Citrus Sinensis ID: 043519

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130
Protein Sequence
MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPSIAI
Secondary Structure (PSIPRED)
cccEEEEccEEEcccEEEEccccccccEEEEccccccccccccccccEEEEEEEccccEEEEEccEEEEccEEccccccccccccccccEEEccccccccccEEEEccccccccccEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEccccccEEEEEEcccccccEEEEcccHHHHHccccccccEEEEEEEccccEEEEEccEEEEccccccccHcccccccccccEEccccccccEEEEEEHHccccccccccccccccccccEcc
Coil and Loop (DISEMBL)
MLRAYVVTSLRrkgsvtyyfrepfandilifksppllqevgytddgvYIKGIVAKEGDVVEACEGklivngvvrnkdfileapfynmtpitvlensnsyDLLVCLDELadhipssldfkyqhhgnpsiai
Flexible Loop (DISEMBL)
mlrayvvtslrrkgsvtyyFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKlivngvvrnkDFILEAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPSIAI
Low Complexity Region (SEG)
MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPSIAI
Disordered region (IsUnstruct)
***AYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKY**********
Disordered Region (DISOPRED)
*LRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPS***
Disordered Region (DISEMBL)
MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPSIAI
Disordered Region (DISPRO)
MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPSIAI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPSIAI
Positional Conservation
no confident homologs detected

---

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	130	2.2.26 [Sep-21-2011]
Q8H0W1	291	Chloroplast processing pe	yes	no	0.653	0.292	0.670	2e-27
Q9M9Z2	367	Probable thylakoidal proc	no	no	0.615	0.217	0.537	1e-17
O04348	340	Thylakoidal processing pe	no	no	0.592	0.226	0.512	1e-15
P72660	196	Probable signal peptidase	N/A	no	0.6	0.397	0.358	2e-07
Q51876	203	Signal peptidase I OS=Pho	N/A	no	0.653	0.418	0.255	0.0002
P73157	218	Probable signal peptidase	N/A	no	0.638	0.380	0.276	0.0004

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

 Score =  121 bits (303), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 63/94 (67%), Positives = 71/94 (75%), Gaps = 9/94 (9%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           V+YYFR+P ANDI+IFKSPP+LQEVGYTD  V+IK IVAKEGD+VE   GKL+VNGV RN
Sbjct: 158 VSYYFRKPCANDIVIFKSPPVLQEVGYTDADVFIKRIVAKEGDLVEVHNGKLMVNGVARN 217

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYD 100
           + FILE P Y MTPI V ENS         NSYD
Sbjct: 218 EKFILEPPGYEMTPIRVPENSVFVMGDNRNNSYD 251

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: 3EC: .EC: 4EC: .EC: 2EC: 1EC: .EC: 8EC: 9

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

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 43/80 (53%), Positives = 58/80 (72%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           V+Y+FR+P  +DI+IFK+PP+L E GY+   V+IK IVA EGD VE C+GKL+VN  V+ 
Sbjct: 230 VSYFFRKPEVSDIVIFKAPPILVEHGYSCADVFIKRIVASEGDWVEVCDGKLLVNDTVQA 289

Query: 76  KDFILEAPFYNMTPITVLEN 95
           +DF+LE   Y M P+ V E 
Sbjct: 290 EDFVLEPIDYEMEPMFVPEG 309

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

 Score = 82.0 bits (201), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 41/80 (51%), Positives = 57/80 (71%), Gaps = 3/80 (3%)

Query: 16  VTYYFREPFANDILIFKSPPLL---QEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGV 72
           V+Y+FR+P  +DI+IFK+PP+L    E GY+ + V+IK IVA EGD VE  +GKL VN +
Sbjct: 200 VSYFFRKPEVSDIVIFKAPPILLEYPEYGYSSNDVFIKRIVASEGDWVEVRDGKLFVNDI 259

Query: 73  VRNKDFILEAPFYNMTPITV 92
           V+ +DF+LE   Y M P+ V
Sbjct: 260 VQEEDFVLEPMSYEMEPMFV 279

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 = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 42/78 (53%)

Query: 15  SVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVR 74
            V+Y+F  P   DI++F  P LLQ  GY     +IK ++A  G  VE   G +  +G   
Sbjct: 59  KVSYHFHPPQVGDIIVFHPPELLQVQGYDLGQAFIKRVIALPGQTVEVNNGIVYRDGQPL 118

Query: 75  NKDFILEAPFYNMTPITV 92
            +++ILE P YN+  + V
Sbjct: 119 QEEYILEPPQYNLPAVRV 136

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 = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 9/94 (9%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           ++Y+F  P   DI++F     L++   + +  +IK ++   G+ V+   G++++NG    
Sbjct: 75  ISYHFNPPRRGDIIVFHPTEALKQQNPSLNEAFIKRVIGLPGETVQVTGGRVLINGQPLE 134

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYD 100
           +++I   P Y   P  V  +S         NSYD
Sbjct: 135 ENYIQSPPDYQWGPEKVPADSFLVLGDNRNNSYD 168

Phormidium laminosum (taxid: 32059)

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 = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 11/94 (11%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           ++Y  R+P   +I++F     L+   + D   +IK I+   GD V   +G + VNG + +
Sbjct: 68  ISYRLRDPERGEIVVFNPTDALKAKNFHD--AFIKRIIGLPGDEVRVSQGNVYVNGKMLD 125

Query: 76  KDFILEAPFYNMTPITVLEN---------SNSYD 100
           +++I   P Y   P+ V ++         +NSYD
Sbjct: 126 ENYIAAPPAYEYGPVKVPDDQYLVLGDNRNNSYD 159

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

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	130
225445220	334	PREDICTED: chloroplast processing peptid	0.807	0.314	0.605	1e-27
297738817	175	unnamed protein product [Vitis vinifera]	0.807	0.6	0.605	2e-27
224142153	202	predicted protein [Populus trichocarpa]	0.807	0.519	0.596	2e-27
449467167	331	PREDICTED: chloroplast processing peptid	0.807	0.317	0.596	9e-27
449518835	331	PREDICTED: chloroplast processing peptid	0.807	0.317	0.596	9e-27
255546463	313	signal peptidase I, putative [Ricinus co	0.807	0.335	0.578	2e-26
413936436	304	hypothetical protein ZEAMMB73_799286 [Ze	0.838	0.358	0.559	3e-26
242061262	302	hypothetical protein SORBIDRAFT_04g00996	0.838	0.360	0.550	4e-26
115445459	298	Os02g0267000 [Oryza sativa Japonica Grou	0.838	0.365	0.559	4e-26
224119740	202	predicted protein [Populus trichocarpa]	0.807	0.519	0.596	4e-26

>gi|225445220|ref|XP_002284378.1| PREDICTED: chloroplast processing peptidase [Vitis vinifera]

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 69/114 (60%), Positives = 81/114 (71%), Gaps = 9/114 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           V+YYFR+P ANDI+IFKSPP+LQEVGYTD+ V+IK IVAKEGD VE  EGKLIVNGVVRN
Sbjct: 174 VSYYFRKPCANDIVIFKSPPVLQEVGYTDEDVFIKRIVAKEGDTVEVREGKLIVNGVVRN 233

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKY 120
           ++FI E P Y+MTPI V EN+         NSYD  V     A +I     F+Y
Sbjct: 234 ENFIFERPSYSMTPIRVPENAVFVMGDNRNNSYDSHVWGSLPAKNILGRSIFRY 287

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738817|emb|CBI28062.3| unnamed protein product [Vitis vinifera]

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 69/114 (60%), Positives = 81/114 (71%), Gaps = 9/114 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           V+YYFR+P ANDI+IFKSPP+LQEVGYTD+ V+IK IVAKEGD VE  EGKLIVNGVVRN
Sbjct: 16  VSYYFRKPCANDIVIFKSPPVLQEVGYTDEDVFIKRIVAKEGDTVEVREGKLIVNGVVRN 75

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKY 120
           ++FI E P Y+MTPI V EN+         NSYD  V     A +I     F+Y
Sbjct: 76  ENFIFERPSYSMTPIRVPENAVFVMGDNRNNSYDSHVWGSLPAKNILGRSIFRY 129

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142153|ref|XP_002324423.1| predicted protein [Populus trichocarpa] gi|222865857|gb|EEF02988.1| predicted protein [Populus trichocarpa]

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 68/114 (59%), Positives = 81/114 (71%), Gaps = 9/114 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           V+YYFR+P  NDI+IF+SPP+LQEVGYTDD V+IK IVAKEGD+VE  EGKLIVNGVVR+
Sbjct: 62  VSYYFRKPCVNDIVIFRSPPVLQEVGYTDDDVFIKRIVAKEGDIVEVHEGKLIVNGVVRS 121

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKY 120
           + FILE+P Y MTP+ V ENS         NSYD  V     A +I     F+Y
Sbjct: 122 EKFILESPLYEMTPVRVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSVFRY 175

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449467167|ref|XP_004151296.1| PREDICTED: chloroplast processing peptidase-like [Cucumis sativus]

 Score =  124 bits (312), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 68/114 (59%), Positives = 80/114 (70%), Gaps = 9/114 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           VTYYFR+P ANDI+IFKSPP+LQEVGYTD+ V+IK IVAKEGD VE  +GKLIVNGV R+
Sbjct: 179 VTYYFRKPCANDIVIFKSPPVLQEVGYTDEDVFIKRIVAKEGDTVEVRKGKLIVNGVERD 238

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKY 120
           + FILE P Y+MTP+ V ENS         NSYD  V     A +I     F+Y
Sbjct: 239 EKFILEPPSYDMTPVQVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSLFRY 292

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449518835|ref|XP_004166441.1| PREDICTED: chloroplast processing peptidase-like [Cucumis sativus]

 Score =  124 bits (312), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 68/114 (59%), Positives = 80/114 (70%), Gaps = 9/114 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           VTYYFR+P ANDI+IFKSPP+LQEVGYTD+ V+IK IVAKEGD VE  +GKLIVNGV R+
Sbjct: 179 VTYYFRKPCANDIVIFKSPPVLQEVGYTDEDVFIKRIVAKEGDTVEVRKGKLIVNGVERD 238

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKY 120
           + FILE P Y+MTP+ V ENS         NSYD  V     A +I     F+Y
Sbjct: 239 EKFILEPPSYDMTPVQVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSLFRY 292

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255546463|ref|XP_002514291.1| signal peptidase I, putative [Ricinus communis] gi|223546747|gb|EEF48245.1| signal peptidase I, putative [Ricinus communis]

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 66/114 (57%), Positives = 82/114 (71%), Gaps = 9/114 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           V+YYFR+P AND++IFKSPP+LQEVGYTD+ V+IK +VAKEGD+VE   GKL+VNGV RN
Sbjct: 170 VSYYFRKPCANDVVIFKSPPVLQEVGYTDNDVFIKRVVAKEGDIVEVRAGKLLVNGVERN 229

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKY 120
           ++FILE+P Y+MTPI V ENS         NSYD  V     A +I     F+Y
Sbjct: 230 ENFILESPSYDMTPIRVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSFFRY 283

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413936436|gb|AFW70987.1| hypothetical protein ZEAMMB73_799286 [Zea mays]

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 66/118 (55%), Positives = 80/118 (67%), Gaps = 9/118 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           VTYYFR+P  NDI+IFKSPP+LQEVGYTD+ V+IK +VA+EGDVVE  EGKL+VNG  RN
Sbjct: 157 VTYYFRKPCVNDIIIFKSPPVLQEVGYTDNDVFIKRVVAREGDVVEVHEGKLVVNGEGRN 216

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHG 124
           ++FILE P Y+M P+ V ENS         NSYD  V     A +I     F+Y   G
Sbjct: 217 EEFILEPPSYDMNPVQVPENSVFVMGDNRNNSYDSHVWGPLPAKNILGRSIFRYWPPG 274

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242061262|ref|XP_002451920.1| hypothetical protein SORBIDRAFT_04g009960 [Sorghum bicolor] gi|241931751|gb|EES04896.1| hypothetical protein SORBIDRAFT_04g009960 [Sorghum bicolor]

 Score =  122 bits (306), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 65/118 (55%), Positives = 80/118 (67%), Gaps = 9/118 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           VTYYFR+P  NDI+IFKSPP+LQEVGYTD+ V+IK +VA+EGDVVE  +GKL+VNG  RN
Sbjct: 155 VTYYFRKPCVNDIVIFKSPPVLQEVGYTDNDVFIKRVVAREGDVVEVHQGKLVVNGEARN 214

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHG 124
           ++FILE P Y+M P+ V ENS         NSYD  V     A +I     F+Y   G
Sbjct: 215 EEFILEPPSYDMNPVQVPENSVFVMGDNRNNSYDSHVWGPLPAKNILGRSIFRYWPPG 272

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115445459|ref|NP_001046509.1| Os02g0267000 [Oryza sativa Japonica Group] gi|50251480|dbj|BAD28619.1| putative signal peptidase I [Oryza sativa Japonica Group] gi|113536040|dbj|BAF08423.1| Os02g0267000 [Oryza sativa Japonica Group] gi|215695176|dbj|BAG90367.1| unnamed protein product [Oryza sativa Japonica Group] gi|222622573|gb|EEE56705.1| hypothetical protein OsJ_06181 [Oryza sativa Japonica Group]

 Score =  122 bits (306), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 66/118 (55%), Positives = 81/118 (68%), Gaps = 9/118 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           VTYYFR+P  NDI+IFKSPP+LQEVGYTD+ V+IK IVA+EGDVVE  +GKL+VNG VRN
Sbjct: 155 VTYYFRKPCINDIVIFKSPPVLQEVGYTDNDVFIKRIVAREGDVVEVHKGKLVVNGEVRN 214

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHG 124
           ++FILE P Y+M P+ V ENS         NSYD  V     + +I     F+Y   G
Sbjct: 215 EEFILEPPSYDMNPVQVPENSVFVMGDNRNNSYDSHVWGPLPSKNILGRSIFRYWPPG 272

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119740|ref|XP_002331149.1| predicted protein [Populus trichocarpa] gi|222873232|gb|EEF10363.1| predicted protein [Populus trichocarpa]

 Score =  122 bits (306), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 68/114 (59%), Positives = 79/114 (69%), Gaps = 9/114 (7%)

Query: 16  VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
           V+YYFR+P  NDI+IFKSPP+LQEVGYTDD V+IK IVAKEGD VE  EGKLIVNGV+R+
Sbjct: 62  VSYYFRKPCVNDIVIFKSPPVLQEVGYTDDDVFIKRIVAKEGDTVEVHEGKLIVNGVMRS 121

Query: 76  KDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKY 120
           + FILE P Y +TPI V ENS         NSYD  V     A +I     F+Y
Sbjct: 122 EKFILEPPSYELTPIHVPENSVFVMGDNRNNSYDSHVWGPLPAKNIIGRSIFRY 175

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	130
TAIR|locus:2091717	291	PLSP1 "plastidic type i signal	0.623	0.278	0.728	2.5e-26
TAIR|locus:2033108	367	Plsp2A "plastidic type I signa	0.607	0.215	0.544	1.6e-17
TAIR|locus:2064337	340	TPP "thylakoid processing pept	0.592	0.226	0.512	3.4e-16

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

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 59/81 (72%), Positives = 67/81 (82%)

Query:    16 VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
             V+YYFR+P ANDI+IFKSPP+LQEVGYTD  V+IK IVAKEGD+VE   GKL+VNGV RN
Sbjct:   158 VSYYFRKPCANDIVIFKSPPVLQEVGYTDADVFIKRIVAKEGDLVEVHNGKLMVNGVARN 217

Query:    76 KDFILEAPFYNMTPITVLENS 96
             + FILE P Y MTPI V ENS
Sbjct:   218 EKFILEPPGYEMTPIRVPENS 238

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 = 217 (81.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 43/79 (54%), Positives = 58/79 (73%)

Query:    16 VTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRN 75
             V+Y+FR+P  +DI+IFK+PP+L E GY+   V+IK IVA EGD VE C+GKL+VN  V+ 
Sbjct:   230 VSYFFRKPEVSDIVIFKAPPILVEHGYSCADVFIKRIVASEGDWVEVCDGKLLVNDTVQA 289

Query:    76 KDFILEAPFYNMTPITVLE 94
             +DF+LE   Y M P+ V E
Sbjct:   290 EDFVLEPIDYEMEPMFVPE 308

GO:0006508 "proteolysis" evidence=IEA;ISS

GO:0008233 "peptidase activity" evidence=ISS

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

GO:0009507 "chloroplast" evidence=ISM

GO:0016020 "membrane" evidence=IEA;ISS

GO:0016021 "integral to membrane" evidence=IEA

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

 Score = 204 (76.9 bits), Expect = 3.4e-16, P = 3.4e-16
 Identities = 41/80 (51%), Positives = 57/80 (71%)

Query:    16 VTYYFREPFANDILIFKSPPLL---QEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGV 72
             V+Y+FR+P  +DI+IFK+PP+L    E GY+ + V+IK IVA EGD VE  +GKL VN +
Sbjct:   200 VSYFFRKPEVSDIVIFKAPPILLEYPEYGYSSNDVFIKRIVASEGDWVEVRDGKLFVNDI 259

Query:    73 VRNKDFILEAPFYNMTPITV 92
             V+ +DF+LE   Y M P+ V
Sbjct:   260 VQEEDFVLEPMSYEMEPMFV 279


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.141   0.414    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      130       130   0.00091  102 3  11 22  0.39    31
                                                     29  0.42    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  3
  No. of states in DFA:  561 (60 KB)
  Total size of DFA:  128 KB (2082 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  11.62u 0.26s 11.88t   Elapsed:  00:00:01
  Total cpu time:  11.62u 0.26s 11.88t   Elapsed:  00:00:01
  Start:  Fri May 10 06:23:58 2013   End:  Fri May 10 06:23:59 2013

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

---

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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00016732001	SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (334 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00019235001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (603 aa)	•			•			•		0.586
	GSVIVG00021597001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (488 aa)	•			•			•		0.461
	GSVIVG00020896001	SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (681 aa)	•						•		0.448
	GSVIVG00024895001	SubName- Full=Chromosome chr4 scaffold_32, whole genome shotgun sequence; (414 aa)	•			•			•		0.440

---

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	130
TIGR02227	163	TIGR02227, sigpep_I_bact, signal peptidase I, bact	9e-08

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

 Score = 47.6 bits (114), Expect = 9e-08
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 18  YYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKD 77
           Y   +P   DI++FK P         +  +YIK ++   GD VE  +GKL +NG   ++ 
Sbjct: 47  YGTSDPKRGDIVVFKDPD-------DNKNIYIKRVIGLPGDKVEFRDGKLYINGKKIDEP 99

Query: 78  FILEAPFYNMTPITVLE 94
           ++    F + +     +
Sbjct: 100 YLKPNGFLDTSEFNTTD 116

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	130
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	99.98
PRK13838	176	conjugal transfer pilin processing protease TraF;	99.94
TIGR02771	171	TraF_Ti conjugative transfer signal peptidase TraF	99.92
KOG1568	174	consensus Mitochondrial inner membrane protease, s	99.92
PF10502	138	Peptidase_S26: Signal peptidase, peptidase S26 ; I	99.92
PRK13884	178	conjugal transfer peptidase TraF; Provisional	99.91
COG4959	173	TraF Type IV secretory pathway, protease TraF [Pos	99.77
TIGR02754	90	sod_Ni_protease nickel-type superoxide dismutase m	99.77
cd06530	85	S26_SPase_I The S26 Type I signal peptidase (SPase	99.66
TIGR02228	158	sigpep_I_arch signal peptidase I, archaeal type. T	99.31
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	99.26
PF00717	70	Peptidase_S24: Peptidase S24-like peptidase classi	99.22
cd06462	84	Peptidase_S24_S26 The S24, S26 LexA/signal peptida	98.45
cd06529	81	S24_LexA-like Peptidase S24 LexA-like proteins are	98.42
COG2932	214	Predicted transcriptional regulator [Transcription	97.88
PRK10276	139	DNA polymerase V subunit UmuD; Provisional	96.96
KOG3342	180	consensus Signal peptidase I [Intracellular traffi	96.89
PRK12423	202	LexA repressor; Provisional	96.86
PRK00215	205	LexA repressor; Validated	96.77
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	96.67
COG0681	166	LepB Signal peptidase I [Intracellular trafficking	95.54
COG1974	201	LexA SOS-response transcriptional repressors (RecA	89.08
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	86.29
COG0361	75	InfA Translation initiation factor 1 (IF-1) [Trans	82.98
TIGR00008	68	infA translation initiation factor IF-1. This fami	81.79
PF05257	124	CHAP: CHAP domain; InterPro: IPR007921 The CHAP (c	80.67

>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type

Probab=100.00  E-value=3.3e-38  Score=225.24  Aligned_cols=117  Identities=24%  Similarity=0.329  Sum_probs=103.8

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL   80 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~   80 (130)
                      |+|||++||+|+++|+.|....+++||+|+|+.|.       ..++.++|||+|+|||+|+++++++||||+.++++|..
T Consensus        30 M~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~-------~~~~~~iKRVig~pGd~v~i~~~~l~vNg~~~~~~~~~  102 (163)
T TIGR02227        30 MEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPD-------DNKNIYVKRVIGLPGDKVEFRDGKLYINGKKIDEPYLK  102 (163)
T ss_pred             cccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCC-------CCCceeEEEEEecCCCEEEEECCEEEECCEECcccccc
Confidence            99999999999999998888899999999999875       35679999999999999999999999999999998765


Q ss_pred             cCCC--------CCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCC
Q 043519           81 EAPF--------YNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHG  124 (130)
Q Consensus        81 ~~~~--------~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~  124 (130)
                      +...        ....+++||+||         +|+||||||+|++++|+|||++++||++
T Consensus       103 ~~~~~~~~~~~~~~~~~~~vp~g~~fvlGDnr~~S~DSR~~G~V~~~~I~Gk~~~~~~p~~  163 (163)
T TIGR02227       103 PNGSLDTSGFNTTDFKPVTVPPGHYFVLGDNRDNSLDSRYFGFVPIDDIIGKVSFVFYPFD  163 (163)
T ss_pred             cccccccccccccccCceEECCCCEEEECCCCCCCcccCCcCcCCHHHeEEEEEEEECCCC
Confidence            3211        123467889998         8999999999999999999999999985

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=8.4e-33  Score=214.92  Aligned_cols=117  Identities=18%  Similarity=0.164  Sum_probs=96.4

Q ss_pred             CccccccCCEEEEEccccCC------------CCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe--CCE
Q 043519            1 MLRAYVVTSLRRKGSVTYYF------------REPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC--EGK   66 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~------------~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~--~~~   66 (130)
                      |+|||..||+|+|+|++|.+            +.|+|||||+|+.|.       +++..+||||||+|||+|+++  +++
T Consensus        92 M~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~-------~~~~~yIKRVIGlPGD~I~~~~~~~~  164 (324)
T PRK10861         92 MMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPE-------DPKLDYIKRVVGLPGDKVTYDPVSKE  164 (324)
T ss_pred             CcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCC-------CCCCcEEEEeeecCCcEEEEEeCCCE
Confidence            99999999999999999863            579999999999987       457889999999999999997  899


Q ss_pred             EEECCEEccccc-----------------cc---------------------------------c-----------CCC-
Q 043519           67 LIVNGVVRNKDF-----------------IL---------------------------------E-----------APF-   84 (130)
Q Consensus        67 l~vng~~~~~~~-----------------~~---------------------------------~-----------~~~-   84 (130)
                      |||||+.+...+                 ..                                 +           .+. 
T Consensus       165 l~iNg~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~l~~~~h~i~~~~~~  244 (324)
T PRK10861        165 VTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFQVPLNETKENGIRLSERKETLGDVTHRILTVPGA  244 (324)
T ss_pred             EEEcCccccccccccccccccccccccccccccccccccccccccccccccccccccccceeEEEecCCccceeeecCCc
Confidence            999997421100                 00                                 0           000 


Q ss_pred             ------------CCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCC
Q 043519           85 ------------YNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHG  124 (130)
Q Consensus        85 ------------~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~  124 (130)
                                  .++.+++||+|+         +|+||||||+||.++|+|+|..++|+++
T Consensus       245 ~~~~~~~~~~~~~~~~~~~vp~g~yf~mgdnr~~S~DSRy~G~Vp~~~i~G~a~~i~~s~d  305 (324)
T PRK10861        245 QDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGKATAIWMSFE  305 (324)
T ss_pred             ccccccccccCCCcCceEEECCCeEEEeCCCCCCCcccCcccccCHHHcEEEEEEEEEEcC
Confidence                        013567999998         8999999999999999999999999986

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

Probab=99.98  E-value=5.6e-33  Score=195.11  Aligned_cols=112  Identities=34%  Similarity=0.383  Sum_probs=98.0

Q ss_pred             Ccccccc-CCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEcccccc
Q 043519            1 MLRAYVV-TSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFI   79 (130)
Q Consensus         1 M~Ptl~~-gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~   79 (130)
                      |+|||++ ||+|++.|++++++.+++||+|++..|.       ...+.+||||+|++||-|++.++.+.+|+..  |.+.
T Consensus        43 M~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~-------~~~~~~cKRIva~eGD~v~v~~~~~~~n~~~--e~~~  113 (176)
T KOG0171|consen   43 MEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPP-------DPKEHICKRIVAMEGDLVEVHDGPLVVNDLV--EKFS  113 (176)
T ss_pred             cCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCC-------CchhhhhheeeccCCceEEEecCCcccchhh--hhcc
Confidence            9998886 5666669999999999999999999998       4678899999999999999999988888664  3332


Q ss_pred             ccCCCCCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCCCCCcC
Q 043519           80 LEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHGNPSIA  129 (130)
Q Consensus        80 ~~~~~~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~g~~  129 (130)
                              .+++||+||         +|+|||+|||||.+.|+||+++++||.+++++.
T Consensus       114 --------~~i~VP~GhVfv~GDN~~nS~DSr~yGplP~glI~gRvv~r~Wp~s~~~~~  164 (176)
T KOG0171|consen  114 --------TPIRVPEGHVFVEGDNRNNSLDSRNYGPLPMGLIQGRVVFRIWPPSRVSGL  164 (176)
T ss_pred             --------ceeeccCceEEEecCCCCCcccccccCCCchhheeeeEEEEecCchhccee
Confidence                    367888888         999999999999999999999999999998764

>PRK13838 conjugal transfer pilin processing protease TraF; Provisional

Probab=99.94  E-value=1.7e-26  Score=166.59  Aligned_cols=112  Identities=16%  Similarity=0.041  Sum_probs=86.9

Q ss_pred             ccCCEEEEEccccCCCCCCCCcEEEEecCCccc-----cccc-C------CCceEEEEEEEeCCCEEEEeCCEEEECCEE
Q 043519            6 VVTSLRRKGSVTYYFREPFANDILIFKSPPLLQ-----EVGY-T------DDGVYIKGIVAKEGDVVEACEGKLIVNGVV   73 (130)
Q Consensus         6 ~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~-----~~~~-~------~~~~~vKRVig~pGD~v~~~~~~l~vng~~   73 (130)
                      .+.+.+.+.++.+..+.++|||+|+|+.|...+     +++| .      ....++|||+|+|||+|++++ +++|||+.
T Consensus        34 T~S~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~~-~v~iNg~~  112 (176)
T PRK13838         34 TPSEPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIGG-SVSIDGRP  112 (176)
T ss_pred             CCCCEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEECC-EEEECCEE
Confidence            457778888887767889999999999886531     1222 1      124699999999999999985 89999999


Q ss_pred             ccccccccCCC--C---CCCCEEeCCCC--------CCCCCCccccccCCCeeeEEEE
Q 043519           74 RNKDFILEAPF--Y---NMTPITVLENS--------NSYDLLVCLDELADHIPSSLDF  118 (130)
Q Consensus        74 ~~~~~~~~~~~--~---~~~~~~vp~g~--------~S~DSR~~G~V~~~~I~Gkv~~  118 (130)
                      +.++|......  .   .+...+||+|+        +|+||||||+|++++|+|+|.-
T Consensus       113 ~~~~~~~~~~~~g~~l~~~~~~~vp~g~~fvlgd~~~S~DSRy~G~V~~~~I~G~a~p  170 (176)
T PRK13838        113 LPSSSVRRRDGEGRPLTPFPGGVVPPGHLFLHSSFAGSYDSRYFGPVPASGLLGLARP  170 (176)
T ss_pred             ccccccccccccCCcCCCCCccCcCCCeEEEECCCCCCCcccccCcccHHHeEEEEEE
Confidence            99987653221  1   12235678887        8999999999999999999963

>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF

Probab=99.92  E-value=3.5e-25  Score=159.20  Aligned_cols=98  Identities=17%  Similarity=0.160  Sum_probs=74.5

Q ss_pred             CCCCCCcEEEEecCCccc-----cccc-CCC------ceEEEEEEEeCCCEEEEeCCEEEECCEEccccccccCC--C--
Q 043519           21 REPFANDILIFKSPPLLQ-----EVGY-TDD------GVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAP--F--   84 (130)
Q Consensus        21 ~~~~rGDiVvf~~p~~~~-----~~~~-~~~------~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~~~~--~--   84 (130)
                      +.++|||+|+|+.|....     .++| +.+      ..++|||+|+|||+|+++++.++|||+.+.+.+.....  +  
T Consensus        45 ~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~~~~v~INg~~~~~~~~~~~~~~g~~  124 (171)
T TIGR02771        45 KPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGQLLPYSKPLATDSSGRP  124 (171)
T ss_pred             CCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEECCEEEECCEEcccccccccccCCCc
Confidence            479999999999886421     1222 122      38999999999999999999999999998876533211  1  


Q ss_pred             -CCCCCEEeCCCC--------CCCCCCccccccCCCeeeEEEE
Q 043519           85 -YNMTPITVLENS--------NSYDLLVCLDELADHIPSSLDF  118 (130)
Q Consensus        85 -~~~~~~~vp~g~--------~S~DSR~~G~V~~~~I~Gkv~~  118 (130)
                       ....+.+||+|.        +|+||||||+|++++|+|||.-
T Consensus       125 l~~~~~~~vp~gyf~lgdn~~~S~DSRy~G~V~~~~IiGk~~p  167 (171)
T TIGR02771       125 LPPFPEGVIPPGFFVVHDTSPTSFDSRYFGPISREQVIGRVKP  167 (171)
T ss_pred             cccCCCcEECCCEEEECCCCCCCCcccccceecHHHeEEEEEE
Confidence             112356666666        8999999999999999999964

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.

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

Probab=99.92  E-value=1.8e-25  Score=156.95  Aligned_cols=100  Identities=22%  Similarity=0.152  Sum_probs=85.2

Q ss_pred             CccccccC------CEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEc
Q 043519            1 MLRAYVVT------SLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVR   74 (130)
Q Consensus         1 M~Ptl~~g------d~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~   74 (130)
                      |.|||+++      |+||++|+.-.-+.+.|||+|+|.+|.       ++++.+||||+|++||++.-.+.         
T Consensus        41 mqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~-------~p~~~~iKRv~alegd~~~t~~~---------  104 (174)
T KOG1568|consen   41 MQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPN-------DPDKVIIKRVAALEGDIMVTEDE---------  104 (174)
T ss_pred             CCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCC-------ChhheeeeeeecccccEeccCCC---------
Confidence            88999874      999999987555678999999999998       57899999999999999977321         


Q ss_pred             cccccccCCCCCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCCCCC
Q 043519           75 NKDFILEAPFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHGNPS  127 (130)
Q Consensus        75 ~~~~~~~~~~~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~g  127 (130)
                                 ....+.||+||         .|+|||.||||+...|.|+|++++||+.|++
T Consensus       105 -----------k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gli~grai~ilwpP~R~~  155 (174)
T KOG1568|consen  105 -----------KEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGLIVGRAIYILWPPVRWQ  155 (174)
T ss_pred             -----------CCCceecCCCcEEEecCCcccccccCccCCcchhheeeeEEEEEcChHHhh
Confidence                       12345566666         9999999999999999999999999999875

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

Probab=99.92  E-value=2e-26  Score=160.55  Aligned_cols=99  Identities=23%  Similarity=0.258  Sum_probs=23.0

Q ss_pred             CCCCCcEEEEecCCccc----cccc-CCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccccCCCCC----CCCEEe
Q 043519           22 EPFANDILIFKSPPLLQ----EVGY-TDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYN----MTPITV   92 (130)
Q Consensus        22 ~~~rGDiVvf~~p~~~~----~~~~-~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~~~~~~~----~~~~~v   92 (130)
                      .++|||+|+|+.|....    +++| ..+..++|||+|+|||+|+++++.++|||+.+.+.+..+..+..    ..+.+|
T Consensus        21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~~~~v~iNG~~~~~~~~~d~~g~~l~~~~~~~~v  100 (138)
T PF10502_consen   21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVTDGGVYINGRPVGEPLATDSDGRPLPQFSGSGTV  100 (138)
T ss_dssp             --------------------------------------------------------------------S-T----TEEE-
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCceEe
Confidence            37999999999997532    3444 45679999999999999999999999999988876654332221    135778


Q ss_pred             CCCC---------CCCCCCccccccCCCeeeEEEEEE
Q 043519           93 LENS---------NSYDLLVCLDELADHIPSSLDFKY  120 (130)
Q Consensus        93 p~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~  120 (130)
                      |+|+         +|+||||||+|++++|+|+|...+
T Consensus       101 p~g~~~v~gd~~~~S~DSRy~G~V~~~~I~g~~~pl~  137 (138)
T PF10502_consen  101 PEGEYFVLGDNRPNSFDSRYFGPVPRSQIIGKARPLW  137 (138)
T ss_dssp             -TTEEEEE-SBTTS--SHHHH--EEGGGEEEEEEEEE
T ss_pred             CCCEEEEecCCCCCccccCEecccCHHHEEEEEEEEE
Confidence            8877         999999999999999999997543

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.

>PRK13884 conjugal transfer peptidase TraF; Provisional

Probab=99.91  E-value=3.8e-24  Score=154.72  Aligned_cols=98  Identities=20%  Similarity=0.233  Sum_probs=74.8

Q ss_pred             CCCCCCcEEEEecCCcc-----ccccc------CC-CceEEEEEEEeCCCEEEEeCCEEEECCEEccccc--cccCC---
Q 043519           21 REPFANDILIFKSPPLL-----QEVGY------TD-DGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDF--ILEAP---   83 (130)
Q Consensus        21 ~~~~rGDiVvf~~p~~~-----~~~~~------~~-~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~--~~~~~---   83 (130)
                      ..+++||+|+|++|+..     .+++|      +. ...++|||+|+|||+|+++++.++|||+.+.+..  ..+..   
T Consensus        49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~~~~l~VNG~~v~~~~~~~~d~~g~~  128 (178)
T PRK13884         49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVTDDGVRVNGELLPLSKPILADGAGRP  128 (178)
T ss_pred             CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEECCEEEECCEEccccccccccccCCc
Confidence            36899999999988742     23343      11 2489999999999999999999999999986543  22211   


Q ss_pred             --CCCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEE
Q 043519           84 --FYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDF  118 (130)
Q Consensus        84 --~~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~  118 (130)
                        .+....++||+|+         +|+||||||+|++++|+|++.-
T Consensus       129 l~~~~~~~~~lp~g~~fvlgd~~~~S~DSRYfG~V~~~~I~G~~~P  174 (178)
T PRK13884        129 LPRYQANSYTLGESELLLMSDVSATSFDGRYFGPINRSQIKTVIRP  174 (178)
T ss_pred             ccccCCCceEECCCEEEEECCCCCCCCcccccCcccHHHEEEEEEE
Confidence              1223345788887         8999999999999999999853

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

Probab=99.77  E-value=2.7e-19  Score=124.89  Aligned_cols=95  Identities=14%  Similarity=0.086  Sum_probs=74.6

Q ss_pred             CCCCcEEEEecCCcc----ccccc-CCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccccCCCCCC----CCEEeC
Q 043519           23 PFANDILIFKSPPLL----QEVGY-TDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEAPFYNM----TPITVL   93 (130)
Q Consensus        23 ~~rGDiVvf~~p~~~----~~~~~-~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~~~~~~~~----~~~~vp   93 (130)
                      +.+||+|++++|...    .++|| +....++|||.|+|||+|++..+.+-|||+.+......+..+..+    ++-.+.
T Consensus        54 vt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci~~~~I~I~G~~v~~sl~~D~~GR~lp~~~gcR~l~  133 (173)
T COG4959          54 VTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCITSQGIAIDGKPVAASLPVDRVGRALPRWQGCRYLA  133 (173)
T ss_pred             cccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEEecceEEECCEEeeeeccccccCCcCCcccCCceec
Confidence            499999999999863    34777 668899999999999999999999999999987654444333221    111233


Q ss_pred             CCC---------CCCCCCccccccCCCeeeEEE
Q 043519           94 ENS---------NSYDLLVCLDELADHIPSSLD  117 (130)
Q Consensus        94 ~g~---------~S~DSR~~G~V~~~~I~Gkv~  117 (130)
                      +++         .||||||||+||.++|+|.+.
T Consensus       134 ~~el~lL~~~~~~SfDsRYfGpipas~vig~aR  166 (173)
T COG4959         134 PSELLLLTDRSSTSFDSRYFGPIPASQVIGVAR  166 (173)
T ss_pred             CCeEEEEeccCCcccccceecccCHHHcceeee
Confidence            333         899999999999999999985

>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease

Probab=99.77  E-value=3.1e-18  Score=110.76  Aligned_cols=81  Identities=15%  Similarity=0.053  Sum_probs=65.9

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL   80 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~   80 (130)
                      |+|||++||+|+++++......+++||+|+|+.|.       .++..++||+++++++.+.+                  
T Consensus         8 M~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~-------~~~~~~vkRv~~~~~~~~~l------------------   62 (90)
T TIGR02754         8 MSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPL-------QPYGLIIKRLAAVDDNGLFL------------------   62 (90)
T ss_pred             ccCccCCCCEEEEEEccccCCCCCCCeEEEEecCC-------CCcceEEEEeeEEcCCeEEE------------------
Confidence            99999999999999865444556789999999875       24689999999997654433                  


Q ss_pred             cCCCCCCCCEEeCCCC-CCCCCCccccccCCCeeeEEE
Q 043519           81 EAPFYNMTPITVLENS-NSYDLLVCLDELADHIPSSLD  117 (130)
Q Consensus        81 ~~~~~~~~~~~vp~g~-~S~DSR~~G~V~~~~I~Gkv~  117 (130)
                                 ..+|. .|.|||++|+|+..+|+|+|+
T Consensus        63 -----------~~dN~~~~~d~~~~g~v~~~~I~G~v~   89 (90)
T TIGR02754        63 -----------LGDNPKASTDSRQLGPVPRSLLLGKVL   89 (90)
T ss_pred             -----------eCCCCCCCCcccccCCCcHHHEEEEEE
Confidence                       23333 689999999999999999985

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=99.66  E-value=4.5e-16  Score=99.39  Aligned_cols=75  Identities=27%  Similarity=0.305  Sum_probs=62.8

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL   80 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~   80 (130)
                      |+||++.||+|++++....+..+++||+|+|+.+.       ..+..++|||++                          
T Consensus        10 M~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~-------~~~~~~vkRv~~--------------------------   56 (85)
T cd06530          10 MEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPG-------DPGKPIIKRVIG--------------------------   56 (85)
T ss_pred             CcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCC-------CCCCEEEEEEEE--------------------------
Confidence            99999999999999876544579999999999975       236899999999                          


Q ss_pred             cCCCCCCCCEEeCCCC-CCCCCCccccccCCCeeeEE
Q 043519           81 EAPFYNMTPITVLENS-NSYDLLVCLDELADHIPSSL  116 (130)
Q Consensus        81 ~~~~~~~~~~~vp~g~-~S~DSR~~G~V~~~~I~Gkv  116 (130)
                              .++.+++. +|.|||+||+++.++|+|++
T Consensus        57 --------~~~~gDn~~ns~d~~~~g~~~~~~i~G~~   85 (85)
T cd06530          57 --------YFVLGDNRNNSLDSRYWGPVPEDDIVGKV   85 (85)
T ss_pred             --------EEEeeCCCCCCCccCCcCCCcHHHeEEeC
Confidence                    12345554 89999999999999999985

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

>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type

Probab=99.31  E-value=1.7e-11  Score=87.26  Aligned_cols=79  Identities=14%  Similarity=0.104  Sum_probs=58.5

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL   80 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~   80 (130)
                      |+|||++||++++++..  ..++++||+|+|+.|.        ..+.++|||+++.++     ++      +.   .   
T Consensus        41 M~Ptl~~GD~vlv~~~~--~~~~~~GDIVvf~~~~--------~~~~iihRVi~v~~~-----~g------~~---~---   93 (158)
T TIGR02228        41 MEPTFNTGDLILVTGAD--PNDIQVGDVITYKSPG--------FNTPVTHRVIEINNS-----GG------EL---G---   93 (158)
T ss_pred             CcCCccCCCEEEEEecc--cCCCCCCCEEEEEECC--------CCccEEEEEEEEECC-----CC------cE---E---
Confidence            99999999999999854  3589999999999875        237899999998643     11      10   0   


Q ss_pred             cCCCCCCCCEEeCCCCCCCCCCccccccCCCeeeEEE
Q 043519           81 EAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSLD  117 (130)
Q Consensus        81 ~~~~~~~~~~~vp~g~~S~DSR~~G~V~~~~I~Gkv~  117 (130)
                              -++-+++..+.|   .++|+.++|+|++.
T Consensus        94 --------~~tkGDnN~~~D---~~~v~~~~IiG~v~  119 (158)
T TIGR02228        94 --------FITKGDNNPAPD---GEPVPSENVIGKYL  119 (158)
T ss_pred             --------EEEEecCCCCCC---cccCCHHHEEEEEE
Confidence                    112233334445   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=99.26  E-value=6.3e-11  Score=83.59  Aligned_cols=104  Identities=18%  Similarity=0.115  Sum_probs=72.5

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccc
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFIL   80 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~   80 (130)
                      |+|||+.||+|+++|++|....+..++++.+  |.       .....++||+++++||++.++++.+++ +..+.+.+..
T Consensus        41 M~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~--~~-------~~~~~~~kr~~~~~GD~i~~~~~~~~~-~~~~~~~~~~  110 (166)
T COG0681          41 MEPTLNVGDRVLVKKFSYGFGKLKVPDIIVL--PA-------VVEGDLIKRVIGLRGDIVVFKDDRLYV-VPIIPRVYGL  110 (166)
T ss_pred             cccccccCCEEEEEeccccccCCccceeeec--CC-------CCCcceEEEeccCCCCEEEEECCEEEe-ecccCcchhh
Confidence            9999999999999999999888999999832  22       357899999999999999999999998 3333332211


Q ss_pred             cCCCCCCCCEEeCCCCCCCCCCccccccCCCeeeEE
Q 043519           81 EAPFYNMTPITVLENSNSYDLLVCLDELADHIPSSL  116 (130)
Q Consensus        81 ~~~~~~~~~~~vp~g~~S~DSR~~G~V~~~~I~Gkv  116 (130)
                      ...  ............+.+++.++.......+.++
T Consensus       111 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (166)
T COG0681         111 VEK--DNGKHLVDVIVNANSSRVFGIITKKDYIKRV  144 (166)
T ss_pred             hhc--ccccccccccccccCccccccccccccccce
Confidence            100  0000011111166777777776666666666

>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification

Probab=99.22  E-value=2.6e-11  Score=74.31  Aligned_cols=52  Identities=23%  Similarity=0.346  Sum_probs=42.3

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeC
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACE   64 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~   64 (130)
                      |+|+|++||+|++++..    .++.||+|+|..+.        ....++||+++.+|+.+.+..
T Consensus         7 M~P~i~~Gd~v~v~~~~----~~~~gdivv~~~~~--------~~~~~iKrv~~~~~~~~~~~~   58 (70)
T PF00717_consen    7 MEPTIKDGDIVLVDPSS----EPKDGDIVVVKIDG--------DEELYIKRVVGEPGGIILISS   58 (70)
T ss_dssp             TGGTSSTTEEEEEEETS-------TTSEEEEEETT--------EESEEEEEEEEETTEEEEE-S
T ss_pred             cccCeeCCCEEEEEEcC----CCccCeEEEEEECC--------ceeeEEEEEEEeCCCEEEEec
Confidence            99999999999999764    78999999999864        124999999999999999864

; 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=98.45  E-value=1.5e-06  Score=54.34  Aligned_cols=52  Identities=19%  Similarity=0.217  Sum_probs=42.9

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCC-CEEEEeC
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEG-DVVEACE   64 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pG-D~v~~~~   64 (130)
                      |+|++.+||+|++++..   ..++.||++++..+         .+..++||+...++ +.+.+..
T Consensus        10 M~P~i~~gd~v~i~~~~---~~~~~G~iv~~~~~---------~~~~~ikrl~~~~~~~~~~l~~   62 (84)
T cd06462          10 MEPTIPDGDLVLVDKSS---YEPKRGDIVVFRLP---------GGELTVKRVIGLPGEGHYFLLG   62 (84)
T ss_pred             ccCcccCCCEEEEEecC---CCCcCCEEEEEEcC---------CCcEEEEEEEEECCCCEEEEEC
Confidence            99999999999999753   14899999999985         24899999999997 6665543

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

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

Probab=98.42  E-value=1.3e-06  Score=54.43  Aligned_cols=50  Identities=14%  Similarity=0.137  Sum_probs=42.7

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeC
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACE   64 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~   64 (130)
                      |+|++++||.|++++..    .++.||++++..+          +..++||+...+++.+.+..
T Consensus        10 M~p~i~~gd~lii~~~~----~~~~g~i~~~~~~----------~~~~ikr~~~~~~~~~~L~s   59 (81)
T cd06529          10 MEPTIPDGDLVLVDPSD----TPRDGDIVVARLD----------GELTVKRLQRRGGGRLRLIS   59 (81)
T ss_pred             cCCccCCCCEEEEcCCC----CCCCCCEEEEEEC----------CEEEEEEEEECCCCcEEEEe
Confidence            99999999999998753    4899999999984          37899999999977776653

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

>COG2932 Predicted transcriptional regulator [Transcription]

Probab=97.88  E-value=4e-05  Score=56.64  Aligned_cols=50  Identities=12%  Similarity=0.146  Sum_probs=41.6

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC   63 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~   63 (130)
                      |+|++++||.++|+.-.    +..+||.|++..-         .+..+|||+.-.+|-.+.+.
T Consensus       133 MeP~~~~Gd~ilVd~~~----~~~~gd~v~v~~~---------g~~~~VK~l~~~~~~~~~l~  182 (214)
T COG2932         133 MEPTYEDGDTLLVDPGV----NTRRGDRVYVETD---------GGELYVKKLQREPGGLLRLV  182 (214)
T ss_pred             ccccccCCCEEEECCCC----ceeeCCEEEEEEe---------CCeEEEEEEEEecCCeEEEE
Confidence            99999999999998643    5678997777653         46899999999999988664

>PRK10276 DNA polymerase V subunit UmuD; Provisional

Probab=96.96  E-value=0.0025  Score=44.16  Aligned_cols=41  Identities=20%  Similarity=0.159  Sum_probs=32.9

Q ss_pred             Cc-cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519            1 ML-RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK   55 (130)
Q Consensus         1 M~-Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~   55 (130)
                      |. |+|..||+|++++-.    .++.||+|++..          .+...+||+.-.
T Consensus        61 M~~~~I~~GD~liVd~~~----~~~~Gdivv~~~----------~g~~~vKrl~~~  102 (139)
T PRK10276         61 MIDAGISDGDLLIVDSAI----TASHGDIVIAAV----------DGEFTVKKLQLR  102 (139)
T ss_pred             CCCCCCCCCCEEEEECCC----CCCCCCEEEEEE----------CCEEEEEEEEEC
Confidence            86 689999999998642    578999999875          356889998753

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

Probab=96.89  E-value=0.00067  Score=47.95  Aligned_cols=45  Identities=16%  Similarity=0.109  Sum_probs=34.8

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEe
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK   55 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~   55 (130)
                      |+|..+.||.++.....  -...+.||+|+|+.+.        ...+.+-||+-+
T Consensus        58 MePaF~RGDlLfL~N~~--~~p~~vGdivVf~veg--------R~IPiVHRviK~  102 (180)
T KOG3342|consen   58 MEPAFHRGDLLFLTNRN--EDPIRVGDIVVFKVEG--------REIPIVHRVIKQ  102 (180)
T ss_pred             cCcccccccEEEEecCC--CCcceeccEEEEEECC--------ccCchhHHHHHH
Confidence            99999999999986422  2346899999999975        456777777754

>PRK12423 LexA repressor; Provisional

Probab=96.86  E-value=0.0058  Score=44.89  Aligned_cols=48  Identities=21%  Similarity=0.223  Sum_probs=36.8

Q ss_pred             Cc-cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe
Q 043519            1 ML-RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC   63 (130)
Q Consensus         1 M~-Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~   63 (130)
                      |. |+|.+||+|+|++-    ..++.||+|++..          .+...+||+.-. ++.+.+.
T Consensus       124 M~~~~i~~Gd~viv~~~----~~~~~Gdivv~~~----------~~~~~vKrl~~~-~~~~~L~  172 (202)
T PRK12423        124 MIDDGILDGDLVGVHRS----PEARDGQIVVARL----------DGEVTIKRLERS-GDRIRLL  172 (202)
T ss_pred             CCCCCcCCCCEEEEeCC----CcCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEEEE
Confidence            86 79999999999863    3678999999986          356899998755 3445443

>PRK00215 LexA repressor; Validated

Probab=96.77  E-value=0.0069  Score=44.26  Aligned_cols=47  Identities=13%  Similarity=0.113  Sum_probs=36.0

Q ss_pred             Cc-cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEE
Q 043519            1 ML-RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEA   62 (130)
Q Consensus         1 M~-Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~   62 (130)
                      |. |++.+||+|+|++-    ..++.||+|++...          +..++||+.-. ++.+.+
T Consensus       128 M~~~~i~~Gd~v~v~~~----~~~~~G~ivv~~~~----------~~~~vKrl~~~-~~~~~L  175 (205)
T PRK00215        128 MIDAGILDGDLVIVRKQ----QTARNGQIVVALID----------DEATVKRFRRE-GGHIRL  175 (205)
T ss_pred             CCCCCcCCCCEEEEeCC----CCCCCCCEEEEEEC----------CEEEEEEEEEe-CCEEEE
Confidence            84 79999999999863    25789999999873          47899999865 334444

>TIGR00498 lexA SOS regulatory protein LexA

Probab=96.67  E-value=0.01  Score=43.17  Aligned_cols=47  Identities=21%  Similarity=0.183  Sum_probs=36.3

Q ss_pred             Cc-cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEE
Q 043519            1 ML-RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEA   62 (130)
Q Consensus         1 M~-Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~   62 (130)
                      |. |++.+||+|++++.    ..++.||+|++..          .+...+||+.-. |+.+.+
T Consensus       121 M~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~----------~~~~~vKrl~~~-~~~i~L  168 (199)
T TIGR00498       121 MVDAGICDGDLLIVRSQ----KDARNGEIVAAMI----------DGEVTVKRFYKD-GTKVEL  168 (199)
T ss_pred             CCCCCCCCCCEEEEecC----CCCCCCCEEEEEE----------CCEEEEEEEEEE-CCEEEE
Confidence            75 68999999999864    3688999999987          357899998754 444444

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.

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

Probab=95.54  E-value=0.023  Score=39.62  Aligned_cols=29  Identities=28%  Similarity=0.415  Sum_probs=24.2

Q ss_pred             CceEEEEEEEeCCCEEEEeCCEEEECCEE
Q 043519           45 DGVYIKGIVAKEGDVVEACEGKLIVNGVV   73 (130)
Q Consensus        45 ~~~~vKRVig~pGD~v~~~~~~l~vng~~   73 (130)
                      ...++||++++|||.+...+..+++||++
T Consensus       137 ~~~~~~~~~~~~gd~~~~~~~~~~~~g~~  165 (166)
T COG0681         137 KKDYIKRVIGLPGDNILYTDDDLPINGKP  165 (166)
T ss_pred             ccccccceEEeeccceeeccCceeecCCC
Confidence            46799999999999999986448888764

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

Probab=89.08  E-value=1.8  Score=31.97  Aligned_cols=46  Identities=11%  Similarity=0.119  Sum_probs=31.7

Q ss_pred             cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEE
Q 043519            3 RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEA   62 (130)
Q Consensus         3 Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~   62 (130)
                      +.+.+||+|+|++-    .....||+|+....         ..+.-+||..-- |+.+.+
T Consensus       125 ~gi~dGDlvvV~~~----~~a~~GdiVvA~i~---------g~e~TvKrl~~~-g~~i~L  170 (201)
T COG1974         125 AGILDGDLVVVDPT----EDAENGDIVVALID---------GEEATVKRLYRD-GNQILL  170 (201)
T ss_pred             CcCCCCCEEEEcCC----CCCCCCCEEEEEcC---------CCcEEEEEEEEe-CCEEEE
Confidence            55678999999863    36788999998874         355788887643 444433

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=86.29  E-value=1.5  Score=33.29  Aligned_cols=61  Identities=15%  Similarity=0.193  Sum_probs=38.4

Q ss_pred             CccccccCCEEEEEcccc-------------CCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEE-------
Q 043519            1 MLRAYVVTSLRRKGSVTY-------------YFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVV-------   60 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~-------------~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v-------   60 (130)
                      |.|.|+.||.|++.-...             .++.++.|-+|-..+..             +-|+++--|--+       
T Consensus       109 ~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~k-------------VpRvig~~~sm~~~l~~~~  175 (239)
T COG1097         109 LRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSK-------------VPRVIGKKGSMLNMLKEKT  175 (239)
T ss_pred             cccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhh-------------cceEecCCCcHHHHhhhhc
Confidence            789999999998763221             23567777777776532             333443333222       


Q ss_pred             -----EEeCCEEEECCEEc
Q 043519           61 -----EACEGKLIVNGVVR   74 (130)
Q Consensus        61 -----~~~~~~l~vng~~~   74 (130)
                           .=.||.+||+++..
T Consensus       176 ~~~I~VG~NG~IWV~~~~~  194 (239)
T COG1097         176 GCEIIVGQNGRIWVDGENE  194 (239)
T ss_pred             CeEEEEecCCEEEecCCCc
Confidence                 22589999999865

>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]

Probab=82.98  E-value=1.4  Score=27.57  Aligned_cols=12  Identities=8%  Similarity=0.338  Sum_probs=6.5

Q ss_pred             CCCCcEEEEecC
Q 043519           23 PFANDILIFKSP   34 (130)
Q Consensus        23 ~~rGDiVvf~~p   34 (130)
                      +..||+|++...
T Consensus        47 I~~GD~V~Ve~~   58 (75)
T COG0361          47 ILPGDVVLVELS   58 (75)
T ss_pred             eCCCCEEEEEec
Confidence            345666665553

>TIGR00008 infA translation initiation factor IF-1

Probab=81.79  E-value=1.5  Score=26.90  Aligned_cols=12  Identities=8%  Similarity=0.058  Sum_probs=7.3

Q ss_pred             CCCCcEEEEecC
Q 043519           23 PFANDILIFKSP   34 (130)
Q Consensus        23 ~~rGDiVvf~~p   34 (130)
                      +..||.|.+...
T Consensus        45 I~~GD~V~Ve~s   56 (68)
T TIGR00008        45 ILPGDKVKVELS   56 (68)
T ss_pred             ECCCCEEEEEEC
Confidence            456666666654

This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).

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

Probab=80.67  E-value=5.6  Score=26.40  Aligned_cols=38  Identities=16%  Similarity=0.198  Sum_probs=23.6

Q ss_pred             CCCCCCCcEEEEecCCcccccccCCCceEEEEEEEe-CCCEEEEeC
Q 043519           20 FREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAK-EGDVVEACE   64 (130)
Q Consensus        20 ~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~-pGD~v~~~~   64 (130)
                      ...|+.||||+|....       ...--.+--|.++ .+++|.+.+
T Consensus        60 ~~~P~~Gdivv~~~~~-------~~~~GHVaIV~~v~~~~~i~v~e   98 (124)
T PF05257_consen   60 GSTPQPGDIVVWDSGS-------GGGYGHVAIVESVNDGGTITVIE   98 (124)
T ss_dssp             CS---TTEEEEEEECT-------TTTT-EEEEEEEE-TTSEEEEEE
T ss_pred             CcccccceEEEeccCC-------CCCCCeEEEEEEECCCCEEEEEE
Confidence            3579999999996221       1333466678888 888988754

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	130
1b12_A	248	Signal peptidase I; serine proteinase, serine-depe	100.0
1kca_A	109	Repressor protein CI; gene regulation, DNA-binding	98.83
1umu_A	116	UMUD'; induced mutagenesis, SOS mutagenesis, DNA r	98.6
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	98.11
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	98.1
2hnf_A	133	Repressor protein CI101-229DM-K192A; viral protein	98.08
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	97.42
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	94.3

>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=8.6e-35  Score=218.48  Aligned_cols=119  Identities=19%  Similarity=0.183  Sum_probs=97.3

Q ss_pred             CccccccCCEEEEEccccC------------CCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCC--E
Q 043519            1 MLRAYVVTSLRRKGSVTYY------------FREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEG--K   66 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~------------~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~--~   66 (130)
                      |+|||+.||+|+|+|++|.            .+.++|||||+|+.|.       ..+..+||||+|+|||+|+++++  +
T Consensus        16 M~Ptl~~GD~vlv~k~~yg~r~P~~~~~l~~~~~~~rGDIvvf~~p~-------~~~~~~iKRViglpGD~v~i~~~~~~   88 (248)
T 1b12_A           16 MMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE-------DPKLDYIKRAVGLPGDKVTYDPVSKE   88 (248)
T ss_dssp             TTTTSCTTEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTT-------CTTSEEEEEEEECTTCEEEEETTTTE
T ss_pred             ccccccCCCEEEEEecccCcccccccccccccCCCCCCcEEEEEeCC-------CCCceEEEEEEeeCCCEEEEEcCceE
Confidence            9999999999999998875            3579999999999986       35679999999999999999999  9


Q ss_pred             EEECC-----------EEccccccc---------------------------------------c-----------CCC-
Q 043519           67 LIVNG-----------VVRNKDFIL---------------------------------------E-----------APF-   84 (130)
Q Consensus        67 l~vng-----------~~~~~~~~~---------------------------------------~-----------~~~-   84 (130)
                      |||||           +.+.+++..                                       +           .+. 
T Consensus        89 l~ING~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ip~~~~~~~~~~~~~~~e~l~~~~~~~~~~p~~  168 (248)
T 1b12_A           89 LTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIA  168 (248)
T ss_dssp             EEEETTCCSSCCCCCCCCEEECCCEEEEEEEEEECGGGSCEEEEEEECCTTCCCTTEEEEEEEEEEETTEEEEEEECTTC
T ss_pred             EEECCccccccccccceeeeeeccccccccccccccccccccccccccccccccccchhhhhHHhhhcCccceeEecCCc
Confidence            99999           655432110                                       0           000 


Q ss_pred             ------C------CCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCCCC
Q 043519           85 ------Y------NMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHGNP  126 (130)
Q Consensus        85 ------~------~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~  126 (130)
                            +      ...+++||+|+         +|.||||||+||+++|+|||++++||+++.
T Consensus       169 ~~~~~~~~~~~~~~~~~~~VP~g~yFvmGDNR~nS~DSR~~G~Vp~~~IvGka~~i~~s~~~~  231 (248)
T 1b12_A          169 QDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDKQ  231 (248)
T ss_dssp             CCCGGGSCCCTTCCTTEEECCTTEEEEECSBTTSCCCHHHHCCEEGGGEEEEEEEEEEEBC--
T ss_pred             cccccchhcccccccccEEeCCCcEEEecCCCcccCCCCcccccCHHHeEEEEEEEEEeCCcc
Confidence                  0      12357899998         899999999999999999999999998865

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

Probab=98.83  E-value=3.3e-08  Score=64.98  Aligned_cols=79  Identities=13%  Similarity=-0.014  Sum_probs=55.5

Q ss_pred             cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccccC
Q 043519            3 RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEA   82 (130)
Q Consensus         3 Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~~~   82 (130)
                      |||.+||+|++++..    +++.||+|++..+         .+..++||++..+| .+.+...         +       
T Consensus        31 p~i~~Gd~v~Vd~~~----~~~~Gdivv~~~~---------~~~~~vKrl~~~~~-~~~L~s~---------N-------   80 (109)
T 1kca_A           31 PSFPDGMLILVDPEQ----AVEPGDFCIARLG---------GDEFTFKKLIRDSG-QVFLQPL---------N-------   80 (109)
T ss_dssp             SCCCTTCEEEEETTS----CCCTTCEEEEECS---------TTCEEEEEEEEETT-EEEEECS---------S-------
T ss_pred             CeeCCCCEEEEecCC----cCCCCCEEEEEEC---------CCeEEEEEEEEeCC-EEEEEEC---------C-------
Confidence            999999999999753    5899999999874         24789999998643 3333210         0       


Q ss_pred             CCCCCCCEEeCCCCCCCCCCccccccCCCeeeEEEEEEeeCCCCC
Q 043519           83 PFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPS  127 (130)
Q Consensus        83 ~~~~~~~~~vp~g~~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~g  127 (130)
                      +  .+.++.+.              ..-.|+|+|+..+||+..||
T Consensus        81 ~--~y~~~~~~--------------~~~~IiG~Vv~~~~~~~~~~  109 (109)
T 1kca_A           81 P--QYPMIPCN--------------ESCSVVGKVIASQWPEETFG  109 (109)
T ss_dssp             T--TSCCEECC--------------TTCEEEEEEEEEECCGGGGC
T ss_pred             C--CCCCEEcC--------------CCcEEEEEEEEEEeCHHHcC
Confidence            1  11223321              13579999999999988775

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

Probab=98.60  E-value=2.9e-07  Score=60.82  Aligned_cols=42  Identities=17%  Similarity=0.111  Sum_probs=36.3

Q ss_pred             Ccc-ccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeC
Q 043519            1 MLR-AYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKE   56 (130)
Q Consensus         1 M~P-tl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~p   56 (130)
                      |+| ||++||+|++++..    .++.||+|++..+          +..++||+...+
T Consensus        37 M~p~~i~~Gd~v~vd~~~----~~~~gdivv~~~~----------~~~~vKr~~~~~   79 (116)
T 1umu_A           37 MIDGGISDGDLLIVDSAI----TASHGDIVIAAVD----------GEFTVKKLQLRP   79 (116)
T ss_dssp             TGGGTCCTTCEEEEETTS----CCCTTCEEEEEET----------TEEEEEEEECSS
T ss_pred             cCCCCCCCCCEEEEEcCC----CCCCCCEEEEEEC----------CEEEEEEEEeCC
Confidence            999 89999999999753    5899999999873          478999999865

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

Probab=98.11  E-value=9.7e-06  Score=58.92  Aligned_cols=79  Identities=11%  Similarity=-0.007  Sum_probs=54.0

Q ss_pred             cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEccccccccC
Q 043519            3 RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILEA   82 (130)
Q Consensus         3 Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~~~   82 (130)
                      |+|.+||+|+|++-.    .+..||+|++...         .+..++||+...+|..+...+     |     ..|    
T Consensus       158 P~i~~Gd~v~vd~~~----~~~~g~ivv~~~~---------~~~~~vKrl~~~~~~~~L~s~-----N-----~~y----  210 (236)
T 3bdn_A          158 PSFPDGMLILVDPEQ----AVEPGDFCIARLG---------GDEFTFKKLIRGSGQVFLQPL-----N-----PQY----  210 (236)
T ss_dssp             SCCCSSCEEEECCSS----CCCTTSEEEEEST---------TTCCCCEEEECCSSSCEEECS-----S-----TTS----
T ss_pred             CcCCCCCEEEECCCC----CCCCCcEEEEEEC---------CCeEEEEEEEEcCCcEEEEeC-----C-----CCC----
Confidence            999999999998743    6899999999873         357899999876554332211     0     111    


Q ss_pred             CCCCCCCEEeCCCCCCCCCCccccccCCCeeeEEEEEEeeCCCCC
Q 043519           83 PFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPS  127 (130)
Q Consensus        83 ~~~~~~~~~vp~g~~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~g  127 (130)
                           .++.+.              ..-.|+|+|+..+||...|+
T Consensus       211 -----~~~~~~--------------~~~~IiG~Vv~~~~~~~~~~  236 (236)
T 3bdn_A          211 -----PMIPCN--------------ESCSVVGKVIASQWPEETFG  236 (236)
T ss_dssp             -----CCBC----------------CCCEEEEEEEECCCCSSSCC
T ss_pred             -----CCeecC--------------CCcEEEEEEEEEEcCHHhcC
Confidence                 111111              23479999999999988774

>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=98.10  E-value=8.2e-06  Score=58.30  Aligned_cols=48  Identities=21%  Similarity=0.254  Sum_probs=40.4

Q ss_pred             Cccc-cccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe
Q 043519            1 MLRA-YVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC   63 (130)
Q Consensus         1 M~Pt-l~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~   63 (130)
                      |+|+ |.+||+|+|++.    ..++.||+|++..          .+..++||+. .+|+.+.+.
T Consensus       120 M~p~~i~~Gd~v~vd~~----~~~~~G~i~v~~~----------~~~~~vKrl~-~~~~~~~l~  168 (202)
T 1jhf_A          120 MKDIGIMDGDLLAVHKT----QDVRNGQVVVARI----------DDEVTVKRLK-KQGNKVELL  168 (202)
T ss_dssp             TGGGTCCTTCEEEEEEC----SCCCTTSEEEEEE----------TTEEEEEEEE-EETTEEEEE
T ss_pred             CCCCCCCCCCEEEEecc----CCcCCCeEEEEEE----------CCEEEEEEEE-EeCCEEEEE
Confidence            9999 999999999874    2589999999986          2579999999 677777664

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

Probab=98.08  E-value=1.3e-05  Score=54.04  Aligned_cols=42  Identities=12%  Similarity=0.088  Sum_probs=35.1

Q ss_pred             cccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCC
Q 043519            3 RAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEG   57 (130)
Q Consensus         3 Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pG   57 (130)
                      |+|.+||+|+|++.    .+++.||+|++...         .+..++||++-.+|
T Consensus        62 p~i~~Gd~v~vd~~----~~~~~Gdivv~~~~---------~~~~~vKrl~~~~~  103 (133)
T 2hnf_A           62 TSFPDGMLILVDPE----QAVEPGDFCIARLG---------GDEFTFAKLIRDSG  103 (133)
T ss_dssp             CCCCTTCEEEEETT----SCCCTTSEEEEEET---------TTEEEEEEEEEETT
T ss_pred             CccCCCCEEEEccC----CCCCCCCEEEEEEC---------CCEEEEEEEEEeCC
Confidence            99999999999974    26899999999874         25789999987543

>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=97.42  E-value=0.00047  Score=49.06  Aligned_cols=42  Identities=12%  Similarity=-0.020  Sum_probs=34.2

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeC
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKE   56 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~p   56 (130)
                      .+|++.+||+|+|++.    ..++.||+|++..          .+..++||+.-.+
T Consensus       120 ~~p~i~~GD~viv~~~----~~~~~G~ivv~~~----------~~~~~vKr~~~~~  161 (196)
T 3k2z_A          120 IEEHICDGDLVLVRRQ----DWAQNGDIVAAMV----------DGEVTLAKFYQRG  161 (196)
T ss_dssp             GGGTCCTTCEEEEEEC----SCCCTTCEEEEEE----------TTEEEEEEEEEET
T ss_pred             CCCCCCCCCEEEEecc----CcCCCCCEEEEEE----------CCcEEEEEEEEEC
Confidence            0699999999999974    2688999999986          3579999997653

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

Probab=94.30  E-value=0.14  Score=35.26  Aligned_cols=43  Identities=5%  Similarity=0.125  Sum_probs=33.8

Q ss_pred             ccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEe
Q 043519            6 VVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEAC   63 (130)
Q Consensus         6 ~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~   63 (130)
                      .+||+|+|++-     .+..|+++++..          .+..+|||+.-.+|+.+.+.
T Consensus       120 ~~Gd~v~Vd~~-----~~~~g~i~vv~~----------~g~~~vKrl~~~~~~~i~L~  162 (189)
T 2fjr_A          120 SEGKIYFVDKQ-----ASLSDGLWLVDI----------KGAISIRELTKLPGRKLHVA  162 (189)
T ss_dssp             ETTEEEEEETT-----CCSCSEEEEEEE----------TTEEEEEEEEEETTTEEEEE
T ss_pred             eCCcEEEEEcC-----CccCCCEEEEEe----------CCeEEEEEEEECCCCEEEEE
Confidence            57999999863     256799999976          35789999998888777664

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	130
d1b12a_	247	Type 1 signal peptidase {Escherichia coli [TaxId:	99.97
d1f39a_	101	lambda repressor C-terminal domain {Bacteriophage	98.39
d1jhfa2	126	LexA C-terminal domain {Escherichia coli [TaxId: 5	97.54
d1umua_	105	UmuD' {Escherichia coli [TaxId: 562]}	97.29

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

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

Probab=99.97  E-value=8.3e-33  Score=204.70  Aligned_cols=118  Identities=18%  Similarity=0.135  Sum_probs=91.2

Q ss_pred             CccccccCCEEEEEccccCCC------------CCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEE
Q 043519            1 MLRAYVVTSLRRKGSVTYYFR------------EPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLI   68 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~------------~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~   68 (130)
                      |+|||+.||+|+|+|++|.++            .+++||+|+|..|.       .....++|||+|+|||+|++.+...+
T Consensus        15 MePTL~~GD~l~V~K~~Yg~r~P~~~~~~~~~~~~~rgdivvf~~p~-------~~~~~~ikR~ig~pGD~i~~~~~~~~   87 (247)
T d1b12a_          15 MMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGHPKRGDIVVFKYPE-------DPKLDYIKRAVGLPGDKVTYDPVSKE   87 (247)
T ss_dssp             TTTTSCTTEEEEEEESEEEEECGGGSCEEEEECCCCTTCEEEEECTT-------CTTSEEEEEEEECTTCEEEEETTTTE
T ss_pred             ccchhccCCEEEEEccccCccCCccCcccccccCcccCceeeecCCC-------CCCccccccccCCCCCeEEEecccce
Confidence            999999999999999998764            45999999999987       46778999999999999999865444


Q ss_pred             ECCEEcccc-------------------ccc--------------------------------------------c----
Q 043519           69 VNGVVRNKD-------------------FIL--------------------------------------------E----   81 (130)
Q Consensus        69 vng~~~~~~-------------------~~~--------------------------------------------~----   81 (130)
                      +|+....+.                   +..                                            .    
T Consensus        88 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (247)
T d1b12a_          88 LTIQPGCSSGQACENALPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIA  167 (247)
T ss_dssp             EEEETTCCSSCCCCCCCCEEECCCEEEEEEEEEECGGGSCEEEEEEECCTTCCCTTEEEEEEEEEEETTEEEEEEECTTC
T ss_pred             EEecccccccceeecceeecccccCcccceeeeeeccCceeccceeeccccccccCceEeeeeeeccCCcceeEEecccc
Confidence            433211000                   000                                            0    


Q ss_pred             ---------CCCCCCCCEEeCCCC---------CCCCCCccccccCCCeeeEEEEEEeeCCC
Q 043519           82 ---------APFYNMTPITVLENS---------NSYDLLVCLDELADHIPSSLDFKYQHHGN  125 (130)
Q Consensus        82 ---------~~~~~~~~~~vp~g~---------~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~  125 (130)
                               ........++||+|+         +|.|||+||+||+++|+|||++++||+++
T Consensus       168 ~~~~~~~~~~~~~~~~~~~Vp~~~yfvmGDNR~nS~DSR~wG~Vp~~~I~Gka~~i~~p~~~  229 (247)
T d1b12a_         168 QDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAIWMSFDK  229 (247)
T ss_dssp             CCCGGGSCCCTTCCTTEEECCTTEEEEECSBTTSCCCHHHHCCEEGGGEEEEEEEEEEEBC-
T ss_pred             hhcccccccCCccccceEEEeCCeEEEecCCCCCCccccccCcCCHHHeEEEEEEEEEECCC
Confidence                     000123457899998         99999999999999999999999999863

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

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

Probab=98.39  E-value=2.7e-06  Score=53.53  Aligned_cols=80  Identities=14%  Similarity=0.020  Sum_probs=54.5

Q ss_pred             ccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEEeCCEEEECCEEcccccccc
Q 043519            2 LRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEACEGKLIVNGVVRNKDFILE   81 (130)
Q Consensus         2 ~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~~~~~l~vng~~~~~~~~~~   81 (130)
                      +|+|.+||+|+|++-    ..++.||+|++...         .+...+||+.-.+| .+.+..         .+      
T Consensus        22 ep~i~~Gd~viVd~~----~~~~~g~ivva~~~---------~~~~~vKr~~~~~~-~~~L~s---------~N------   72 (101)
T d1f39a_          22 KPSFPDGMLILVDPE----QAVEPGDFCIARLG---------GDEFTFKKLIRDSG-QVFLQP---------LN------   72 (101)
T ss_dssp             SSCCCTTCEEEEETT----SCCCTTCEEEEECT---------TSCEEEEEEEEETT-EEEEEC---------SS------
T ss_pred             CCCcCCCCEEEEEec----CccCCCCEEEEEEC---------CCeEEEEEEEEcCC-EEEEEE---------CC------
Confidence            799999999999974    36899999998764         35678999975533 333321         00      


Q ss_pred             CCCCCCCCEEeCCCCCCCCCCccccccCCCeeeEEEEEEeeCCCCC
Q 043519           82 APFYNMTPITVLENSNSYDLLVCLDELADHIPSSLDFKYQHHGNPS  127 (130)
Q Consensus        82 ~~~~~~~~~~vp~g~~S~DSR~~G~V~~~~I~Gkv~~~~~P~~~~g  127 (130)
                       +  +..++.+.+              .-.|+|+|+..+||-.-||
T Consensus        73 -~--~y~~i~~~~--------------~~~IiG~Vv~s~~p~~~~~  101 (101)
T d1f39a_          73 -P--QYPMIPCNE--------------SCSVVGKVIASQWPEETFG  101 (101)
T ss_dssp             -T--TSCCEECST--------------TCEEEEEEEEEECCGGGGC
T ss_pred             -C--CCCCCcCCC--------------CcEEEEEEEEEECcHHHCC
Confidence             1  112333321              2479999999999987665

>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=97.54  E-value=0.00014  Score=46.94  Aligned_cols=47  Identities=17%  Similarity=0.191  Sum_probs=37.9

Q ss_pred             Cccc-cccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEEEeCCCEEEE
Q 043519            1 MLRA-YVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIVAKEGDVVEA   62 (130)
Q Consensus         1 M~Pt-l~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVig~pGD~v~~   62 (130)
                      |+|+ +.+||+|++++-    .+++.||+|++..          .++.++||+.-.+ +.+.+
T Consensus        48 M~~~~i~~gd~viv~~~----~~~~~G~ivv~~~----------~ge~~vKrl~~~~-~~~~L   95 (126)
T d1jhfa2          48 MKDIGIMDGDLLAVHKT----QDVRNGQVVVARI----------DDEVTVKRLKKQG-NKVEL   95 (126)
T ss_dssp             TGGGTCCTTCEEEEEEC----SCCCTTSEEEEEE----------TTEEEEEEEEEET-TEEEE
T ss_pred             ccCcccCCCEEEEEecc----ccccCCCEEEEEE----------CCEEEEEEEEEcC-CEEEE
Confidence            9998 999999999874    3789999999997          3579999998653 33443

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

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

Probab=97.29  E-value=0.00023  Score=44.70  Aligned_cols=39  Identities=18%  Similarity=0.078  Sum_probs=32.7

Q ss_pred             CccccccCCEEEEEccccCCCCCCCCcEEEEecCCcccccccCCCceEEEEEE
Q 043519            1 MLRAYVVTSLRRKGSVTYYFREPFANDILIFKSPPLLQEVGYTDDGVYIKGIV   53 (130)
Q Consensus         1 M~Ptl~~gd~vlv~k~~~~~~~~~rGDiVvf~~p~~~~~~~~~~~~~~vKRVi   53 (130)
                      +.|.+.+||++++++-.    +++.||+|++..          .++.++||+.
T Consensus        31 ~~~gI~~GDlliVd~~~----~~~~g~ivva~i----------~ge~~vKrl~   69 (105)
T d1umua_          31 IDGGISDGDLLIVDSAI----TASHGDIVIAAV----------DGEFTVKKLQ   69 (105)
T ss_dssp             GGGTCCTTCEEEEETTS----CCCTTCEEEEEE----------TTEEEEEEEE
T ss_pred             ccCccCCCCEEEEEccc----ccccCcEEEEEE----------CCEEEEEEEE
Confidence            05889999999999843    689999999998          3579999975