Citrus Sinensis ID: 045468

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-
MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIRHST
ccccccccccccccccHHHHHHHHHHHHHcccccEEEEEccccHHHHHHHHHHHHHcccEEEEEcccHHHHHHHHHHcccccccccccccHHHHcccccccEEEEEcccccHHHHHHHHHHcccccccccccccEEEEEcccccccHHHHHHHHHHHHHcccEEEccccccccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHccccccc
ccccccccccccccccHHHHHHHHHHHHHHccccEEEEEHHHHHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHHHcccEEcccccEEcHHHHHccccccEEEEEccccccHHHHHHHHHcccccEEEEccccEEEEEcccccccHHHHHHHHHHHHHccccEEEcccccEEEcccccHHHHHHHHHHcccccEccccHHHHHHHHHHHHHHHccccccc
mmsdstnvlspgrttsesVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAawkdgkapidpstlvkvedidayapkdllivttgsqaepRAALNLAsyggshslkltnEDVILYSAKVIPGNESRVMKMLNRISEIGSTIvmgrneglhtsghgyrGELEEVLKLvkpqhflpihgelLFLKEHellgrstgirhst
mmsdstnvlspgrttsesvvkDALMRHVSAAKGRVIttqfasnihrlgsvkaaadltgRKLVFVGMSLRTYLDaawkdgkapidpstlvkvediDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKvipgnesrVMKMLNRISEIGSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELlflkehellgrstgirhst
MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIRHST
**********************ALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELL**********
MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGR*TGI****
***************SESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIRHST
*************TTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGI****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIRHST
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 ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query221 2.2.26 [Sep-21-2011]
P54122 718 Ribonuclease J OS=Coryneb yes no 0.981 0.302 0.373 8e-36
Q7A171 565 Ribonuclease J 1 OS=Staph yes no 0.986 0.385 0.357 7e-35
Q6GAC5 565 Ribonuclease J 1 OS=Staph yes no 0.986 0.385 0.357 7e-35
Q6GHZ6 565 Ribonuclease J 1 OS=Staph yes no 0.986 0.385 0.357 7e-35
Q7A682 565 Ribonuclease J 1 OS=Staph yes no 0.986 0.385 0.357 7e-35
Q99V09 565 Ribonuclease J 1 OS=Staph yes no 0.986 0.385 0.357 7e-35
Q5HGZ5 565 Ribonuclease J 1 OS=Staph yes no 0.986 0.385 0.357 7e-35
Q2FZG9 565 Ribonuclease J 1 OS=Staph yes no 0.986 0.385 0.357 7e-35
Q2FHZ1 565 Ribonuclease J 1 OS=Staph N/A no 0.986 0.385 0.357 7e-35
Q2YX35 565 Ribonuclease J 1 OS=Staph yes no 0.986 0.385 0.357 7e-35
>sp|P54122|RNJ_CORGL Ribonuclease J OS=Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) GN=Cgl1970 PE=3 SV=2 Back     alignment and function desciption
 Score =  150 bits (378), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 81/217 (37%), Positives = 132/217 (60%)

Query: 1   MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRK 60
           M+ DSTN  +PG + SE+ V   L R V  AK RVI   FASN++R+ +   AA  + RK
Sbjct: 338 MLCDSTNATTPGVSGSEADVAPTLKRLVGDAKQRVILASFASNVYRVQAAVDAAVASNRK 397

Query: 61  LVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLA 120
           + F G S+   ++ A K G       T++ ++D    AP  ++++TTG+Q EP AAL+  
Sbjct: 398 VAFNGRSMIRNMEIAEKLGYLKAPRGTIISMDDASRMAPHKVMLITTGTQGEPMAALSRM 457

Query: 121 SYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYR 180
           +      + + + D+I+ S+ ++PGNE  V  ++N +++IG+T+V GR+  +HTSGHGY 
Sbjct: 458 ARREHRQITVRDGDLIILSSSLVPGNEEAVFGVINMLAQIGATVVTGRDAKVHTSGHGYS 517

Query: 181 GELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGI 217
           GEL  +    +P++ +P+HGE   L+ ++ L  STG+
Sbjct: 518 GELLFLYNAARPKNAMPVHGEWRHLRANKELAISTGV 554

Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (taxid: 196627)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>sp|Q7A171|RNJ1_STAAW Ribonuclease J 1 OS=Staphylococcus aureus (strain MW2) GN=MW0972 PE=3 SV=1 Back     alignment and function description
>sp|Q6GAC5|RNJ1_STAAS Ribonuclease J 1 OS=Staphylococcus aureus (strain MSSA476) GN=SAS1024 PE=3 SV=1 Back     alignment and function description
>sp|Q6GHZ6|RNJ1_STAAR Ribonuclease J 1 OS=Staphylococcus aureus (strain MRSA252) GN=SAR1063 PE=1 SV=1 Back     alignment and function description
>sp|Q7A682|RNJ1_STAAN Ribonuclease J 1 OS=Staphylococcus aureus (strain N315) GN=SA0940 PE=1 SV=1 Back     alignment and function description
>sp|Q99V09|RNJ1_STAAM Ribonuclease J 1 OS=Staphylococcus aureus (strain Mu50 / ATCC 700699) GN=SAV1089 PE=1 SV=1 Back     alignment and function description
>sp|Q5HGZ5|RNJ1_STAAC Ribonuclease J 1 OS=Staphylococcus aureus (strain COL) GN=SACOL1098 PE=3 SV=1 Back     alignment and function description
>sp|Q2FZG9|RNJ1_STAA8 Ribonuclease J 1 OS=Staphylococcus aureus (strain NCTC 8325) GN=SAOUHSC_01035 PE=3 SV=1 Back     alignment and function description
>sp|Q2FHZ1|RNJ1_STAA3 Ribonuclease J 1 OS=Staphylococcus aureus (strain USA300) GN=SAUSA300_0989 PE=3 SV=1 Back     alignment and function description
>sp|Q2YX35|RNJ1_STAAB Ribonuclease J 1 OS=Staphylococcus aureus (strain bovine RF122 / ET3-1) GN=SAB0955c PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query221
297734394 1659 unnamed protein product [Vitis vinifera] 1.0 0.133 0.927 1e-118
147856240 1616 hypothetical protein VITISV_026006 [Viti 1.0 0.136 0.927 1e-118
225456284 886 PREDICTED: ribonuclease J-like [Vitis vi 1.0 0.249 0.927 1e-118
356507349 888 PREDICTED: ribonuclease J-like [Glycine 0.995 0.247 0.913 1e-115
449501401 909 PREDICTED: LOW QUALITY PROTEIN: ribonucl 1.0 0.243 0.927 1e-115
449440566 909 PREDICTED: ribonuclease J-like [Cucumis 1.0 0.243 0.927 1e-115
255540285 880 conserved hypothetical protein [Ricinus 1.0 0.251 0.904 1e-115
356516571 874 PREDICTED: ribonuclease J-like [Glycine 0.995 0.251 0.909 1e-115
224119634 890 predicted protein [Populus trichocarpa] 1.0 0.248 0.914 1e-115
356565270 886 PREDICTED: ribonuclease J-like [Glycine 1.0 0.249 0.848 1e-112
>gi|297734394|emb|CBI15641.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  431 bits (1107), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 205/221 (92%), Positives = 217/221 (98%)

Query: 1    MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRK 60
            MMSDSTNVLSPGRT SESVV DAL+RH+S+AKGRVITTQFASNIHRLGSVKAAADLTGRK
Sbjct: 1037 MMSDSTNVLSPGRTISESVVADALLRHISSAKGRVITTQFASNIHRLGSVKAAADLTGRK 1096

Query: 61   LVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLA 120
            LVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLA
Sbjct: 1097 LVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLA 1156

Query: 121  SYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYR 180
            SYG SHSLKL+ ED+ILYSAKVIPGNE+RVMKMLNR+SEIGSTI+MG+NEGLHTSGHGYR
Sbjct: 1157 SYGSSHSLKLSKEDIILYSAKVIPGNETRVMKMLNRVSEIGSTIIMGKNEGLHTSGHGYR 1216

Query: 181  GELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIRHST 221
            GELEEVLK+VKPQHFLPIHGELLFLKEHELLG+STGIRH+T
Sbjct: 1217 GELEEVLKIVKPQHFLPIHGELLFLKEHELLGKSTGIRHTT 1257

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|147856240|emb|CAN81787.1| hypothetical protein VITISV_026006 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225456284|ref|XP_002279798.1| PREDICTED: ribonuclease J-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|356507349|ref|XP_003522430.1| PREDICTED: ribonuclease J-like [Glycine max] Back     alignment and taxonomy information
>gi|449501401|ref|XP_004161356.1| PREDICTED: LOW QUALITY PROTEIN: ribonuclease J-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449440566|ref|XP_004138055.1| PREDICTED: ribonuclease J-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255540285|ref|XP_002511207.1| conserved hypothetical protein [Ricinus communis] gi|223550322|gb|EEF51809.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|356516571|ref|XP_003526967.1| PREDICTED: ribonuclease J-like [Glycine max] Back     alignment and taxonomy information
>gi|224119634|ref|XP_002318122.1| predicted protein [Populus trichocarpa] gi|222858795|gb|EEE96342.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356565270|ref|XP_003550865.1| PREDICTED: ribonuclease J-like [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query221
TAIR|locus:2167336 911 emb2746 "embryo defective 2746 1.0 0.242 0.864 2.7e-100
TIGR_CMR|NSE_0829 542 NSE_0829 "metallo-beta-lactama 0.972 0.396 0.383 5.7e-36
UNIPROTKB|Q81WN9 556 BAS3648 "Ribonuclease J" [Baci 0.981 0.390 0.364 8.4e-35
TIGR_CMR|BA_3933 556 BA_3933 "metallo-beta-lactamas 0.981 0.390 0.364 8.4e-35
TIGR_CMR|CHY_1157 554 CHY_1157 "metallo-beta-lactama 0.986 0.393 0.357 4.1e-34
UNIPROTKB|Q81SK8 549 BA_1640 "Ribonuclease J" [Baci 0.981 0.395 0.351 4.9e-34
TIGR_CMR|BA_1640 549 BA_1640 "metallo-beta-lactamas 0.981 0.395 0.351 4.9e-34
UNIPROTKB|Q6GHZ6 565 SAR1063 "Ribonuclease J 1" [St 0.981 0.384 0.359 1.1e-33
TIGR_CMR|SPO_2760 555 SPO_2760 "metallo-beta-lactama 0.968 0.385 0.368 1.9e-31
TIGR_CMR|DET_0438 551 DET_0438 "metallo-beta-lactama 0.977 0.392 0.376 3e-31
TAIR|locus:2167336 emb2746 "embryo defective 2746" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 995 (355.3 bits), Expect = 2.7e-100, P = 2.7e-100
 Identities = 191/221 (86%), Positives = 210/221 (95%)

Query:     1 MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRK 60
             MMSDSTNVLSPGRT SE VV DAL+R+V AAKGRVITTQFASNIHRLGS+KAAAD+TGRK
Sbjct:   296 MMSDSTNVLSPGRTISEKVVADALVRNVMAAKGRVITTQFASNIHRLGSIKAAADITGRK 355

Query:    61 LVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLA 120
             LVFVGMSLRTYL+AAW+DGKAPIDPS+L+KVEDI+AYAPKDLLIVTTGSQAEPRAALNLA
Sbjct:   356 LVFVGMSLRTYLEAAWRDGKAPIDPSSLIKVEDIEAYAPKDLLIVTTGSQAEPRAALNLA 415

Query:   121 SYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYR 180
             SYG SH+ KLT ED+ILYSAKVIPGNESRVMKM+NRI++IG  I+MG+NE LHTSGH YR
Sbjct:   416 SYGSSHAFKLTKEDIILYSAKVIPGNESRVMKMMNRIADIGPNIIMGKNEMLHTSGHAYR 475

Query:   181 GELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIRHST 221
             GELEEVLK+VKPQHFLPIHGELLFLKEHELLG+STGIRH+T
Sbjct:   476 GELEEVLKIVKPQHFLPIHGELLFLKEHELLGKSTGIRHTT 516
GO:0003677 "DNA binding" evidence=IEA
GO:0003824 "catalytic activity" evidence=ISS
GO:0008152 "metabolic process" evidence=ISS
GO:0009793 "embryo development ending in seed dormancy" evidence=NAS
GO:0016787 "hydrolase activity" evidence=IEA
GO:0009507 "chloroplast" evidence=IDA
GO:0015979 "photosynthesis" evidence=RCA
GO:0045333 "cellular respiration" evidence=RCA
TIGR_CMR|NSE_0829 NSE_0829 "metallo-beta-lactamase family, beta-CASP subfamily" [Neorickettsia sennetsu str. Miyayama (taxid:222891)] Back     alignment and assigned GO terms
UNIPROTKB|Q81WN9 BAS3648 "Ribonuclease J" [Bacillus anthracis (taxid:1392)] Back     alignment and assigned GO terms
TIGR_CMR|BA_3933 BA_3933 "metallo-beta-lactamase family protein" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_1157 CHY_1157 "metallo-beta-lactamase family protein" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
UNIPROTKB|Q81SK8 BA_1640 "Ribonuclease J" [Bacillus anthracis (taxid:1392)] Back     alignment and assigned GO terms
TIGR_CMR|BA_1640 BA_1640 "metallo-beta-lactamase family protein" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
UNIPROTKB|Q6GHZ6 SAR1063 "Ribonuclease J 1" [Staphylococcus aureus subsp. aureus MRSA252 (taxid:282458)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_2760 SPO_2760 "metallo-beta-lactamase family protein" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
TIGR_CMR|DET_0438 DET_0438 "metallo-beta-lactamase family protein" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms

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 ?Alignment Graph ?Length ? Definition ? E-value ?
Query221
COG0595 555 COG0595, COG0595, mRNA degradation ribonucleases J 1e-58
TIGR00649422 TIGR00649, MG423, conserved hypothetical protein 2e-41
pfam0752143 pfam07521, RMMBL, RNA-metabolising metallo-beta-la 9e-08
>gnl|CDD|223668 COG0595, COG0595, mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair] Back     alignment and domain information 
 Score =  192 bits (491), Expect = 1e-58
 Identities = 82/221 (37%), Positives = 133/221 (60%), Gaps = 2/221 (0%)

Query: 1   MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRK 60
           ++SDSTN  +PG T SES V + L   +  AKGRVI T FASNI R+ ++  AA+  GRK
Sbjct: 195 LISDSTNAENPGFTPSESEVGENLEDIIRNAKGRVIVTTFASNIERIQTIIDAAEKLGRK 254

Query: 61  LVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLA 120
           +V  G S+   +  A + G   +   + +++ ++  Y  +++LI+ TGSQ EP AAL+  
Sbjct: 255 VVVTGRSMERLIAIARRLGYLKLPDESFIEIREVKRYPDEEVLIICTGSQGEPMAALSR- 313

Query: 121 SYGGSH-SLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGY 179
              G H  +K+   D +++S+  IPGNE+ V ++LNR+ + G+ ++ G ++ +H SGH  
Sbjct: 314 MANGEHRYVKIKEGDTVIFSSSPIPGNEAAVYRLLNRLYKAGAKVITGGDKKVHVSGHAS 373

Query: 180 RGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIRHS 220
           R EL+ ++ L++P++ +P+HGE   L  H  L    GI   
Sbjct: 374 REELKLMINLLRPKYLIPVHGEYRMLVAHAKLAEEEGIPQE 414

Length = 555
>gnl|CDD|233071 TIGR00649, MG423, conserved hypothetical protein Back     alignment and domain information
>gnl|CDD|203663 pfam07521, RMMBL, RNA-metabolising metallo-beta-lactamase Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 221
COG0595 555 mRNA degradation ribonucleases J1/J2 (metallo-beta 100.0
TIGR00649422 MG423 conserved hypothetical protein. Contains an 100.0
TIGR03675630 arCOG00543 arCOG00543 universal archaeal KH-domain 99.8
COG1782637 Predicted metal-dependent RNase, consists of a met 99.79
COG1236427 YSH1 Predicted exonuclease of the beta-lactamase f 99.54
PF0752143 RMMBL: RNA-metabolising metallo-beta-lactamase; In 99.33
KOG1136501 consensus Predicted cleavage and polyadenylation s 99.27
KOG1137 668 consensus mRNA cleavage and polyadenylation factor 99.05
KOG1137668 consensus mRNA cleavage and polyadenylation factor 97.55
KOG1361481 consensus Predicted hydrolase involved in interstr 96.13
PF07522110 DRMBL: DNA repair metallo-beta-lactamase; InterPro 93.98
PF13483163 Lactamase_B_3: Beta-lactamase superfamily domain; 91.6
PF10996126 Beta-Casp: Beta-Casp domain; InterPro: IPR022712 T 91.51
TIGR03588 380 PseC UDP-4-keto-6-deoxy-N-acetylglucosamine 4-amin 91.05
PRK00685228 metal-dependent hydrolase; Provisional 90.15
PRK11706 375 TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisio 89.36
PF12706194 Lactamase_B_2: Beta-lactamase superfamily domain; 88.33
PRK11709355 putative L-ascorbate 6-phosphate lactonase; Provis 88.03
TIGR02379 376 ECA_wecE TDP-4-keto-6-deoxy-D-glucose transaminase 87.24
PRK00055270 ribonuclease Z; Reviewed 84.68
PF01041 363 DegT_DnrJ_EryC1: DegT/DnrJ/EryC1/StrS aminotransfe 84.27
PRK11658 379 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate amin 83.76
COG1167 459 ARO8 Transcriptional regulators containing a DNA-b 83.21
COG0399 374 WecE Predicted pyridoxal phosphate-dependent enzym 82.26
PRK06702 432 O-acetylhomoserine aminocarboxypropyltransferase; 82.03
cd06451 356 AGAT_like Alanine-glyoxylate aminotransferase (AGA 80.58
cd00616 352 AHBA_syn 3-amino-5-hydroxybenzoic acid synthase fa 80.19
>COG0595 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair] Back     alignment and domain information 
Probab=100.00  E-value=4.5e-50  Score=360.39  Aligned_cols=219  Identities=37%  Similarity=0.633  Sum_probs=210.7

Q ss_pred             CccccCCCCCCCCCCCHHHHHHHHHHHHHhcCCcEEEEeccccHHHHHHHHHHHHHcCCeEEEEcccHHHHHHHHHHCCC
Q 045468            1 MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAAWKDGK   80 (221)
Q Consensus         1 Li~EsT~~~~~~~~~sE~~v~~~i~~~~~~~~g~viv~~~a~ni~Rl~~i~~~a~~~gR~~vi~~~~~~~~~~~~~~~g~   80 (221)
                      |||||||+.+++.+.||+++.+.+.+++.+++|||+|+||++|++|+|+++++|.++||+++++|++|..+...+.+.|+
T Consensus       195 LisdsTna~~pg~t~SE~~v~~~l~~i~~~a~grVIv~tfaSni~Ri~~i~~~A~~~gR~vvv~GrSm~~~~~~a~~lg~  274 (555)
T COG0595         195 LISDSTNAENPGFTPSESEVGENLEDIIRNAKGRVIVTTFASNIERIQTIIDAAEKLGRKVVVTGRSMERLIAIARRLGY  274 (555)
T ss_pred             EEeCCcccCCCCCCCCHHHHHHHHHHHHHhCCCcEEEEEchhhHHHHHHHHHHHHHcCCeEEEEcHhHHHHHHHHhhccc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccChhhhhhcCCCCEEEEecCCCccHHHHHHHHhcCCCCCcccCCCCEEEEEecCCCCcHHHHHHHHHHHHHc
Q 045468           81 APIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEI  160 (221)
Q Consensus        81 ~~~~~~~~v~~~~~~~~~~~~~vi~~~g~~~e~~~~l~~~~~~~~~~~~~~~~~~vI~s~~~~pg~e~~~~~~~~~l~~~  160 (221)
                      +..+++.+++.++++.++.++++++|||+||||++.|.+++.++|..+++.++|++|||+.++||+|.....+.|+|.+.
T Consensus       275 ~~~~~~~~i~~~~~~~~~~~~~lii~TG~qgep~aaL~r~a~~~h~~~~i~~gD~vIfss~~ipgne~~~~~~~n~l~~~  354 (555)
T COG0595         275 LKLPDESFIEIREVKRYPDEEVLIICTGSQGEPMAALSRMANGEHRYVKIKEGDTVIFSSSPIPGNEAAVYRLLNRLYKA  354 (555)
T ss_pred             ccCccccccCHHHhccccccceEEEEeCCCCCchhhhhHhhcCCccceecCCCCeEEEeccCcCCcHHHHHHHHHHHHhc
Confidence            98876688999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeEEecCCceeeeecCCCHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHhcCCCC
Q 045468          161 GSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIRH  219 (221)
Q Consensus       161 g~~v~~~~~~~~h~SGHA~~~dL~~~i~~i~Pk~iiPVHge~~~~~~~~~~~~~~g~~~  219 (221)
                      |++++......+|+||||+++||+.|++.++|+++||||||++++.+|+++|.++|++.
T Consensus       355 g~~i~~~~~~~~hvSGHas~eel~~mi~~l~Pky~iPvHGeyr~~~~~a~la~~~G~~~  413 (555)
T COG0595         355 GAKVITGGDKKVHVSGHASREELKLMINLLRPKYLIPVHGEYRMLVAHAKLAEEEGIPQ  413 (555)
T ss_pred             CcEEeecccceeEecCCCChHHHHHHHHhhCCceecccCCCcHHHHHHHHHHHhcCCCc
Confidence            99999765567999999999999999999999999999999999999999999999865

>TIGR00649 MG423 conserved hypothetical protein Back     alignment and domain information
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein Back     alignment and domain information
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only] Back     alignment and domain information
>COG1236 YSH1 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF07521 RMMBL: RNA-metabolising metallo-beta-lactamase; InterPro: IPR011108 The metallo-beta-lactamase fold contains five sequence motifs Back     alignment and domain information
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification] Back     alignment and domain information
>KOG1137 consensus mRNA cleavage and polyadenylation factor II complex, BRR5 (CPSF subunit) [RNA processing and modification] Back     alignment and domain information
>KOG1137 consensus mRNA cleavage and polyadenylation factor II complex, BRR5 (CPSF subunit) [RNA processing and modification] Back     alignment and domain information
>KOG1361 consensus Predicted hydrolase involved in interstrand cross-link repair [Replication, recombination and repair] Back     alignment and domain information
>PF07522 DRMBL: DNA repair metallo-beta-lactamase; InterPro: IPR011084 The metallo-beta-lactamase fold contains five sequence motifs Back     alignment and domain information
>PF13483 Lactamase_B_3: Beta-lactamase superfamily domain; PDB: 1VJN_B 3KL7_A Back     alignment and domain information
>PF10996 Beta-Casp: Beta-Casp domain; InterPro: IPR022712 The beta-CASP domain is found C-terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease Back     alignment and domain information
>TIGR03588 PseC UDP-4-keto-6-deoxy-N-acetylglucosamine 4-aminotransferase Back     alignment and domain information
>PRK00685 metal-dependent hydrolase; Provisional Back     alignment and domain information
>PRK11706 TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional Back     alignment and domain information
>PF12706 Lactamase_B_2: Beta-lactamase superfamily domain; PDB: 3BV6_F 1WW1_A 2E7Y_A 3RPC_D 3ZWF_A 3JXP_A 1XTO_A 2CBN_A 3G1P_B 3P2U_A Back     alignment and domain information
>PRK11709 putative L-ascorbate 6-phosphate lactonase; Provisional Back     alignment and domain information
>TIGR02379 ECA_wecE TDP-4-keto-6-deoxy-D-glucose transaminase Back     alignment and domain information
>PRK00055 ribonuclease Z; Reviewed Back     alignment and domain information
>PF01041 DegT_DnrJ_EryC1: DegT/DnrJ/EryC1/StrS aminotransferase family; InterPro: IPR000653 This entry represents a family that are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions Back     alignment and domain information
>PRK11658 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase; Provisional Back     alignment and domain information
>COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism] Back     alignment and domain information
>COG0399 WecE Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>PRK06702 O-acetylhomoserine aminocarboxypropyltransferase; Validated Back     alignment and domain information
>cd06451 AGAT_like Alanine-glyoxylate aminotransferase (AGAT) family Back     alignment and domain information
>cd00616 AHBA_syn 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn) Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query221
3zq4_A 555 Unusual, Dual Endo- And Exo-Nuclease Activity In Th 1e-31
3t3n_A 562 Molecular Basis For The Recognition And Cleavage Of 1e-28
3bk1_A 562 Crystal Structure Analysis Of Rnase J Length = 562 7e-28
>pdb|3ZQ4|A Chain A, Unusual, Dual Endo- And Exo-Nuclease Activity In The Degradosome Explained By Crystal Structure Analysis Of Rnase J1 Length = 555 Back     alignment and structure 
Iteration: 1

 Score =  133 bits (334), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 75/217 (34%), Positives = 117/217 (53%)
Query: 1   MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRK 60
           ++SDSTN  +P  T SE  V +++        GR+I   FASNIHRL  V  AA   GRK
Sbjct: 192 LLSDSTNSENPEFTMSERRVGESIHDIFRKVDGRIIFATFASNIHRLQQVIEAAVQNGRK 251
Query: 61  LVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLA 120
           +   G S+ + ++     G      +T ++  +I+      + I+ TGSQ EP AAL+  
Sbjct: 252 VAVFGRSMESAIEIGQTLGYINCPKNTFIEHNEINRMPANKVTILCTGSQGEPMAALSRI 311
Query: 121 SYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYR 180
           + G    + +   D +++S+  IPGN   V + +N++   G+ ++ G    +HTSGHG +
Sbjct: 312 ANGTHRQISINPGDTVVFSSSPIPGNTISVSRTINQLYRAGAEVIHGPLNDIHTSGHGGQ 371
Query: 181 GELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGI 217
            E + +L+L+KP+ F+PIHGE    K H  L    GI
Sbjct: 372 EEQKLMLRLIKPKFFMPIHGEYRMQKMHVKLATDCGI 408
>pdb|3T3N|A Chain A, Molecular Basis For The Recognition And Cleavage Of Rna (Uuccgu) By The Bifunctional 5'-3' ExoENDORIBONUCLEASE RNASE J Length = 562 Back     alignment and structure
>pdb|3BK1|A Chain A, Crystal Structure Analysis Of Rnase J Length = 562 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query221
3bk2_A 562 RNAse J, metal dependent hydrolase; endoribonuclea 2e-80
3zq4_A 555 Ribonuclease J 1, RNAse J1; hydrolase, RNA maturat 9e-75
2az4_A429 Hypothetical protein EF2904; structural genomics, 9e-63
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-04
>3bk2_A RNAse J, metal dependent hydrolase; endoribonuclease, exoribonuclease, metallo-beta-lactamase; HET: U5P; 2.10A {Thermus thermophilus} PDB: 3bk1_A* 3t3o_A* 3t3n_A* Length = 562 Back     alignment and structure
 Score =  249 bits (638), Expect = 2e-80
 Identities = 71/217 (32%), Positives = 115/217 (52%), Gaps = 1/217 (0%)

Query: 1   MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRK 60
           +++D+TN   PG T SE  +   L R +  A GRV  T FAS+IHR+ SV  AA+  GRK
Sbjct: 208 LIADATNAERPGYTPSEMEIAKELDRVIGRAPGRVFVTTFASHIHRIQSVIWAAEKYGRK 267

Query: 61  LVFVGMSLRTYLDAAWKDGKAPIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLA 120
           +   G S+  +   A + G   +    L  +E++       +LI+ TGSQ +P + L+  
Sbjct: 268 VAMEGRSMLKFSRIALELGYLKV-KDRLYTLEEVKDLPDHQVLILATGSQGQPMSVLHRL 326

Query: 121 SYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEIGSTIVMGRNEGLHTSGHGYR 180
           ++ G   + +   D ++ S+  IPGNE  V +++NR+  +G+ ++      +H SGH  +
Sbjct: 327 AFEGHAKMAIKPGDTVILSSSPIPGNEEAVNRVINRLYALGAYVLYPPTYKVHASGHASQ 386

Query: 181 GELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGI 217
            EL+ +L L  P+ FLP HGE+      + L  S   
Sbjct: 387 EELKLILNLTTPRFFLPWHGEVRHQMNFKWLAESMSR 423
>3zq4_A Ribonuclease J 1, RNAse J1; hydrolase, RNA maturation; 3.00A {Bacillus subtilis} Length = 555 Back     alignment and structure
>2az4_A Hypothetical protein EF2904; structural genomics, PSI, protein STR initiative, midwest center for structural genomics, MCSG, U function; 2.00A {Enterococcus faecalis} SCOP: d.157.1.10 Length = 429 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query221
3zq4_A 555 Ribonuclease J 1, RNAse J1; hydrolase, RNA maturat 100.0
3bk2_A 562 RNAse J, metal dependent hydrolase; endoribonuclea 100.0
2az4_A429 Hypothetical protein EF2904; structural genomics, 99.95
3af5_A651 Putative uncharacterized protein PH1404; archaeal 99.92
2ycb_A636 Beta-CAsp RNAse, cleavage and polyadenylation spec 99.92
3zdk_A336 5' exonuclease apollo; hydrolase; HET: TLA; 2.16A 99.92
2xr1_A640 Cleavage and polyadenylation specificity factor 1 99.92
3iek_A431 Ribonuclease TTHA0252; metallo beta lactamase fold 99.79
2i7t_A459 Cleavage and polyadenylation specificity factor 73 99.75
4b87_A367 DNA cross-LINK repair 1A protein; dclre1A, DCLRE, 99.33
2i7x_A 717 Protein CFT2; polyadenylation, metallo-B-lactamase 99.27
3rpc_A264 Possible metal-dependent hydrolase; structural gen 90.92
1vjn_A220 Zn-dependent hydrolase of metallo-beta-lactamase s 90.33
2i7x_A717 Protein CFT2; polyadenylation, metallo-B-lactamase 87.98
3ju7_A 377 Putative PLP-dependent aminotransferase; NP_978343 86.38
3g1p_A258 Protein PHNP; C-P lyase, phosphodiesterase, phosph 85.5
3tcm_A 500 Alanine aminotransferase 2; pyridoxal phosphate (P 84.02
3kl7_A235 Putative metal-dependent hydrolase; structural gen 83.96
3isl_A 416 Purine catabolism protein PUCG; pyridoxalphosphate 82.62
1e5d_A402 Rubredoxin\:oxygen oxidoreductase; oxygenreductase 82.08
3euc_A 367 Histidinol-phosphate aminotransferase 2; YP_297314 80.19
>3zq4_A Ribonuclease J 1, RNAse J1; hydrolase, RNA maturation; 3.00A {Bacillus subtilis} Back     alignment and structure
Probab=100.00  E-value=1.6e-47  Score=348.69  Aligned_cols=219  Identities=34%  Similarity=0.535  Sum_probs=207.7

Q ss_pred             CccccCCCCCCCCCCCHHHHHHHHHHHHHhcCCcEEEEeccccHHHHHHHHHHHHHcCCeEEEEcccHHHHHHHHHHCCC
Q 045468            1 MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLTGRKLVFVGMSLRTYLDAAWKDGK   80 (221)
Q Consensus         1 Li~EsT~~~~~~~~~sE~~v~~~i~~~~~~~~g~viv~~~a~ni~Rl~~i~~~a~~~gR~~vi~~~~~~~~~~~~~~~g~   80 (221)
                      ||+||||+.+++++.+|.++.+.+.+++.+++|+|+|++||+|++|+|+++++|.++||+++++|++|..+++.+.+.|+
T Consensus       192 Li~esT~~~~~~~~~se~~v~~~i~~~~~~~~grvii~~fasnv~R~q~il~~a~~~gr~v~v~grs~~~~~~~~~~~g~  271 (555)
T 3zq4_A          192 LLSDSTNSENPEFTMSERRVGESIHDIFRKVDGRIIFATFASNIHRLQQVIEAAVQNGRKVAVFGRSMESAIEIGQTLGY  271 (555)
T ss_dssp             EEEECTTTTCCSCCCCHHHHHHHHHHHHHHCCSCEEEECCTTCHHHHHHHHHHHHTTTCEEEEESHHHHHHHHHHHGGGS
T ss_pred             EEecCcccCCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEChhHHHHHHHHHHHHHHHCCEEEEeCHHHHHHHHHHHHcCC
Confidence            68999999999999999999999999998878999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccChhhhhhcCCCCEEEEecCCCccHHHHHHHHhcCCCCCcccCCCCEEEEEecCCCCcHHHHHHHHHHHHHc
Q 045468           81 APIDPSTLVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSLKLTNEDVILYSAKVIPGNESRVMKMLNRISEI  160 (221)
Q Consensus        81 ~~~~~~~~v~~~~~~~~~~~~~vi~~~g~~~e~~~~l~~~~~~~~~~~~~~~~~~vI~s~~~~pg~e~~~~~~~~~l~~~  160 (221)
                      +++++..+++.++++.+++++++|++||+|||++++|.+++.++|..++++++|++|||+|++||+|....++.|++.+.
T Consensus       272 l~~p~~~~v~~~~~~~~~~~~~vii~tgsqGe~~~~L~r~a~~~~~~~~~~~~d~vi~s~~~ipGne~~~~~~~~~l~~~  351 (555)
T 3zq4_A          272 INCPKNTFIEHNEINRMPANKVTILCTGSQGEPMAALSRIANGTHRQISINPGDTVVFSSSPIPGNTISVSRTINQLYRA  351 (555)
T ss_dssp             CCCCGGGEECGGGTTTSCGGGEEEEECCTTCCTTSHHHHHHSSCCSSCCCCTTCEEEECSCCCTTCHHHHHHHHHHHHHT
T ss_pred             ccCCcccEeCHHHHhhCCCCCEEEEeCCCCchHHHHHHHHhcCCCCccccCCCCEEEEECCCCCCcHHHHHHHHHHHHHC
Confidence            98876678889999999888999999999999999999999999999999999999999999999999888999999999


Q ss_pred             CCeEEecCCceeeeecCCCHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHhcCCCC
Q 045468          161 GSTIVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIRH  219 (221)
Q Consensus       161 g~~v~~~~~~~~h~SGHA~~~dL~~~i~~i~Pk~iiPVHge~~~~~~~~~~~~~~g~~~  219 (221)
                      |++|+......+|+||||+++||+.|++.++|+++||||||++++.+|+++|+++|+++
T Consensus       352 g~~v~~~~~~~~h~SgHa~~~eL~~~~~~~~Pk~~ipvHGe~~~~~~~~~~a~~~G~~~  410 (555)
T 3zq4_A          352 GAEVIHGPLNDIHTSGHGGQEEQKLMLRLIKPKFFMPIHGEYRMQKMHVKLATDCGIPE  410 (555)
T ss_dssp             TCEEECSSSSCCCCCSSCCHHHHHHHHHHSCEEEEEEESBCHHHHHHHHHHHHHTTCCG
T ss_pred             CCEEEecCCcceEEeCCCCHHHHHHHHHHhCCCEEEEcCCCHHHHHHHHHHHHHcCCCc
Confidence            99998655567999999999999999999999999999999999999999999999963
>3bk2_A RNAse J, metal dependent hydrolase; endoribonuclease, exoribonuclease, metallo-beta-lactamase; HET: U5P; 2.10A {Thermus thermophilus} PDB: 3bk1_A* 3t3o_A* 3t3n_A* Back     alignment and structure
>2az4_A Hypothetical protein EF2904; structural genomics, PSI, protein STR initiative, midwest center for structural genomics, MCSG, U function; 2.00A {Enterococcus faecalis} SCOP: d.157.1.10 Back     alignment and structure
>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp family, KH domain, ribonuclease, ME beta-lactamase superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB: 3af6_A* Back     alignment and structure
>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor; hydrolase, KH, metallo-beta-lactamase; 3.10A {Methanothermobacter thermautotrophicusorganism_taxid} Back     alignment and structure
>3zdk_A 5' exonuclease apollo; hydrolase; HET: TLA; 2.16A {Homo sapiens} Back     alignment and structure
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit; hydrolase, metallo-beta-lactamase, beta-CAsp, RNA processing; 2.59A {Methanosarcina mazei} Back     alignment and structure
>3iek_A Ribonuclease TTHA0252; metallo beta lactamase fold, endonuclease, hydrolase, metal- nuclease, RNA-binding, rRNA processing; HET: FLC; 2.05A {Thermus thermophilus} SCOP: d.157.1.10 PDB: 2dkf_A* 3iel_A* 3iem_A* 2zdf_A* 3idz_A* 2zdd_A* 3ie0_A* 2zde_A* 3ie1_A* 2zdw_A* 3a4y_A* 2yvd_A* 3ie2_A* Back     alignment and structure
>2i7t_A Cleavage and polyadenylation specificity factor 73 kDa subunit; metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination; 2.10A {Homo sapiens} SCOP: d.157.1.10 PDB: 2i7v_A Back     alignment and structure
>4b87_A DNA cross-LINK repair 1A protein; dclre1A, DCLRE, interstrand crosslink repair, hydrolase, NIT mustard, cancer, chemotherapy, PSO2 homolog,; HET: DNA; 2.16A {Homo sapiens} Back     alignment and structure
>2i7x_A Protein CFT2; polyadenylation, metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination, double-strand break repair; 2.50A {Saccharomyces cerevisiae} SCOP: d.157.1.10 Back     alignment and structure
>3rpc_A Possible metal-dependent hydrolase; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 1.49A {Veillonella parvula} Back     alignment and structure
>1vjn_A Zn-dependent hydrolase of metallo-beta-lactamase superfamily TM0207; metallo-hydrolase/oxidoreductase fold, structural genomics; 2.00A {Thermotoga maritima} SCOP: d.157.1.4 Back     alignment and structure
>2i7x_A Protein CFT2; polyadenylation, metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J recombination, double-strand break repair; 2.50A {Saccharomyces cerevisiae} SCOP: d.157.1.10 Back     alignment and structure
>3ju7_A Putative PLP-dependent aminotransferase; NP_978343.1, struct genomics, joint center for structural genomics, JCSG; HET: LLP PGE; 2.19A {Bacillus cereus atcc 10987} Back     alignment and structure
>3g1p_A Protein PHNP; C-P lyase, phosphodiesterase, phosphonate utilization, alkylphosphonate uptake; 1.40A {Escherichia coli} PDB: 3p2u_A Back     alignment and structure
>3tcm_A Alanine aminotransferase 2; pyridoxal phosphate (PLP)-binding; HET: DCS; 2.71A {Hordeum vulgare} Back     alignment and structure
>3kl7_A Putative metal-dependent hydrolase; structural genomics, JOI for structural genomics, JCSG; 2.30A {Parabacteroides distasonis atcc 8503} Back     alignment and structure
>3isl_A Purine catabolism protein PUCG; pyridoxalphosphate, PLP dependent enzymes, purine metabolism transaminases, aminotransferases; HET: PLP; 2.06A {Bacillus subtilis} Back     alignment and structure
>1e5d_A Rubredoxin\:oxygen oxidoreductase; oxygenreductase, DIIRON-centre, flavoproteins, lactamase-fold; HET: FMN; 2.5A {Desulfovibrio gigas} SCOP: c.23.5.1 d.157.1.3 Back     alignment and structure
>3euc_A Histidinol-phosphate aminotransferase 2; YP_297314.1, structur genomics, joint center for structural genomics, JCSG; HET: MSE; 2.05A {Ralstonia eutropha JMP134} SCOP: c.67.1.0 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 221
d2i7xa1514 d.157.1.10 (A:1-422,A:626-717) Cleavage factor two 5e-13
d2i7ta1451 d.157.1.10 (A:9-459) Cleavage and polyadenylation 2e-11
d2dkfa1431 d.157.1.10 (A:1-431) Putative RNA-degradation prot 2e-09
>d2i7xa1 d.157.1.10 (A:1-422,A:626-717) Cleavage factor two protein 2, CFT2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 514 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Metallo-hydrolase/oxidoreductase
superfamily: Metallo-hydrolase/oxidoreductase
family: beta-CASP RNA-metabolising hydrolases
domain: Cleavage factor two protein 2, CFT2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 64.8 bits (157), Expect = 5e-13
 Identities = 24/291 (8%), Positives = 66/291 (22%), Gaps = 74/291 (25%)

Query: 1   MMSDSTNVLSPGRTTSESVVKDALMRHVSAAKGRVITTQFASNI---------HRLGSVK 51
           +++      S       S +    ++   ++ G VI     S             L    
Sbjct: 210 IITTLDRFGSSQPFKKRSKIFKDTLKKGLSSDGSVIIPVDMSGKFLDLFTQVHELLFEST 269

Query: 52  AAADLTGRKLVFVGMSLRTYLDAAW----------------KDGKAPIDPSTLVKVEDID 95
                T   ++ +  +    L  A                 ++  +P +  + +K+   +
Sbjct: 270 KINAHTQVPVLILSYARGRTLTYAKSMLEWLSPSLLKTWENRNNTSPFEIGSRIKIIAPN 329

Query: 96  AYA--PKDLLIVTTGSQAEPRAALN-------------LASYGGSHSL------------ 128
             +  P   +   +   A     +                S+  + SL            
Sbjct: 330 ELSKYPGSKICFVSEVGALINEVIIKVGNSEKTTLILTKPSFECASSLDKILEIVEQDER 389

Query: 129 ------------------KLTNEDVILYSAKVIPGNESRVMKMLN----RISEIGSTIVM 166
                              +        S +    +    +K+      R     +  + 
Sbjct: 390 NWKTFPEDGKSFLCDNYISIDTIKEEPLSKEETNFDNLDYLKIDKTLSKRTISTVNVQLK 449

Query: 167 GRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGI 217
                L+      +     +   +K +  +    + +  +E         I
Sbjct: 450 CSVVILNLQSLVDQRSASIIWPSLKSRKIVLSAPKQIQNEEITAKLIKKNI 500
>d2i7ta1 d.157.1.10 (A:9-459) Cleavage and polyadenylation specificity factor subunit 3 {Human (Homo sapiens) [TaxId: 9606]} Length = 451 Back     information, alignment and structure
>d2dkfa1 d.157.1.10 (A:1-431) Putative RNA-degradation protein TTHA0252 {Thermus thermophilus [TaxId: 274]} Length = 431 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query221
d2i7xa1514 Cleavage factor two protein 2, CFT2 {Baker's yeast 99.88
d2dkfa1431 Putative RNA-degradation protein TTHA0252 {Thermus 99.87
d2i7ta1451 Cleavage and polyadenylation specificity factor su 99.56
d1vjna_209 Hypothetical protein TM0207 {Thermotoga maritima [ 91.72
d1mdoa_ 376 Aminotransferase ArnB {Salmonella typhimurium [Tax 86.99
>d2i7xa1 d.157.1.10 (A:1-422,A:626-717) Cleavage factor two protein 2, CFT2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Metallo-hydrolase/oxidoreductase
superfamily: Metallo-hydrolase/oxidoreductase
family: beta-CASP RNA-metabolising hydrolases
domain: Cleavage factor two protein 2, CFT2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.88  E-value=1.6e-22  Score=180.54  Aligned_cols=206  Identities=8%  Similarity=0.068  Sum_probs=139.8

Q ss_pred             CccccCCCCCCC--CCCCHHHHHHHHHHHHHhcCCcEEEEeccccHHHHHHHHHHHHHc-----------CCeEEEEccc
Q 045468            1 MMSDSTNVLSPG--RTTSESVVKDALMRHVSAAKGRVITTQFASNIHRLGSVKAAADLT-----------GRKLVFVGMS   67 (221)
Q Consensus         1 Li~EsT~~~~~~--~~~sE~~v~~~i~~~~~~~~g~viv~~~a~ni~Rl~~i~~~a~~~-----------gR~~vi~~~~   67 (221)
                      |++|+|+.....  +...|+.+.+.+.++++ .+|+|+||+||  ++|+|+++.++.+.           +.+++++|+.
T Consensus       209 lli~~t~~~~~~~~~~~~~~~l~~~i~~~~~-~gG~VlIP~fa--~gR~QEil~~l~~~~~~~~~~~~~~~~pI~~~~~~  285 (514)
T d2i7xa1         209 AIITTLDRFGSSQPFKKRSKIFKDTLKKGLS-SDGSVIIPVDM--SGKFLDLFTQVHELLFESTKINAHTQVPVLILSYA  285 (514)
T ss_dssp             EEEECCSCCCCSSCHHHHHHHHHHHHHHHTS-TTCEEEEEECT--TTHHHHHHHHHHHHHTTC-------CCCEEEECTT
T ss_pred             EEEEcCCCCCCCCChHHHHHHHHHHHHHHHh-CCCEEEEEEcC--chHHHHHHHHHHHHHHHHHhhccCCCceEEEEChH
Confidence            366777765433  23455667777777764 58999999999  77999999888765           3488999877


Q ss_pred             HHHHHHHHHHC----------------CCCCCCCCC---ccChhhhhhcCCCCEEEEecCCCccHHHHHHHHhcCCCCCc
Q 045468           68 LRTYLDAAWKD----------------GKAPIDPST---LVKVEDIDAYAPKDLLIVTTGSQAEPRAALNLASYGGSHSL  128 (221)
Q Consensus        68 ~~~~~~~~~~~----------------g~~~~~~~~---~v~~~~~~~~~~~~~vi~~~g~~~e~~~~l~~~~~~~~~~~  128 (221)
                      +..+++.+...                +.-++....   ..+.+++.+++. ..||++|+++|+...+|.+++.+     
T Consensus       286 ~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~pf~~~~~~~i~~~~~l~~~~~-p~VIiat~~~G~~~~~l~~~a~d-----  359 (514)
T d2i7xa1         286 RGRTLTYAKSMLEWLSPSLLKTWENRNNTSPFEIGSRIKIIAPNELSKYPG-SKICFVSEVGALINEVIIKVGNS-----  359 (514)
T ss_dssp             TTHHHHHHHTCGGGSCHHHHHHHHSSSSCCTTCCTTTEEECCGGGGGGCCS-CEEEEEESCHHHHHHHHHHHSSC-----
T ss_pred             HHHHHHHHHHhHhhcCHHHHHHHhhhcCCCchhccCceeccCHHHHHhccC-CcEEEEcCCCchHHHHHHHHhcC-----
Confidence            66666555331                111111111   124556666655 45788888889999999999876     


Q ss_pred             ccCCCCEEEEE--ecCCCCcHHHHHHHHHHHHHc-------CC-------------------------------------
Q 045468          129 KLTNEDVILYS--AKVIPGNESRVMKMLNRISEI-------GS-------------------------------------  162 (221)
Q Consensus       129 ~~~~~~~vI~s--~~~~pg~e~~~~~~~~~l~~~-------g~-------------------------------------  162 (221)
                         ++++|+|.  +++.+|+.....+...+....       +.                                     
T Consensus       360 ---~~n~Vi~t~~g~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~  436 (514)
T d2i7xa1         360 ---EKTTLILTKPSFECASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISIDTIKEEPLSKEETNFDNLDYLKIDKTL  436 (514)
T ss_dssp             ---TTEEEEECSSCCTTCHHHHHHHHHHHTCC--------CCCCEECCEEEEEEEEEEEESCSCCCCCSCCGGGSCSSCC
T ss_pred             ---CCCEEEEecCCCcccccHHHHHhhhhhhccccccccccccccccCcceeecccccccccccccCccccccccccccc
Confidence               78899998  444443322211111100000       00                                     


Q ss_pred             --------e-EEecCCceeeeecCCCHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHhcCCC
Q 045468          163 --------T-IVMGRNEGLHTSGHGYRGELEEVLKLVKPQHFLPIHGELLFLKEHELLGRSTGIR  218 (221)
Q Consensus       163 --------~-v~~~~~~~~h~SGHA~~~dL~~~i~~i~Pk~iiPVHge~~~~~~~~~~~~~~g~~  218 (221)
                              . .+.++...+|+||||++++|+.|++.++|+++||||||.+++.++++.+++.|++
T Consensus       437 ~~~~~~~~~~~v~~~v~~i~~SgHad~~el~~~~~~~~P~~vvlvHGe~~~~~~~a~~l~~~g~~  501 (514)
T d2i7xa1         437 SKRTISTVNVQLKCSVVILNLQSLVDQRSASIIWPSLKSRKIVLSAPKQIQNEEITAKLIKKNIE  501 (514)
T ss_dssp             EEEEEEEEEEEECSEEEECCCCCSCCHHHHHHHGGGSCCSEEEECSCGGGSCHHHHHHHHHTTCE
T ss_pred             ceeecccceEEEEEEEEEEEeeecCCHHHHHHHHHhhCCCEEEEeCCCHHHHHHHHHHHHHCCCe
Confidence                    0 0112224689999999999999999999999999999999999999999999974
>d2dkfa1 d.157.1.10 (A:1-431) Putative RNA-degradation protein TTHA0252 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2i7ta1 d.157.1.10 (A:9-459) Cleavage and polyadenylation specificity factor subunit 3 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vjna_ d.157.1.4 (A:) Hypothetical protein TM0207 {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1mdoa_ c.67.1.4 (A:) Aminotransferase ArnB {Salmonella typhimurium [TaxId: 90371]} Back     information, alignment and structure