Citrus Sinensis ID: 031049

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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------
Protein Sequence
MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQPCSKPEDILPDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPPNCT
Secondary Structure (PSIPRED)
ccEEEEEEccHHHHHHHHHHHHHHHHccccccccccccccEEEEEccccccccccccccccccccccEEEcEEEEEcccccEEEEEEEccHHHHHHHHHHHHHHHHccccccccccccccccEEEEccccccccHHHHHHHHHHccccEEEEEEEEEEEEEccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEccHHHHHHHHHHHHHHHHccccccccccccccEEEEEEcccccHHHHHHHHHcccccccEEEEEEEEccccccEEEEcccccHHHHHHHHHHHHHHHHcccccccccccccccccccEcccccHHHHHHHHHHHHHcccccEEEEEEEEEEEEccccc
Coil and Loop (DISEMBL)
MQYAIKLYFDDALKSKILDSMKLVRElnipnlikpedephitllvtqpcskpedilpdsiplvdkfpislslfsvlprkNNLLCLLIAQSLNLRELHDNLYEALATKglqidkeyvpgvwfphcmlapsvptdrvgnVCNILAKvklplqgdvehvrlvqlppnct
Flexible Loop (DISEMBL)
MQYAIKLyfddalkskildsMKLVRELNIPnlikpedepHITLLVTQPCSKPEDILPDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKvklplqgdvehvrlvqlppnct
Low Complexity Region (SEG)
MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQPCSKPEDILPDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPPNCT
Disordered region (IsUnstruct)
**YAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQPCSKPEDILPDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQ******
Disordered Region (DISOPRED)
MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQPCSKPEDILPDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPPN**
Disordered Region (DISEMBL)
MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQPCSKPEDILPDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPPNCT
Disordered Region (DISPRO)
MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQPCSKPEDILPDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPPNCT
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQPCSKPEDILPDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPPNCT
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	166
224055517	184	predicted protein [Populus trichocarpa]	0.969	0.875	0.365	3e-19
225452536	183	PREDICTED: uncharacterized protein LOC10	0.963	0.874	0.357	4e-19
296087705	257	unnamed protein product [Vitis vinifera]	0.963	0.622	0.357	5e-19
255552670	183	calmodulin binding protein, putative [Ri	0.969	0.879	0.353	1e-18
449449194	183	PREDICTED: uncharacterized protein LOC10	0.963	0.874	0.357	2e-18
147844702	183	hypothetical protein VITISV_002643 [Viti	0.963	0.874	0.351	3e-18
388496900	182	unknown [Lotus japonicus] gi|388513163|g	0.975	0.890	0.353	2e-16
294460847	183	unknown [Picea sitchensis]	0.963	0.874	0.327	8e-16
224141313	181	predicted protein [Populus trichocarpa]	0.945	0.867	0.327	8e-14
356550070	182	PREDICTED: uncharacterized protein LOC10	0.939	0.857	0.329	2e-13

>gi|224055517|ref|XP_002298518.1| predicted protein [Populus trichocarpa] gi|222845776|gb|EEE83323.1| predicted protein [Populus trichocarpa]

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 91/164 (55%), Gaps = 3/164 (1%)

Query: 3   YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQPC--SKPEDILPDS 59
           YAI+LYFD AL++++L +  ++    I + LI+ E  PHITL  T     +K E I+   
Sbjct: 6   YAIELYFDPALENQVLKAWNVLARRQISSQLIEIESRPHITLYSTPFIDPTKLESIIKTF 65

Query: 60  IPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGV 119
               +  P+SLS    LP  NN+L L    SL+L + H  L +A+  +G++I +EY P  
Sbjct: 66  ASKQEPLPLSLSTIGCLPNDNNILFLAPTPSLSLLQFHSQLCDAMRKEGIEISEEYRPDN 125

Query: 120 WFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
           W P+C +A  VP  R+G    +L  +KLP+ G    + LV+  P
Sbjct: 126 WIPYCAVAQDVPKARMGESLCVLRDLKLPVAGYAMDIGLVEFSP 169

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225452536|ref|XP_002279925.1| PREDICTED: uncharacterized protein LOC100249281 isoform 1 [Vitis vinifera]

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 91/165 (55%), Gaps = 5/165 (3%)

Query: 3   YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQPCSKP---EDILPD 58
           YAI+LYFD AL++++L +  ++    I   LI+ E  PHITL  + P  +P   E+I+  
Sbjct: 5   YAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLF-SSPLIEPARLENIIKS 63

Query: 59  SIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPG 118
                +  P+S S    LP   N+L L    +L+L + H  L +AL  +G++I +EY P 
Sbjct: 64  FAGKQEPLPLSFSSIGSLPNDKNVLFLAPTPTLSLLQFHSQLCDALKKEGIEIGEEYRPD 123

Query: 119 VWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
            W PHC +A  VP  R+G   ++L  +KLP+ G    + LV+  P
Sbjct: 124 SWIPHCPVAQEVPKIRMGEAFSVLRDLKLPVTGYAMDIGLVEFSP 168

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087705|emb|CBI34961.3| unnamed protein product [Vitis vinifera]

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 91/165 (55%), Gaps = 5/165 (3%)

Query: 3   YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQPCSKP---EDILPD 58
           YAI+LYFD AL++++L +  ++    I   LI+ E  PHITL  + P  +P   E+I+  
Sbjct: 79  YAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLF-SSPLIEPARLENIIKS 137

Query: 59  SIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPG 118
                +  P+S S    LP   N+L L    +L+L + H  L +AL  +G++I +EY P 
Sbjct: 138 FAGKQEPLPLSFSSIGSLPNDKNVLFLAPTPTLSLLQFHSQLCDALKKEGIEIGEEYRPD 197

Query: 119 VWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
            W PHC +A  VP  R+G   ++L  +KLP+ G    + LV+  P
Sbjct: 198 SWIPHCPVAQEVPKIRMGEAFSVLRDLKLPVTGYAMDIGLVEFSP 242

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552670|ref|XP_002517378.1| calmodulin binding protein, putative [Ricinus communis] gi|223543389|gb|EEF44920.1| calmodulin binding protein, putative [Ricinus communis]

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 58/164 (35%), Positives = 89/164 (54%), Gaps = 3/164 (1%)

Query: 3   YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQPC--SKPEDILPDS 59
           +AI+LYFD AL++++L +  ++    I   LI+ E  PHITL  +     +K E I+   
Sbjct: 5   FAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLYSSSFVEPTKLESIVKTF 64

Query: 60  IPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGV 119
               +  P+SLS    LP  NN+L L    SL+L +    L +AL  +G++I +EY P  
Sbjct: 65  ASKQEPLPLSLSAIGGLPNDNNVLFLAPTPSLSLLQFQSQLCDALKKEGIEISEEYKPDS 124

Query: 120 WFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
           W P+C +A  VP  R+G    +L  +KLP+ G    + LV+  P
Sbjct: 125 WIPYCAVAQDVPRARIGEAFCVLRDLKLPVSGYAMDIGLVEFSP 168

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449449194|ref|XP_004142350.1| PREDICTED: uncharacterized protein LOC101208638 [Cucumis sativus] gi|449492681|ref|XP_004159070.1| PREDICTED: uncharacterized protein LOC101226201 [Cucumis sativus]

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 91/165 (55%), Gaps = 5/165 (3%)

Query: 3   YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVT---QPCSKPEDILPD 58
           +AI+LYFD AL++++L +  ++    I   LI+ E  PHITL  T   +P +K E I+ +
Sbjct: 5   FAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLFSTPFLEP-TKVESIVKN 63

Query: 59  SIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPG 118
                +   +SLS    LP  NN+L L  A S++L +    L EA+  +G++I +EY  G
Sbjct: 64  FASKQEPLALSLSSIGSLPSDNNILFLGPAPSISLLQFQSQLCEAMRKEGIEIGEEYRLG 123

Query: 119 VWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
            W PHC +A  VP  R+     +L  +KLP+ G    + LV+  P
Sbjct: 124 SWIPHCAVAQEVPKARMAEAFCVLRDLKLPVSGYAIDIGLVEFSP 168

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147844702|emb|CAN82133.1| hypothetical protein VITISV_002643 [Vitis vinifera]

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 58/165 (35%), Positives = 90/165 (54%), Gaps = 5/165 (3%)

Query: 3   YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQPCSKP---EDILPD 58
           YAI+LYFD AL++++L +  ++    I   LI+ E  PHITL  + P  +P   E+I+  
Sbjct: 5   YAIELYFDPALENQVLKAWNVLARRQISTQLIEIESRPHITLF-SSPLIEPARLENIIKS 63

Query: 59  SIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPG 118
                +   +S S    LP   N+L L    +L+L + H  L +AL  +G++I +EY P 
Sbjct: 64  FAGKQEPLXLSFSSIGSLPNDKNVLFLAPTPTLSLLQFHSQLCDALKKEGIEIGEEYRPD 123

Query: 119 VWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
            W PHC +A  VP  R+G   ++L  +KLP+ G    + LV+  P
Sbjct: 124 SWIPHCPVAQEVPKIRMGEAFSVLRDLKLPVTGYAMDIGLVEFSP 168

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388496900|gb|AFK36516.1| unknown [Lotus japonicus] gi|388513163|gb|AFK44643.1| unknown [Lotus japonicus]

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 59/167 (35%), Positives = 85/167 (50%), Gaps = 5/167 (2%)

Query: 1   MQYAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVT---QPCSKPEDIL 56
           M YAI+LY D AL++++L +  ++    I   LI+ E  PHITL  T   +P SK E +L
Sbjct: 1   MGYAIELYMDPALENQVLKAWNVIARRQISTQLIEMESRPHITLFSTPFLEP-SKLEPLL 59

Query: 57  PDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYV 116
                  D FP+S S     P  +N L L    SL+L      L +A+  +G+ +  EY 
Sbjct: 60  KTLSTKHDPFPLSFSSVGAFPGDHNTLFLSPTPSLSLLHFQSQLCDAIRKEGVDVPDEYA 119

Query: 117 PGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
            G W P C +A  VP  R+    ++L  +KLP+ G    V +VQ  P
Sbjct: 120 LGSWIPFCSVAHQVPKARMAEAFSLLRDLKLPVSGYAVDVAVVQFSP 166

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294460847|gb|ADE75997.1| unknown [Picea sitchensis]

 Score = 88.6 bits (218), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 54/165 (32%), Positives = 85/165 (51%), Gaps = 5/165 (3%)

Query: 3   YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQPCSKP---EDILPD 58
           YA++LYFD AL++++L +  ++    I   LI+ E  PHITLL + P   P   ++I+ +
Sbjct: 5   YAVELYFDPALENQVLKAWNVLARRQISTQLIEIEARPHITLL-SSPTLDPLKLQNIIRN 63

Query: 59  SIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPG 118
                +   ++LS         N+L L    SL++   H  LYE L   G++    Y P 
Sbjct: 64  FSAKQEPLALTLSSVGSFSTDENVLFLAPTPSLSILTFHGQLYELLKRGGIEAGDSYQPD 123

Query: 119 VWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
            W PHC +A  VP +R+    +IL   KLP+ G +  + LV+  P
Sbjct: 124 NWVPHCTVAQDVPRNRMAEAFSILRDFKLPISGYILDIGLVEFSP 168

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224141313|ref|XP_002324018.1| predicted protein [Populus trichocarpa] gi|222867020|gb|EEF04151.1| predicted protein [Populus trichocarpa]

 Score = 82.0 bits (201), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 54/165 (32%), Positives = 88/165 (53%), Gaps = 8/165 (4%)

Query: 3   YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQPC---SKPEDILPD 58
           YAI+LY D AL++++L +  ++    I + LI+ E  PH+TL  + P    +K E I+  
Sbjct: 6   YAIELYLDPALENQVLKAWNVLARRQISSQLIEIESRPHLTL-YSAPFIDPTKLESIIKT 64

Query: 59  SIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPG 118
                +  P+SLS        NNLL L    +L+L + H  L +A+  +G++I ++Y P 
Sbjct: 65  FASKQEPLPLSLSTIGC---HNNLLFLAPTPTLSLLQFHSQLCDAMRREGIEISEDYRPE 121

Query: 119 VWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
            W P+C +A  VP  R+     +L  +KLP+ G    + LV+  P
Sbjct: 122 NWIPYCAVAQDVPKARMAESLCVLRDLKLPVAGYAMDIGLVEFSP 166

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550070|ref|XP_003543413.1| PREDICTED: uncharacterized protein LOC100777475 [Glycine max]

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 55/167 (32%), Positives = 89/167 (53%), Gaps = 11/167 (6%)

Query: 3   YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQPCSKPEDILPDSIP 61
           +AI+LY + AL++++L +  ++    I   LI+ E  PHITL  + P  +P  +  DS+ 
Sbjct: 6   FAIELYLEPALENQVLKAWNVLARRQISTELIEMESRPHITLF-SAPFLEPSKL--DSLL 62

Query: 62  LV-----DKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYV 116
            V     D  P++ S  +  P  NNLL L    SL+L      L +A+  +G++I  E+ 
Sbjct: 63  KVFASKHDPLPLTFSSLATFP--NNLLFLAPTPSLSLLHFQSQLCDAIRKEGIEIAHEFA 120

Query: 117 PGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
              W P+C +A  VP +R+    ++L ++KLP+ G    V LVQ  P
Sbjct: 121 FNSWIPYCSVAHHVPQNRMPEAFSLLRELKLPVSGYAMDVALVQFSP 167

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	166
TAIR|locus:2173792	183	AT5G40190 [Arabidopsis thalian	0.969	0.879	0.317	4.1e-17
TAIR|locus:2091378	184	AT3G28140 [Arabidopsis thalian	0.969	0.875	0.333	6.9e-15

TAIR|locus:2173792 AT5G40190 [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 4.1e-17, P = 4.1e-17
 Identities = 52/164 (31%), Positives = 81/164 (49%)

Query:     3 YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQ--PCSKPEDILPDS 59
             YAI+LYFD AL++++L +  +     I   LI  E  PHITL  T     ++ E ++ + 
Sbjct:     5 YAIELYFDPALENQVLKAWNVFARRQISTKLINTESRPHITLFSTSFFDSTRLESVIKNF 64

Query:    60 IPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGV 119
             +   +   IS S        NN+L L    SL+L +L   L + L  + + I +EY    
Sbjct:    65 VSKQEPISISFSTIGSFSSDNNVLFLSPTPSLSLLQLQTQLCDMLKKESVDIGEEYRVDS 124

Query:   120 WFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
             W P C +A  VP  R+    ++L  +KLP+ G    + LV+  P
Sbjct:   125 WVPFCPVALDVPKSRMAEAFSVLRDLKLPVNGYGMEIGLVEFSP 168

GO:0003824 "catalytic activity" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0016070 "RNA metabolic process" evidence=IEA

GO:0005516 "calmodulin binding" evidence=TAS;IPI

GO:0006661 "phosphatidylinositol biosynthetic process" evidence=RCA

TAIR|locus:2091378 AT3G28140 [Arabidopsis thaliana (taxid:3702)]

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 55/165 (33%), Positives = 78/165 (47%)

Query:     3 YAIKLYFDDALKSKILDSMKLVRELNIPN-LIKPEDEPHITLLVTQPCSKPEDILPDSIP 61
             YAI+LYFD AL++++L +  +     I   LI  E  PHITL  T        + P    
Sbjct:     5 YAIELYFDPALENQVLKAWNVFARRQISTYLINNESRPHITLFSTTSSIDSTKLEPIIKS 64

Query:    62 LVDKF-PISLSLFSV--LPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPG 118
                K  PISLS  S+      +N L L    SL+L +L   L E +  +G +I +EY   
Sbjct:    65 FSSKQEPISLSFSSIGSFSSDDNALFLSPTPSLSLIQLQLQLCEVIKKEGFEIGEEYRVD 124

Query:   119 VWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLPP 163
              W P C +A  VP  R+     +L  +KL + G    + LV+  P
Sbjct:   125 SWVPFCSVAVDVPKSRISEGFLVLRDLKLLVYGYAMDIGLVEFSP 169


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.141   0.425    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      166       166   0.00097  107 3  11 22  0.37    32
                                                     30  0.46    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:  2
  No. of states in DFA:  587 (62 KB)
  Total size of DFA:  148 KB (2090 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:  15.52u 0.07s 15.59t   Elapsed:  00:00:01
  Total cpu time:  15.52u 0.07s 15.59t   Elapsed:  00:00:01
  Start:  Fri May 10 09:03:06 2013   End:  Fri May 10 09:03:07 2013

GO:0003824 "catalytic activity" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0016070 "RNA metabolic process" evidence=IEA

GO:0005516 "calmodulin binding" evidence=ISS

GO:0006661 "phosphatidylinositol biosynthetic process" evidence=RCA

---

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	166
pfam13563	152	pfam13563, 2_5_RNA_ligase2, 2'-5' RNA ligase super	1e-05

>gnl|CDD|222224 pfam13563, 2_5_RNA_ligase2, 2'-5' RNA ligase superfamily

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 30/130 (23%), Positives = 48/130 (36%), Gaps = 14/130 (10%)

Query: 37  DEPHITLLVTQPCSKPEDILPDSIPLV-------DKFPISLSLFSVLPRKNNLLCLLIAQ 89
             PHITL         ++ L + +  +         F ++L           +  L +  
Sbjct: 24  WPPHITLAY---PFVADESLEELLEALARLAAETPPFELTLGGLGSFGGGRVVY-LKVEG 79

Query: 90  SLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPL 149
           S  LR L   L EAL    L  D+   PG + PH  +A  +       +   LA+   P+
Sbjct: 80  SEELRALRAALREALPGHLLAQDE---PGPFTPHLTIAYKLDDAPAAALLEALARELPPI 136

Query: 150 QGDVEHVRLV 159
              V+ + LV
Sbjct: 137 SFTVDELALV 146

This family contains proteins related to pfam02834. These proteins are likely to be enzymes, but they may not share the RNA ligase activity. Length = 152

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	166
COG1514	180	LigT 2'-5' RNA ligase [Translation, ribosomal stru	99.97
PRK15124	176	2'-5' RNA ligase; Provisional	99.96
TIGR02258	179	2_5_ligase 2'-5' RNA ligase. This protein family c	99.95
PRK13679	168	hypothetical protein; Provisional	99.95
PF13563	153	2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB	99.9
PHA02574	149	57B hypothetical protein; Provisional	99.88
PF10469	209	AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; Inte	99.68
PLN00108	257	unknown protein; Provisional	99.33
PF02834	87	LigT_PEase: LigT like Phosphoesterase; InterPro: I	99.33
PF07823	196	CPDase: Cyclic phosphodiesterase-like protein; Int	99.25
PF05213	248	Corona_NS2A: Coronavirus NS2A protein; InterPro: I	98.76
PF09749	239	HVSL: Uncharacterised conserved protein; InterPro:	98.63
TIGR03223	228	Phn_opern_protn putative phosphonate metabolism pr	98.36
PF02834	87	LigT_PEase: LigT like Phosphoesterase; InterPro: I	98.34
PHA02977	201	hypothetical protein; Provisional	97.57
PF06299	160	DUF1045: Protein of unknown function (DUF1045); In	97.48
PF08302	257	tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase	95.65
KOG2814	345	consensus Transcription coactivator complex, P50 c	94.05
PF13563	153	2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB	93.95
PRK13679	168	hypothetical protein; Provisional	93.89
TIGR02258	179	2_5_ligase 2'-5' RNA ligase. This protein family c	93.65
PF07823	196	CPDase: Cyclic phosphodiesterase-like protein; Int	93.22
COG1514	180	LigT 2'-5' RNA ligase [Translation, ribosomal stru	93.04
PRK15124	176	2'-5' RNA ligase; Provisional	89.24
KOG3102	269	consensus Uncharacterized conserved protein [Funct	87.03

>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=1.4e-29  Score=189.15  Aligned_cols=157  Identities=20%  Similarity=0.268  Sum_probs=131.2

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCcCceeEEEeeeee
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLVDKFPISLSLFSV   75 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~~~f~l~l~~~g~   75 (166)
                      |=|||++.+|+++++.|.++++.++..+...|+ ..+|+||||+|+++     .+.+.++|.++++.. ||+|+++|+|+
T Consensus         1 ~RlFiAl~~p~~i~~~i~~~~~~~~~~~~~k~v-~~en~HiTL~flGev~e~~~~~l~~~l~~i~~~~-~f~i~l~g~g~   78 (180)
T COG1514           1 MRLFIALDPPAEIAERLARIRARLKGARAIKWV-EPENLHITLKFLGEVDEDKADELIEALARIAAPE-PFPITLDGAGS   78 (180)
T ss_pred             CeeEEEecCCHHHHHHHHHHHHhcCcccccccc-cccCceEEEEccCCcCchHHHHHHHHHHHhhcCC-ceEEEEeeEcc
Confidence            668999999999999999999999987522233 67899999999754     677888888888777 99999999999


Q ss_pred             cCC--CCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCCCchhHHHHHHHHhhcCcCceEEE
Q 031049           76 LPR--KNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDV  153 (166)
Q Consensus        76 F~~--~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~~~~~~~~~~~~l~~~~~p~~~~v  153 (166)
                      |++  +++|+|+++.++++|.+|++.+.+.+...|  +....++  |+|||||||+.......++...+.+.... ++.|
T Consensus        79 F~~~~~~rvi~~~v~~~~~L~~L~~~l~~~~~~~g--~~~~~r~--F~PHvTl~r~k~~~~~~~~~~~~~~~~~~-~~~v  153 (180)
T COG1514          79 FPNPRRPRVIWVGVEETEELRALAEELERALARLG--LRPEERP--FVPHVTLARVKSKDKLVEALGEFKNVEFG-EMEV  153 (180)
T ss_pred             cCCCCCCcEEEEcCCCcHHHHHHHHHHHHHHHhcC--CCCCCCC--cCCCEEEEeecccchhhhhhhhhcccccc-ceEe
Confidence            995  799999999888899999999999999998  4555565  99999999977655666666666653333 7799


Q ss_pred             eEEEEEecCCC
Q 031049          154 EHVRLVQLPPN  164 (166)
Q Consensus       154 ~~i~L~~~~p~  164 (166)
                      ++++||+|..+
T Consensus       154 d~~~L~~S~l~  164 (180)
T COG1514         154 DRFSLYSSTLT  164 (180)
T ss_pred             eEEEEEEEeeC
Confidence            99999999764

>PRK15124 2'-5' RNA ligase; Provisional

Probab=99.96  E-value=3.4e-28  Score=181.56  Aligned_cols=149  Identities=14%  Similarity=0.123  Sum_probs=115.9

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCcCceeEEEeeeee
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLVDKFPISLSLFSV   75 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~~~f~l~l~~~g~   75 (166)
                      |=+||++.+|+++++++.++++.+.......|+ .++|+||||.|+++     ++.+.++++++  ..+||+++++|+|+
T Consensus         5 ~RlFiAl~~p~~~~~~l~~~~~~~~~~~~~rwv-~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~--~~~pF~l~l~~~g~   81 (176)
T PRK15124          5 KRLFFAIDLPDEIRQQIIHWRATHFPPEAGRPV-AAANLHLTLAFLGEVSAEKQQALSQLAGRI--RQPGFTLTLDDAGQ   81 (176)
T ss_pred             eEEEEEeCCCHHHHHHHHHHHHHhccccCcccc-cccccEEEEEecCCCCHHHHHHHHHHHHhc--ccCCeEEEECcccC
Confidence            458999999999999999999888653222343 57899999999876     34455555554  46899999999999


Q ss_pred             cCCCCcEEEEEec-CChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCCCchhHHHHHHHHhhcCcCceEEEe
Q 031049           76 LPRKNNLLCLLIA-QSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVE  154 (166)
Q Consensus        76 F~~~~~vl~l~~~-~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~~~~~~~~~~~~l~~~~~p~~~~v~  154 (166)
                      ||+ |+|+|++++ +++.|.+||+++.++++..|  +..+.++  |+|||||||.......      +.....+..|.|+
T Consensus        82 Fp~-prvlwlg~~~~~~~L~~L~~~l~~~l~~~G--~~~e~r~--f~PHiTLaR~~~~~~~------~~~~~~~~~~~v~  150 (176)
T PRK15124         82 WPR-SRVVWLGMRQPPRGLLQLANMLRSQAARSG--CYQSPQP--FHPHITLLRDASRPVA------IPPPGFNWSFPVT  150 (176)
T ss_pred             cCC-CCEEEEEcCCCCHHHHHHHHHHHHHHHHcC--CCCCCCC--CCCCEeeccCCCCccc------ccCCCCCCceEcC
Confidence            984 899999996 46799999999999999999  4666677  9999999996543211      1111223468899


Q ss_pred             EEEEEecCC
Q 031049          155 HVRLVQLPP  163 (166)
Q Consensus       155 ~i~L~~~~p  163 (166)
                      ++.||+|..
T Consensus       151 ~~~L~~S~l  159 (176)
T PRK15124        151 EFTLYASSF  159 (176)
T ss_pred             EEEEEEEec
Confidence            999999964

>TIGR02258 2_5_ligase 2'-5' RNA ligase

Probab=99.95  E-value=2.8e-27  Score=176.59  Aligned_cols=156  Identities=22%  Similarity=0.252  Sum_probs=122.3

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHh-cCCCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCcCceeEEEeeee
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVREL-NIPNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLVDKFPISLSLFS   74 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~-~~~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~~~f~l~l~~~g   74 (166)
                      |=+||++.+++++.++|.++++.+++. ....+. +++++||||.|.++     .+.+.+.+++++  .++|+++++|+|
T Consensus         1 ~R~FiAl~~p~~~~~~l~~~~~~l~~~~~~~r~~-~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~--~~~f~l~l~~~~   77 (179)
T TIGR02258         1 MRLFIAIDLPPEIREQLSRIQRKLKSPLDGIKWV-PPENLHITLKFLGEVDEEQVEELEDALAKIA--EPPFTLKLEGIG   77 (179)
T ss_pred             CeEEEEecCCHHHHHHHHHHHHHhhccCCCcEEC-ChHHCEEEEEEccCCCHHHHHHHHHHHHHhc--CCCeEEEEeeee
Confidence            668999999999999999999999842 222332 67799999999754     455777787776  367999999999


Q ss_pred             ecCC--CCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCCCch-hHHHHHHHHhhcCcCceE
Q 031049           75 VLPR--KNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTD-RVGNVCNILAKVKLPLQG  151 (166)
Q Consensus        75 ~F~~--~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~~~~-~~~~~~~~l~~~~~p~~~  151 (166)
                      +|++  +++|+|++++.+++|.+|++++.+.+...|.  ..+.++  |+|||||||..... .+.+.++.... ..+.+|
T Consensus        78 ~F~~~~~~~vl~l~~~~~~~L~~L~~~l~~~~~~~g~--~~~~~~--f~PHiTlar~~~~~~~~~~~~~~~~~-~~~~~~  152 (179)
T TIGR02258        78 VFGNPKRPRVLWAGVEQSEELTQLHADLERELAKLGF--SKEERP--FTPHITLARKKSGKPGVPEFLQEFAN-EEFGSF  152 (179)
T ss_pred             eCCCCCCCeEEEEeeCCCHHHHHHHHHHHHHHHHcCC--CCCCCC--cCCCEEEEEecCCcHhHHHHHHHhCC-CCCCce
Confidence            9986  5789999998888999999999999999884  333344  99999999866543 33333333333 247899


Q ss_pred             EEeEEEEEecCCC
Q 031049          152 DVEHVRLVQLPPN  164 (166)
Q Consensus       152 ~v~~i~L~~~~p~  164 (166)
                      +|++|+||+|...
T Consensus       153 ~v~~i~L~~S~~~  165 (179)
T TIGR02258       153 HVDEFHLYSSTLT  165 (179)
T ss_pred             EeeEEEEEEeecc
Confidence            9999999999754

This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.

>PRK13679 hypothetical protein; Provisional

Probab=99.95  E-value=4.6e-27  Score=174.20  Aligned_cols=150  Identities=17%  Similarity=0.206  Sum_probs=123.5

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCcCceeEEEeeeee
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLVDKFPISLSLFSV   75 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~~~f~l~l~~~g~   75 (166)
                      |.|+|++.+|+++.+.+.++++.+...+      ...+|||||.|.++     .+.+.++++++++...||+++++++|+
T Consensus         1 ~~~~iai~~p~~~~~~l~~~~~~~~~~~------~~v~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~   74 (168)
T PRK13679          1 MKYGIVLFPSKKIQDFANSYRKRYDPHY------ALIPPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSS   74 (168)
T ss_pred             CeeEEEEcCCHHHHHHHHHHHHhhCccc------ccCCCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEecccc
Confidence            8999999999999999999988775321      22467999998643     466788998998888999999999999


Q ss_pred             cCCCCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCCCchhHHHHHHHHhhcCcCceEEEeE
Q 031049           76 LPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEH  155 (166)
Q Consensus        76 F~~~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~~~~~~~~~~~~l~~~~~p~~~~v~~  155 (166)
                      |++.++|||+++++++.|.+||++++..+.  +   ..+.++  |+|||||||..+.++..++.+.+.+...+..++|++
T Consensus        75 F~~~~~vl~l~~~~~~~L~~L~~~l~~~~~--~---~~~~~~--f~PHiTlar~~~~~~~~~~~~~l~~~~~~~~~~v~~  147 (168)
T PRK13679         75 FAPTNNVIYFKVEKTEELEELHERLHSGDF--Y---GEAEYA--FVPHITIGQGLSDDEHEDVLGQLKMADVDHEETIDR  147 (168)
T ss_pred             CCCCCCEEEEEccCCHHHHHHHHHHHhccc--c---cccCCC--CCCeEEeeCCCCcHHHHHHHHHHhcCCcceeEEECe
Confidence            986679999999988999999999987653  1   223344  999999999988888888888887655667889999


Q ss_pred             EEEEecCC
Q 031049          156 VRLVQLPP  163 (166)
Q Consensus       156 i~L~~~~p  163 (166)
                      |.||....
T Consensus       148 i~L~~~~~  155 (168)
T PRK13679        148 FHLLYQLE  155 (168)
T ss_pred             EEEEEECC
Confidence            99987643

>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A

Probab=99.90  E-value=3.2e-25  Score=160.71  Aligned_cols=145  Identities=24%  Similarity=0.301  Sum_probs=85.0

Q ss_pred             cChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCC----CCChhhhhcccCCCcCceeEEEeeeeecCCCCcEEE
Q 031049            9 FDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQP----CSKPEDILPDSIPLVDKFPISLSLFSVLPRKNNLLC   84 (166)
Q Consensus         9 ~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~----~~~~~~~l~~~~~~~~~f~l~l~~~g~F~~~~~vl~   84 (166)
                      ||+++.++|.++.   +..+....  ...+|||||.+...    .+.+.+.+.+++++.++|+++|+++|+|+++++|||
T Consensus         1 pp~~~~~~i~~lr---~~~~~~~~--~~~~pHITL~~~~~~~~~~~~~~~~l~~~~~~~~~f~l~l~~~~~F~~~~~vi~   75 (153)
T PF13563_consen    1 PPDELAEEIEALR---RQKGDKRY--PRWPPHITLAFPFDIDDSLDELVEALARLAAGFPPFELRLDGFGSFPGKGRVIF   75 (153)
T ss_dssp             ------------G---T-TTEEE----GGG-EEEEEEEEE--GGGHHHHHHHHHHHHHS--EEEEEEEEEEESSSSSSEE
T ss_pred             Ccccccccchhhh---cccCCCCC--CCCCCEeEEEecCcccccHHHHHHHHHHHHccCCCeEEEEccEEEcCCCCCEEE
Confidence            5677777766665   13332222  45679999987432    378999999998889999999999999985456999


Q ss_pred             EEecCChhHHHHHHHHHHHHHhcCCCCCCCC-CCCCeecceeecCCCCchhHHHHHHHHhhcCcCceEEEeEEEEEecC
Q 031049           85 LLIAQSLNLRELHDNLYEALATKGLQIDKEY-VPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQLP  162 (166)
Q Consensus        85 l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~-~~~~f~PHiTLar~~~~~~~~~~~~~l~~~~~p~~~~v~~i~L~~~~  162 (166)
                      +.+.+++.|.+||++|.+.+...+.  ..+. ++  |+||||||++........+++.+.....+.+|+|++|.|++++
T Consensus        76 l~~~~~~~L~~L~~~l~~~~~~~~~--~~~~~~~--~~PHiTia~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~L~~~~  150 (153)
T PF13563_consen   76 LNVEPSPELEALHRALREALRPFGF--KQDSYRP--FRPHITIARRLSPKQAAEAIEKLQSEFPPISFTVDELALVRSD  150 (153)
T ss_dssp             EEEEE-HHHHHHHHHHHHHHHHHHG--GGGGGS------EEEEEEESS-----------------EEEEE-EEEEEEEE
T ss_pred             EEcCCCHHHHHHHHHHHHHHHHcCC--ccccCCC--cceEEEEeccCCcchhHHHHHHHhCcCCCcEEEEeEEEEEEEC
Confidence            9999999999999999999999862  2222 44  9999999998887777888888855567899999999999975

>PHA02574 57B hypothetical protein; Provisional

Probab=99.88  E-value=2.2e-22  Score=145.49  Aligned_cols=113  Identities=19%  Similarity=0.127  Sum_probs=90.9

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCC-CCChhhhhcccCCCcCceeEEEeeeeecCC-
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQP-CSKPEDILPDSIPLVDKFPISLSLFSVLPR-   78 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~-~~~~~~~l~~~~~~~~~f~l~l~~~g~F~~-   78 (166)
                      |=.|+++++|++++++|.++++++..  ++ ++ .++|+||||+|..+ ++.+..       +.++|+++++|+|.|++ 
T Consensus         9 ~RlF~Al~~~~~~r~~L~~lq~~l~~--~r-~V-~~enLHlTL~F~~~~v~~l~~-------~~~~F~l~l~glG~F~~~   77 (149)
T PHA02574          9 QGTYVAAKFSEATLDALERLQRTLRI--PN-PV-PRDKLHSTIVYSRVYVPFIPA-------SGSTEVASSGHLEVWETQ   77 (149)
T ss_pred             ceEEEEEcCCHHHHHHHHHHHHhccC--Cc-cc-CHHHCEEEEecCHHHhHHHhc-------cCCCeEEEeccccccCCC
Confidence            34689999999999999999999643  22 33 67899999999433 433322       56999999999999985 


Q ss_pred             CCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCCCch
Q 031049           79 KNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTD  133 (166)
Q Consensus        79 ~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~~~~  133 (166)
                      +++|+|++++ +++|.+|++++.+++...+      +++  |+|||||||+....
T Consensus        78 ~~rvlWlg~~-~~~L~~L~~~l~~~l~~~~------~r~--F~PHITLaR~~~~~  123 (149)
T PHA02574         78 DKNALVLVLE-SEYLQCRHKYARALGATHD------FDD--YTPHITLSYDVGPL  123 (149)
T ss_pred             CCCEEEEEeC-CHHHHHHHHHHHHHhhcCC------CCC--cCCcEEEeecCCCc
Confidence            6899999998 9999999999999988743      344  99999999954433

>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7

Probab=99.68  E-value=7.9e-16  Score=117.66  Aligned_cols=159  Identities=17%  Similarity=0.205  Sum_probs=113.5

Q ss_pred             CceEEEEec-ChhHHHHHHHHHHHHHHh--cC-CCCCCCCCCCeeEEeec--CC---CCChhhhhcccC-------CCcC
Q 031049            1 MQYAIKLYF-DDALKSKILDSMKLVREL--NI-PNLIKPEDEPHITLLVT--QP---CSKPEDILPDSI-------PLVD   64 (166)
Q Consensus         1 m~~~i~l~~-~~~~~~~i~~l~~~L~~~--~~-~~~~~~~~~~HiTL~~~--~~---~~~~~~~l~~~~-------~~~~   64 (166)
                      .+|||++-+ .+++.+.+.++++.+...  ++ .....++..+||||.++  .+   .+...++|+.+.       ....
T Consensus         1 pthFl~ipl~~~~i~~~~~~fq~~v~~~~~~~~~~~~i~~~~lHlTL~vl~L~~~~~i~~a~~~L~~~~~~i~~~~~~~~   80 (209)
T PF10469_consen    1 PTHFLCIPLNSPEIQEKFKEFQNEVLSKDPGLDESAFIPPEKLHLTLGVLSLDTDEEIEKAKEALKSLKQEIKDQLQNPP   80 (209)
T ss_pred             CCeEEEEECCCHHHHHHHHHHHHHHHhhcCCCCHHHcCCcccceEEEEEeeCCCHHHHHHHHHHHHHHHHHHhhhccCCC
Confidence            489999997 677899999999998864  34 22234778999999873  21   444445554442       1248


Q ss_pred             ceeEEEeeeeecCC---CCcEEEEEecC---ChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCCC-----ch
Q 031049           65 KFPISLSLFSVLPR---KNNLLCLLIAQ---SLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVP-----TD  133 (166)
Q Consensus        65 ~f~l~l~~~g~F~~---~~~vl~l~~~~---~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~~-----~~  133 (166)
                      |+.++|.|+|+|++   .++|||+++.+   ...|.++.+.|.+.+...|+....+ +...|+||+||++...     ..
T Consensus        81 ~~~i~l~Gl~~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~-~~~~~~~H~Tl~n~~~~~~~~~~  159 (209)
T PF10469_consen   81 PLKITLKGLGYFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDD-RRFSFKPHITLMNTSYRKKKKRR  159 (209)
T ss_pred             CceEEeeechhhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccc-cCCCcceEEEEEecccccccccc
Confidence            99999999999985   57899999985   3799999999999999999633222 2223899999996332     11


Q ss_pred             -----hHHHHHHHHhhcCcCceEEEeEEEEEec
Q 031049          134 -----RVGNVCNILAKVKLPLQGDVEHVRLVQL  161 (166)
Q Consensus       134 -----~~~~~~~~l~~~~~p~~~~v~~i~L~~~  161 (166)
                           ...++++...+..+ ..+.|++|.|.+.
T Consensus       160 ~~~~~d~~~~~~~~~~~~f-G~~~v~~i~Lc~m  191 (209)
T PF10469_consen  160 QGNKFDASELLEKYKDFDF-GEQPVEEIQLCSM  191 (209)
T ss_pred             ccCccccHHHHHHcCCCcc-ceEEECEEEEEeC
Confidence                 23344444444322 3679999999988

This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.

>PLN00108 unknown protein; Provisional

Probab=99.33  E-value=4.1e-11  Score=93.48  Aligned_cols=156  Identities=14%  Similarity=0.113  Sum_probs=107.6

Q ss_pred             CceEEEEec--ChhHHHHHHHHHHHHHHh---------------cC-CCCCCCCCCCeeEEeec--CC---CCChhhhhc
Q 031049            1 MQYAIKLYF--DDALKSKILDSMKLVREL---------------NI-PNLIKPEDEPHITLLVT--QP---CSKPEDILP   57 (166)
Q Consensus         1 m~~~i~l~~--~~~~~~~i~~l~~~L~~~---------------~~-~~~~~~~~~~HiTL~~~--~~---~~~~~~~l~   57 (166)
                      +||||++-+  .+++.+.+.++++.+-+.               |+ ...-..+..+||||.++  .+   ++...+.|+
T Consensus        36 ~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~~~~~~f~~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~L~  115 (257)
T PLN00108         36 FTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDKDPLKFQSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILK  115 (257)
T ss_pred             CCeEEEEEcCCCHHHHHHHHHHHHHHHhccccccccccccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHHHH
Confidence            589999999  599999999999987652               22 12223677999999763  21   333333333


Q ss_pred             -------ccCCCcCceeEEEeeeeecCC---CCcEEEEEecCC---hhHHHHHHHHHHHHHhcCCCCCCCC-CCCCeecc
Q 031049           58 -------DSIPLVDKFPISLSLFSVLPR---KNNLLCLLIAQS---LNLRELHDNLYEALATKGLQIDKEY-VPGVWFPH  123 (166)
Q Consensus        58 -------~~~~~~~~f~l~l~~~g~F~~---~~~vl~l~~~~~---~~L~~L~~~l~~~l~~~g~~~~~~~-~~~~f~PH  123 (166)
                             ++. .-.|+.|++.|+++|++   ..+|||+.++..   ..|..+.+.|.+.+...|. ...+. ++  ..+|
T Consensus       116 s~~~~i~~~l-~~~pl~I~lkGL~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL-~~~d~~~~--vKLH  191 (257)
T PLN00108        116 SICSNVRQAL-KDRPVFIRLRGLDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGF-AGKDAKSR--LKLH  191 (257)
T ss_pred             HHHHHHHHhh-CCCCeEEEEEeehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCC-cccccCcc--eeeE
Confidence                   332 35899999999999974   478999988743   5799999999999999996 33333 34  9999


Q ss_pred             eeecCCC----Cc-----hhHHHHHHHHhhcCcCceEEEeEEEEEec
Q 031049          124 CMLAPSV----PT-----DRVGNVCNILAKVKLPLQGDVEHVRLVQL  161 (166)
Q Consensus       124 iTLar~~----~~-----~~~~~~~~~l~~~~~p~~~~v~~i~L~~~  161 (166)
                      +||..-.    ..     -+..++++.+.+..+ .+..|++|.|-+-
T Consensus       192 ~TlmNt~~rk~k~~k~~sFDA~~Il~~f~d~~F-G~~~i~~vhls~r  237 (257)
T PLN00108        192 ATLMNASYRKDKSKKMDTFDAREIHKEFENKDW-GTYLIREAHISQR  237 (257)
T ss_pred             eEEechhhhhcccCccccccHHHHHHhccCccc-ceEEecEEEEEee
Confidence            9999521    11     123345555554332 5778999887653

>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases

Probab=99.33  E-value=8.4e-13  Score=87.27  Aligned_cols=76  Identities=16%  Similarity=0.304  Sum_probs=62.3

Q ss_pred             EecChhHHHHHHHHHHHHHHh----cCCCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCcCceeEEEeeeeecC
Q 031049            7 LYFDDALKSKILDSMKLVREL----NIPNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLVDKFPISLSLFSVLP   77 (166)
Q Consensus         7 l~~~~~~~~~i~~l~~~L~~~----~~~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~~~f~l~l~~~g~F~   77 (166)
                      +.+|++++++|.++++.|++.    |+ .+. .+.++||||+|.++     .+.+.+++.+++....||+++++++|.|+
T Consensus         1 i~~p~~~~~~L~~l~~~l~~~~~~~~~-r~~-~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~f~~~~~~~~~f~   78 (87)
T PF02834_consen    1 IDLPEEIKEQLNQLQERLRQALPPLGI-RWV-RPFNPHITLAFLGEVPPDQLPELIEALANIASRFPPFTLTVDGFGLFP   78 (87)
T ss_dssp             EE-THHHHHHHHHHHHHHHHHCCSCTE-EEG-SCGGSEEEEEEEEEESHHHHHHHHHHHHHHHCCCB-EEEEEEEEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHHhhhccccCC-ccc-CCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhccCCCeEEEEeEEEEeC
Confidence            467999999999999999953    32 233 78899999999653     67788889988888999999999999998


Q ss_pred             C--CCcEEE
Q 031049           78 R--KNNLLC   84 (166)
Q Consensus        78 ~--~~~vl~   84 (166)
                      +  +++|+|
T Consensus        79 s~~~~rvi~   87 (87)
T PF02834_consen   79 SRLRPRVIW   87 (87)
T ss_dssp             EEETCEEEE
T ss_pred             CCCCCCCcC
Confidence            5  689998

These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.

>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes

Probab=99.25  E-value=4.5e-11  Score=90.69  Aligned_cols=162  Identities=15%  Similarity=0.170  Sum_probs=89.3

Q ss_pred             CceEEEEecCh--hHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeec--CC-CCChhhhhcccCCCcCce-----eEEE
Q 031049            1 MQYAIKLYFDD--ALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVT--QP-CSKPEDILPDSIPLVDKF-----PISL   70 (166)
Q Consensus         1 m~~~i~l~~~~--~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~--~~-~~~~~~~l~~~~~~~~~f-----~l~l   70 (166)
                      |+|+|=+.|+.  ...+.+..+...|+.......  +.=.|||||...  .+ .+++.+.|+..+....++     .++|
T Consensus         1 M~~SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~~--p~F~PHiTL~s~i~~~~~~~~~~~L~~~~~~~~~~~~~~~~v~~   78 (196)
T PF07823_consen    1 MPYSLWLVPPPGSPLYERLKTLISSLASLFPGSP--PPFEPHITLTSGISLDSSDDVQKVLDSAAAALKPLPKNHFTVRF   78 (196)
T ss_dssp             --EEEEEEE-T--TTHHHHHHHHHHHHHHST-----------EEEEEEEEE--HHHHHHHHHHHHHH-B-E-----EEEE
T ss_pred             CeEEEEEcCCCCccHHHHHHHHHHHHHHHCCCCC--CCcCCeEEEeCCCccCCHHHHHHHHHHHHHhccCcccceeEEEe
Confidence            99999999999  999999999999997532111  334799999753  22 566677777766677888     9999


Q ss_pred             eeeeecCCCCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCC--CCCCCCCeecceeecCC-CCchhH---HHHHHHHhh
Q 031049           71 SLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQID--KEYVPGVWFPHCMLAPS-VPTDRV---GNVCNILAK  144 (166)
Q Consensus        71 ~~~g~F~~~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~--~~~~~~~f~PHiTLar~-~~~~~~---~~~~~~l~~  144 (166)
                      +++..=...-+-+|+.+..+++|..|++.+++.+........  .......|.||++|... ....+.   ......+.+
T Consensus        79 ~~v~~g~~yfq~vyl~v~~t~~L~~l~~~~r~~~~~~~~~~~~~~~~~~~~y~PHlSLlY~d~~~~e~~~~~~~~~~i~~  158 (196)
T PF07823_consen   79 DKVASGDKYFQCVYLEVEKTPELMSLAQIARELFVEGPPDEVKAAEWPREPYMPHLSLLYGDLPPEEKAEAAEIAQRIDD  158 (196)
T ss_dssp             EEEEEEEETTEEEEEEE---HHHHHHHCHHHHCT----------T----S----EEEEE-----HHHHHHHHHHHHHH-T
T ss_pred             eeEeeCCeEEEEEEEEecCChhHHHHHHHHHHHhhhccccccccccccCCCCCCeEEEEEcCCCcccHHHHHHHHHHhcc
Confidence            998753223478999999999999999999988744210000  01111249999999984 332222   222223333


Q ss_pred             c------CcCceEEEeEEEEEecCCC
Q 031049          145 V------KLPLQGDVEHVRLVQLPPN  164 (166)
Q Consensus       145 ~------~~p~~~~v~~i~L~~~~p~  164 (166)
                      .      .....|.+.++.|++..-.
T Consensus       159 ~l~~~~~~~~~~~~~~~l~lv~t~g~  184 (196)
T PF07823_consen  159 ALGVDSGISGLGWEGGELKLVRTDGP  184 (196)
T ss_dssp             T------GTT-EEEEEEEEEEE--TT
T ss_pred             cccccccCCCCCEeccEEEEEEcCCC
Confidence            2      2235889999999987643

The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.

>PF05213 Corona_NS2A: Coronavirus NS2A protein; InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins

Probab=98.76  E-value=6.8e-08  Score=72.94  Aligned_cols=116  Identities=16%  Similarity=0.191  Sum_probs=78.5

Q ss_pred             ceEEEEecC--hhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeec--C-C-CCChhhhhcccCCC--cCceeEEEeee
Q 031049            2 QYAIKLYFD--DALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVT--Q-P-CSKPEDILPDSIPL--VDKFPISLSLF   73 (166)
Q Consensus         2 ~~~i~l~~~--~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~--~-~-~~~~~~~l~~~~~~--~~~f~l~l~~~   73 (166)
                      +|||.+.+-  +..-....++|.+|-+.|++..  ....|||||.++  . + ...+..+++++...  ....+++++..
T Consensus         7 ~HFin~Pl~~f~~f~~~~~~LQ~~~~~eG~d~k--~QkaPHlSl~mL~Isd~~i~~V~~~iq~ViddM~~~~~~it~tnp   84 (248)
T PF05213_consen    7 THFINFPLVQFEGFMLNFKDLQFQLLEEGVDCK--LQKAPHLSLGMLDISDEDIPDVETAIQKVIDDMVWFEGDITFTNP   84 (248)
T ss_pred             CceeeccchhhhhHHHHHHHHHHHHHHcCCCcc--ccccCeeEEEEEEcChhhhhhHHHHHHHHHHHhhcccceEEecCc
Confidence            456666443  2455677789999999998653  334899999864  2 2 66666444444322  34458888876


Q ss_pred             eecCCCCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecC
Q 031049           74 SVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAP  128 (166)
Q Consensus        74 g~F~~~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar  128 (166)
                      -..+   +...+   ..+++.+||..|...++..|..+. ..|.  |.||||||.
T Consensus        85 ~MLg---~~yV~---nV~Gv~slh~ki~n~~~~kgit~g-QSRm--wIPHiTia~  130 (248)
T PF05213_consen   85 HMLG---RCYVA---NVKGVLSLHDKIVNVFRKKGITFG-QSRM--WIPHITIAQ  130 (248)
T ss_pred             eeec---cEEEE---ecccHHHHHHHHHHHHHHhCcCcC-cccc--cccceehhh
Confidence            6654   33334   356899999999999999985332 2355  999999996

Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.

>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans

Probab=98.63  E-value=9.9e-07  Score=68.89  Aligned_cols=121  Identities=18%  Similarity=0.161  Sum_probs=86.2

Q ss_pred             EEEecChhHHHHHHHHHHHHHHhcCCCC----------CCCCCCCeeEEe--e-cCC--CCChhhhhcccC--CCcCcee
Q 031049            5 IKLYFDDALKSKILDSMKLVRELNIPNL----------IKPEDEPHITLL--V-TQP--CSKPEDILPDSI--PLVDKFP   67 (166)
Q Consensus         5 i~l~~~~~~~~~i~~l~~~L~~~~~~~~----------~~~~~~~HiTL~--~-~~~--~~~~~~~l~~~~--~~~~~f~   67 (166)
                      |.+.++++..+.+.++.+.+........          .....++||+|.  + +..  .+...+.|++..  +...+|.
T Consensus        46 i~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~s~lg~~~~lHISLSr~~~lr~~~id~f~~~lr~~l~~~~~~~F~  125 (239)
T PF09749_consen   46 IEWPPSEDQRELLEKLISKANSICPKLHSEFEPLLYSDLGSPDPLHISLSRTFPLRTHQIDPFVDSLRQALRSSNIRPFY  125 (239)
T ss_pred             EEecCcHHHHHHHHHHHHHHHhhhhhhhhhcccccccccCCCCCeEEEeCCCccccHHHHHHHHHHHHHHHhhcCCceEE
Confidence            6777888888888888888776532110          013568999995  2 222  555555555555  6889999


Q ss_pred             EEEeeeeecCC-CCcEEEEEe--cC-Ch-hHHHHHHHHHHHHHhcCCCCCCCC-CCCCeecceeecCC
Q 031049           68 ISLSLFSVLPR-KNNLLCLLI--AQ-SL-NLRELHDNLYEALATKGLQIDKEY-VPGVWFPHCMLAPS  129 (166)
Q Consensus        68 l~l~~~g~F~~-~~~vl~l~~--~~-~~-~L~~L~~~l~~~l~~~g~~~~~~~-~~~~f~PHiTLar~  129 (166)
                      +.++++.+|.+ .....|++.  .. .. .|..|.+.+.+.+...|  .+.+| ..  -.|||+||-.
T Consensus       126 v~f~~~~~~~N~e~TR~FL~l~V~~~~~~~l~~l~~~i~~~l~~~~--lp~~Y~~~--~~fHvSIAw~  189 (239)
T PF09749_consen  126 VSFSGLDVYTNDEKTRSFLALRVSEGSNNELKRLLDRINEVLKEFG--LPPFYDED--PSFHVSIAWT  189 (239)
T ss_pred             EEeCceEEEecCCCCeEEEEEEecccccHHHHHHHHHHHHHHHHhC--CCcccCCC--CCCEEEEEEE
Confidence            99999999997 333344443  32 23 39999999999999988  67777 65  7899999963

It contains two conserved motifs, HxSL and FHVSL. The function is unknown.

>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein

Probab=98.36  E-value=2.6e-06  Score=65.71  Aligned_cols=119  Identities=14%  Similarity=0.003  Sum_probs=83.0

Q ss_pred             CCCCeeEEee---c--CC-CCChhhhhcccCCCcCceeEE---EeeeeecCCCCcEEEEEecCChhHHHHHHHHHHHHHh
Q 031049           36 EDEPHITLLV---T--QP-CSKPEDILPDSIPLVDKFPIS---LSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALAT  106 (166)
Q Consensus        36 ~~~~HiTL~~---~--~~-~~~~~~~l~~~~~~~~~f~l~---l~~~g~F~~~~~vl~l~~~~~~~L~~L~~~l~~~l~~  106 (166)
                      +-..|+||+-   +  +. ..++.++++++|+...||++.   +..+|-|     +-+....++++|..|+.++.+.|..
T Consensus        55 rYGfHaTLKaPFrLa~g~~~a~L~~al~~fA~~~~pf~i~~L~l~~Lg~F-----lAL~P~~~~~~L~~LAa~~V~~~d~  129 (228)
T TIGR03223        55 RYGFHATLKAPFRLAPGVTEAELLAAVAAFAATRAPFALPPLRVALLGGF-----LALRPAAPCPALQALAAACVRELDP  129 (228)
T ss_pred             hcccceeecCCcccCCCCCHHHHHHHHHHHHhcCCCccCCcceeeeeCCE-----EEEeeCCCCHHHHHHHHHHHHhhhh
Confidence            4479999984   2  22 788999999999999999875   3334333     1122235779999999999888855


Q ss_pred             cCC--------------------------CCCCCCCCCCeecceeecCCCCchhHHHHHHHHhhcC---cCceEEEeEEE
Q 031049          107 KGL--------------------------QIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVK---LPLQGDVEHVR  157 (166)
Q Consensus       107 ~g~--------------------------~~~~~~~~~~f~PHiTLar~~~~~~~~~~~~~l~~~~---~p~~~~v~~i~  157 (166)
                      +-.                          +++.-.  +.|.-||||.-+++......+...+....   .+-.+.|++|+
T Consensus       130 fRAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~--deFrFHmTLTg~l~~~~~~~~~~~l~~~~~~~l~~p~~id~la  207 (228)
T TIGR03223       130 FRAPLTEAELARRRPDQLTPRQRALLERWGYPYVL--EEFRFHMTLTGRLDEEERAAVLARLEARFAPLLADPLAVDGLA  207 (228)
T ss_pred             ccCCCCHHHHhhcCccCCCHHHHHHHHHcCCCcee--cceEEEEEecCCCChHHHHHHHHHHHHHhhhccCCCeeeeeEE
Confidence            321                          023222  34999999998888777766666666543   33477899999


Q ss_pred             EEec
Q 031049          158 LVQL  161 (166)
Q Consensus       158 L~~~  161 (166)
                      |+.-
T Consensus       208 Lf~e  211 (228)
T TIGR03223       208 LFVE  211 (228)
T ss_pred             EEec
Confidence            9863

This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.

>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases

Probab=98.34  E-value=2.8e-07  Score=60.63  Aligned_cols=68  Identities=29%  Similarity=0.395  Sum_probs=49.8

Q ss_pred             ChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecC--CCCchhHHHHHHHHhhc---CcCceEEEeEEEEEecC
Q 031049           90 SLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAP--SVPTDRVGNVCNILAKV---KLPLQGDVEHVRLVQLP  162 (166)
Q Consensus        90 ~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar--~~~~~~~~~~~~~l~~~---~~p~~~~v~~i~L~~~~  162 (166)
                      .+.|.++++.+.+.+...|  +... ++  +.|||||++  ..+.+.+.++.+.+...   ..|++++++++++|.|.
T Consensus         8 ~~~L~~l~~~l~~~~~~~~--~r~~-~~--~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~f~~~~~~~~~f~s~   80 (87)
T PF02834_consen    8 KEQLNQLQERLRQALPPLG--IRWV-RP--FNPHITLAFLGEVPPDQLPELIEALANIASRFPPFTLTVDGFGLFPSR   80 (87)
T ss_dssp             HHHHHHHHHHHHHHCCSCT--EEEG-SC--GGSEEEEEEEEEESHHHHHHHHHHHHHHHCCCB-EEEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHhhhccccC--Cccc-CC--CCCeEEEEeCCCCCHHHHHHHHHHHHhhhccCCCeEEEEeEEEEeCCC
Confidence            3678888888888776766  3333 55  999999997  44456677776666643   35789999999999883

These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.

>PHA02977 hypothetical protein; Provisional

Probab=97.57  E-value=0.00074  Score=48.49  Aligned_cols=109  Identities=17%  Similarity=0.228  Sum_probs=69.7

Q ss_pred             CCCCCCCCCCeeEEeecC-C----CCChhhhhcccCCCcCceeEEEeeeeecCC---------CCcEEEEEecCChhHHH
Q 031049           30 PNLIKPEDEPHITLLVTQ-P----CSKPEDILPDSIPLVDKFPISLSLFSVLPR---------KNNLLCLLIAQSLNLRE   95 (166)
Q Consensus        30 ~~~~~~~~~~HiTL~~~~-~----~~~~~~~l~~~~~~~~~f~l~l~~~g~F~~---------~~~vl~l~~~~~~~L~~   95 (166)
                      +.+....-.|||||.... |    .+...+...++  ....++++-...-.||.         ..+-+.+..+.+++|..
T Consensus        61 kymtgcdi~phitlgian~dq~~~f~~fk~~~~d~--dl~sis~~cke~icfpqs~askelga~g~avvmkle~sddlka  138 (201)
T PHA02977         61 KYMTGCDIFPHITLGIANKDQCDNFENFKELIKDI--DLQSISFTCKEEICFPQSNASKELGAKGCAVVMKLEASDDLKA  138 (201)
T ss_pred             hhhccCCCCcceeeeccCccHhHHHHHHHHHhhcc--cceeEEEEeeeeEeccccchhhhhCcCccEEEEEEEechHHHH
Confidence            344445568999998753 2    44455555555  67888999999999983         23466777888999999


Q ss_pred             HHHHHHHHHHh----cCCCCCCCCCCCCeecceeecCC-CC-chhHHHHHHHHhh
Q 031049           96 LHDNLYEALAT----KGLQIDKEYVPGVWFPHCMLAPS-VP-TDRVGNVCNILAK  144 (166)
Q Consensus        96 L~~~l~~~l~~----~g~~~~~~~~~~~f~PHiTLar~-~~-~~~~~~~~~~l~~  144 (166)
                      |..-|-.+...    +|. +- ...  .|-||+|+|.- .+ .+.-.+.++....
T Consensus       139 lrnvl~n~vp~pkdifg~-i~-~d~--~w~phitigyv~~dd~dnk~r~ie~~~~  189 (201)
T PHA02977        139 LRNVLFNAVPCPKDIFGD-IL-SDN--PWCPHITIGYVKADDEDNKKRFIECAEA  189 (201)
T ss_pred             HHHHhhcccCCcHHhhcc-cc-cCC--CCCCceEEEeecccchhhHHHHHHHHHH
Confidence            98887665422    121 11 112  49999999962 22 2344455554443

>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species

Probab=97.48  E-value=0.001  Score=48.75  Aligned_cols=105  Identities=16%  Similarity=0.100  Sum_probs=74.2

Q ss_pred             CCChhhhhcccCCCcCceeEE---EeeeeecCCCCcEEEEEec-CChhHHHHHHHHHHHHHhcCC---------------
Q 031049           49 CSKPEDILPDSIPLVDKFPIS---LSLFSVLPRKNNLLCLLIA-QSLNLRELHDNLYEALATKGL---------------  109 (166)
Q Consensus        49 ~~~~~~~l~~~~~~~~~f~l~---l~~~g~F~~~~~vl~l~~~-~~~~L~~L~~~l~~~l~~~g~---------------  109 (166)
                      ..++.++++.+|+...||.+.   +..+|.|      +-+-+. +++.|..|+..+.+.|..+-.               
T Consensus        14 ~~~L~~a~~~~a~~~~pf~l~~L~v~~lg~F------lALvp~~~~~~L~~LAa~cV~~~d~fRAPls~aelaRR~~~~L   87 (160)
T PF06299_consen   14 EADLLAALAAFAARFAPFELPGLEVARLGGF------LALVPAGPCPALQALAAACVRAFDPFRAPLSEAELARRRPAGL   87 (160)
T ss_pred             HHHHHHHHHHHhccCCCccCCceeEeeECCE------EEEeeCCCCHHHHHHHHHHHHhhhhccCCCChHHHhhcCcccC
Confidence            677999999999999999755   4554443      334444 568999999998877766421               


Q ss_pred             -----------CCCCCCCCCCeecceeecCCCCchhHHHHHHHHhhcC---cCceEEEeEEEEEec
Q 031049          110 -----------QIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVK---LPLQGDVEHVRLVQL  161 (166)
Q Consensus       110 -----------~~~~~~~~~~f~PHiTLar~~~~~~~~~~~~~l~~~~---~p~~~~v~~i~L~~~  161 (166)
                                 +++  |--+.|..||||.-+++......+...++...   .+-...|++|+|+.-
T Consensus        88 s~~Q~~~L~rWGYP--YV~deFRFHmTLTg~l~~~~~~~~~~~l~~~f~~~l~~p~~id~laLf~e  151 (160)
T PF06299_consen   88 SPRQRANLERWGYP--YVMDEFRFHMTLTGRLDPAERARVEAALEAHFAPLLPEPLRIDSLALFGE  151 (160)
T ss_pred             CHHHHHHHHHhCCC--ceeCcCEeeEEeCCCCCHHHHHHHHHHHHHHHHhhcCCCeeecceEEEec
Confidence                       122  22235999999998888777777766666543   234678999999864

The function of this family is unknown.

>PF08302 tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase domain; InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []

Probab=95.65  E-value=0.28  Score=38.82  Aligned_cols=65  Identities=8%  Similarity=0.114  Sum_probs=36.9

Q ss_pred             cCceeEEEeeeeecCCCCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecC---CCCchhHHHHH
Q 031049           63 VDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAP---SVPTDRVGNVC  139 (166)
Q Consensus        63 ~~~f~l~l~~~g~F~~~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar---~~~~~~~~~~~  139 (166)
                      ...+++++..+- |-.  +++.+.+.-...-..-..       ..+      ....+..||||+|.   .+++.+-..++
T Consensus       160 ~~~~~v~L~rlv-wd~--rimai~V~~~~~~~~~~~-------~~~------~~c~N~~~HITVGT~~~~VkP~eSN~Ll  223 (257)
T PF08302_consen  160 LGSCDVRLERLV-WDD--RIMAIVVRIVPPEDEEDE-------VPE------WECTNKIPHITVGTRDPGVKPKESNDLL  223 (257)
T ss_pred             cceEEEEEEEEE-ECC--cEEEEEEEccCccccccc-------cCC------cccCCCCCEEEEEcCCCCCCcchHHHHH
Confidence            356899999997 765  898888763211000000       111      12234799999994   34455555555


Q ss_pred             HHHh
Q 031049          140 NILA  143 (166)
Q Consensus       140 ~~l~  143 (166)
                      +.+.
T Consensus       224 ~~~~  227 (257)
T PF08302_consen  224 ERWL  227 (257)
T ss_pred             HHHH
Confidence            5444

Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]

Probab=94.05  E-value=0.23  Score=40.37  Aligned_cols=91  Identities=19%  Similarity=0.196  Sum_probs=58.7

Q ss_pred             CCCCCCeeEEeec---CC--CCChhhhhccc------CCCcCceeEEEeeeeecCC---CCcEEEEEecCCh---hHHHH
Q 031049           34 KPEDEPHITLLVT---QP--CSKPEDILPDS------IPLVDKFPISLSLFSVLPR---KNNLLCLLIAQSL---NLREL   96 (166)
Q Consensus        34 ~~~~~~HiTL~~~---~~--~~~~~~~l~~~------~~~~~~f~l~l~~~g~F~~---~~~vl~l~~~~~~---~L~~L   96 (166)
                      ..+...|+|+.+.   .+  +.+..+.|+..      .-.-.|+.+.+.|+..++.   ..+|+|+.+++..   .|...
T Consensus       173 ~~p~~~HLTvgm~~L~~dd~vq~a~e~les~~~e~~~~~~~kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e~~l~~~  252 (345)
T KOG2814|consen  173 QGPGTFHLTVGMLKLLNDDDVQKALEILESTFQEIRIDVGEKPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYEKFLQHR  252 (345)
T ss_pred             cCCceeeEEEEEEEecChHHHHHHHHHHHHHHHHHHhccCCCceeeeccchhhhcCCHhHheeeeeeccCcchHHHHHHH
Confidence            3677999999863   22  44444444331      1256899999999999985   3679999998643   34333


Q ss_pred             H-HHHHHHHHhcCCCCCCCCCCCCeecceeec
Q 031049           97 H-DNLYEALATKGLQIDKEYVPGVWFPHCMLA  127 (166)
Q Consensus        97 ~-~~l~~~l~~~g~~~~~~~~~~~f~PHiTLa  127 (166)
                      - +.+-.++..+|. +..+.++  -.=|||+.
T Consensus       253 ~~~~i~~~f~~~~l-i~k~~~~--~kLH~Tvm  281 (345)
T KOG2814|consen  253 CGERILERFVASGL-IKKESSS--LKLHCTVM  281 (345)
T ss_pred             HHHHHHHHHHHhcc-hhccccc--cEEEEEEe
Confidence            3 555666666663 3333333  67799998

>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A

Probab=93.95  E-value=0.26  Score=34.91  Aligned_cols=74  Identities=8%  Similarity=0.055  Sum_probs=29.6

Q ss_pred             EEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCCCCChhhhhcccCCCcCceeEEEeeeeecC
Q 031049            4 AIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQPCSKPEDILPDSIPLVDKFPISLSLFSVLP   77 (166)
Q Consensus         4 ~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~~~~~~~~l~~~~~~~~~f~l~l~~~g~F~   77 (166)
                      ++.+..++++.+--.++.+.+...+...-......|||||.-........+.++.+.....+.+.+++++..+.
T Consensus        75 ~l~~~~~~~L~~L~~~l~~~~~~~~~~~~~~~~~~PHiTia~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~L~~  148 (153)
T PF13563_consen   75 FLNVEPSPELEALHRALREALRPFGFKQDSYRPFRPHITIARRLSPKQAAEAIEKLQSEFPPISFTVDELALVR  148 (153)
T ss_dssp             EEEEEE-HHHHHHHHHHHHHHHHHHGGGGGGS----EEEEEEESS-----------------EEEEE-EEEEEE
T ss_pred             EEEcCCCHHHHHHHHHHHHHHHHcCCccccCCCcceEEEEeccCCcchhHHHHHHHhCcCCCcEEEEeEEEEEE
Confidence            34444455555555555555555443111014568999998754322223333333345678899999988764

>PRK13679 hypothetical protein; Provisional

Probab=93.89  E-value=0.25  Score=36.28  Aligned_cols=69  Identities=13%  Similarity=0.260  Sum_probs=43.2

Q ss_pred             EEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecC--CCCchhHHHHHHHHhhc---CcCceEEEeEEEE
Q 031049           84 CLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAP--SVPTDRVGNVCNILAKV---KLPLQGDVEHVRL  158 (166)
Q Consensus        84 ~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar--~~~~~~~~~~~~~l~~~---~~p~~~~v~~i~L  158 (166)
                      ++++.+++++.+.-+++.+.+..       .++.  +-|||||.-  .++.+++.++.+.++..   ..|++.++++++-
T Consensus         4 ~iai~~p~~~~~~l~~~~~~~~~-------~~~~--v~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~   74 (168)
T PRK13679          4 GIVLFPSKKIQDFANSYRKRYDP-------HYAL--IPPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSS   74 (168)
T ss_pred             EEEEcCCHHHHHHHHHHHHhhCc-------cccc--CCCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEecccc
Confidence            45666677777777777665532       1233  788999984  45555555555544432   3577888888876


Q ss_pred             Eec
Q 031049          159 VQL  161 (166)
Q Consensus       159 ~~~  161 (166)
                      +..
T Consensus        75 F~~   77 (168)
T PRK13679         75 FAP   77 (168)
T ss_pred             CCC
Confidence            643

>TIGR02258 2_5_ligase 2'-5' RNA ligase

Probab=93.65  E-value=0.6  Score=34.30  Aligned_cols=72  Identities=22%  Similarity=0.314  Sum_probs=43.9

Q ss_pred             EEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeec----ceeec--CCCCchhHHHHHHHHhhcC-cCceEEEeE
Q 031049           83 LCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFP----HCMLA--PSVPTDRVGNVCNILAKVK-LPLQGDVEH  155 (166)
Q Consensus        83 l~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~P----HiTLa--r~~~~~~~~~~~~~l~~~~-~p~~~~v~~  155 (166)
                      +|+++..++++.+.-.++.+.+....    ..   .+|.|    ||||+  -..+.+++..+.+.+.... .++++.+++
T Consensus         3 ~FiAl~~p~~~~~~l~~~~~~l~~~~----~~---~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~f~l~l~~   75 (179)
T TIGR02258         3 LFIAIDLPPEIREQLSRIQRKLKSPL----DG---IKWVPPENLHITLKFLGEVDEEQVEELEDALAKIAEPPFTLKLEG   75 (179)
T ss_pred             EEEEecCCHHHHHHHHHHHHHhhccC----CC---cEECChHHCEEEEEEccCCCHHHHHHHHHHHHHhcCCCeEEEEee
Confidence            57777777666655555555554211    11   23665    99998  2455566666655554432 357888999


Q ss_pred             EEEEec
Q 031049          156 VRLVQL  161 (166)
Q Consensus       156 i~L~~~  161 (166)
                      +..+..
T Consensus        76 ~~~F~~   81 (179)
T TIGR02258        76 IGVFGN   81 (179)
T ss_pred             eeeCCC
Confidence            988864

This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.

>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes

Probab=93.22  E-value=0.25  Score=37.41  Aligned_cols=69  Identities=23%  Similarity=0.245  Sum_probs=30.8

Q ss_pred             EEEEEecCC-hhHHHHHHHHHHHHHh-cCCCCCCCCCCCCeecceeecCCCC---chhHHHHHHHHhhcCcCc-----eE
Q 031049           82 LLCLLIAQS-LNLRELHDNLYEALAT-KGLQIDKEYVPGVWFPHCMLAPSVP---TDRVGNVCNILAKVKLPL-----QG  151 (166)
Q Consensus        82 vl~l~~~~~-~~L~~L~~~l~~~l~~-~g~~~~~~~~~~~f~PHiTLar~~~---~~~~~~~~~~l~~~~~p~-----~~  151 (166)
                      -||+-|.++ +.-..|+..| ..+.. .+  .    .+..|.|||||.-.+.   .+++.+.+........++     ..
T Consensus         4 SlWl~P~~~~~~~~~L~~lI-~~L~~~~~--~----~~p~F~PHiTL~s~i~~~~~~~~~~~L~~~~~~~~~~~~~~~~v   76 (196)
T PF07823_consen    4 SLWLVPPPGSPLYERLKTLI-SSLASLFP--G----SPPPFEPHITLTSGISLDSSDDVQKVLDSAAAALKPLPKNHFTV   76 (196)
T ss_dssp             EEEEEE-T--TTHHHHHHHH-HHHHHHST---------------EEEEEEEEE--HHHHHHHHHHHHHH-B-E-----EE
T ss_pred             EEEEcCCCCccHHHHHHHHH-HHHHHHCC--C----CCCCcCCeEEEeCCCccCCHHHHHHHHHHHHHhccCcccceeEE
Confidence            489888753 4455566555 44443 32  1    1234999999996443   344555554433323344     55


Q ss_pred             EEeEEE
Q 031049          152 DVEHVR  157 (166)
Q Consensus       152 ~v~~i~  157 (166)
                      +++++.
T Consensus        77 ~~~~v~   82 (196)
T PF07823_consen   77 RFDKVA   82 (196)
T ss_dssp             EEEEEE
T ss_pred             EeeeEe
Confidence            565554

The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.

>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]

Probab=93.04  E-value=0.62  Score=34.85  Aligned_cols=75  Identities=16%  Similarity=0.131  Sum_probs=52.9

Q ss_pred             EEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecC--CCCchhHHHHHHHHhhcCc--CceEEEeEEEE
Q 031049           83 LCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAP--SVPTDRVGNVCNILAKVKL--PLQGDVEHVRL  158 (166)
Q Consensus        83 l~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar--~~~~~~~~~~~~~l~~~~~--p~~~~v~~i~L  158 (166)
                      +|+++..++++.+.-.++.+.+...+ . ..-+.+  =.+||||.-  +++.....++.+.++....  +++.++++++.
T Consensus         3 lFiAl~~p~~i~~~i~~~~~~~~~~~-~-~k~v~~--en~HiTL~flGev~e~~~~~l~~~l~~i~~~~~f~i~l~g~g~   78 (180)
T COG1514           3 LFIALDPPAEIAERLARIRARLKGAR-A-IKWVEP--ENLHITLKFLGEVDEDKADELIEALARIAAPEPFPITLDGAGS   78 (180)
T ss_pred             eEEEecCCHHHHHHHHHHHHhcCccc-c-cccccc--cCceEEEEccCCcCchHHHHHHHHHHHhhcCCceEEEEeeEcc
Confidence            57788888888777777777666654 1 122334  578999983  6677777777777766543  78889999998


Q ss_pred             Eec
Q 031049          159 VQL  161 (166)
Q Consensus       159 ~~~  161 (166)
                      +-.
T Consensus        79 F~~   81 (180)
T COG1514          79 FPN   81 (180)
T ss_pred             cCC
Confidence            875

>PRK15124 2'-5' RNA ligase; Provisional

Probab=89.24  E-value=2.3  Score=31.41  Aligned_cols=76  Identities=9%  Similarity=0.077  Sum_probs=42.3

Q ss_pred             cEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeec--CCCCchhHHHHHHHHhhc-CcCceEEEeEEE
Q 031049           81 NLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLA--PSVPTDRVGNVCNILAKV-KLPLQGDVEHVR  157 (166)
Q Consensus        81 ~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLa--r~~~~~~~~~~~~~l~~~-~~p~~~~v~~i~  157 (166)
                      -.+|+++..++++.+--.++.+.+....  ......+++|  ||||.  -.++.+.+..+...+... ..|++..++++.
T Consensus         5 ~RlFiAl~~p~~~~~~l~~~~~~~~~~~--~~rwv~~~nl--HiTL~FlG~v~~~~~~~l~~~l~~~~~~pF~l~l~~~g   80 (176)
T PRK15124          5 KRLFFAIDLPDEIRQQIIHWRATHFPPE--AGRPVAAANL--HLTLAFLGEVSAEKQQALSQLAGRIRQPGFTLTLDDAG   80 (176)
T ss_pred             eEEEEEeCCCHHHHHHHHHHHHHhcccc--Cccccccccc--EEEEEecCCCCHHHHHHHHHHHHhcccCCeEEEECccc
Confidence            3578887766555443333333332211  0111122223  99998  356667766666666543 257888888888


Q ss_pred             EEe
Q 031049          158 LVQ  160 (166)
Q Consensus       158 L~~  160 (166)
                      .+-
T Consensus        81 ~Fp   83 (176)
T PRK15124         81 QWP   83 (176)
T ss_pred             CcC
Confidence            774

>KOG3102 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.03  E-value=1.3  Score=34.01  Aligned_cols=88  Identities=14%  Similarity=0.179  Sum_probs=61.2

Q ss_pred             CCCCeeEEe---ecC--CCCChhhhhcccCCCcCceeEEEeeeeecCC--CCcEEEEEec-CC---hhHHHHHHHHHHHH
Q 031049           36 EDEPHITLL---VTQ--PCSKPEDILPDSIPLVDKFPISLSLFSVLPR--KNNLLCLLIA-QS---LNLRELHDNLYEAL  104 (166)
Q Consensus        36 ~~~~HiTL~---~~~--~~~~~~~~l~~~~~~~~~f~l~l~~~g~F~~--~~~vl~l~~~-~~---~~L~~L~~~l~~~l  104 (166)
                      ..-.||+|.   ++.  .+.....+|++..+...-|-+++.++..|-+  +.|+ |++.+ .+   +.+.++-+.+.+.+
T Consensus       119 ~~~fHlSLsr~VvLr~HqI~~fi~~L~~~l~s~~rf~~t~n~~~iytN~e~TRt-Fi~leitt~~~~~~~~~i~~vd~Vm  197 (269)
T KOG3102|consen  119 GREFHLSLSRNVVLRVHQINSFISMLRQKLQSQKRFLITFNKWEIYTNDEHTRT-FISLEITTSGLSEISKQIDAVDEVM  197 (269)
T ss_pred             cceEEEeeccceEEEeehhhHHHHHHHHHHhhhhhheEeecceEEEecccccee-EEEEEechhhHHHHHHHHHHHHHHH
Confidence            457899995   232  1666777777777777889999999999987  3444 44443 33   45566777888888


Q ss_pred             HhcCCCCCCCCCCCCeecceeecC
Q 031049          105 ATKGLQIDKEYVPGVWFPHCMLAP  128 (166)
Q Consensus       105 ~~~g~~~~~~~~~~~f~PHiTLar  128 (166)
                      ..+.  ++..|+..  .+|++|+=
T Consensus       198 ~~~n--L~~FY~DP--sfHiSL~W  217 (269)
T KOG3102|consen  198 KLHN--LPEFYKDP--SFHISLVW  217 (269)
T ss_pred             HHcC--chhhhcCC--CCCceEEE
Confidence            8876  66666432  77998884

---

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	166
2d4g_A	171	Hypothetical protein BSU11850; beta barrel, alpha	5e-09
1vgj_A	184	Hypothetical protein PH0099; alpha+beta, LIGT-like	1e-04

>2d4g_A Hypothetical protein BSU11850; beta barrel, alpha helix, structural genomics, unknown function; 2.30A {Bacillus subtilis} Length = 171

 Score = 51.7 bits (124), Expect = 5e-09
 Identities = 20/134 (14%), Positives = 48/134 (35%), Gaps = 16/134 (11%)

Query: 38  EPHITLLVTQPCSKPEDILPDSIPLVDK-------FPISLSLFSVLPRKNNLLCLLIAQS 90
            PH+TL         E+     +  +           + ++ +S     NN++ +    +
Sbjct: 32  PPHLTLRA--SFECAEEKADQLVSHLRNIAKESHPLVLKMTKYSSFAPVNNVIYIKAEPT 89

Query: 91  LNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQ 150
             L+ L++ LY  +     + +       + PH  +  ++  D   +V   L   ++  +
Sbjct: 90  EELKTLNEKLYTGVLAGEQEYN-------FVPHVTVGQNLSDDEHSDVLGQLKMQEVSHE 142

Query: 151 GDVEHVRLVQLPPN 164
             V+   L+    N
Sbjct: 143 EIVDRFHLLYQLEN 156

>1vgj_A Hypothetical protein PH0099; alpha+beta, LIGT-like, structural genomics, ligase; 1.94A {Pyrococcus horikoshii} PDB: 1vdx_A 2fyh_A Length = 184

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 26/164 (15%), Positives = 58/164 (35%), Gaps = 16/164 (9%)

Query: 7   LYFDDALKSKILDSMKLVRELNIP-NLIKPEDEPHITL--LVTQPCSKPEDI---LPDSI 60
           +  +++++  ++ +   +         ++ E+  HITL  L      + E+I   L    
Sbjct: 7   IDVNESVRDSLVRAQDYIGSKEAKIKFVERENL-HITLKFLGEITEEQAEEIKNILKKIA 65

Query: 61  PLVDKFPISLSLFSVLPRKNN--LLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPG 118
               K  + +    V P  N   ++   I     +RE+   + + LA  G + +  +V  
Sbjct: 66  EKYKKHEVKVKGIGVFPNPNYIRVIWAGIENDEIIREMAREIEDELAKLGFKKEGNFV-- 123

Query: 119 VWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGD--VEHVRLVQ 160
               H  L           +   L ++     G   V+ + L +
Sbjct: 124 ---AHITLGRVKFVKDKLGLTMKLKELANEDFGSFVVDAIELKK 164

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	166
1vgj_A	184	Hypothetical protein PH0099; alpha+beta, LIGT-like	99.96
1iuh_A	198	2'-5' RNA ligase; riken structural genomics/proteo	99.95
2d4g_A	171	Hypothetical protein BSU11850; beta barrel, alpha	99.95
1jh6_A	189	Cyclic phosphodiesterase; ADP-ribose 1'',2''-cycli	99.94
2vfk_A	205	AKAP18 delta; APO, hydrolase; HET: AMP; 1.50A {Hom	99.94
2fsq_A	243	ATU0111 protein; alpha-beta barrel, structural gen	97.86
2d4g_A	171	Hypothetical protein BSU11850; beta barrel, alpha	94.2
1iuh_A	198	2'-5' RNA ligase; riken structural genomics/proteo	93.76
1vgj_A	184	Hypothetical protein PH0099; alpha+beta, LIGT-like	92.42
2vfk_A	205	AKAP18 delta; APO, hydrolase; HET: AMP; 1.50A {Hom	91.05
1jh6_A	189	Cyclic phosphodiesterase; ADP-ribose 1'',2''-cycli	89.52

>1vgj_A Hypothetical protein PH0099; alpha+beta, LIGT-like, structural genomics, ligase; 1.94A {Pyrococcus horikoshii} PDB: 1vdx_A 2fyh_A

Probab=99.96  E-value=3.5e-30  Score=191.35  Aligned_cols=155  Identities=16%  Similarity=0.179  Sum_probs=125.4

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHhcC-CCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCcCceeEEEeeee
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVRELNI-PNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLVDKFPISLSLFS   74 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~~~-~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~~~f~l~l~~~g   74 (166)
                      |=|||++.+|+++.+.|.++++.+...+. ..|+ +++++||||.|.++     ++++.++|++++++.+||+++++|+|
T Consensus         1 mR~Fial~~p~~~~~~l~~~~~~l~~~~~~~~~v-~~~~lHiTL~flg~~~~~~~~~l~~~l~~~~~~~~pf~l~l~g~g   79 (184)
T 1vgj_A            1 MRAFIAIDVNESVRDSLVRAQDYIGSKEAKIKFV-ERENLHITLKFLGEITEEQAEEIKNILKKIAEKYKKHEVKVKGIG   79 (184)
T ss_dssp             CEEEEEEECCHHHHHHHHHHHHHHCSSSEEEEEC-CGGGCEEEEEEEESCCHHHHHHHHHHHHHHHTTSBCEEEEEEEEE
T ss_pred             CeEEEEEcCCHHHHHHHHHHHHHHhhcCCCcEec-CccccEEEEEeecCCCHHHHHHHHHHHHHHHccCCCeEEEEeeEe
Confidence            77999999999999999999999976422 1232 56799999999753     56778899998888999999999999


Q ss_pred             ecCC--CCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCCCch---hHHHHHHHHhhcCcCc
Q 031049           75 VLPR--KNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTD---RVGNVCNILAKVKLPL  149 (166)
Q Consensus        75 ~F~~--~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~~~~---~~~~~~~~l~~~~~p~  149 (166)
                      +|++  +|+|+|++++++++|.+|+++|.+.+...|+  ..+. +  |+|||||||.....   .+.+.++.+.+ ..+.
T Consensus        80 ~F~~~~~p~vl~~~v~~~~~L~~L~~~l~~~l~~~g~--~~~~-~--f~PHiTLar~~~~~~~~~~~~~~~~~~~-~~~~  153 (184)
T 1vgj_A           80 VFPNPNYIRVIWAGIENDEIIREMAREIEDELAKLGF--KKEG-N--FVAHITLGRVKFVKDKLGLTMKLKELAN-EDFG  153 (184)
T ss_dssp             EEECSSSEEEEEEEEETCHHHHHHHHHHHHHHHTTTC--CCCC-C--CCCEEEEEEEEEESCHHHHHHHHHHTTT-CEEE
T ss_pred             eCCCCCCCcEEEEEecCCHHHHHHHHHHHHHHHHcCC--CCCC-C--ccceEEEEeecccCcHHHHHHHHHHhcC-CCCC
Confidence            9986  4699999999889999999999999999884  4433 4  99999999965433   34444444443 2345


Q ss_pred             eEEEeEEEEEecC
Q 031049          150 QGDVEHVRLVQLP  162 (166)
Q Consensus       150 ~~~v~~i~L~~~~  162 (166)
                      +|+|++|.||+|.
T Consensus       154 ~~~v~~~~L~~s~  166 (184)
T 1vgj_A          154 SFVVDAIELKKST  166 (184)
T ss_dssp             EEEECEEEEEEEE
T ss_pred             cEEEeEEEEEEee
Confidence            8999999999986

>1iuh_A 2'-5' RNA ligase; riken structural genomics/proteomics initiative, RSGI, structural genomics; 2.50A {Thermus thermophilus} SCOP: d.61.1.2

Probab=99.95  E-value=5.2e-29  Score=187.77  Aligned_cols=150  Identities=17%  Similarity=0.203  Sum_probs=119.5

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCcCceeEEEeeeee
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLVDKFPISLSLFSV   75 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~~~f~l~l~~~g~   75 (166)
                      |=|||++.+|+++.+.|.++++.|+......|+ .++++||||+|.++     ++++.++|++++++.+||+++++|+|+
T Consensus         1 mRlFial~~p~~~~~~l~~~~~~l~~~~~~r~v-~~~~~HiTL~flgev~~~~~~~l~~~l~~~~~~~~pf~l~l~g~g~   79 (198)
T 1iuh_A            1 MRLFYAVFLPEEVRAALVEAQTKVRPFRGWKPV-PPHQLHLTLLFLGERPEEELPDYLALGHRLARLEAPFRARLRGTGY   79 (198)
T ss_dssp             CEEEEEEECCHHHHHHHHHHHGGGTTCTTEEEC-CGGGCEEEEEEEEECCGGGHHHHHHHHHHHHHHSCCEEEEEEEEEE
T ss_pred             CEEEEEEeCCHHHHHHHHHHHHHhhhhcCCccc-CCCCCEEEEEeCCcCCHHHHHHHHHHHHHHhccCCCeEEEEcceEE
Confidence            779999999999999999999999762111333 57799999998643     556678888887778999999999999


Q ss_pred             cCC--CCcEEEEEecCChhHHHHHHHHHHHHHhc-C-----CCCCCCCCCCCeecceeecCCCCchhHHHHHHHHhhcCc
Q 031049           76 LPR--KNNLLCLLIAQSLNLRELHDNLYEALATK-G-----LQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKL  147 (166)
Q Consensus        76 F~~--~~~vl~l~~~~~~~L~~L~~~l~~~l~~~-g-----~~~~~~~~~~~f~PHiTLar~~~~~~~~~~~~~l~~~~~  147 (166)
                      |++  +++|||+++ ++++|.+||++|++.+... |     +  ..+.++  |+|||||||......  +    +.....
T Consensus        80 F~~~~~p~vl~l~v-~~~~L~~L~~~l~~~l~~~~g~~~~~~--~~~~~~--f~PHiTLar~~~~~~--~----l~~~l~  148 (198)
T 1iuh_A           80 FPNEGTPRVWFAKA-EAEGFLRLAEGLRAGVEELLGEEAVRI--PGWDKP--FKPHITLARRKAPAP--R----VPPVLF  148 (198)
T ss_dssp             ESSSSSCSEEEEEE-ECHHHHHHHHHHHHHHHHHHGGGGGGS--TTTTSC--CCCEEEEEEESSCCC--C----CCCCCC
T ss_pred             CCCCCCCCEEEEEC-CCHHHHHHHHHHHHHHHHhcCCCcccc--cCCCCC--CCCcEEeEeccCcch--h----HHHhhc
Confidence            986  479999999 8899999999999999998 7     4  223344  999999998654332  1    111112


Q ss_pred             CceEEEeEEEEEecC
Q 031049          148 PLQGDVEHVRLVQLP  162 (166)
Q Consensus       148 p~~~~v~~i~L~~~~  162 (166)
                      +++|+|++|+||+|.
T Consensus       149 ~~~~~v~~~~L~~S~  163 (198)
T 1iuh_A          149 GLEWPVEGFALVRSE  163 (198)
T ss_dssp             CEEEEECEEEEEEEE
T ss_pred             CceEEecEEEEEEEE
Confidence            669999999999986

>2d4g_A Hypothetical protein BSU11850; beta barrel, alpha helix, structural genomics, unknown function; 2.30A {Bacillus subtilis}

Probab=99.95  E-value=1.3e-27  Score=175.57  Aligned_cols=149  Identities=17%  Similarity=0.260  Sum_probs=119.5

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCcCceeEEEeeeee
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLVDKFPISLSLFSV   75 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~~~f~l~l~~~g~   75 (166)
                      |=|||++.+|+++.+.|.++++++.. +.+ +    .++||||+|.++     .+++.+++++++++.+||+++++|+|+
T Consensus         1 mR~Fiai~~~~~~~~~l~~~~~~~~~-~~~-~----v~pHiTL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~g~   74 (171)
T 2d4g_A            1 MKYGIVLFPSKKLQDLANSYRKRYDP-SYS-L----IPPHLTLRASFECAEEKADQLVSHLRNIAKESHPLVLKMTKYSS   74 (171)
T ss_dssp             CEEEEEBCCCHHHHHHHHHHHHHHCG-GGG-T----SCSCBCCSSCEECCGGGHHHHHHHHHHHHHTCCCEEEEEEEEEE
T ss_pred             CeEEEEEeCCHHHHHHHHHHHHHhCc-ccC-C----CCCeEEeecCCcCChHHHHHHHHHHHHHHccCCCEEEEECCcEE
Confidence            78999999999999999999999843 222 2    245999998542     566788888888788999999999999


Q ss_pred             cCCCCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCCCchhHHHHHHHHhhcCcCceEEEeE
Q 031049           76 LPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQGDVEH  155 (166)
Q Consensus        76 F~~~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~~~~~~~~~~~~l~~~~~p~~~~v~~  155 (166)
                      |+++..|+|++++++++|.+||+++.+.+...     .+.++  |+|||||||+.....+.++++.+.....+.+|+|++
T Consensus        75 F~~~~~vl~l~~~~~~~L~~L~~~l~~~~~~~-----~~~~~--f~PHiTLar~~~~~~~~~~~~~~~~~~~~~~~~v~~  147 (171)
T 2d4g_A           75 FAPVNNVIYIKAEPTEELKTLNEKLYTGVLAG-----EQEYN--FVPHVTVGQNLSDDEHSDVLGQLKMQEVSHEEIVDR  147 (171)
T ss_dssp             CTTTCCCEEEEECCCHHHHHHHHHTTSGGGCS-----CCCSC--CCCEEEEECSCCHHHHHHHHHHHTTSCCCEEEEECE
T ss_pred             eCCCCcEEEEEccCChHHHHHHHHHHhccccc-----ccCCC--CCCeEEeecCCCHHHHHHHHHHhcCCCCceeEEECe
Confidence            98533499999998999999999999876541     22344  999999999887766777666654323467999999


Q ss_pred             EEEEecC
Q 031049          156 VRLVQLP  162 (166)
Q Consensus       156 i~L~~~~  162 (166)
                      |.||+|.
T Consensus       148 i~L~~s~  154 (171)
T 2d4g_A          148 FHLLYQL  154 (171)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEEC
Confidence            9999983

>1jh6_A Cyclic phosphodiesterase; ADP-ribose 1'',2''-cyclic phosphate, RNA processing, 2',3'-C nucleotide phosphodiesterase, hydrolase; 1.80A {Arabidopsis thaliana} SCOP: d.61.1.1 PDB: 1fsi_A 1jh7_A*

Probab=99.94  E-value=3e-26  Score=171.60  Aligned_cols=150  Identities=13%  Similarity=0.144  Sum_probs=119.2

Q ss_pred             eEEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeec--CCCCChhhhhcccCCCcCceeEEEeeeeecCCCC
Q 031049            3 YAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVT--QPCSKPEDILPDSIPLVDKFPISLSLFSVLPRKN   80 (166)
Q Consensus         3 ~~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~--~~~~~~~~~l~~~~~~~~~f~l~l~~~g~F~~~~   80 (166)
                      |++.+.+|+++++.|.++++.|+....  .  .+.++||||.-.  .+.+++.++|++++++.+||+++++|+|+|++.+
T Consensus         9 ~~f~~~pp~~~~~~l~~~~~~l~~~~~--~--~~~~~HiTLlG~~~~~~~~l~~~L~~~a~~~~pf~l~l~g~g~~~~~~   84 (189)
T 1jh6_A            9 YSVWALPDEESEPRFKKLMEALRSEFT--G--PRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFF   84 (189)
T ss_dssp             EEEEEEECTTTHHHHHHHHHHHHHHHT--C--CCCCCCEEEEEEEEECHHHHHHHHHHHHHTCBCEEEEEEEEEEEEETT
T ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHcC--C--CCCCCEEEEeCCCCCCHHHHHHHHHHHHhhCCCeEEEEcceeccCccc
Confidence            889999999999999999999987422  1  457999999421  2266788999999888899999999999976678


Q ss_pred             cEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCC-CchhHHHHHHHHhhc---CcCceEEEeEE
Q 031049           81 NLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSV-PTDRVGNVCNILAKV---KLPLQGDVEHV  156 (166)
Q Consensus        81 ~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~-~~~~~~~~~~~l~~~---~~p~~~~v~~i  156 (166)
                      +|||++++++++|.+||+++++.   +|+  .. .++  |+|||||||.. ......++.+.++..   ....+|+|++|
T Consensus        85 rvlw~~v~~~~~L~~L~~~v~~~---~g~--~~-~~~--f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~  156 (189)
T 1jh6_A           85 QCVFLLLQTTPEVMEAGEHCKNH---FNC--ST-TTP--YMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRL  156 (189)
T ss_dssp             EEEEEEECCCHHHHHHHHHHHHH---TTC--CC-CSC--CCCEEEEECCCCCHHHHHHHHHHHHHHCTTCTTCEEEEEEE
T ss_pred             eEEEEeecCCHHHHHHHHHHHHH---hCC--CC-CCC--CCCeEEEEEecCCHHHHHHHHHHHHhhccCCCCCcEEeeEE
Confidence            99999999889999999999986   463  33 244  99999999843 555555565655432   23468999999


Q ss_pred             EEEecCCC
Q 031049          157 RLVQLPPN  164 (166)
Q Consensus       157 ~L~~~~p~  164 (166)
                      .||+|++.
T Consensus       157 ~L~~s~~~  164 (189)
T 1jh6_A          157 ALCKTDTE  164 (189)
T ss_dssp             EEEECCTT
T ss_pred             EEEEeCCC
Confidence            99999973

>2vfk_A AKAP18 delta; APO, hydrolase; HET: AMP; 1.50A {Homo sapiens} PDB: 2vfl_A* 2vfy_A

Probab=99.94  E-value=6.5e-27  Score=176.64  Aligned_cols=155  Identities=14%  Similarity=0.179  Sum_probs=117.1

Q ss_pred             CceEEEEecCh-hHHHHHHHHHHHHHHh--cC-CCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCc------Cc
Q 031049            1 MQYAIKLYFDD-ALKSKILDSMKLVREL--NI-PNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLV------DK   65 (166)
Q Consensus         1 m~~~i~l~~~~-~~~~~i~~l~~~L~~~--~~-~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~------~~   65 (166)
                      |.|||++.+++ ++.+.|.++++.+...  +. ..|+ .++++||||.|+++     ++++.++|++++...      +|
T Consensus         3 ~r~Fial~~~~~~~~~~l~~~~~~l~~~~~~~~~~~v-~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~~~~~~p   81 (205)
T 2vfk_A            3 PNYFLSIPITNKKITAGIKVLQNSILRQDNRLTKAMV-GDGSFHITLLVMQLLNEDEVNIGTDALLELKPFVEEILEGKH   81 (205)
T ss_dssp             CCEEEEEECCCHHHHHHHHHHHHHHHHHCGGGGGGBC-CTTCCEEEEEEECCCSHHHHHHHHHHHHHHHHHHHHHTTTSC
T ss_pred             CCEEEEEEcCCHHHHHHHHHHHHHHHhcCcchHHHhC-CcCccEEEEEEEEcCCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            88999999997 8999999999999853  32 2343 67799999999754     455666776654333      89


Q ss_pred             eeEEEeeeeecCCCCcEEEEEecCC---hhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCCCc---h-----h
Q 031049           66 FPISLSLFSVLPRKNNLLCLLIAQS---LNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSVPT---D-----R  134 (166)
Q Consensus        66 f~l~l~~~g~F~~~~~vl~l~~~~~---~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~~~---~-----~  134 (166)
                      |+++++|+|+|++  +|||++++++   +.|.+|+++|.+.+...|+. ..+.++  |+|||||||....   .     .
T Consensus        82 f~l~l~g~~~F~~--~vl~~~v~~~~~~~~L~~L~~~l~~~~~~~g~~-~~~~~~--f~PHiTlar~~~~~~~~~~~~~~  156 (205)
T 2vfk_A           82 LTLPFHGIGTFQG--QVGFVKLADGDHVSALLEIAETAKRTFQEKGIL-AGESRT--FKPHLTFMKLSKAPMLWKKGVRK  156 (205)
T ss_dssp             CEEEEEEEEEETT--TEEEEEECCSHHHHHHHHHHHHHHHHHHTTTCC-BCCSSC--CCCCEEEEEGGGCHHHHHTTCSS
T ss_pred             cEEEEechhhCCC--cEEEEeecccccHHHHHHHHHHHHHHHHHcCCC-cCCCCC--cceEEEEEecccchhhhhccccc
Confidence            9999999999987  7999999875   68999999999999998841 224455  9999999985432   1     1


Q ss_pred             H-HHHHHHHhhcCcCceEEEeEEEEEecC
Q 031049          135 V-GNVCNILAKVKLPLQGDVEHVRLVQLP  162 (166)
Q Consensus       135 ~-~~~~~~l~~~~~p~~~~v~~i~L~~~~  162 (166)
                      + .++++.+.+ ....+|+|++|.||++.
T Consensus       157 ~~~~~l~~~~~-~~~~~~~v~~i~L~~~~  184 (205)
T 2vfk_A          157 IEPGLYEQFID-HRFGEEILYQIDLCSML  184 (205)
T ss_dssp             CCGGGGGGGTT-CEEEEEECCEEEEEESS
T ss_pred             cCHHHHHHhcC-CcCcEEEeCEEEEEEcC
Confidence            2 133333332 12358999999999865

>2fsq_A ATU0111 protein; alpha-beta barrel, structural genomics, PSI, protein structu initiative, midwest center for structural genomics; HET: MSE; 1.40A {Agrobacterium tumefaciens str} SCOP: d.61.1.4

Probab=97.86  E-value=0.00018  Score=55.18  Aligned_cols=115  Identities=13%  Similarity=0.115  Sum_probs=70.2

Q ss_pred             eEEEEecCh--hHHHHHHHHHHHHHHhcC-CCCC-CCCCCCeeEEee--cC----------C---CC-------Chhhhh
Q 031049            3 YAIKLYFDD--ALKSKILDSMKLVRELNI-PNLI-KPEDEPHITLLV--TQ----------P---CS-------KPEDIL   56 (166)
Q Consensus         3 ~~i~l~~~~--~~~~~i~~l~~~L~~~~~-~~~~-~~~~~~HiTL~~--~~----------~---~~-------~~~~~l   56 (166)
                      |.|.-.+++  +..+++.+++++|++... ..+. -+.+-.|+||+=  .+          +   ..       .+.+.+
T Consensus        43 nTvI~~l~~~s~~~~~l~~iq~~L~~~~~~~~~~~lPpsS~HMTvfdgv~e~~r~~~~wP~~L~~d~~l~~~~~~~~~~l  122 (243)
T 2fsq_A           43 NTVVCHLVEGSQTESAIVSTRQRFLDMPEASQLAFTPVSSLHMTVFQGVIESRRALPYWPQTLPLDTPIDAVTDYYRDRL  122 (243)
T ss_dssp             EEEEEEBCTTSHHHHHHHHHHHHHHTSGGGGGEEECCGGGCEEEEEEEEETTCCSTTSSCTTSCTTCCHHHHHHHHHHHG
T ss_pred             CeEEEecCCCChHHHHHHHHHHHHHhccccCceeeCCchhhhhhhccccccccccCCCCCccCcccchHHHHHHHHHHHH
Confidence            344444444  457899999999997533 1121 377899999973  11          0   11       223355


Q ss_pred             cccCCCcCceeEEEeeeeecCCCCcEEEEEecC-C--hhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCC
Q 031049           57 PDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQ-S--LNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPS  129 (166)
Q Consensus        57 ~~~~~~~~~f~l~l~~~g~F~~~~~vl~l~~~~-~--~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~  129 (166)
                      +... ...||.+.+.+++  +   ..|-+.+.. .  ..|.++.++|.+.+   |+..+ +..  .|+.|||||..
T Consensus       123 ~~~~-~~~p~~~~v~~l~--~---~~v~L~Pade~~~~~L~~~R~~l~q~l---Gi~~p-~hd--~y~fHITLgY~  186 (243)
T 2fsq_A          123 STFP-TLPAFNMRVTGLR--P---VGMVMKGATAEDDSIVALWRDTFADFF---GYRHP-DHD--TYEFHITLSYI  186 (243)
T ss_dssp             GGCC-CCCCCCEEEEEEE--T---TEEEEEESSHHHHHHHHHHHHHHHHHH---TCCCT-TGG--GCCEEEECEEE
T ss_pred             hccc-CCCCeEEEEeccc--c---ceEEEecCCHHHHHHHHHHHHHHHHHh---CCCCC-CCc--ceEEEEEEEec
Confidence            5553 3488999999882  2   244454442 2  47888888887754   63222 222  39999999963

>2d4g_A Hypothetical protein BSU11850; beta barrel, alpha helix, structural genomics, unknown function; 2.30A {Bacillus subtilis}

Probab=94.20  E-value=0.2  Score=35.31  Aligned_cols=69  Identities=14%  Similarity=0.238  Sum_probs=44.3

Q ss_pred             EEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecC--CCCchhHHHHHHHHhhc---CcCceEEEeEEE
Q 031049           83 LCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAP--SVPTDRVGNVCNILAKV---KLPLQGDVEHVR  157 (166)
Q Consensus        83 l~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar--~~~~~~~~~~~~~l~~~---~~p~~~~v~~i~  157 (166)
                      +|+++..++++.+.-.++.+.+.. +      .+.  +.|||||.-  .++.+.+.++.+.++..   ..|++++++++.
T Consensus         3 ~Fiai~~~~~~~~~l~~~~~~~~~-~------~~~--v~pHiTL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~g   73 (171)
T 2d4g_A            3 YGIVLFPSKKLQDLANSYRKRYDP-S------YSL--IPPHLTLRASFECAEEKADQLVSHLRNIAKESHPLVLKMTKYS   73 (171)
T ss_dssp             EEEEBCCCHHHHHHHHHHHHHHCG-G------GGT--SCSCBCCSSCEECCGGGHHHHHHHHHHHHHTCCCEEEEEEEEE
T ss_pred             EEEEEeCCHHHHHHHHHHHHHhCc-c------cCC--CCCeEEeecCCcCChHHHHHHHHHHHHHHccCCCEEEEECCcE
Confidence            577777777766666666666532 1      232  778999984  45555555554444432   367899999988


Q ss_pred             EEe
Q 031049          158 LVQ  160 (166)
Q Consensus       158 L~~  160 (166)
                      .+.
T Consensus        74 ~F~   76 (171)
T 2d4g_A           74 SFA   76 (171)
T ss_dssp             ECT
T ss_pred             EeC
Confidence            774

>1iuh_A 2'-5' RNA ligase; riken structural genomics/proteomics initiative, RSGI, structural genomics; 2.50A {Thermus thermophilus} SCOP: d.61.1.2

Probab=93.76  E-value=0.18  Score=36.73  Aligned_cols=71  Identities=8%  Similarity=0.002  Sum_probs=44.6

Q ss_pred             EEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCee----cceeecC--CCCchhHHHHHHHHhhc---CcCceEEE
Q 031049           83 LCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWF----PHCMLAP--SVPTDRVGNVCNILAKV---KLPLQGDV  153 (166)
Q Consensus        83 l~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~----PHiTLar--~~~~~~~~~~~~~l~~~---~~p~~~~v  153 (166)
                      +|+++..++++.+.-.++.+.+.. +  ..     .+|+    |||||+-  .++.+.+.++.+.+...   ..|++.++
T Consensus         3 lFial~~p~~~~~~l~~~~~~l~~-~--~~-----~r~v~~~~~HiTL~flgev~~~~~~~l~~~l~~~~~~~~pf~l~l   74 (198)
T 1iuh_A            3 LFYAVFLPEEVRAALVEAQTKVRP-F--RG-----WKPVPPHQLHLTLLFLGERPEEELPDYLALGHRLARLEAPFRARL   74 (198)
T ss_dssp             EEEEEECCHHHHHHHHHHHGGGTT-C--TT-----EEECCGGGCEEEEEEEEECCGGGHHHHHHHHHHHHHHSCCEEEEE
T ss_pred             EEEEEeCCHHHHHHHHHHHHHhhh-h--cC-----CcccCCCCCEEEEEeCCcCCHHHHHHHHHHHHHHhccCCCeEEEE
Confidence            577777777665555555554432 1  10     1255    7999984  45666666555544432   46899999


Q ss_pred             eEEEEEec
Q 031049          154 EHVRLVQL  161 (166)
Q Consensus       154 ~~i~L~~~  161 (166)
                      +++..+..
T Consensus        75 ~g~g~F~~   82 (198)
T 1iuh_A           75 RGTGYFPN   82 (198)
T ss_dssp             EEEEEESS
T ss_pred             cceEECCC
Confidence            99998865

>1vgj_A Hypothetical protein PH0099; alpha+beta, LIGT-like, structural genomics, ligase; 1.94A {Pyrococcus horikoshii} PDB: 1vdx_A 2fyh_A

Probab=92.42  E-value=0.37  Score=34.26  Aligned_cols=72  Identities=14%  Similarity=0.147  Sum_probs=45.7

Q ss_pred             EEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCee-c---ceeecC--CCCchhHHHHHHHHhhc---CcCceEEE
Q 031049           83 LCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWF-P---HCMLAP--SVPTDRVGNVCNILAKV---KLPLQGDV  153 (166)
Q Consensus        83 l~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~-P---HiTLar--~~~~~~~~~~~~~l~~~---~~p~~~~v  153 (166)
                      +|+++..++++.+.-.++.+.+...+  .  .   .+|+ |   ||||+-  .++.+.+.++.+.+...   ..|+++++
T Consensus         3 ~Fial~~p~~~~~~l~~~~~~l~~~~--~--~---~~~v~~~~lHiTL~flg~~~~~~~~~l~~~l~~~~~~~~pf~l~l   75 (184)
T 1vgj_A            3 AFIAIDVNESVRDSLVRAQDYIGSKE--A--K---IKFVERENLHITLKFLGEITEEQAEEIKNILKKIAEKYKKHEVKV   75 (184)
T ss_dssp             EEEEEECCHHHHHHHHHHHHHHCSSS--E--E---EEECCGGGCEEEEEEEESCCHHHHHHHHHHHHHHHTTSBCEEEEE
T ss_pred             EEEEEcCCHHHHHHHHHHHHHHhhcC--C--C---cEecCccccEEEEEeecCCCHHHHHHHHHHHHHHHccCCCeEEEE
Confidence            57777777776666666666664321  0  1   1254 4   999984  56666666555555432   36889999


Q ss_pred             eEEEEEec
Q 031049          154 EHVRLVQL  161 (166)
Q Consensus       154 ~~i~L~~~  161 (166)
                      +++..+..
T Consensus        76 ~g~g~F~~   83 (184)
T 1vgj_A           76 KGIGVFPN   83 (184)
T ss_dssp             EEEEEEEC
T ss_pred             eeEeeCCC
Confidence            99998864

>2vfk_A AKAP18 delta; APO, hydrolase; HET: AMP; 1.50A {Homo sapiens} PDB: 2vfl_A* 2vfy_A

Probab=91.05  E-value=0.91  Score=32.83  Aligned_cols=72  Identities=14%  Similarity=0.055  Sum_probs=42.7

Q ss_pred             EEEEEecCCh-hHHHHHHHHHHHHHhc--CCCCCCCCCCCCeec----ceeec--CCCCchhHHHHHHHHhhc---C---
Q 031049           82 LLCLLIAQSL-NLRELHDNLYEALATK--GLQIDKEYVPGVWFP----HCMLA--PSVPTDRVGNVCNILAKV---K---  146 (166)
Q Consensus        82 vl~l~~~~~~-~L~~L~~~l~~~l~~~--g~~~~~~~~~~~f~P----HiTLa--r~~~~~~~~~~~~~l~~~---~---  146 (166)
                      .+|+++..++ ++.+--.++.+.+...  |  ..     .+|+|    ||||+  -.++.+.+.++.+.+...   .   
T Consensus         4 r~Fial~~~~~~~~~~l~~~~~~l~~~~~~--~~-----~~~v~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~~   76 (205)
T 2vfk_A            4 NYFLSIPITNKKITAGIKVLQNSILRQDNR--LT-----KAMVGDGSFHITLLVMQLLNEDEVNIGTDALLELKPFVEEI   76 (205)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHHHHHHCGG--GG-----GGBCCTTCCEEEEEEECCCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCHHHHHHHHHHHHHHHhcCcc--hH-----HHhCCcCccEEEEEEEEcCCHHHHHHHHHHHHHHHHHHHHH
Confidence            4677776553 5555555555555421  2  10     12554    99998  355666666665555442   1   


Q ss_pred             ---cCceEEEeEEEEEe
Q 031049          147 ---LPLQGDVEHVRLVQ  160 (166)
Q Consensus       147 ---~p~~~~v~~i~L~~  160 (166)
                         .|++++++++..+.
T Consensus        77 ~~~~pf~l~l~g~~~F~   93 (205)
T 2vfk_A           77 LEGKHLTLPFHGIGTFQ   93 (205)
T ss_dssp             TTTSCCEEEEEEEEEET
T ss_pred             hCCCCcEEEEechhhCC
Confidence               57899999988775

>1jh6_A Cyclic phosphodiesterase; ADP-ribose 1'',2''-cyclic phosphate, RNA processing, 2',3'-C nucleotide phosphodiesterase, hydrolase; 1.80A {Arabidopsis thaliana} SCOP: d.61.1.1 PDB: 1fsi_A 1jh7_A*

Probab=89.52  E-value=1.4  Score=31.72  Aligned_cols=44  Identities=16%  Similarity=0.113  Sum_probs=26.4

Q ss_pred             eecceeecCCCCc--hhHHHHHHHHhhcCcCceEEEeEEEEEecCC
Q 031049          120 WFPHCMLAPSVPT--DRVGNVCNILAKVKLPLQGDVEHVRLVQLPP  163 (166)
Q Consensus       120 f~PHiTLar~~~~--~~~~~~~~~l~~~~~p~~~~v~~i~L~~~~p  163 (166)
                      +.|||||.-....  +++.+.++.+.....|++.++++++-....|
T Consensus        39 ~~~HiTLlG~~~~~~~~l~~~L~~~a~~~~pf~l~l~g~g~~~~~~   84 (189)
T 1jh6_A           39 FVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFF   84 (189)
T ss_dssp             CCCCEEEEEEEEECHHHHHHHHHHHHHTCBCEEEEEEEEEEEEETT
T ss_pred             CCCEEEEeCCCCCCHHHHHHHHHHHHhhCCCeEEEEcceeccCccc
Confidence            8999999532222  3333444444322468899999988744444

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	166
d1jh6a_	181	d.61.1.1 (A:) tRNA splicing product Appr>p cyclic	3e-06

>d1jh6a_ d.61.1.1 (A:) tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 181

class: Alpha and beta proteins (a+b)
fold: LigT-like
superfamily: LigT-like
family: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase
domain: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 43.3 bits (101), Expect = 3e-06
 Identities = 18/166 (10%), Positives = 45/166 (27%), Gaps = 18/166 (10%)

Query: 1   MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITL--LVTQPCSKPEDILPD 58
             Y++    D+  + +    M+ +R         P   PH+T+         + + +   
Sbjct: 7   DVYSVWALPDEESEPRFKKLMEALRS----EFTGPRFVPHVTVAVSAYLTADEAKKMFES 62

Query: 59  SIPLVDKFPISLSLFSVLPRKNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPG 118
           +   +  +  ++   S        + LL+  +  + E  ++                   
Sbjct: 63  ACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHF--------NCSTTT 114

Query: 119 VWFPHCMLA----PSVPTDRVGNVCNILAKVKLPLQGDVEHVRLVQ 160
            + PH  L                   L      L   +  + L +
Sbjct: 115 PYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCK 160

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	166
d1iuha_	183	2'-5' RNA ligase LigT {Thermus thermophilus [TaxId	99.92
d1jh6a_	181	tRNA splicing product Appr>p cyclic nucleotide pho	99.91
d2fsqa1	232	Putative phosphoesterase Atu0111 {Agrobacterium tu	97.94
d1jh6a_	181	tRNA splicing product Appr>p cyclic nucleotide pho	96.85
d1iuha_	183	2'-5' RNA ligase LigT {Thermus thermophilus [TaxId	90.82

>d1iuha_ d.61.1.2 (A:) 2'-5' RNA ligase LigT {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: LigT-like
superfamily: LigT-like
family: 2'-5' RNA ligase LigT
domain: 2'-5' RNA ligase LigT
species: Thermus thermophilus [TaxId: 274]

Probab=99.92  E-value=1.8e-26  Score=169.66  Aligned_cols=155  Identities=17%  Similarity=0.191  Sum_probs=115.2

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCC-----CCChhhhhcccCCCcCceeEEEeeeee
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQP-----CSKPEDILPDSIPLVDKFPISLSLFSV   75 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~-----~~~~~~~l~~~~~~~~~f~l~l~~~g~   75 (166)
                      |=.||++.+++++.++|.++++.+.......|+ +++++||||.|.++     .+.+.++++++++..+||+++++++|+
T Consensus         1 ~RlFial~~p~~~~~~l~~~~~~l~~~~~~r~~-~~~~lHiTL~flg~~~~~~~~~l~~~l~~~~~~~~pf~l~~~~~~~   79 (183)
T d1iuha_           1 MRLFYAVFLPEEVRAALVEAQTKVRPFRGWKPV-PPHQLHLTLLFLGERPEEELPDYLALGHRLARLEAPFRARLRGTGY   79 (183)
T ss_dssp             CEEEEEEECCHHHHHHHHHHHGGGTTCTTEEEC-CGGGCEEEEEEEEECCGGGHHHHHHHHHHHHHHSCCEEEEEEEEEE
T ss_pred             CeEEEEEcCCHHHHHHHHHHHHHcccccccccC-CcccCEEEEEcCCCCCHHHHHHHHHHHHHHHhcCCCeEEEeccccc
Confidence            567999999999999999999999764322333 67799999998643     567788888888889999999999999


Q ss_pred             cCC-CCcEEEEEecCChhHHHHHHHHHHHHHhc----CCCCCCCCCCCCeecceeecCCCCchhHHHHHHHHhhcCcCce
Q 031049           76 LPR-KNNLLCLLIAQSLNLRELHDNLYEALATK----GLQIDKEYVPGVWFPHCMLAPSVPTDRVGNVCNILAKVKLPLQ  150 (166)
Q Consensus        76 F~~-~~~vl~l~~~~~~~L~~L~~~l~~~l~~~----g~~~~~~~~~~~f~PHiTLar~~~~~~~~~~~~~l~~~~~p~~  150 (166)
                      |++ +..++|+...+++.+.+|+++|.+++...    +.+.+.+.++  |+|||||||.......      +.....+.+
T Consensus        80 f~~~~~~~v~~~~~~~~~~~~L~~~l~~~l~~~~~~~~~~~~~~~r~--f~PHITlar~~~~~~~------~~~~~~~~~  151 (183)
T d1iuha_          80 FPNEGTPRVWFAKAEAEGFLRLAEGLRAGVEELLGEEAVRIPGWDKP--FKPHITLARRKAPAPR------VPPVLFGLE  151 (183)
T ss_dssp             ESSSSSCSEEEEEEECHHHHHHHHHHHHHHHHHHGGGGGGSTTTTSC--CCCEEEEEEESSCCCC------CCCCCCCEE
T ss_pred             CCCCCCcEEEEEecCChHHHHHHHHHHHHHHHHhhhhccCCCccCCC--cCCCEEEEeEcCCchh------hhcccCCce
Confidence            986 33344444456778888888887777653    2235555666  9999999984332210      112345789


Q ss_pred             EEEeEEEEEecCCC
Q 031049          151 GDVEHVRLVQLPPN  164 (166)
Q Consensus       151 ~~v~~i~L~~~~p~  164 (166)
                      |+|++|.||+|...
T Consensus       152 ~~v~~~~L~~S~~~  165 (183)
T d1iuha_         152 WPVEGFALVRSELK  165 (183)
T ss_dssp             EEECEEEEEEEEEC
T ss_pred             EEeeEEEEEEEecc
Confidence            99999999997643

>d1jh6a_ d.61.1.1 (A:) tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: LigT-like
superfamily: LigT-like
family: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase
domain: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.91  E-value=6.6e-24  Score=155.72  Aligned_cols=150  Identities=13%  Similarity=0.137  Sum_probs=117.5

Q ss_pred             CceEEEEecChhHHHHHHHHHHHHHHhcCCCCCCCCCCCeeEEeecCC--CCChhhhhcccCCCcCceeEEEeeeeecCC
Q 031049            1 MQYAIKLYFDDALKSKILDSMKLVRELNIPNLIKPEDEPHITLLVTQP--CSKPEDILPDSIPLVDKFPISLSLFSVLPR   78 (166)
Q Consensus         1 m~~~i~l~~~~~~~~~i~~l~~~L~~~~~~~~~~~~~~~HiTL~~~~~--~~~~~~~l~~~~~~~~~f~l~l~~~g~F~~   78 (166)
                      |.|+|.+.|+++...+|+++++.|++....    +..+|||||.+..+  .+.+.+.++.+++...||+++++|+|+|+.
T Consensus         7 ~~yslwl~P~~~~~~~l~~l~~~l~~~~~~----~~~~pHiTL~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~~   82 (181)
T d1jh6a_           7 DVYSVWALPDEESEPRFKKLMEALRSEFTG----PRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTF   82 (181)
T ss_dssp             EEEEEEEEECTTTHHHHHHHHHHHHHHHTC----CCCCCCEEEEEEEEECHHHHHHHHHHHHHTCBCEEEEEEEEEEEEE
T ss_pred             CcEEEEEECCHHHHHHHHHHHHHHHHhhCC----CCCCCeEEEeecCcCCHHHHHHHHHHHHhhCCCeEEEecccccCCC
Confidence            479999999999999999999999986321    23479999998654  556777777777788999999999999986


Q ss_pred             CCcEEEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCCC-CchhHHHHHHHH---hhcCcCceEEEe
Q 031049           79 KNNLLCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPSV-PTDRVGNVCNIL---AKVKLPLQGDVE  154 (166)
Q Consensus        79 ~~~vl~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~~-~~~~~~~~~~~l---~~~~~p~~~~v~  154 (166)
                      ..+++|+++..+++|..||+.+.+.+.      ..+.++  |+|||||||.. ..+....+...+   .....+.+|+++
T Consensus        83 ~~~~v~~~~~~~~~L~~l~~~l~~~~~------~~~~~~--f~PHiTLa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vd  154 (181)
T d1jh6a_          83 FFQCVFLLLQTTPEVMEAGEHCKNHFN------CSTTTP--YMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLN  154 (181)
T ss_dssp             TTEEEEEEECCCHHHHHHHHHHHHHTT------CCCCSC--CCCEEEEECCCCCHHHHHHHHHHHHHHCTTCTTCEEEEE
T ss_pred             CceEEEEccCCCHHHHHHHHHHHHhcC------cccCCC--CCCeEEEEecCCChhhHHHHHHHHHHhcccCCCccEEEe
Confidence            678999999999999999999877642      222344  99999999854 444444444333   333457899999


Q ss_pred             EEEEEecC
Q 031049          155 HVRLVQLP  162 (166)
Q Consensus       155 ~i~L~~~~  162 (166)
                      +|+||++.
T Consensus       155 ~i~L~~s~  162 (181)
T d1jh6a_         155 RLALCKTD  162 (181)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEEEC
Confidence            99999985

>d2fsqa1 d.61.1.4 (A:6-237) Putative phosphoesterase Atu0111 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a+b)
fold: LigT-like
superfamily: LigT-like
family: Atu0111-like
domain: Putative phosphoesterase Atu0111
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.94  E-value=2.5e-05  Score=57.77  Aligned_cols=115  Identities=13%  Similarity=0.120  Sum_probs=65.8

Q ss_pred             eEEEEecC--hhHHHHHHHHHHHHHHhcC-CCCC-CCCCCCeeEEeec-----------CC-------CCChhh----hh
Q 031049            3 YAIKLYFD--DALKSKILDSMKLVRELNI-PNLI-KPEDEPHITLLVT-----------QP-------CSKPED----IL   56 (166)
Q Consensus         3 ~~i~l~~~--~~~~~~i~~l~~~L~~~~~-~~~~-~~~~~~HiTL~~~-----------~~-------~~~~~~----~l   56 (166)
                      +.|.-.++  .++.++|.++|++|++... ..+. -+++-.|+||+=+           ++       .+++..    .+
T Consensus        36 nTiI~~i~~~s~~~~~l~~~q~~l~~~~~~~~~~~LP~sSfHMTLfd~~n~~~r~~~~wP~~l~~d~~~~~~~~~~~~rl  115 (232)
T d2fsqa1          36 NTVVCHLVEGSQTESAIVSTRQRFLDMPEASQLAFTPVSSLHMTVFQGVIESRRALPYWPQTLPLDTPIDAVTDYYRDRL  115 (232)
T ss_dssp             EEEEEEBCTTSHHHHHHHHHHHHHHTSGGGGGEEECCGGGCEEEEEEEEETTCCSTTSSCTTSCTTCCHHHHHHHHHHHG
T ss_pred             CEEEEecCCCchHHHHHHHHHHHHHhcCcccceeeCChhhhhHHHhcccccccccCCCCCccCCcccCHHHHHHHHHHHH
Confidence            34444444  4477999999999998533 1111 3778899999721           11       111222    22


Q ss_pred             cccCCCcCceeEEEeeeeecCCCCcEEEEEecCC---hhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecCC
Q 031049           57 PDSIPLVDKFPISLSLFSVLPRKNNLLCLLIAQS---LNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAPS  129 (166)
Q Consensus        57 ~~~~~~~~~f~l~l~~~g~F~~~~~vl~l~~~~~---~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar~  129 (166)
                      +.. ....+|.+.+.+.+   +  -.|.+.+...   ..|.++.++|.+.+   |...+.++   .|++|||||.-
T Consensus       116 ~~~-~~~~~~~~~~~~~~---~--~~v~L~p~~e~d~~~L~~~R~~l~~l~---gi~~~~h~---~Y~fHITLaY~  179 (232)
T d2fsqa1         116 STF-PTLPAFNMRVTGLR---P--VGMVMKGATAEDDSIVALWRDTFADFF---GYRHPDHD---TYEFHITLSYI  179 (232)
T ss_dssp             GGC-CCCCCCCEEEEEEE---T--TEEEEEESSHHHHHHHHHHHHHHHHHH---TCCCTTGG---GCCEEEECEEE
T ss_pred             hcC-CCCcceEEEEeccc---c--cEEEEecCCHHHHHHHHHHHHHHHHHh---ccCCCCCc---eeEEEEEEEec
Confidence            222 24567888887654   2  2344554422   35677777776643   43233332   39999999963

>d1jh6a_ d.61.1.1 (A:) tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: LigT-like
superfamily: LigT-like
family: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase
domain: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=96.85  E-value=0.0019  Score=45.00  Aligned_cols=71  Identities=13%  Similarity=0.105  Sum_probs=46.1

Q ss_pred             EEEEEecCC--hhHHHHHHHHHHHHHhcCCCCCCCCCCCCeecceeecC--CCCchhHHHHHHHHhhcCcCceEEEeEEE
Q 031049           82 LLCLLIAQS--LNLRELHDNLYEALATKGLQIDKEYVPGVWFPHCMLAP--SVPTDRVGNVCNILAKVKLPLQGDVEHVR  157 (166)
Q Consensus        82 vl~l~~~~~--~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~PHiTLar--~~~~~~~~~~~~~l~~~~~p~~~~v~~i~  157 (166)
                      -||+-+...  +.|.++.+.+.+..   |  .      ..|.|||||+-  ..+.+.....++.+.....|+++++++++
T Consensus        10 slwl~P~~~~~~~l~~l~~~l~~~~---~--~------~~~~pHiTL~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~   78 (181)
T d1jh6a_          10 SVWALPDEESEPRFKKLMEALRSEF---T--G------PRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVS   78 (181)
T ss_dssp             EEEEEECTTTHHHHHHHHHHHHHHH---T--C------CCCCCCEEEEEEEEECHHHHHHHHHHHHHTCBCEEEEEEEEE
T ss_pred             EEEEECCHHHHHHHHHHHHHHHHhh---C--C------CCCCCeEEEeecCcCCHHHHHHHHHHHHhhCCCeEEEecccc
Confidence            467776432  35666666665543   3  1      13889999994  44556666666666654568899999998


Q ss_pred             EEecCC
Q 031049          158 LVQLPP  163 (166)
Q Consensus       158 L~~~~p  163 (166)
                      .+...+
T Consensus        79 ~~~~~~   84 (181)
T d1jh6a_          79 TGTFFF   84 (181)
T ss_dssp             EEEETT
T ss_pred             cCCCCc
Confidence            876543

>d1iuha_ d.61.1.2 (A:) 2'-5' RNA ligase LigT {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: LigT-like
superfamily: LigT-like
family: 2'-5' RNA ligase LigT
domain: 2'-5' RNA ligase LigT
species: Thermus thermophilus [TaxId: 274]

Probab=90.82  E-value=0.33  Score=32.89  Aligned_cols=71  Identities=11%  Similarity=0.056  Sum_probs=42.0

Q ss_pred             EEEEecCChhHHHHHHHHHHHHHhcCCCCCCCCCCCCeec----ceeecC--CCCchhHHHHHHHH---hhcCcCceEEE
Q 031049           83 LCLLIAQSLNLRELHDNLYEALATKGLQIDKEYVPGVWFP----HCMLAP--SVPTDRVGNVCNIL---AKVKLPLQGDV  153 (166)
Q Consensus        83 l~l~~~~~~~L~~L~~~l~~~l~~~g~~~~~~~~~~~f~P----HiTLar--~~~~~~~~~~~~~l---~~~~~p~~~~v  153 (166)
                      +|+++..++++.+--.++.+.+..       .+. .+|+|    ||||.-  .++.+....+.+.+   .....|++.++
T Consensus         3 lFial~~p~~~~~~l~~~~~~l~~-------~~~-~r~~~~~~lHiTL~flg~~~~~~~~~l~~~l~~~~~~~~pf~l~~   74 (183)
T d1iuha_           3 LFYAVFLPEEVRAALVEAQTKVRP-------FRG-WKPVPPHQLHLTLLFLGERPEEELPDYLALGHRLARLEAPFRARL   74 (183)
T ss_dssp             EEEEEECCHHHHHHHHHHHGGGTT-------CTT-EEECCGGGCEEEEEEEEECCGGGHHHHHHHHHHHHHHSCCEEEEE
T ss_pred             EEEEEcCCHHHHHHHHHHHHHccc-------ccc-cccCCcccCEEEEEcCCCCCHHHHHHHHHHHHHHHhcCCCeEEEe
Confidence            577777776544433444433322       111 14777    999973  55655555544433   33246889999


Q ss_pred             eEEEEEec
Q 031049          154 EHVRLVQL  161 (166)
Q Consensus       154 ~~i~L~~~  161 (166)
                      ++++.+..
T Consensus        75 ~~~~~f~~   82 (183)
T d1iuha_          75 RGTGYFPN   82 (183)
T ss_dssp             EEEEEESS
T ss_pred             cccccCCC
Confidence            99998854