct: 126 GEATSGFFEVPKNET 140

>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 = 52.3 bits (124), Expect = 5e-09
 Identities = 27/106 (25%), Positives = 40/106 (37%)

Query: 78  SYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSLYVNGIAQNEDF 137
           S + +  S  +     + F      E      R+  +   L  V    L V         
Sbjct: 114 SDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGM 173

Query: 138 IAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGR 183
             + P        VP G  +++GDNR+NS DS  WG +P  N+ GR
Sbjct: 174 YYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGR 219

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	194
d1b12a_	247	Type 1 signal peptidase {Escherichia coli [TaxId:	100.0
d1f39a_	101	lambda repressor C-terminal domain {Bacteriophage	99.08
d1jhfa2	126	LexA C-terminal domain {Escherichia coli [TaxId: 5	98.82
d1umua_	105	UmuD' {Escherichia coli [TaxId: 562]}	98.57

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

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

Probab=100.00  E-value=1.7e-37  Score=253.07  Aligned_cols=139  Identities=37%  Similarity=0.470  Sum_probs=113.2

Q ss_pred             HhcceEEEecCCCcccccCCCCEEEEEeeeeccC------------CCCcceEEEEecCCCCCCCCCCceEEEEEEEeCC
Q 029367           49 STFSEIRFIPSSSMYPTLRIGDRIIVEKASYYFR------------NPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAG  116 (194)
Q Consensus        49 ~~~~~~~~V~~~SM~Ptl~~Gd~vlv~k~~~~~~------------~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpG  116 (194)
                      +|+++.+.|+|+||+|||..||+++|+|++|.++            .+++||+|+|..|.     .+...++|||+|+||
T Consensus         2 ~f~~~~f~IPs~SMePTL~~GD~l~V~K~~Yg~r~P~~~~~~~~~~~~~rgdivvf~~p~-----~~~~~~ikR~ig~pG   76 (247)
T d1b12a_           2 SFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE-----DPKLDYIKRAVGLPG   76 (247)
T ss_dssp             BCCEEEEECCSCTTTTTSCTTEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTT-----CTTSEEEEEEEECTT
T ss_pred             EEEEEEEEeCcccccchhccCCEEEEEccccCccCCccCcccccccCcccCceeeecCCC-----CCCccccccccCCCC
Confidence            5789999999999999999999999999988655            45999999999988     467789999999999


Q ss_pred             CeEEEeCCEEEECCEEcccc-------------------hh---------------------------------------
Q 029367          117 DLVQVRDGSLYVNGIAQNED-------------------FI---------------------------------------  138 (194)
Q Consensus       117 D~V~i~~~~v~vnG~~~~~~-------------------~~---------------------------------------  138 (194)
                      |+|++++...++|++...+.                   +.                                       
T Consensus        77 D~i~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (247)
T d1b12a_          77 DKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGD  156 (247)
T ss_dssp             CEEEEETTTTEEEEETTCCSSCCCCCCCCEEECCCEEEEEEEEEECGGGSCEEEEEEECCTTCCCTTEEEEEEEEEEETT
T ss_pred             CeEEEecccceEEecccccccceeecceeecccccCcccceeeeeeccCceeccceeeccccccccCceEeeeeeeccCC
Confidence            99999755444433211000                   00                                       


Q ss_pred             ------------------ccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCC
Q 029367          139 ------------------AEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS  192 (194)
Q Consensus       139 ------------------~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~  192 (194)
                                        ..........++||+|+|||||||+++|.|||+||+||+++|+|||..+|||.+
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Vp~~~yfvmGDNR~nS~DSR~wG~Vp~~~I~Gka~~i~~p~~  228 (247)
T d1b12a_         157 VTHRILTVPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFD  228 (247)
T ss_dssp             EEEEEEECTTCCCCGGGSCCCTTCCTTEEECCTTEEEEECSBTTSCCCHHHHCCEEGGGEEEEEEEEEEEBC
T ss_pred             cceeEEecccchhcccccccCCccccceEEEeCCeEEEecCCCCCCccccccCcCCHHHeEEEEEEEEEECC
Confidence                              000122345789999999999999999999999999999999999999999975

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

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

Probab=99.08  E-value=5.6e-10  Score=77.76  Aligned_cols=87  Identities=15%  Similarity=0.179  Sum_probs=64.1

Q ss_pred             eEEEecCCCc------ccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEEeCCCeEEEeCCEE
Q 029367           53 EIRFIPSSSM------YPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVAKAGDLVQVRDGSL  126 (194)
Q Consensus        53 ~~~~V~~~SM------~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvglpGD~V~i~~~~v  126 (194)
                      ...+|.|+||      +|++++||+++|++.    .+++.||+|++...       .+...+||+.-.            
T Consensus         6 F~l~V~GdSM~~~~~~ep~i~~Gd~viVd~~----~~~~~g~ivva~~~-------~~~~~vKr~~~~------------   62 (101)
T d1f39a_           6 FWLEVEGNSMTAPTGSKPSFPDGMLILVDPE----QAVEPGDFCIARLG-------GDEFTFKKLIRD------------   62 (101)
T ss_dssp             EEEECCSSTTCCCTTCSSCCCTTCEEEEETT----SCCCTTCEEEEECT-------TSCEEEEEEEEE------------
T ss_pred             EEEEEeCCccCCCcccCCCcCCCCEEEEEec----CccCCCCEEEEEEC-------CCeEEEEEEEEc------------
Confidence            3568999999      899999999999975    67899999988773       446789998732            


Q ss_pred             EECCEEcccchhccCCCCCCceeeecCCeEEEecCCCCCCCCCCccccccCCCeeEEEEEEEeCCC
Q 029367          127 YVNGIAQNEDFIAEHPKYTSDLTYVPVGYVYVLGDNRNNSFDSHVWGPLPVKNIAGRYLTRCYRPS  192 (194)
Q Consensus       127 ~vnG~~~~~~~~~~~~~~~~~~~~vp~g~yfvlGDn~~~S~DSR~~G~V~~~~I~Gkv~~~~~p~~  192 (194)
                                                +|++++..+|+..  ......  ..-+|+|+|+..+||.+
T Consensus        63 --------------------------~~~~~L~s~N~~y--~~i~~~--~~~~IiG~Vv~s~~p~~   98 (101)
T d1f39a_          63 --------------------------SGQVFLQPLNPQY--PMIPCN--ESCSVVGKVIASQWPEE   98 (101)
T ss_dssp             --------------------------TTEEEEECSSTTS--CCEECS--TTCEEEEEEEEEECCGG
T ss_pred             --------------------------CCEEEEEECCCCC--CCCcCC--CCcEEEEEEEEEECcHH
Confidence                                      2456666777621  112111  24589999999999975

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

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

Probab=98.82  E-value=1.8e-08  Score=72.53  Aligned_cols=49  Identities=22%  Similarity=0.291  Sum_probs=43.0

Q ss_pred             eEEEecCCCcccc-cCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEEE
Q 029367           53 EIRFIPSSSMYPT-LRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIVA  113 (194)
Q Consensus        53 ~~~~V~~~SM~Pt-l~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVvg  113 (194)
                      ...+|.|+||+|+ +.+||++++++.    .+++.||+|++..        .+...+||+.-
T Consensus        39 f~lrV~GdSM~~~~i~~gd~viv~~~----~~~~~G~ivv~~~--------~ge~~vKrl~~   88 (126)
T d1jhfa2          39 FLLRVSGMSMKDIGIMDGDLLAVHKT----QDVRNGQVVVARI--------DDEVTVKRLKK   88 (126)
T ss_dssp             EEEECCSSTTGGGTCCTTCEEEEEEC----SCCCTTSEEEEEE--------TTEEEEEEEEE
T ss_pred             EEEEEcCCcccCcccCCCEEEEEecc----ccccCCCEEEEEE--------CCEEEEEEEEE
Confidence            4678999999997 999999999875    6899999999998        45789999874

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

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

Probab=98.57  E-value=1.9e-07  Score=65.10  Aligned_cols=48  Identities=25%  Similarity=0.254  Sum_probs=41.8

Q ss_pred             eEEEecCCCc-ccccCCCCEEEEEeeeeccCCCCcceEEEEecCCCCCCCCCCceEEEEEE
Q 029367           53 EIRFIPSSSM-YPTLRIGDRIIVEKASYYFRNPSIHDIVTFRAPFQYPGLGEEDVFIKRIV  112 (194)
Q Consensus        53 ~~~~V~~~SM-~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~vKRVv  112 (194)
                      ...+|.|+|| .|.+.+||.+++++.    .+++.||+|++..        .++..+||..
T Consensus        21 f~~rV~GdSM~~~gI~~GDlliVd~~----~~~~~g~ivva~i--------~ge~~vKrl~   69 (105)
T d1umua_          21 YFVKASGDSMIDGGISDGDLLIVDSA----ITASHGDIVIAAV--------DGEFTVKKLQ   69 (105)
T ss_dssp             EEEECCSSTTGGGTCCTTCEEEEETT----SCCCTTCEEEEEE--------TTEEEEEEEE
T ss_pred             EEEEEcCCccccCccCCCCEEEEEcc----cccccCcEEEEEE--------CCEEEEEEEE
Confidence            3578999999 588999999999985    6889999999998        4578999975