Citrus Sinensis ID: 028218

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210--
Protein Sequence
MLGKSVASPLLSASPCPSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLKKWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHEEEEHHHHHHccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccHHHHHcccccHHHHHHHHHHHHHccccHHHHHHHHHHcccEEEcccccccHHHHHHHHHcccccHHHHHHHHHHcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccEcccccccccccccccccccEEEccccccccccHEEEEcccHHHcccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccHHHHccccccHHHHHHHHHHHHHccccHHHHHHHHHHccHEccccHHHHHHHHHHHHHHHcccccHHHHHHHHHcccEcccccccccccccccccEEEEc
Coil and Loop (DISEMBL)
mlgksvaspllsaspcpsapdistttpnnvplnvnlsnglppnairvpwsshvYLKKWAIYSTAQVQSITLNDEERKKWEACRQALStfnfsteeEDKILGKAFGHIHSAywseerkretpelETVSEILGYLRNLSLSDDDIRKLLKKFpevlgcdiehELRNNVQILGKDWGIEGKYLRNLLlrnpkvlgynvdckgdcmaqctrcwvrf
Flexible Loop (DISEMBL)
mlgksvaspllsaspcpsAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLKKWAIYSTAQVQSITLNDEERKKWEACRQALstfnfsteeeDKILGKAFGHIHSAywseerkretpELETVSEILGYLRNLSLSDDDIRKLLKKFPEvlgcdiehelrnnvqilgkdWGIEGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF
Low Complexity Region (SEG)
MLGKSVaspllsaspcpsapDIstttpnnvplnvnlsnglppnAIRVPWSSHVYLKKWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF
Disordered region (IsUnstruct)
*********************************VNLSNGLPPNAIRVPWSSHVYLKKWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSE********LETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWV**
Disordered Region (DISOPRED)
***********SASPCPSAPDISTTTPN******************************AIYSTAQ*************WEACRQALSTFNFSTEEEDKILGKAFGHIHSAYW***********ETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF
Disordered Region (DISEMBL)
***************CPSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLKKWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWS***********TVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF
Disordered Region (DISPRO)
***********SASPCPSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLKKWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLGKSVASPLLSASPCPSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLKKWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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	212
225460737	212	PREDICTED: uncharacterized protein LOC10	0.981	0.981	0.680	6e-80
255571762	222	conserved hypothetical protein [Ricinus	0.976	0.932	0.611	5e-74
224135523	215	predicted protein [Populus trichocarpa]	0.995	0.981	0.629	1e-72
449490118	216	PREDICTED: uncharacterized protein LOC10	1.0	0.981	0.578	2e-67
449441758	216	PREDICTED: uncharacterized protein LOC10	1.0	0.981	0.578	4e-67
255645600	216	unknown [Glycine max]	0.995	0.976	0.576	1e-66
356576155	235	PREDICTED: uncharacterized protein LOC10	0.995	0.897	0.571	2e-65
297813391	214	hypothetical protein ARALYDRAFT_489815 [	0.971	0.962	0.550	1e-60
15810253	210	unknown protein [Arabidopsis thaliana]	0.966	0.976	0.562	1e-59
30681137	212	Mitochondrial transcription termination	0.966	0.966	0.562	1e-59

>gi|225460737|ref|XP_002272640.1| PREDICTED: uncharacterized protein LOC100241910 [Vitis vinifera] gi|296081139|emb|CBI18165.3| unnamed protein product [Vitis vinifera]

 Score =  302 bits (773), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 147/216 (68%), Positives = 170/216 (78%), Gaps = 8/216 (3%)

Query: 1   MLGKSVASPLLS----ASPCPSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLK 56
           MLGKS ASPLL+    A    S+ D++T  PNN+    N SNG+ PN  R   +S    K
Sbjct: 1   MLGKSFASPLLTLDFTARLSFSSTDLATAAPNNL----NFSNGILPNVTRGACTSLAATK 56

Query: 57  KWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEER 116
           KW ++STAQ  SITLNDE+ K WEAC+QALS F FS EEEDKILGKAFGH+HS YWSEER
Sbjct: 57  KWELHSTAQTASITLNDEDGKAWEACKQALSVFQFSDEEEDKILGKAFGHVHSPYWSEER 116

Query: 117 KRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIE 176
           K+E P+ E VSE L YLR+L+LSDDD+ KLLKKFPEVLGC +E ELRNNVQ+L K+WGIE
Sbjct: 117 KKEVPQFEIVSEKLEYLRSLNLSDDDLGKLLKKFPEVLGCSLEEELRNNVQVLAKEWGIE 176

Query: 177 GKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
           GK L+N+LLRNPKVLGYNVDC+GDCMAQCTRCWVRF
Sbjct: 177 GKSLKNVLLRNPKVLGYNVDCRGDCMAQCTRCWVRF 212

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255571762|ref|XP_002526824.1| conserved hypothetical protein [Ricinus communis] gi|223533828|gb|EEF35559.1| conserved hypothetical protein [Ricinus communis]

 Score =  282 bits (722), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 132/216 (61%), Positives = 165/216 (76%), Gaps = 9/216 (4%)

Query: 1   MLGKSVASPLLSASPCPS----APDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLK 56
           MLG+S  SPLL+     S     PD++T   N     V     L  N  +  W+SH+  K
Sbjct: 12  MLGRSPVSPLLTLDSGISLSFLGPDLATAARN-----VKFCGALSSNTFQGAWTSHLSPK 66

Query: 57  KWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEER 116
           KW ++STAQ+ ++ LNDE++K WEACR+ALS F FS +E+DKILGKAFGH+HS YW EER
Sbjct: 67  KWIVHSTAQIDNLALNDEQKKTWEACREALSAFEFSAQEKDKILGKAFGHVHSPYWGEER 126

Query: 117 KRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIE 176
           K++ P++E VS I+ YLR+L LSDD++ K++KKFPEVLGC +EH+L+NNV+IL KDWGI+
Sbjct: 127 KQQVPDIEIVSGIIDYLRSLGLSDDELYKVVKKFPEVLGCSLEHDLKNNVKILEKDWGIK 186

Query: 177 GKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
           GK LRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF
Sbjct: 187 GKTLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 222

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135523|ref|XP_002327239.1| predicted protein [Populus trichocarpa] gi|222835609|gb|EEE74044.1| predicted protein [Populus trichocarpa]

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 136/216 (62%), Positives = 161/216 (74%), Gaps = 5/216 (2%)

Query: 1   MLGKSVASPLLS----ASPCPSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLK 56
           MLG+S+ASPLL+    A      PD+ T  PN   LNVN S  LP N  R   +SH   +
Sbjct: 1   MLGRSLASPLLTFDSAARSSCVTPDLVTAAPNAACLNVN-SLALPSNVTRGYCTSHFSPR 59

Query: 57  KWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEER 116
           KWAI STAQ  + T ++E+RK WEACR+ALS FNF+ EE+DKILGKAFGH+HS YW E+R
Sbjct: 60  KWAIQSTAQADNTTFSNEDRKTWEACREALSAFNFNAEEKDKILGKAFGHVHSPYWGEQR 119

Query: 117 KRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIE 176
           K E P+ E V E L YLR+L LS+DD+ KLLKKFPEVLGC +E EL+ NV+IL KDWGI+
Sbjct: 120 KLEVPKFEIVCETLDYLRSLGLSEDDLFKLLKKFPEVLGCSLEQELKTNVKILEKDWGIK 179

Query: 177 GKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
           GK L+ LLLRNPK LGYNVDCKGDC+AQCTRCW RF
Sbjct: 180 GKSLQKLLLRNPKALGYNVDCKGDCIAQCTRCWARF 215

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449490118|ref|XP_004158513.1| PREDICTED: uncharacterized protein LOC101229745 isoform 1 [Cucumis sativus] gi|449490122|ref|XP_004158514.1| PREDICTED: uncharacterized protein LOC101229745 isoform 2 [Cucumis sativus]

 Score =  261 bits (666), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 125/216 (57%), Positives = 162/216 (75%), Gaps = 4/216 (1%)

Query: 1   MLGKSVASPLLSASP----CPSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLK 56
           MLGKS+ASP+ +       C S    +T   + V  +V+ S     + I+     + Y +
Sbjct: 1   MLGKSLASPISTIDSATRFCCSTRCTATAISDAVCSHVSFSCHSAKHTIKGVRRQNSYPR 60

Query: 57  KWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEER 116
           KW I S+ QV+S+ L+DE++K WEACRQALS F+FS EE+DK+LGKAFGHIHS YW E+R
Sbjct: 61  KWEICSSTQVESLILSDEDKKTWEACRQALSVFSFSVEEQDKMLGKAFGHIHSPYWGEDR 120

Query: 117 KRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIE 176
           +++ P +E V++IL YLR L LS+DD+ KLLKKFPEVLGC++E EL+ NVQ+L K+WGI+
Sbjct: 121 EKKVPNIEIVNDILEYLRTLGLSNDDLSKLLKKFPEVLGCNLEQELKTNVQLLDKEWGIQ 180

Query: 177 GKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
           GK LRNLLLRNPKVLGY VDCKGDC+A+CTRCWVRF
Sbjct: 181 GKSLRNLLLRNPKVLGYYVDCKGDCIAKCTRCWVRF 216

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449441758|ref|XP_004138649.1| PREDICTED: uncharacterized protein LOC101218603 isoform 1 [Cucumis sativus] gi|449441760|ref|XP_004138650.1| PREDICTED: uncharacterized protein LOC101218603 isoform 2 [Cucumis sativus]

 Score =  259 bits (663), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 125/216 (57%), Positives = 162/216 (75%), Gaps = 4/216 (1%)

Query: 1   MLGKSVASPLLSASP----CPSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLK 56
           MLGKS+ASP+ +       C S    +T   + V  +V+ S     + I+     + Y +
Sbjct: 1   MLGKSLASPISTIDSATRFCCSTRCTATAISDAVCSHVSFSCHSAKHTIKGVRRQNPYPR 60

Query: 57  KWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEER 116
           KW I S+ QV+S+ L+DE++K WEACRQALS F+FS EE+DK+LGKAFGHIHS YW E+R
Sbjct: 61  KWEICSSTQVESLILSDEDKKTWEACRQALSVFSFSVEEQDKMLGKAFGHIHSPYWGEDR 120

Query: 117 KRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIE 176
           +++ P +E V++IL YLR L LS+DD+ KLLKKFPEVLGC++E EL+ NVQ+L K+WGI+
Sbjct: 121 EKKVPNIEIVNDILEYLRTLGLSNDDLSKLLKKFPEVLGCNLEQELKTNVQLLDKEWGIQ 180

Query: 177 GKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
           GK LRNLLLRNPKVLGY VDCKGDC+A+CTRCWVRF
Sbjct: 181 GKSLRNLLLRNPKVLGYYVDCKGDCIAKCTRCWVRF 216

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255645600|gb|ACU23294.1| unknown [Glycine max]

 Score =  258 bits (660), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 125/217 (57%), Positives = 165/217 (76%), Gaps = 6/217 (2%)

Query: 1   MLGKSVASPLL----SASPCPSAPDISTTTPNNVPL-NVNLSNGLPPNAIRVPWSSHVYL 55
           MLGK + SPLL    SA  C    D++  + +++PL N+  S    P+     W+S++  
Sbjct: 1   MLGKRLNSPLLIIDSSAQFCYCKTDLAAAS-SSIPLPNMRFSCRFSPSVAAETWTSNLSS 59

Query: 56  KKWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEE 115
           K+W ++STAQ+++I  ++E++  WEAC+QALS FNFS EE+DKILGKAFG IHS YW EE
Sbjct: 60  KQWILHSTAQIENIITSNEDQSMWEACKQALSAFNFSDEEKDKILGKAFGLIHSPYWGEE 119

Query: 116 RKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGI 175
           R +E P+L+TV+ +L YLR+L+LSDDD+  LLKKFPEVLGC++E EL+ NV+IL + WGI
Sbjct: 120 RSKEVPKLKTVNGVLDYLRSLNLSDDDLSILLKKFPEVLGCNLEEELKGNVKILEEQWGI 179

Query: 176 EGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
           +G +LR LLLRNPKVLGYNVDCKGDC+AQCTRCW RF
Sbjct: 180 KGNFLRKLLLRNPKVLGYNVDCKGDCIAQCTRCWARF 216

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576155|ref|XP_003556199.1| PREDICTED: uncharacterized protein LOC100797265 [Glycine max]

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 124/217 (57%), Positives = 163/217 (75%), Gaps = 6/217 (2%)

Query: 1   MLGKSVASPLL----SASPCPSAPDISTTTPNNVPL-NVNLSNGLPPNAIRVPWSSHVYL 55
           MLGK + SPLL    SA  C    D++  + +++PL N+  S    P+     W+S++  
Sbjct: 20  MLGKRLNSPLLIIDSSAQFCYCKTDLAAAS-SSIPLPNMRFSCRFSPSVAAETWTSNLSS 78

Query: 56  KKWAIYSTAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEE 115
           K+W ++STAQ+++I  ++E++  WEAC+QALS FNFS EE+DKILGKAFG IHS YW EE
Sbjct: 79  KQWILHSTAQIENIITSNEDQSMWEACKQALSAFNFSDEEKDKILGKAFGLIHSPYWGEE 138

Query: 116 RKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGI 175
           R +E P+L+TV+ +L YLR+L+LSDDD+  LLKKFPEVLGC++E EL+ NV+IL + W I
Sbjct: 139 RSKEVPKLKTVNGVLDYLRSLNLSDDDLSILLKKFPEVLGCNLEEELKGNVKILEEQWSI 198

Query: 176 EGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
           +G  LR LLLRNPKVLGYNVDCKGDC+AQCTRCW RF
Sbjct: 199 KGNSLRKLLLRNPKVLGYNVDCKGDCIAQCTRCWARF 235

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297813391|ref|XP_002874579.1| hypothetical protein ARALYDRAFT_489815 [Arabidopsis lyrata subsp. lyrata] gi|297320416|gb|EFH50838.1| hypothetical protein ARALYDRAFT_489815 [Arabidopsis lyrata subsp. lyrata]

 Score =  238 bits (608), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 120/218 (55%), Positives = 159/218 (72%), Gaps = 12/218 (5%)

Query: 1   MLGKSVASPLLSASPC-----PSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYL 55
           M+G S+ASPL +  P      P+   ++ TT   + LN N S       +R   +S +  
Sbjct: 3   MVGNSLASPLATLGPAKCFRHPTGDLVTYTTVLPLSLNSNSSYHGVIGGVR---TSLISR 59

Query: 56  KKWAIY-STAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSE 114
           KKW ++ ST QV++   ++E+ K WE C++ALS F+FS EE+DKILGKAFGHIHS YW+E
Sbjct: 60  KKWIVFCSTTQVET---SNEDPKTWEECKEALSCFDFSVEEKDKILGKAFGHIHSPYWTE 116

Query: 115 ERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWG 174
           ER +E P++ET+++IL +LR+L LSD+D+ K++KKFPEVLGC +E E++ N+ IL   WG
Sbjct: 117 ERVKENPKVETLNQILEFLRSLGLSDEDLHKVMKKFPEVLGCSLEEEMKPNIGILENQWG 176

Query: 175 IEGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
           I GK LRNLLLRNPKVLGYNVDCKGDC+AQCTRCWVRF
Sbjct: 177 ITGKQLRNLLLRNPKVLGYNVDCKGDCVAQCTRCWVRF 214

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15810253|gb|AAL07014.1| unknown protein [Arabidopsis thaliana]

 Score =  235 bits (599), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 122/217 (56%), Positives = 161/217 (74%), Gaps = 12/217 (5%)

Query: 1   MLGKSVASPL--LSASPC--PSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLK 56
           M+G S+ASPL  L ++ C   SA D+ T T N +PL +N S       +R   +S     
Sbjct: 1   MVGNSLASPLATLGSAKCFRHSAVDLVTYT-NVLPLRLNSSYHGVNGGVR---TSSYSRS 56

Query: 57  KWAIY-STAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEE 115
           KW ++ ST QV++   ++E+   WE C++ALS F+FS EE+DKILGKAFGHIHS YW+EE
Sbjct: 57  KWIVFCSTTQVET---SNEDPNIWEECKEALSCFDFSVEEKDKILGKAFGHIHSPYWTEE 113

Query: 116 RKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGI 175
           R +E P++ET+++IL +LR+L LSD+D+ K++KKFPEVLGC +E E++ N+ IL   WGI
Sbjct: 114 RVKENPKVETLNQILEFLRSLGLSDEDLHKVMKKFPEVLGCSLEEEMKPNIGILENQWGI 173

Query: 176 EGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
           +GK LRNLLLRNPKVLGYNVDCKGDC+AQCTRCWVRF
Sbjct: 174 KGKQLRNLLLRNPKVLGYNVDCKGDCVAQCTRCWVRF 210

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30681137|ref|NP_192700.2| Mitochondrial transcription termination factor family protein [Arabidopsis thaliana] gi|332657372|gb|AEE82772.1| Mitochondrial transcription termination factor family protein [Arabidopsis thaliana]

 Score =  234 bits (598), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 122/217 (56%), Positives = 160/217 (73%), Gaps = 12/217 (5%)

Query: 1   MLGKSVASPL--LSASPC--PSAPDISTTTPNNVPLNVNLSNGLPPNAIRVPWSSHVYLK 56
           M+G S+ASPL  L ++ C   SA D+ T T N +PL +N S       +R   +S     
Sbjct: 3   MVGNSLASPLATLGSAKCFRHSAVDLVTYT-NVLPLRLNSSYHGVNGGVR---TSSYSRS 58

Query: 57  KWAIY-STAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEE 115
           KW ++ ST QV++   ++E+   WE C++ALS F+FS EE+DKILGKAFGHIHS YW+EE
Sbjct: 59  KWIVFCSTTQVET---SNEDPNIWEECKEALSCFDFSVEEKDKILGKAFGHIHSPYWTEE 115

Query: 116 RKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGI 175
           R +E P++ET+++IL +LR+L LSD+D+ K++KKFPEVLGC +E E++ N+ IL   WGI
Sbjct: 116 RVKENPKVETLNQILEFLRSLGLSDEDLHKVMKKFPEVLGCSLEEEMKPNIGILENQWGI 175

Query: 176 EGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
            GK LRNLLLRNPKVLGYNVDCKGDC+AQCTRCWVRF
Sbjct: 176 TGKQLRNLLLRNPKVLGYNVDCKGDCVAQCTRCWVRF 212

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	212
TAIR|locus:2136902	212	AT4G09620 "AT4G09620" [Arabido	0.721	0.721	0.643	2.3e-55

TAIR|locus:2136902 AT4G09620 "AT4G09620" [Arabidopsis thaliana (taxid:3702)]

 Score = 571 (206.1 bits), Expect = 2.3e-55, P = 2.3e-55
 Identities = 101/157 (64%), Positives = 130/157 (82%)

Query:    57 KWAIY-STAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEE 115
             KW ++ ST QV++   ++E+   WE C++ALS F+FS EE+DKILGKAFGHIHS YW+EE
Sbjct:    59 KWIVFCSTTQVET---SNEDPNIWEECKEALSCFDFSVEEKDKILGKAFGHIHSPYWTEE 115

Query:   116 RKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGI 175
             R +E P++ET+++IL +LR+L LSD+D+ K++KKFPEVLGC +E E++ N+ IL   WGI
Sbjct:   116 RVKENPKVETLNQILEFLRSLGLSDEDLHKVMKKFPEVLGCSLEEEMKPNIGILENQWGI 175

Query:   176 EGKYLRNLLLRNPKVLGYNVDCKGDCMAQCTRCWVRF 212
              GK LRNLLLRNPKVLGYNVDCKGDC+AQCTRCWVRF
Sbjct:   176 TGKQLRNLLLRNPKVLGYNVDCKGDCVAQCTRCWVRF 212


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        0.320   0.136   0.428    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      212       177   0.00084  109 3  11 22  0.41    32
                                                     31  0.50    34


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:  1
  No. of states in DFA:  597 (63 KB)
  Total size of DFA:  186 KB (2106 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:  19.71u 0.08s 19.79t   Elapsed:  00:00:01
  Total cpu time:  19.71u 0.08s 19.79t   Elapsed:  00:00:01
  Start:  Fri May 10 08:07:01 2013   End:  Fri May 10 08:07:02 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	212
PLN03196	487	PLN03196, PLN03196, MOC1-like protein; Provisional	7e-05

>gnl|CDD|215628 PLN03196, PLN03196, MOC1-like protein; Provisional

 Score = 42.4 bits (100), Expect = 7e-05
 Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 13/83 (15%)

Query: 128 EILG------------YLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGI 175
           EILG            YL +L L    + ++L+K P +LG D+E  ++ NV+ L  ++G+
Sbjct: 222 EILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECL-LEFGV 280

Query: 176 EGKYLRNLLLRNPKVLGYNVDCK 198
             + L +++ + P +LG ++  K
Sbjct: 281 RKEALPSVIAQYPDILGLDLKAK 303

Length = 487

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	212
PF02536	345	mTERF: mTERF; InterPro: IPR003690 This family curr	99.73
PLN03196	487	MOC1-like protein; Provisional	99.7
PLN03196	487	MOC1-like protein; Provisional	99.6
PF02536	345	mTERF: mTERF; InterPro: IPR003690 This family curr	99.52
KOG1267	413	consensus Mitochondrial transcription termination	99.11
KOG1267	413	consensus Mitochondrial transcription termination	99.09
smart00733	31	Mterf Mitochondrial termination factor repeats. Hu	97.58
smart00733	31	Mterf Mitochondrial termination factor repeats. Hu	91.8
PF04695	136	Pex14_N: Peroxisomal membrane anchor protein (Pex1	91.05
PF07499	47	RuvA_C: RuvA, C-terminal domain; InterPro: IPR0111	88.87
PF14490	94	HHH_4: Helix-hairpin-helix containing domain; PDB:	88.77
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	87.62
COG1725	125	Predicted transcriptional regulators [Transcriptio	86.75
PF07499	47	RuvA_C: RuvA, C-terminal domain; InterPro: IPR0111	86.67
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	86.26
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	81.97
PRK02249	343	DNA primase large subunit; Validated	81.16

>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []

Probab=99.73  E-value=2.2e-18  Score=152.59  Aligned_cols=123  Identities=21%  Similarity=0.376  Sum_probs=94.7

Q ss_pred             cChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhh--------------------h-hhcCCChhhHHHH
Q 028218           71 LNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEE--------------------R-KRETPELETVSEI  129 (212)
Q Consensus        71 ~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a--------------------~-~~~v~s~e~i~ak  129 (212)
                      +.-+..++|+..+++|+.+|++.+++.+++.+.+.+.....-+..                    . .....+.+++..+
T Consensus       167 l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~  246 (345)
T PF02536_consen  167 LLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPK  246 (345)
T ss_dssp             HCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHH
T ss_pred             hccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHH
Confidence            333444679999999999999999999999998887433321100                    0 0011457789999


Q ss_pred             HHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeecccccc
Q 028218          130 LGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCK  198 (212)
Q Consensus       130 lefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~R  198 (212)
                      ++||+++|||++||.+++.++|.||++|+| +|+++++||++++|++    .++|+++|++|+||||+|
T Consensus       247 i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e-~l~~k~~fl~~~m~~~----~~~i~~~P~~l~~sLe~r  310 (345)
T PF02536_consen  247 IEFLQSLGFSEEEIAKMVRRFPQILSYSIE-KLKPKFEFLVKEMGLP----LEEIVEFPQYLSYSLEKR  310 (345)
T ss_dssp             HHHHHTTT--HHHHHHHHHHSGGGGGS-HH-HHHHHHHHHHHCCT------HHHHHHSCHHHCS-HHHH
T ss_pred             HHHHHHhcCcHHHHHHHHHhCcchhhcchh-hhhHHHHHHHHHhCcC----HHHHhhCCceeEechhhh
Confidence            999999999999999999999999999955 5999999999999997    789999999999999986

The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.

>PLN03196 MOC1-like protein; Provisional

Probab=99.70  E-value=3.8e-17  Score=155.48  Aligned_cols=106  Identities=15%  Similarity=0.282  Sum_probs=87.5

Q ss_pred             HHHHHHHHHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceee
Q 028218           77 KKWEACRQAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLG  155 (212)
Q Consensus        77 ~~we~~v~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg  155 (212)
                      ++++..+++| +.+|++++++..++.+++.+.+            .+++++.+|++||+++||+++||.++|+|+|++|+
T Consensus       302 ~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~------------lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~  369 (487)
T PLN03196        302 AKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVS------------LNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILA  369 (487)
T ss_pred             HhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhc------------ccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceee
Confidence            3445555555 4666666666666555543322            47899999999999999999999999999999999


Q ss_pred             cCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccccc
Q 028218          156 CDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKG  199 (212)
Q Consensus       156 ~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~Rg  199 (212)
                      +|+ ++|+++++||++++|++    .++|+++|++|+||||+|=
T Consensus       370 ~S~-~~l~~k~dFlvneMg~~----~~~Iv~fP~~LsySLEkRI  408 (487)
T PLN03196        370 LNL-EIMKPSLEFFKKEMKRP----LKELVEFPAYFTYGLESRI  408 (487)
T ss_pred             ccH-HHHHHHHHHHHHHhCCC----HHHHHhChHHhccChhhhh
Confidence            995 89999999999999997    8999999999999999883

>PLN03196 MOC1-like protein; Provisional

Probab=99.60  E-value=2.1e-15  Score=143.62  Aligned_cols=120  Identities=19%  Similarity=0.343  Sum_probs=80.9

Q ss_pred             HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccch----------hhhhhh-------------h--cCCChhhHHHHHH
Q 028218           77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAY----------WSEERK-------------R--ETPELETVSEILG  131 (212)
Q Consensus        77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~----------fr~a~~-------------~--~v~s~e~i~akle  131 (212)
                      +++.-.++||+.+|++..++.+++.+.+.++++..          ++....             .  ..--+.++..+++
T Consensus       122 ~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~  201 (487)
T PLN03196        122 KNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVA  201 (487)
T ss_pred             hhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHH
Confidence            45555666666666666666666666655533321          110000             0  0011346778888


Q ss_pred             HHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccc
Q 028218          132 YLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDC  197 (212)
Q Consensus       132 fLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~  197 (212)
                      ||+++|+++++|++++.++|+||+++++++|+|+++||.+ +|++.+++.++|.++|.+|++|+|+
T Consensus       202 fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~-lGv~~~~I~~il~~~P~iL~~sle~  266 (487)
T PLN03196        202 YLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLES-LGLPRLAVARILEKRPYILGFDLEE  266 (487)
T ss_pred             HHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHH-cCCCHHHHHHHHHhCCceeEcCHHH
Confidence            8888888888888888888888888888888888888874 7888888888888888888888875

>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []

Probab=99.52  E-value=6e-15  Score=130.73  Aligned_cols=109  Identities=24%  Similarity=0.455  Sum_probs=95.1

Q ss_pred             HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeec
Q 028218           77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGC  156 (212)
Q Consensus        77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~  156 (212)
                      ..|++.+++|..+|++++....++.+.+.+...           .+++++.++++||+++||+++++.+++.++|.+|++
T Consensus       137 ~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~-----------~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~  205 (345)
T PF02536_consen  137 EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLS-----------DSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSL  205 (345)
T ss_dssp             HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCG-----------SCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGC
T ss_pred             hHHHHHHHHHHHhCCCchhhcccccccchhhcc-----------ccHHHHHHHHHHHHhhcccchhhhHHhhcccceecc
Confidence            789999999999999999999999998644322           356889999999999999999999999999999999


Q ss_pred             Cccc--------------------------------hhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccc
Q 028218          157 DIEH--------------------------------ELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDC  197 (212)
Q Consensus       157 SVEe--------------------------------~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~  197 (212)
                      |+++                                +++++++||.+ .|++.+++.+++.++|+||+||+|+
T Consensus       206 s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~-lG~s~~ei~~mv~~~P~iL~~s~e~  277 (345)
T PF02536_consen  206 SVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIEK  277 (345)
T ss_dssp             GCHC---------------------------THHHHHHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HHH
T ss_pred             cccccccccccccccccccccccccccccccccchHhHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchhh
Confidence            9876                                69999999996 8999999999999999999999986

The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.

>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]

Probab=99.11  E-value=9.1e-11  Score=108.71  Aligned_cols=124  Identities=22%  Similarity=0.274  Sum_probs=102.3

Q ss_pred             cChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccch-----------------hhhhhhhcCCChhhHHHHHHHH
Q 028218           71 LNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAY-----------------WSEERKRETPELETVSEILGYL  133 (212)
Q Consensus        71 ~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~-----------------fr~a~~~~v~s~e~i~aklefL  133 (212)
                      +.-.--++.++.+++|+.+||+.+++..|+.|.+.+++-.-                 .++.. ....++.++..++|||
T Consensus       258 ~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~~~~~~k~p~-~l~~s~~~l~~~ie~l  336 (413)
T KOG1267|consen  258 LSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKNPKHILKFPQ-LLRSSEDKLKPRIEFL  336 (413)
T ss_pred             hcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhcchhhhhhhh-hhhccchhhhhhHHHH
Confidence            44445578999999999999999999999999997632210                 01111 0124556799999999


Q ss_pred             HhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccccc
Q 028218          134 RNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKG  199 (212)
Q Consensus       134 ksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~Rg  199 (212)
                      ..+|+++.++.++++++|+++++|+|..++++.+|+.+.++..    -+.+...|.+++|++|+|-
T Consensus       337 ~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p----~~~~~~~p~~~~y~le~ri  398 (413)
T KOG1267|consen  337 LSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRP----LSALVSFPAFFGYSLEKRI  398 (413)
T ss_pred             HHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCch----HHHHhccchhhccchhhcc
Confidence            9999999999999999999999998889999999999988763    5899999999999999984

>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]

Probab=99.09  E-value=1.2e-10  Score=107.89  Aligned_cols=76  Identities=22%  Similarity=0.475  Sum_probs=70.3

Q ss_pred             CChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccc---------------------------hhhhhhhhhhhcc
Q 028218          121 PELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEH---------------------------ELRNNVQILGKDW  173 (212)
Q Consensus       121 ~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe---------------------------~LkpkveFL~~~v  173 (212)
                      .+++++..|+++|+++||+.+||..+++|+|++|++|++.                           +|.+++|||.. .
T Consensus       261 ~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~~~~~~k~p~~l~~s~~~l~~~ie~l~~-~  339 (413)
T KOG1267|consen  261 SSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKNPKHILKFPQLLRSSEDKLKPRIEFLLS-L  339 (413)
T ss_pred             cccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhcchhhhhhhhhhhccchhhhhhHHHHHH-c
Confidence            4789999999999999999999999999999999999665                           39999999996 6


Q ss_pred             CcCchhHHHHHHhCCceeeccccc
Q 028218          174 GIEGKYLRNLLLRNPKVLGYNVDC  197 (212)
Q Consensus       174 GL~g~~l~~~I~r~P~ILgYSLE~  197 (212)
                      |++...+..++.++|++++||+|+
T Consensus       340 g~~~~q~~~~~~~~Pq~l~~s~~~  363 (413)
T KOG1267|consen  340 GFSDVQILEMVKRFPQYLSFSLEK  363 (413)
T ss_pred             CCcHHHHHHHHhhccHHhhhhHHh
Confidence            999999999999999999999994

>smart00733 Mterf Mitochondrial termination factor repeats

Probab=97.58  E-value=3.2e-05  Score=45.15  Aligned_cols=29  Identities=45%  Similarity=0.885  Sum_probs=26.9

Q ss_pred             HHHhhcCceeecCccchhhhhhhhhhhccCc
Q 028218          145 KLLKKFPEVLGCDIEHELRNNVQILGKDWGI  175 (212)
Q Consensus       145 k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL  175 (212)
                      +++.++|.||++| +++|+++++||. ++|+
T Consensus         2 ~~~~~~P~il~~~-~~~l~~~~~~l~-~~g~   30 (31)
T smart00733        2 KILKKFPQILGYS-EKKLKPKVEFLK-ELGF   30 (31)
T ss_pred             chhhhCcCccccc-HHHhhHHHHHHH-HcCC
Confidence            5789999999999 999999999999 6887

Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.

>smart00733 Mterf Mitochondrial termination factor repeats

Probab=91.80  E-value=0.17  Score=28.95  Aligned_cols=18  Identities=17%  Similarity=0.377  Sum_probs=16.4

Q ss_pred             ChhhHHHHHHHHHhCCCC
Q 028218          122 ELETVSEILGYLRNLSLS  139 (212)
Q Consensus       122 s~e~i~aklefLksLG~S  139 (212)
                      +++++..+++||+++|++
T Consensus        14 ~~~~l~~~~~~l~~~g~~   31 (31)
T smart00733       14 SEKKLKPKVEFLKELGFS   31 (31)
T ss_pred             cHHHhhHHHHHHHHcCCC
Confidence            579999999999999985

Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.

>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes

Probab=91.05  E-value=0.24  Score=40.23  Aligned_cols=29  Identities=14%  Similarity=0.326  Sum_probs=23.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHHhhcCcee
Q 028218          126 VSEILGYLRNLSLSDDDIRKLLKKFPEVL  154 (212)
Q Consensus       126 i~aklefLksLG~Sd~eI~k~vkK~P~IL  154 (212)
                      +.+|++||++=|++++||..++++.+.-=
T Consensus        23 ~~~k~~FL~sKGLt~~EI~~al~~a~~~~   51 (136)
T PF04695_consen   23 LEKKIAFLESKGLTEEEIDEALGRAGSPP   51 (136)
T ss_dssp             HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence            66999999999999999999999977655

Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.

>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction

Probab=88.87  E-value=0.3  Score=32.78  Aligned_cols=41  Identities=24%  Similarity=0.376  Sum_probs=28.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhh
Q 028218          127 SEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQ  167 (212)
Q Consensus       127 ~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~Lkpkve  167 (212)
                      ...++-|.+|||++.|+.+++++-..-=+.++|+-||..+.
T Consensus         4 ~d~~~AL~~LGy~~~e~~~av~~~~~~~~~~~e~~ik~aLk   44 (47)
T PF07499_consen    4 EDALEALISLGYSKAEAQKAVSKLLEKPGMDVEELIKQALK   44 (47)
T ss_dssp             HHHHHHHHHTTS-HHHHHHHHHHHHHSTTS-HHHHHHHHHC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHh
Confidence            46778899999999999999998754334456666655443

The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.

>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A

Probab=88.77  E-value=1.5  Score=33.09  Aligned_cols=73  Identities=22%  Similarity=0.182  Sum_probs=47.0

Q ss_pred             HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeec
Q 028218           77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGC  156 (212)
Q Consensus        77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~  156 (212)
                      ..-++.+.+|..+|+++..+.++..+-                                 |   ++...+|+..|+.|..
T Consensus         6 ~~~~~~~~~L~~~gl~~~~a~kl~~~y---------------------------------g---~~ai~~l~~nPY~L~~   49 (94)
T PF14490_consen    6 RGLRELMAFLQEYGLSPKLAMKLYKKY---------------------------------G---DDAIEILKENPYRLIE   49 (94)
T ss_dssp             ---HHHHHHHHHTT--HHHHHHHHHHH-------------------------------------TTHHHHHHH-STCCCB
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHH---------------------------------h---HHHHHHHHHChHHHHH
Confidence            334667788888888888887776653                                 1   2445778899999999


Q ss_pred             CccchhhhhhhhhhhccCcCchhHHHHHH
Q 028218          157 DIEHELRNNVQILGKDWGIEGKYLRNLLL  185 (212)
Q Consensus       157 SVEe~LkpkveFL~~~vGL~g~~l~~~I~  185 (212)
                      ++..-==.++|.+-..+|++.++..++.+
T Consensus        50 ~i~gi~F~~aD~iA~~~g~~~~d~~Ri~A   78 (94)
T PF14490_consen   50 DIDGIGFKTADKIALKLGIEPDDPRRIRA   78 (94)
T ss_dssp             -SSSSBHHHHHHHHHTTT--TT-HHHHHH
T ss_pred             HccCCCHHHHHHHHHHcCCCCCCHHHHHH
Confidence            87777778888888889998777666544

>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators

Probab=87.62  E-value=1.8  Score=36.29  Aligned_cols=21  Identities=19%  Similarity=0.523  Sum_probs=18.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHH
Q 028218          126 VSEILGYLRNLSLSDDDIRKL  146 (212)
Q Consensus       126 i~aklefLksLG~Sd~eI~k~  146 (212)
                      ..+=.+||.++|+|++|+..+
T Consensus       147 p~~h~~~l~~~g~~~~~~~~i  167 (172)
T cd04790         147 PEAHQEFLQSLGIPEDEIERI  167 (172)
T ss_pred             cHHHHHHHHHcCCCHHHHHHH
Confidence            348899999999999999875

Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=86.75  E-value=1.7  Score=35.47  Aligned_cols=88  Identities=17%  Similarity=0.194  Sum_probs=59.4

Q ss_pred             hhhhhhhcccChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc------cccchhhhhhhhcC-------CChhhHHH
Q 028218           62 STAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGH------IHSAYWSEERKRET-------PELETVSE  128 (212)
Q Consensus        62 ~~~~~~~~~~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl------~~S~~fr~a~~~~v-------~s~e~i~a  128 (212)
                      --.+...-++.++|+  -=..++.-..+|.+|-++.++..-..+-      ++.++|-.+.....       ...+.+..
T Consensus        20 Ik~~I~~g~l~pGdk--LPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~~~~~~~~~l~~   97 (125)
T COG1725          20 IKEQIASGELKPGDK--LPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQLKRELAEEELEE   97 (125)
T ss_pred             HHHHHHhCCcCCCCC--CCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHHHHHHHHHHHHH
Confidence            333444444555432  1234555589999999998888776543      78888876542222       33444667


Q ss_pred             HHHHHHhCCCCHHHHHHHHhhcC
Q 028218          129 ILGYLRNLSLSDDDIRKLLKKFP  151 (212)
Q Consensus       129 klefLksLG~Sd~eI~k~vkK~P  151 (212)
                      .|+-++.+|+|.++|..++++..
T Consensus        98 ~I~~~~~~G~s~eei~~~~~~~~  120 (125)
T COG1725          98 FIEEAKALGLSLEEILELLKEIY  120 (125)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHH
Confidence            77778899999999999998764

>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction

Probab=86.67  E-value=0.98  Score=30.29  Aligned_cols=27  Identities=26%  Similarity=0.386  Sum_probs=23.8

Q ss_pred             HHHHHHHHhhhCCCChHHHHHHHHhhh
Q 028218           78 KWEACRQALSTFNFSTEEEDKILGKAF  104 (212)
Q Consensus        78 ~we~~v~~L~~LGfspe~v~~il~rA~  104 (212)
                      .+++++++|.+|||++.++..++.++.
T Consensus         2 ~~~d~~~AL~~LGy~~~e~~~av~~~~   28 (47)
T PF07499_consen    2 ALEDALEALISLGYSKAEAQKAVSKLL   28 (47)
T ss_dssp             HHHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence            468999999999999999999999985

The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=86.26  E-value=0.77  Score=44.73  Aligned_cols=93  Identities=20%  Similarity=0.214  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHHhhhCCCChHH--HHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCC----HHHHHHHH
Q 028218           74 EERKKWEACRQALSTFNFSTEE--EDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLS----DDDIRKLL  147 (212)
Q Consensus        74 ~~~~~we~~v~~L~~LGfspe~--v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~S----d~eI~k~v  147 (212)
                      .+.++||++|+.++.+.=...+  .++.+.+|.                 -.-+-.++.++++.||++    ++||.++-
T Consensus       332 l~le~~e~AV~d~~~a~q~~~s~e~r~~l~~A~-----------------~aLkkSkRkd~ykilGi~~~as~~eikkay  394 (486)
T KOG0550|consen  332 LALEKWEEAVEDYEKAMQLEKDCEIRRTLREAQ-----------------LALKKSKRKDWYKILGISRNASDDEIKKAY  394 (486)
T ss_pred             HHHHHHHHHHHHHHHHHhhccccchHHHHHHHH-----------------HHHHHhhhhhHHHHhhhhhhcccchhhhHH
Confidence            4678999999999654443333  666777764                 123455789999999996    56699888


Q ss_pred             hhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCC
Q 028218          148 KKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNP  188 (212)
Q Consensus       148 kK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P  188 (212)
                      +|-|-+..-+....=+..-|..-+++|-     .-.|++.|
T Consensus       395 rk~AL~~Hpd~~agsq~eaE~kFkevge-----Ay~il~d~  430 (486)
T KOG0550|consen  395 RKLALVHHPDKNAGSQKEAEAKFKEVGE-----AYTILSDP  430 (486)
T ss_pred             HHHHHHhCCCcCcchhHHHHHHHHHHHH-----HHHHhcCH
Confidence            7777776655433335566777677775     45666665

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=81.97  E-value=6.1  Score=33.66  Aligned_cols=80  Identities=13%  Similarity=0.171  Sum_probs=48.2

Q ss_pred             HHHhh-hCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccch
Q 028218           83 RQALS-TFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHE  161 (212)
Q Consensus        83 v~~L~-~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~  161 (212)
                      .+.|. .=|+.++.+.+++....+....  +.............+...+++|.+||+++.++.++++++-.- ..++++-
T Consensus       107 ~~~L~~v~Gig~k~A~~I~~~l~~~~~~--~~~~~~~~~~~~~~~~ev~~aL~~LG~~~~~a~~~~~~~~~~-~~~~~~~  183 (192)
T PRK00116        107 VKALTKVPGIGKKTAERIVLELKDKLAA--AASAAAAAAAASSALEEAVSALVALGYKPKEASKAVAKILKE-AASVEEL  183 (192)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHhhc--ccccccccccccchHHHHHHHHHHcCCCHHHHHHHHHHHhcc-CCCHHHH
Confidence            34564 4499999999998775443321  000000000112236789999999999999999999988321 2344444


Q ss_pred             hhhh
Q 028218          162 LRNN  165 (212)
Q Consensus       162 Lkpk  165 (212)
                      ||..
T Consensus       184 i~~a  187 (192)
T PRK00116        184 IREA  187 (192)
T ss_pred             HHHH
Confidence            4433

>PRK02249 DNA primase large subunit; Validated

Probab=81.16  E-value=1.4  Score=41.33  Aligned_cols=74  Identities=24%  Similarity=0.395  Sum_probs=47.1

Q ss_pred             CChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHH-HhCCceeeccccccc
Q 028218          121 PELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLL-LRNPKVLGYNVDCKG  199 (212)
Q Consensus       121 ~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I-~r~P~ILgYSLE~Rg  199 (212)
                      ++-..--+-.-||+++|++-+|+..+++..|   .++ |+.-+=++++..   |.+|.  .+|. -..-+|++|     |
T Consensus       239 L~h~~R~~l~~FL~~iG~~~deil~~~~~~~---~f~-e~~~~Y~irH~~---G~~G~--~~Y~p~sC~~m~s~-----g  304 (343)
T PRK02249        239 LPHTARFAITSFLLNIGMSVDEIVELFRNAP---DFD-EEKTRYQVEHIA---GETGG--TEYTPPSCETMRTY-----G  304 (343)
T ss_pred             CChHHHHHHHHHHHhcCCCHHHHHHHHhhCC---Ccc-HHHHHHHHHHHh---cccCC--CCCCCccHHHHHHc-----C
Confidence            3444445667799999999999999999887   344 444455666654   55443  1111 111144444     8


Q ss_pred             ccccccchh
Q 028218          200 DCMAQCTRC  208 (212)
Q Consensus       200 ~c~~~c~rc  208 (212)
                      +|.+-|..|
T Consensus       305 ~C~~~d~lC  313 (343)
T PRK02249        305 LCVGKDDLC  313 (343)
T ss_pred             CCCCchhhh
Confidence            898888766

---

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

ID	Length	Definition	E-value
Query	212
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	3e-11
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	3e-10
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	9e-10
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	2e-08
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	7e-05
3mva_O	343	Transcription termination factor, mitochondrial; a	6e-09
3mva_O	343	Transcription termination factor, mitochondrial; a	1e-05
3mva_O	343	Transcription termination factor, mitochondrial; a	2e-05
3mva_O	343	Transcription termination factor, mitochondrial; a	1e-04
3mva_O	343	Transcription termination factor, mitochondrial; a	4e-04

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A Length = 270

 Score = 60.2 bits (146), Expect = 3e-11
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 127 SEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLR 186
           SE L  L  L +    I K  +    +L  D E +++  +  L KD GIE   L   L +
Sbjct: 6   SETLQKLVLLGVDLSKIEKHPEAANLLLRLDFEKDIKQMLLFL-KDVGIEDNQLGAFLTK 64

Query: 187 NPKVLGYNVD 196
           N  +   +++
Sbjct: 65  NHAIFSEDLE 74

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A Length = 270

 Score = 57.1 bits (138), Expect = 3e-10
 Identities = 20/87 (22%), Positives = 43/87 (49%), Gaps = 1/87 (1%)

Query: 123 LETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRN 182
           LE +   + YL + + S  D+ ++++K P +L   +E  L N +    K+  +  K  R+
Sbjct: 73  LENLKTRVAYLHSKNFSKADVAQMVRKAPFLLNFSVER-LDNRLGFFQKELELSVKKTRD 131

Query: 183 LLLRNPKVLGYNVDCKGDCMAQCTRCW 209
           L++R P++L  +++   + M       
Sbjct: 132 LVVRLPRLLTGSLEPVKENMKVYRLEL 158

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A Length = 270

 Score = 56.0 bits (135), Expect = 9e-10
 Identities = 13/73 (17%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 124 ETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNL 183
           + + ++L +L+++ + D+ +   L K   +   D+E+ L+  V  L          +  +
Sbjct: 39  KDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSEDLEN-LKTRVAYL-HSKNFSKADVAQM 96

Query: 184 LLRNPKVLGYNVD 196
           + + P +L ++V+
Sbjct: 97  VRKAPFLLNFSVE 109

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A Length = 270

 Score = 52.1 bits (125), Expect = 2e-08
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 123 LETVSEILGYLRN-LSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLR 181
           +E +   LG+ +  L LS    R L+ + P +L   +E    N       + G +   ++
Sbjct: 108 VERLDNRLGFFQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVYR-LELGFKHNEIQ 166

Query: 182 NLLLRNPKVLGYNVD 196
           +++ R PK+L  N  
Sbjct: 167 HMITRIPKMLTANKM 181

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A Length = 270

 Score = 41.7 bits (98), Expect = 7e-05
 Identities = 9/68 (13%), Positives = 25/68 (36%), Gaps = 5/68 (7%)

Query: 129 ILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNP 188
           +  Y   L    ++I+ ++ + P++L  +    L      +     I        +++ P
Sbjct: 151 MKVYRLELGFKHNEIQHMITRIPKMLTANKMK-LTETFDFVHNVMSIPHHI----IVKFP 205

Query: 189 KVLGYNVD 196
           +V    + 
Sbjct: 206 QVFNTRLF 213

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A* Length = 343

 Score = 53.9 bits (129), Expect = 6e-09
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 123 LETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGC-DIEHELRNNVQILGKDWGIEGKYLR 181
            E +S+     R +  SD +I  +L++ PE     +    L NN++ L    G+  K L 
Sbjct: 83  PENLSKRWDLWRKIVTSDLEIVNILERSPESFFRSNNNLNLENNIKFL-YSVGLTRKCLC 141

Query: 182 NLLLRNPKVLGYNVD 196
            LL   P+    ++D
Sbjct: 142 RLLTNAPRTFSNSLD 156

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A* Length = 343

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 121 PELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYL 180
            E     ++L  L  + +   DI    K+ P V    I +  ++    L    G   + +
Sbjct: 14  SEPLKNEDLLKNLLTMGV---DIDMARKRQPGVFHRMITN-EQDLKMFL-LSKGASKEVI 68

Query: 181 RNLLLRNPKVLGYNVDC 197
            +++ R P+ +    + 
Sbjct: 69  ASIISRYPRAITRTPEN 85

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A* Length = 343

 Score = 43.9 bits (103), Expect = 2e-05
 Identities = 10/76 (13%), Positives = 30/76 (39%), Gaps = 2/76 (2%)

Query: 123 LETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRN 182
           +    ++  +L +   S + I  ++ ++P  +    E+ L     +  +        + N
Sbjct: 48  ITNEQDLKMFLLSKGASKEVIASIISRYPRAITRTPEN-LSKRWDLW-RKIVTSDLEIVN 105

Query: 183 LLLRNPKVLGYNVDCK 198
           +L R+P+    + +  
Sbjct: 106 ILERSPESFFRSNNNL 121

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A* Length = 343

 Score = 40.8 bits (95), Expect = 1e-04
 Identities = 18/106 (16%), Positives = 44/106 (41%), Gaps = 9/106 (8%)

Query: 100 LGKAFGHIHSAYWSEERKRETPEL-----ETVSEILGYLRN-LSLSDDDIRKLL-KKFPE 152
            G + GH   A +  +   + P +     + V   + +LR+  +L+ +++  L+     E
Sbjct: 168 AGLSLGHNDPADFVRKIIFKNPFILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAE 227

Query: 153 VLGCDIEHELRN--NVQILGKDWGIEGKYLRNLLLRNPKVLGYNVD 196
           +L    ++  R+  N++      G   + ++  +L  P V+     
Sbjct: 228 ILDLSNDYARRSYANIKEKLFSLGCTEEEVQKFVLSYPDVIFLAEK 273

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A* Length = 343

 Score = 39.6 bits (92), Expect = 4e-04
 Identities = 12/83 (14%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 120 TPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKY 179
           +     +   + +L ++ L+   + +LL   P      ++   +  V+ L +  G+   +
Sbjct: 117 SNNNLNLENNIKFLYSVGLTRKCLCRLLTNAPRTFSNSLDL-NKQMVEFL-QAAGLSLGH 174

Query: 180 ------LRNLLLRNPKVLGYNVD 196
                 +R ++ +NP +L  +  
Sbjct: 175 NDPADFVRKIIFKNPFILIQSTK 197

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	212
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	99.69
3m66_A	270	Mterf3, mterf domain-containing protein 1, mitocho	99.65
3mva_O	343	Transcription termination factor, mitochondrial; a	99.59
4fp9_B	335	Mterf domain-containing protein 2; modification en	99.57
4fp9_B	335	Mterf domain-containing protein 2; modification en	99.57
3mva_O	343	Transcription termination factor, mitochondrial; a	99.54
3ff5_A	54	PEX14P, peroxisomal biogenesis factor 14; protein	92.33
4fzv_B	239	Mterf domain-containing protein 2; mterf fold, met	92.16
4ae4_A	118	Ubiquitin-associated protein 1; protein transport,	90.12
2w84_A	70	Peroxisomal membrane protein PEX14; zellweger synd	90.01
2knz_A	53	Ubiquilin-4; cytoplasm, endoplasmic reticulum, nuc	85.31

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A

Probab=99.69  E-value=4.8e-17  Score=139.65  Aligned_cols=103  Identities=14%  Similarity=0.300  Sum_probs=89.5

Q ss_pred             HHHHHHHHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHH-HhCCCCHHHHHHHHhhcCceee
Q 028218           78 KWEACRQAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYL-RNLSLSDDDIRKLLKKFPEVLG  155 (212)
Q Consensus        78 ~we~~v~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefL-ksLG~Sd~eI~k~vkK~P~ILg  155 (212)
                      ++...+++| +.+|++.+++.+++.+.+.+.+            .+.++++++++|+ +++|||++||.++|.++|.||+
T Consensus       110 ~l~~~v~~L~~~lG~~~~~i~~ll~~~P~il~------------~s~e~~~~~v~~l~~~~G~s~~ei~~~v~~~P~il~  177 (270)
T 3m66_A          110 RLDNRLGFFQKELELSVKKTRDLVVRLPRLLT------------GSLEPVKENMKVYRLELGFKHNEIQHMITRIPKMLT  177 (270)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHSGGGGT------------SCSHHHHHHHHHHHHTSCCCHHHHHHHHHHCGGGGT
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHhCCccee------------echHHHHHHHHHHHHHcCCCHHHHHHHHHhCChhhe
Confidence            477888888 6788888888888877765543            3568899999976 5999999999999999999999


Q ss_pred             cCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeecccccc
Q 028218          156 CDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCK  198 (212)
Q Consensus       156 ~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~R  198 (212)
                      +| +++|+++++||++++|++    +++|+++|.+|+||+| |
T Consensus       178 ~s-~~~l~~k~~fL~~~mg~~----~~~i~~~P~~l~~Sle-r  214 (270)
T 3m66_A          178 AN-KMKLTETFDFVHNVMSIP----HHIIVKFPQVFNTRLF-K  214 (270)
T ss_dssp             SC-HHHHHHHHHHHHTTSCCC----HHHHHHCGGGGGSCHH-H
T ss_pred             ec-HHHHHHHHHHHHHHhCCC----HHHHHhCchHhhCCHH-H
Confidence            99 589999999999999998    7899999999999998 6

>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial; mitochondrion, DNA binding protein, transcription factor, transcription termination; 1.60A {Homo sapiens} PDB: 3opg_A 3my3_A

Probab=99.65  E-value=2.1e-16  Score=135.66  Aligned_cols=108  Identities=21%  Similarity=0.353  Sum_probs=97.9

Q ss_pred             HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeec
Q 028218           77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGC  156 (212)
Q Consensus        77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~  156 (212)
                      ++....+++|..+|++++++.+++.+.+.++.+            +.+++..+++||+++|+++++|.++++++|.+|++
T Consensus        39 ~~l~~~l~fL~~lG~~~~~i~~il~~~P~lL~~------------~~e~l~p~v~~L~~~Gls~~~i~~~l~~~P~lL~~  106 (270)
T 3m66_A           39 KDIKQMLLFLKDVGIEDNQLGAFLTKNHAIFSE------------DLENLKTRVAYLHSKNFSKADVAQMVRKAPFLLNF  106 (270)
T ss_dssp             HHTHHHHHHHHHHTCCGGGHHHHHHHCTTGGGS------------CHHHHHHHHHHHHHTTCCHHHHHHHHHHSTTGGGS
T ss_pred             hhHHHHHHHHHHcCCCHHHHHHHHHhCChhhhC------------CHHHHHHHHHHHHHcCCCHHHHHHHHHhCCHHHcC
Confidence            566889999999999999999999999877654            35779999999999999999999999999999999


Q ss_pred             CccchhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccc
Q 028218          157 DIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDC  197 (212)
Q Consensus       157 SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~  197 (212)
                      |+| +++|+++||.+++|++++++.++|.++|.+|++|+|+
T Consensus       107 s~~-~l~~~v~~L~~~lG~~~~~i~~ll~~~P~il~~s~e~  146 (270)
T 3m66_A          107 SVE-RLDNRLGFFQKELELSVKKTRDLVVRLPRLLTGSLEP  146 (270)
T ss_dssp             CHH-HHHHHHHHHHHHHCCCHHHHHHHHHHSGGGGTSCSHH
T ss_pred             CHH-HHHHHHHHHHHHhCCCHHHHHHHHHhCCcceeechHH
Confidence            977 6999999997679999999999999999999999885

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A*

Probab=99.59  E-value=2.1e-15  Score=134.34  Aligned_cols=104  Identities=18%  Similarity=0.323  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHhh-hCCCChHHHHHHHHhhhh-ccccchhhhhhhhcCCChhhHHHHHHHHH----hCCCCHHHHHHHHhh
Q 028218           76 RKKWEACRQALS-TFNFSTEEEDKILGKAFG-HIHSAYWSEERKRETPELETVSEILGYLR----NLSLSDDDIRKLLKK  149 (212)
Q Consensus        76 ~~~we~~v~~L~-~LGfspe~v~~il~rA~g-l~~S~~fr~a~~~~v~s~e~i~aklefLk----sLG~Sd~eI~k~vkK  149 (212)
                      .++|++.+++|+ .+|++++++..++.+... +.+            .+.+.++++++|+.    ++|||++||..+|.+
T Consensus       196 ~~~i~~~v~fL~~~~G~~~~~~~~~i~~~~~~~l~------------~s~~~l~~~~~~l~e~~~~lG~s~~ev~~~v~~  263 (343)
T 3mva_O          196 TKRVKANIEFLRSTFNLNSEELLVLICGPGAEILD------------LSNDYARRSYANIKEKLFSLGCTEEEVQKFVLS  263 (343)
T ss_dssp             HHHHHHHHHHHHHHSCCCHHHHHHHHHTTTGGGGG------------CCTTHHHHHHHHHHHHHHTTTCCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHhcCChHHhh------------ccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            368999999997 699999999888877432 111            24566777765554    899999999999999


Q ss_pred             cCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeecccccc
Q 028218          150 FPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCK  198 (212)
Q Consensus       150 ~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~R  198 (212)
                      +|.||++| +++|+++++||.+ +|++    .++|+++|++|+||+| |
T Consensus       264 ~P~il~~s-~~~l~~k~~fl~~-mg~~----~~~i~~~P~~l~~sle-r  305 (343)
T 3mva_O          264 YPDVIFLA-EKKFNDKIDCLME-ENIS----ISQIIENPRVLDSSIS-T  305 (343)
T ss_dssp             CGGGGGSC-HHHHHHHHHHHHT-TTCC----HHHHHHSGGGGGSCHH-H
T ss_pred             CCchhccc-HHHHHHHHHHHHH-cCCC----HHHHHhCCHHHhcCHH-H
Confidence            99999999 5579999999999 9998    7899999999999999 5

>4fp9_B Mterf domain-containing protein 2; modification enzyme, transferase; HET: SAM; 2.90A {Homo sapiens}

Probab=99.57  E-value=4.1e-15  Score=134.52  Aligned_cols=114  Identities=16%  Similarity=0.182  Sum_probs=87.9

Q ss_pred             HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccc---------hhhhh----------hh----hcCCChhhHHHHHHHH
Q 028218           77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSA---------YWSEE----------RK----RETPELETVSEILGYL  133 (212)
Q Consensus        77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~---------~fr~a----------~~----~~v~s~e~i~aklefL  133 (212)
                      ++++..+++|..|||+++.+.+|+.+.+.+++.+         +|+..          ..    ....+.+++..++.||
T Consensus        76 ~~l~~~i~~L~~LGls~e~V~kiL~k~P~lL~~s~e~L~~~l~fL~~lGl~~~~i~~ll~~~P~lL~~s~e~i~~~v~~L  155 (335)
T 4fp9_B           76 QQLLDIISEFILLGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVLYCCPEIFTMRQQDINDTVRLL  155 (335)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHCGGGGGSCHHHHHHHHHHHHHTTCTTTTHHHHHHHCGGGGTSCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHcCCCHHHHHHHHHhChhhccCCHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhccChHHHHHHHHHH
Confidence            4467788889889999999999999888774332         11111          00    1116677888888888


Q ss_pred             H-hCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeecccc
Q 028218          134 R-NLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVD  196 (212)
Q Consensus       134 k-sLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE  196 (212)
                      + ++|||++||.++|.++|.||++| +++|+++++||++++|++    ...|++ |++|+||+|
T Consensus       156 ~~~lGfS~~ev~~mv~r~P~lL~~S-~e~L~~K~efLv~~Mgl~----~~eIvk-P~~l~ySLe  213 (335)
T 4fp9_B          156 KEKCLFTVQQVTKILHSCPSVLRED-LGQLEYKFQYAYFRMGIK----HPDIVK-SEYLQYSLT  213 (335)
T ss_dssp             HHTSCCCHHHHHHHHHHCGGGGTSC-HHHHHHHHHHHHTTTCCC----HHHHHH-TTGGGSCHH
T ss_pred             HHHcCCCHHHHHHHHHhCChhhhCC-HHHHHHHHHHHHHHhCCC----HHHccc-cchhhccHH
Confidence            6 88999999999999999999999 668999999999999997    566676 899999987

>4fp9_B Mterf domain-containing protein 2; modification enzyme, transferase; HET: SAM; 2.90A {Homo sapiens}

Probab=99.57  E-value=3.5e-15  Score=134.96  Aligned_cols=106  Identities=22%  Similarity=0.316  Sum_probs=95.4

Q ss_pred             HHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCcee
Q 028218           75 ERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVL  154 (212)
Q Consensus        75 ~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~IL  154 (212)
                      -+.+||..++.|..+||+++.+.+++.+.++++               .+++..++.||.+||++.++|.++|+|+|.||
T Consensus        42 ~~~~~e~~l~~L~d~Gfs~~~i~~il~~~P~il---------------~~~l~~~i~~L~~LGls~e~V~kiL~k~P~lL  106 (335)
T 4fp9_B           42 GSLELERVMSSLLDMGFSNAHINELLSVRRGAS---------------LQQLLDIISEFILLGLNPEPVCVVLKKSPQLL  106 (335)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHCSSCC---------------HHHHHHHHHHHHHTTCCHHHHHHHHHHCGGGG
T ss_pred             ccccHHHHHHHHHHCCCCHHHHHHHHHhCcccc---------------hhHHHHHHHHHHHcCCCHHHHHHHHHhChhhc
Confidence            355799999999999999999999999976442               36677899999999999999999999999999


Q ss_pred             ecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccc
Q 028218          155 GCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDC  197 (212)
Q Consensus       155 g~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~  197 (212)
                      ++|+ ++|+++++||.+ +|+++..+.++|.++|++|+||.+.
T Consensus       107 ~~s~-e~L~~~l~fL~~-lGl~~~~i~~ll~~~P~lL~~s~e~  147 (335)
T 4fp9_B          107 KLPI-MQMRKRSSYLQK-LGLGEGKLKRVLYCCPEIFTMRQQD  147 (335)
T ss_dssp             GSCH-HHHHHHHHHHHH-TTCTTTTHHHHHHHCGGGGTSCHHH
T ss_pred             cCCH-HHHHHHHHHHHH-cCCCHHHHHHHHHhCchhhccChHH
Confidence            9996 489999999986 9999999999999999999999885

>3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A*

Probab=99.54  E-value=6.1e-15  Score=131.32  Aligned_cols=107  Identities=23%  Similarity=0.283  Sum_probs=95.8

Q ss_pred             HHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCc-eeec
Q 028218           78 KWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPE-VLGC  156 (212)
Q Consensus        78 ~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~-ILg~  156 (212)
                      ..++.+++|..+|++.+++.+++.+.+.++..            +.+++.++++||+++|+++++|.++|.++|. ++++
T Consensus        50 ~~~~vl~fL~~~G~s~~~i~~iv~~~P~lL~~------------~~~~l~p~l~fL~~lG~s~~~i~~il~~~P~iLl~s  117 (343)
T 3mva_O           50 NEQDLKMFLLSKGASKEVIASIISRYPRAITR------------TPENLSKRWDLWRKIVTSDLEIVNILERSPESFFRS  117 (343)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHHHCGGGGGC------------CHHHHHHHHHHHTTTSSCHHHHHHHHHHCSHHHHSC
T ss_pred             cHHHHHHHHHHcCCCHHHHHHHHHhCcHHHhC------------CHHHHHHHHHHHHHcCCCHHHHHHHHHHCCHHHhCC
Confidence            34688999999999999999999999876543            3578999999999999999999999999999 5566


Q ss_pred             CccchhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccc
Q 028218          157 DIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDC  197 (212)
Q Consensus       157 SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~  197 (212)
                      +.+++|+|+++||. ++|++.+++.+++.++|.+|+|++|+
T Consensus       118 ~~~~~l~p~v~fL~-~lGl~~~~i~~ll~~~P~il~~~~e~  157 (343)
T 3mva_O          118 NNNLNLENNIKFLY-SVGLTRKCLCRLLTNAPRTFSNSLDL  157 (343)
T ss_dssp             CCHHHHHHHHHHHH-HTTCCHHHHHHHHHHCGGGGTSCHHH
T ss_pred             ChHhhHHHHHHHHH-HhCCCHHHHHHHHHhCChhheeCHHH
Confidence            63359999999999 59999999999999999999999986

>3ff5_A PEX14P, peroxisomal biogenesis factor 14; protein import, peroxin, 3 helices bundle, protein transport; HET: DPW; 1.80A {Rattus norvegicus}

Probab=92.33  E-value=0.13  Score=35.42  Aligned_cols=24  Identities=17%  Similarity=0.426  Sum_probs=22.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHHhh
Q 028218          126 VSEILGYLRNLSLSDDDIRKLLKK  149 (212)
Q Consensus       126 i~aklefLksLG~Sd~eI~k~vkK  149 (212)
                      +..|++||++=|++++||..+++|
T Consensus        30 ~~~K~~FL~sKGLt~~EI~~Al~r   53 (54)
T 3ff5_A           30 LATRRAFLKKKGLTDEEIDLAFQQ   53 (54)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHc
Confidence            669999999999999999999987

>4fzv_B Mterf domain-containing protein 2; mterf fold, methyltransferase fold, rRNA methyltransferase, mitochondria, transferase; HET: MSE SAM; 2.00A {Homo sapiens}

Probab=92.16  E-value=0.12  Score=43.46  Aligned_cols=93  Identities=17%  Similarity=0.312  Sum_probs=51.1

Q ss_pred             hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhh
Q 028218           87 STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNV  166 (212)
Q Consensus        87 ~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~Lkpkv  166 (212)
                      -.||++||-+-.++++.+.+..-|            --.++.+-.||..||+-+..+.+++--.|+|..+. ...+...+
T Consensus        41 illglnpepvcvvlkkspqllklp------------imqmrkrssylqklglgegklkrvlyccpeiftmr-qqdindtv  107 (239)
T 4fzv_B           41 ILLGLNPEPVCVVLKKSPQLLKLP------------IMQMRKRSSYLQKLGLGEGKLKRVLYCCPEIFTMR-QQDINDTV  107 (239)
T ss_dssp             HHHCCCTTHHHHHHHSCGGGGTSC------------HHHHHHHHHHHHHHTTCSSCCHHHHHHCGGGGTSC-HHHHHHHH
T ss_pred             HhhcCCCCceEEEecCCHHHhcCh------------HHHHHHHHHHHHHhCCCccchhhheecCcHHHHHH-HhhHhHHH
Confidence            478999999999999887663222            12233444555555555555555555555555555 44444445


Q ss_pred             hhhhhccCcCchhHHHHHHhCCceee
Q 028218          167 QILGKDWGIEGKYLRNLLLRNPKVLG  192 (212)
Q Consensus       167 eFL~~~vGL~g~~l~~~I~r~P~ILg  192 (212)
                      ..|.+..=+.-..+.+++-..|.+|.
T Consensus       108 rllkekclftvqqvtkilhscpsvlr  133 (239)
T 4fzv_B          108 RLLKEKCLFTVQQVTKILHSCPSVLR  133 (239)
T ss_dssp             HHHHHHSCCCHHHHHHHHHHCGGGGT
T ss_pred             HHHHHhHHhhHHHHHHHHHhCcHHHH
Confidence            44444433333444445555555443

>4ae4_A Ubiquitin-associated protein 1; protein transport, endosomal sorting, tetherin, VPU, HIV-1, monoubiquitin; HET: NHE; 1.65A {Homo sapiens} PDB: 4ae4_B*

Probab=90.12  E-value=1.6  Score=33.89  Aligned_cols=29  Identities=17%  Similarity=0.321  Sum_probs=22.6

Q ss_pred             cChHHHHHHHHHHHHhhhCCCChHHHHHHHHhh
Q 028218           71 LNDEERKKWEACRQALSTFNFSTEEEDKILGKA  103 (212)
Q Consensus        71 ~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA  103 (212)
                      |++++    .++++-|-.+||+.+++.+++...
T Consensus         4 l~~~e----~~~v~~l~~MGFp~~~~~kAl~~~   32 (118)
T 4ae4_A            4 MSPSE----RQCVETVVNMGYSYECVLRAMKAA   32 (118)
T ss_dssp             SCHHH----HHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCHHH----HHHHHHHHHcCCCHHHHHHHHHHH
Confidence            55554    468888999999999998887653

>2w84_A Peroxisomal membrane protein PEX14; zellweger syndrome, alternative splicing, phosphoprotein, protein complex, disease mutation, peroxisome; NMR {Homo sapiens} PDB: 2w85_A

Probab=90.01  E-value=0.29  Score=35.42  Aligned_cols=25  Identities=16%  Similarity=0.381  Sum_probs=23.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHHhhc
Q 028218          126 VSEILGYLRNLSLSDDDIRKLLKKF  150 (212)
Q Consensus       126 i~aklefLksLG~Sd~eI~k~vkK~  150 (212)
                      +..|++||++=|++++||..++++.
T Consensus        35 ~~~K~~FL~sKGLt~eEI~~Al~ra   59 (70)
T 2w84_A           35 LATRRAFLKKKGLTDEEIDMAFQQS   59 (70)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHc
Confidence            6699999999999999999999985

>2knz_A Ubiquilin-4; cytoplasm, endoplasmic reticulum, nucleus, phosphoprotein, protein binding; NMR {Mus musculus}

Probab=85.31  E-value=2.4  Score=28.24  Aligned_cols=44  Identities=16%  Similarity=0.183  Sum_probs=34.7

Q ss_pred             HHHHHHHHHhhhCCC-ChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCC
Q 028218           77 KKWEACRQALSTFNF-STEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLS  139 (212)
Q Consensus        77 ~~we~~v~~L~~LGf-spe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~S  139 (212)
                      ..|++.++-|..+|| +.+.+..++....                   .++..-+++|-+.+.|
T Consensus         9 ~~~~~~l~~L~~MGF~~~~~~~~AL~~t~-------------------gnve~Ave~L~~~~~s   53 (53)
T 2knz_A            9 VRFQQQLEQLNSMGFINREANLQALIATG-------------------GDINAAIERLLGSQLS   53 (53)
T ss_dssp             HHHHHHHHHHHTTTCCCHHHHHHHHHHHT-------------------SCHHHHHHHHHHCCCC
T ss_pred             hHHHHHHHHHHHcCCCCHHHHHHHHHHhC-------------------CCHHHHHHHHHHcCCC
Confidence            468999999999999 8888888888763                   3466888888876643

---

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	212
d1vg5a_	73	Rhomboid family protein At3g58460 {Thale cress (Ar	84.02
d1wgna_	63	Ubiquitin-associated protein 1, UBAP1 {Human (Homo	82.76
d1oqya1	41	DNA repair protein Hhr23a {Human (Homo sapiens) [T	80.47

>d1vg5a_ a.5.2.1 (A:) Rhomboid family protein At3g58460 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Rhomboid family protein At3g58460
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.02  E-value=0.57  Score=31.84  Aligned_cols=38  Identities=18%  Similarity=0.187  Sum_probs=31.0

Q ss_pred             HHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhC
Q 028218           80 EACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNL  136 (212)
Q Consensus        80 e~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksL  136 (212)
                      |+.++-|..+||+.+.+.+.|..+.                   .++..-++||-+.
T Consensus        30 ee~i~~L~~MGF~~~~a~~AL~~~~-------------------~n~e~A~~~Ll~~   67 (73)
T d1vg5a_          30 EEQIQKLVAMGFDRTQVEVALAAAD-------------------DDLTVAVEILMSQ   67 (73)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHT-------------------SCHHHHHHHHHTC
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHhC-------------------CCHHHHHHHHHhC
Confidence            6788999999999999998888874                   4566888888643

>d1wgna_ a.5.2.1 (A:) Ubiquitin-associated protein 1, UBAP1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: Ubiquitin-associated protein 1, UBAP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.76  E-value=0.62  Score=30.90  Aligned_cols=50  Identities=24%  Similarity=0.302  Sum_probs=36.7

Q ss_pred             hhhhhcccChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhC
Q 028218           64 AQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNL  136 (212)
Q Consensus        64 ~~~~~~~~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksL  136 (212)
                      ++.+...+++.|    |++++-|-.+||+.+.+.+.+.+..                   .++.+-++||-++
T Consensus         8 ~~s~~~~~~~~d----e~~v~~L~~MGF~~~~a~~AL~~~~-------------------~n~e~A~~~Lls~   57 (63)
T d1wgna_           8 AYSELQMLSPSE----RQCVETVVNMGYSYECVLRAMKKKG-------------------ENIEQILDYLFAH   57 (63)
T ss_dssp             STHHHHTCCHHH----HHHHHHHHHHHCCHHHHHHHHHHHC-------------------SCHHHHHHHHHHH
T ss_pred             CccccccCCchh----HHHHHHHHHcCCCHHHHHHHHHHcC-------------------CCHHHHHHHHHhC
Confidence            334444566655    6789999999999999988888863                   3455888888754

>d1oqya1 a.5.2.1 (A:160-200) DNA repair protein Hhr23a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: UBA domain
domain: DNA repair protein Hhr23a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.47  E-value=0.97  Score=27.56  Aligned_cols=38  Identities=11%  Similarity=0.123  Sum_probs=30.2

Q ss_pred             hHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhh
Q 028218          125 TVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILG  170 (212)
Q Consensus       125 ~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~  170 (212)
                      ....+|+-|.++||+++++.+++++.        ..++-..++||.
T Consensus         3 ~~e~~i~~L~~MGF~~~~a~~AL~~~--------~~N~e~A~~~Ll   40 (41)
T d1oqya1           3 EYETMLTEIMSMGYERERVVAALRAS--------YNNPHRAVEYLL   40 (41)
T ss_dssp             THHHHHHHHHTTTCCSHHHHHHHHHS--------CSSTTHHHHTTT
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHHHh--------CCCHHHHHHHHh
Confidence            34588999999999999999999874        345667777764