Citrus Sinensis ID: 029664

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190
Protein Sequence
MEAPETVVVDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSPD
Secondary Structure (PSIPRED)
cccccccccccccccEEEEEEEccHHHHHHHHHHHHHHHHHccccccccEEEEcccccccHHHHHHHHHHHHccccccEEEEEEEEEccEEEEEEEEEEEcccccccHHHHHHcccccccccccccEEEEEcccccHHHHHHHHHHHHHcccccccccEEEcEEEEEEEcccccccccEEEEEEEEcccc
Secondary Structure Prediction (SSPRO)
cccccccEccccccEEEEEEEEcccccHHHHHHHHHHHHHHcccccccccEEEEEEEEEccHHHHHHHHHHHccccccEEEccEEEEEEEccEEEEEEccccHHHHccccccccccccccccccccEEEEEcccccHHHHHHHHHHHccccccccccEEEccEEEEEEcccccccccccEEEEEEEcccc
Coil and Loop (DISEMBL)
meapetvvvdknkkgfysvwaippdEVRARVKKLMEGLrsefggpqfdphVTVVGAMSLTADDALEKFKSACnglkaynctvnrVATGTFFYQCVFLLlhptpevaepsshccghfgyksstpymphlsllygdltDDEKKIAQEKAHKLdesigslsfpitrlqlwktdtedttLKSWEMVAECNLSPD
Flexible Loop (DISEMBL)
meapetvvvdknkkgfysvwaippdeVRARVKKLMEGLRsefggpqfdpHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAhkldesigslsfpitrlqlwKTDTEDTTLKSWEMVAECNLSPD
Low Complexity Region (SEG)
MEAPETVVVDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSPD
Disordered region (IsUnstruct)
*******VVDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTD***************SIGSLSFPITRLQLWKTDTEDTTLKSWEMVA*******
Disordered Region (DISOPRED)
************KK*FYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSP*
Disordered Region (DISEMBL)
********VDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSPD
Disordered Region (DISPRO)
*****TVVVDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLS**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEAPETVVVDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSPD
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	190	2.2.26 [Sep-21-2011]
O04147	181	Cyclic phosphodiesterase	yes	no	0.952	1.0	0.624	9e-62
Q6CGD3	216	2',3'-cyclic-nucleotide 3	yes	no	0.731	0.643	0.217	0.0004
P62809	51	Cyclic phosphodiesterase	N/A	no	0.121	0.450	0.782	0.0007

>sp|O04147|CPD_ARATH Cyclic phosphodiesterase OS=Arabidopsis thaliana GN=At4g18930 PE=1 SV=1

 Score =  236 bits (601), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 113/181 (62%), Positives = 138/181 (76%)

Query: 9   VDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKF 68
           +++ KK  YSVWA+P +E   R KKLME LRSEF GP+F PHVTV  +  LTAD+A + F
Sbjct: 1   MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMF 60

Query: 69  KSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHL 128
           +SAC+GLKAY  TV+RV+TGTFF+QCVFLLL  TPEV E   HC  HF   ++TPYMPHL
Sbjct: 61  ESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHL 120

Query: 129 SLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLS 188
           SLLY +LT++EKK AQEKA+ LD S+  LSF + RL L KTDTED TL++WE VA CNL+
Sbjct: 121 SLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLN 180

Query: 189 P 189
           P
Sbjct: 181 P 181

Hydrolyzes APD-ribose 1",2"-cyclic phosphate (Appr>1) that is produced during tRNA splicing into ADP-ribose 1"-phosphate (Appr-1"p). Acts also on nucloside 2',3'-cyclic phosphates.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 4EC: .EC: -

>sp|Q6CGD3|CPD1_YARLI 2',3'-cyclic-nucleotide 3'-phosphodiesterase OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=CPD1 PE=3 SV=2

 Score = 44.7 bits (104), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 39/179 (21%), Positives = 75/179 (41%), Gaps = 40/179 (22%)

Query: 18  SVWAIPPDE--VRARVKKLMEGLRSEFGGPQ-FDPHVTVVGAMSLT----ADDALEKFKS 70
           S+W  PP    +  ++   ++GL+  F   + F+PH+T+   +S+      D  L++  +
Sbjct: 4   SLWLQPPRNSPIWQQLATTIQGLKPIFSDSENFEPHITLTSNISVNTQGQVDFVLDRAVA 63

Query: 71  ACNGL-KAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYK---------- 119
           A   + + +   ++ V  G+ F++ V+L + PTPE+   +  C   F Y           
Sbjct: 64  AAKCVPQGFQIHLSSVKYGSRFFKKVYLQVEPTPELLSLARICREDFVYMPEAMSQARNY 123

Query: 120 ----------------------SSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGS 156
                                 +   Y PH+SL+Y DL   E    +    +L+++ GS
Sbjct: 124 QAMSAEERQKIDTQVGQRAAEWTRNEYDPHVSLVYSDLYPVEDADRRTIETRLEDTFGS 182

Involved in the metabolism of ADP-ribose 1',2'-cyclic phosphate which is produced as a consequence of tRNA splicing.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: .

EC: 3

EC: 7

>sp|P62809|CPD_WHEAT Cyclic phosphodiesterase (Fragments) OS=Triticum aestivum PE=1 SV=1

 Score = 43.9 bits (102), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/23 (78%), Positives = 22/23 (95%)

Query: 118 YKSSTPYMPHLSLLYGDLTDDEK 140
           Y ++TPYMPH+SLLYGDLTD+EK
Sbjct: 29  YTATTPYMPHVSLLYGDLTDEEK 51

Hydrolyzes APD-ribose 1",2"-cyclic phosphate (Appr>1) that is produced during tRNA splicing into ADP-ribose 1"-phosphate (Appr-1"p).

Triticum aestivum (taxid: 4565)

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: .

EC: -

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	190
224116504	190	predicted protein [Populus trichocarpa]	0.994	0.994	0.751	5e-80
255562558	190	Cyclic phosphodiesterase, putative [Rici	1.0	1.0	0.721	5e-77
225443670	185	PREDICTED: cyclic phosphodiesterase [Vit	0.942	0.967	0.731	1e-73
357519169	184	Cyclic phosphodiesterase [Medicago trunc	0.936	0.967	0.657	3e-69
356512549	180	PREDICTED: cyclic phosphodiesterase-like	0.936	0.988	0.629	1e-65
449433716	192	PREDICTED: cyclic phosphodiesterase-like	0.989	0.979	0.610	1e-64
15234068	181	cyclic phosphodiesterase [Arabidopsis th	0.952	1.0	0.624	5e-60
11513544	189	Chain A, Crystal Structure Of Cyclic Nuc	0.952	0.957	0.624	6e-60
224097496	190	predicted protein [Populus trichocarpa]	0.952	0.952	0.616	3e-59
297804254	181	cyclic phosphodiesterase [Arabidopsis ly	0.952	1.0	0.635	1e-56

>gi|224116504|ref|XP_002317317.1| predicted protein [Populus trichocarpa] gi|222860382|gb|EEE97929.1| predicted protein [Populus trichocarpa]

 Score =  302 bits (773), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 142/189 (75%), Positives = 159/189 (84%)

Query: 1   MEAPETVVVDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLT 60
           ME P+      +KK  YSVWAIPP++V  R+K+LM GL SEFGGPQF+PH+TVVGA+ LT
Sbjct: 1   MEIPQGTSTPADKKHVYSVWAIPPEDVGTRLKRLMAGLASEFGGPQFEPHITVVGAIGLT 60

Query: 61  ADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKS 120
             DALEKF SAC+GL+AY  TV+RVATGTFFYQCV+LLLHP PEV E S+HC GHFGYKS
Sbjct: 61  EQDALEKFHSACDGLQAYTATVDRVATGTFFYQCVYLLLHPLPEVVEASAHCSGHFGYKS 120

Query: 121 STPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWE 180
           STPYMPHLSLLYGDLTDDEKK AQEKA+ LDESI  LSFPITRL LWKTDTED TLKSWE
Sbjct: 121 STPYMPHLSLLYGDLTDDEKKEAQEKANILDESISGLSFPITRLALWKTDTEDLTLKSWE 180

Query: 181 MVAECNLSP 189
            +AEC+LSP
Sbjct: 181 KIAECSLSP 189

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562558|ref|XP_002522285.1| Cyclic phosphodiesterase, putative [Ricinus communis] gi|223538538|gb|EEF40143.1| Cyclic phosphodiesterase, putative [Ricinus communis]

 Score =  292 bits (747), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 137/190 (72%), Positives = 158/190 (83%)

Query: 1   MEAPETVVVDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLT 60
           ME P T      +K  YSVWAIP ++V AR+KKLME LRSEFGGPQF+PHVTVVGA+SLT
Sbjct: 1   MEIPATATDITAQKYVYSVWAIPAEDVSARLKKLMEDLRSEFGGPQFEPHVTVVGAISLT 60

Query: 61  ADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKS 120
            ++ALEKF+S+C+GL  Y  TV+RVATGTFFYQC++LLL+P+PEV   S+HC GHFGYKS
Sbjct: 61  EEEALEKFRSSCDGLTRYIATVDRVATGTFFYQCIYLLLNPSPEVVRASAHCTGHFGYKS 120

Query: 121 STPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWE 180
           STPYMPHLSLLYGDLTDDEKK AQEK + LDESI  LSF I+RL LWKTDTED TLKSWE
Sbjct: 121 STPYMPHLSLLYGDLTDDEKKKAQEKTNILDESINGLSFQISRLALWKTDTEDRTLKSWE 180

Query: 181 MVAECNLSPD 190
            +AEC LSP+
Sbjct: 181 KIAECTLSPN 190

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443670|ref|XP_002263343.1| PREDICTED: cyclic phosphodiesterase [Vitis vinifera] gi|297740575|emb|CBI30757.3| unnamed protein product [Vitis vinifera]

 Score =  281 bits (719), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 131/179 (73%), Positives = 155/179 (86%)

Query: 11  KNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKS 70
           +++K  YSVW IPP+EV ARVKK+MEGLRSEFGGP F+PHVTVVGA+SLT  DAL KF+S
Sbjct: 6   ESRKEVYSVWGIPPEEVGARVKKVMEGLRSEFGGPAFEPHVTVVGAISLTEADALHKFRS 65

Query: 71  ACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSL 130
           AC+GLKAY+ +V+ VATGTFFYQCV+LLLHP PEV E S+HC GHFG++SSTPYMPHLSL
Sbjct: 66  ACDGLKAYDASVDSVATGTFFYQCVYLLLHPMPEVVEASAHCTGHFGFRSSTPYMPHLSL 125

Query: 131 LYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSP 189
           LYGDL++++KK AQEKA  LDESIGSL+F I+ L L+KTDTED TL SWE V+ECNL P
Sbjct: 126 LYGDLSEEDKKKAQEKAKVLDESIGSLNFTISCLALYKTDTEDKTLTSWEKVSECNLIP 184

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357519169|ref|XP_003629873.1| Cyclic phosphodiesterase [Medicago truncatula] gi|355523895|gb|AET04349.1| Cyclic phosphodiesterase [Medicago truncatula] gi|388520963|gb|AFK48543.1| unknown [Medicago truncatula]

 Score =  266 bits (679), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 117/178 (65%), Positives = 151/178 (84%)

Query: 13  KKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSAC 72
           KK  YSVWAIPP++VR R+ KLM  LRS+FGGPQF+PH+TVVGA+ LT DDAL+K +SA 
Sbjct: 7   KKEVYSVWAIPPEDVRDRLTKLMTSLRSDFGGPQFEPHMTVVGAIELTPDDALKKLRSAS 66

Query: 73  NGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLY 132
            G+K++  TV+RV+ GTFFYQCV+LLLHPTP++ E ++HCC HFGYK+STPYMPH+SL+Y
Sbjct: 67  EGVKSFQVTVDRVSAGTFFYQCVYLLLHPTPQILETNAHCCTHFGYKNSTPYMPHVSLVY 126

Query: 133 GDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSPD 190
           GDLTD+EK+ AQE+A+ LD S+  LSF I++L L+KTDTED +LKSWE +AEC L+P+
Sbjct: 127 GDLTDEEKQKAQERANILDNSLSGLSFQISKLALYKTDTEDKSLKSWEKIAECTLTPN 184

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512549|ref|XP_003524981.1| PREDICTED: cyclic phosphodiesterase-like [Glycine max]

 Score =  254 bits (649), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 112/178 (62%), Positives = 143/178 (80%)

Query: 13  KKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSAC 72
            +  YSVWAIPP++V AR   LM  LRSEFGGP F PH+TVVGA+ LT +DA+ K +SAC
Sbjct: 3   NQAVYSVWAIPPEDVGARCANLMTALRSEFGGPHFHPHITVVGAIKLTPEDAVTKLRSAC 62

Query: 73  NGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLY 132
             L+ ++ TV+RVA G+FFYQCV+LLL P P + E S+HCC HFGY +STPYMPHLSLLY
Sbjct: 63  QALRPFHVTVDRVAAGSFFYQCVYLLLRPDPHLLETSAHCCTHFGYTNSTPYMPHLSLLY 122

Query: 133 GDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSPD 190
           GDL+D+EK+ AQE+A+ +D+++G L+F ITRL L+KTDTED TLKSWE +AEC L+P+
Sbjct: 123 GDLSDEEKRKAQERANAIDDTLGGLTFQITRLALYKTDTEDKTLKSWEKIAECTLTPN 180

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433716|ref|XP_004134643.1| PREDICTED: cyclic phosphodiesterase-like [Cucumis sativus]

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 116/190 (61%), Positives = 148/190 (77%), Gaps = 2/190 (1%)

Query: 1   MEAPETVVV--DKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMS 58
           M  PE+  +  D+ +   YSVWA+PP++V AR++ LM+ LRSEFGGP F+PH+TVVGA+ 
Sbjct: 1   MMNPESASIQSDEEETHVYSVWALPPEDVSARIENLMKSLRSEFGGPLFEPHITVVGAIR 60

Query: 59  LTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGY 118
           LTA+DAL KF++AC G+KAY  TV+ V TGTFFYQCVFLL+HPT EV E SSH C HF +
Sbjct: 61  LTAEDALTKFRTACQGIKAYQATVDHVTTGTFFYQCVFLLIHPTTEVVETSSHFCKHFDF 120

Query: 119 KSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKS 178
           KSSTPYMPH+SLLY  ++D+++K A+E A KLDE++  L FPITRL L KTDT D TLKS
Sbjct: 121 KSSTPYMPHMSLLYSHISDEKRKQAKEIADKLDEAVNGLRFPITRLALCKTDTADETLKS 180

Query: 179 WEMVAECNLS 188
           W+ + E +LS
Sbjct: 181 WDKIVEHDLS 190

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15234068|ref|NP_193628.1| cyclic phosphodiesterase [Arabidopsis thaliana] gi|51315738|sp|O04147.1|CPD_ARATH RecName: Full=Cyclic phosphodiesterase; Short=CPDase gi|2065013|emb|CAA72363.1| cyclic phosphodiesterase [Arabidopsis thaliana] gi|2832621|emb|CAA16750.1| putative protein [Arabidopsis thaliana] gi|7268687|emb|CAB78895.1| putative protein [Arabidopsis thaliana] gi|17065492|gb|AAL32900.1| protein kinase - like protein [Arabidopsis thaliana] gi|20148603|gb|AAM10192.1| protein kinase-like protein [Arabidopsis thaliana] gi|332658708|gb|AEE84108.1| cyclic phosphodiesterase [Arabidopsis thaliana]

 Score =  236 bits (601), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 113/181 (62%), Positives = 138/181 (76%)

Query: 9   VDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKF 68
           +++ KK  YSVWA+P +E   R KKLME LRSEF GP+F PHVTV  +  LTAD+A + F
Sbjct: 1   MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMF 60

Query: 69  KSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHL 128
           +SAC+GLKAY  TV+RV+TGTFF+QCVFLLL  TPEV E   HC  HF   ++TPYMPHL
Sbjct: 61  ESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHL 120

Query: 129 SLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLS 188
           SLLY +LT++EKK AQEKA+ LD S+  LSF + RL L KTDTED TL++WE VA CNL+
Sbjct: 121 SLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLN 180

Query: 189 P 189
           P
Sbjct: 181 P 181

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|11513544|pdb|1FSI|A Chain A, Crystal Structure Of Cyclic Nucleotide Phosphodiesterase Of Appr>p From Arabidopsis Thaliana gi|11513545|pdb|1FSI|B Chain B, Crystal Structure Of Cyclic Nucleotide Phosphodiesterase Of Appr>p From Arabidopsis Thaliana gi|11513546|pdb|1FSI|C Chain C, Crystal Structure Of Cyclic Nucleotide Phosphodiesterase Of Appr>p From Arabidopsis Thaliana gi|18655429|pdb|1JH6|A Chain A, Semi-Reduced Cyclic Nucleotide Phosphodiesterase From Arabidopsis Thaliana gi|18655430|pdb|1JH6|B Chain B, Semi-Reduced Cyclic Nucleotide Phosphodiesterase From Arabidopsis Thaliana gi|18655431|pdb|1JH7|A Chain A, Semi-Reduced Inhibitor-Bound Cyclic Nucleotide Phosphodiesterase From Arabidopsis Thaliana

 Score =  235 bits (600), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 113/181 (62%), Positives = 138/181 (76%)

Query: 9   VDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKF 68
           +++ KK  YSVWA+P +E   R KKLME LRSEF GP+F PHVTV  +  LTAD+A + F
Sbjct: 1   MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMF 60

Query: 69  KSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHL 128
           +SAC+GLKAY  TV+RV+TGTFF+QCVFLLL  TPEV E   HC  HF   ++TPYMPHL
Sbjct: 61  ESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHL 120

Query: 129 SLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLS 188
           SLLY +LT++EKK AQEKA+ LD S+  LSF + RL L KTDTED TL++WE VA CNL+
Sbjct: 121 SLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLN 180

Query: 189 P 189
           P
Sbjct: 181 P 181

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224097496|ref|XP_002334607.1| predicted protein [Populus trichocarpa] gi|222873410|gb|EEF10541.1| predicted protein [Populus trichocarpa]

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 114/185 (61%), Positives = 140/185 (75%), Gaps = 4/185 (2%)

Query: 7   VVVDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALE 66
           VV +KN    YSVWAIPP+ V  ++KKLM  LRSEFGGP+  PH+TVVGA SLT +DAL+
Sbjct: 9   VVAEKND---YSVWAIPPEVVGEKLKKLMGVLRSEFGGPEIPPHITVVGATSLTEEDALK 65

Query: 67  KFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMP 126
           KF+SAC GLKAY+   + V +G F  QC++LL H TPEV + S HCC +FGYK S  YMP
Sbjct: 66  KFRSACEGLKAYHAKADLVVSGAFPSQCLYLLFHSTPEVMDASEHCCRYFGYKRSNRYMP 125

Query: 127 HLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDT-TLKSWEMVAEC 185
           HLSLLYG LT+DEK  A+EKA+ LDESI  L+F I+RL LWKTD +D  TL+SW  +AEC
Sbjct: 126 HLSLLYGTLTEDEKNKAREKAYVLDESIDGLNFQISRLALWKTDRKDKGTLESWRQIAEC 185

Query: 186 NLSPD 190
           +LSP+
Sbjct: 186 SLSPN 190

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297804254|ref|XP_002870011.1| cyclic phosphodiesterase [Arabidopsis lyrata subsp. lyrata] gi|297315847|gb|EFH46270.1| cyclic phosphodiesterase [Arabidopsis lyrata subsp. lyrata]

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 115/181 (63%), Positives = 140/181 (77%)

Query: 9   VDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKF 68
           +++ KK  YSVWA+P +E   R +KLME LRSEF GP+FDPHVTVVGA +LT D+A + F
Sbjct: 1   MEEVKKDVYSVWALPDEESEPRFRKLMEALRSEFTGPRFDPHVTVVGATNLTEDEAKKMF 60

Query: 69  KSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHL 128
           KSAC+G K+Y  TV+RV+TGTFF+QCVFLLL  TPEV E   HC  HF   ++TPYMPHL
Sbjct: 61  KSACDGFKSYRATVDRVSTGTFFFQCVFLLLQSTPEVTEAGEHCKNHFNCSTTTPYMPHL 120

Query: 129 SLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLS 188
           SLLY +LT++EKK AQEKA+ LD S+  LSF + RL L KTDTED TL+SWE VA CNL+
Sbjct: 121 SLLYAELTEEEKKKAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLESWETVAVCNLN 180

Query: 189 P 189
           P
Sbjct: 181 P 181

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	190
TAIR|locus:2117099	181	AT4G18930 [Arabidopsis thalian	0.952	1.0	0.624	6.6e-58
TAIR|locus:2117114	196	AT4G18940 [Arabidopsis thalian	0.968	0.938	0.470	3.5e-43

TAIR|locus:2117099 AT4G18930 [Arabidopsis thaliana (taxid:3702)]

 Score = 595 (214.5 bits), Expect = 6.6e-58, P = 6.6e-58
 Identities = 113/181 (62%), Positives = 138/181 (76%)

Query:     9 VDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKF 68
             +++ KK  YSVWA+P +E   R KKLME LRSEF GP+F PHVTV  +  LTAD+A + F
Sbjct:     1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMF 60

Query:    69 KSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHL 128
             +SAC+GLKAY  TV+RV+TGTFF+QCVFLLL  TPEV E   HC  HF   ++TPYMPHL
Sbjct:    61 ESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHL 120

Query:   129 SLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLS 188
             SLLY +LT++EKK AQEKA+ LD S+  LSF + RL L KTDTED TL++WE VA CNL+
Sbjct:   121 SLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLN 180

Query:   189 P 189
             P
Sbjct:   181 P 181

GO:0003824 "catalytic activity" evidence=IEA

GO:0004112 "cyclic-nucleotide phosphodiesterase activity" evidence=IEA;IDA

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM;IDA

GO:0016070 "RNA metabolic process" evidence=IEA

GO:0006388 "tRNA splicing, via endonucleolytic cleavage and ligation" evidence=TAS

TAIR|locus:2117114 AT4G18940 [Arabidopsis thaliana (taxid:3702)]

 Score = 456 (165.6 bits), Expect = 3.5e-43, P = 3.5e-43
 Identities = 89/189 (47%), Positives = 124/189 (65%)

Query:     1 MEAPETVVVDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAM--S 58
             ++ P+T   D+ +K  Y++WA+P D+V  R+++LMEGLRSEFGGP FDPH+T+VG     
Sbjct:     9 LQPPQTQEDDEEEKAMYAIWAVPEDDVEDRLQRLMEGLRSEFGGPAFDPHLTLVGPFPYK 68

Query:    59 LTADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGY 118
             LTA +A   FKSAC G K Y  TV++V+ GT ++QC+++ L  T EV   + H   HF  
Sbjct:    69 LTASEAKRMFKSACEGFKVYPATVDQVSAGTSYFQCLYVSLRHTVEVMNAAGHFMAHFKP 128

Query:   119 KSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKS 178
              +   Y+PH+S+LYGDLT+ EKK A EKA+ LD S+  L+F I R+ LW TD +   + S
Sbjct:   129 FTGKFYVPHMSILYGDLTEREKKKALEKAYTLDSSLDGLNFKINRVALWITDAD---VGS 185

Query:   179 WEMVAECNL 187
             W  V E  L
Sbjct:   186 WVKVDEHTL 194


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        0.317   0.133   0.412    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      190       190   0.00091  110 3  11 22  0.47    32
                                                     31  0.42    35


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:  605 (64 KB)
  Total size of DFA:  185 KB (2106 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  19.19u 0.14s 19.33t   Elapsed:  00:00:01
  Total cpu time:  19.19u 0.14s 19.33t   Elapsed:  00:00:01
  Start:  Sat May 11 06:29:15 2013   End:  Sat May 11 06:29:16 2013

GO:0003824 "catalytic activity" evidence=IEA

GO:0004112 "cyclic-nucleotide phosphodiesterase activity" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0016070 "RNA metabolic process" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O04147	CPD_ARATH	3, ., 1, ., 4, ., -	0.6243	0.9526	1.0	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.4.37	LOW CONFIDENCE prediction!
3rd Layer	3.1.4	0.691

---

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	190
pfam07823	192	pfam07823, CPDase, Cyclic phosphodiesterase-like p	4e-45
pfam13563	152	pfam13563, 2_5_RNA_ligase2, 2'-5' RNA ligase super	2e-09

>gnl|CDD|219597 pfam07823, CPDase, Cyclic phosphodiesterase-like protein

 Score =  147 bits (372), Expect = 4e-45
 Identities = 58/182 (31%), Positives = 97/182 (53%), Gaps = 21/182 (11%)

Query: 24  PDEVRARVKKLMEGLRSEFGG--PQFDPHVTVVGAMSL-TADDALEKFKSACNGLKAY-N 79
            D    R+++L+E L++ F G  P F+PH+T+   +SL T DD     +SAC GLK+   
Sbjct: 14  SDPEYERLQRLIESLQTLFPGESPSFEPHITLTSGISLDTKDDVKRVLESACAGLKSLPL 73

Query: 80  CTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHF--------GYKSSTPYMPHLSLL 131
              + V++G  ++Q V+L + PTPE+   +      F           +S  Y PHLSLL
Sbjct: 74  VKFDGVSSGDSYFQKVYLEVEPTPELLSLADIIRELFVEIPPQRADEWTSEEYHPHLSLL 133

Query: 132 YGDLTDDEKKIAQEKAHKLDESIG------SLSFPITRLQLWKTDTEDTTLKSWEMVAEC 185
           YGDL+  +K  A+E A ++D+++        L + I RL+L + +     ++ WE++   
Sbjct: 134 YGDLSPSDKAEAREIAQRIDDALDVHLNISGLGWNIGRLKLVRCEGP---VEEWEVLGSI 190

Query: 186 NL 187
           +L
Sbjct: 191 DL 192

Cyclic phosphodiesterase (CPDase) is involved in the tRNA splicing pathway. This protein exhibits a bilobal arrangement of two alpha-beta modules. Two antiparallel helices are found on the outer side of each lobe and frame an antiparallel beta-sheet that is wrapped around an accessible cleft. Moreover, the beta-strands of each lobe interact with the other lobe. The central water-filled cavity houses the enzyme's active site. Length = 192

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

 Score = 53.6 bits (129), Expect = 2e-09
 Identities = 33/159 (20%), Positives = 58/159 (36%), Gaps = 21/159 (13%)

Query: 23  PPDEVRARVKKLMEGLRSEFGGPQF---DPHVTVVGAMSLTA--DDALEKFKSACNGLKA 77
           PP E+ AR+    E LR E   P +    PH+T+          ++ LE           
Sbjct: 1   PPPELAARI----ERLRRELFDPLYPRWPPHITLAYPFVADESLEELLEALARLAAETPP 56

Query: 78  YNCTVNRVATGTF-FYQCVFLLLHPTPEVAEPSSHCCGHFGY-----KSSTPYMPHLSLL 131
           +  T+  +  G+F   + V+L +  + E+    +                 P+ PHL++ 
Sbjct: 57  FELTLGGL--GSFGGGRVVYLKVEGSEELRALRAALREALPGHLLAQDEPGPFTPHLTIA 114

Query: 132 YGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTD 170
           Y      +   A      L   +  +SF +  L L + D
Sbjct: 115 YKL----DDAPAAALLEALARELPPISFTVDELALVRRD 149

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	190
PF07823	196	CPDase: Cyclic phosphodiesterase-like protein; Int	100.0
COG1514	180	LigT 2'-5' RNA ligase [Translation, ribosomal stru	99.96
PRK15124	176	2'-5' RNA ligase; Provisional	99.94
PRK13679	168	hypothetical protein; Provisional	99.93
TIGR02258	179	2_5_ligase 2'-5' RNA ligase. This protein family c	99.93
PF13563	153	2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB	99.81
PHA02574	149	57B hypothetical protein; Provisional	99.79
PF10469	209	AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; Inte	99.39
PF02834	87	LigT_PEase: LigT like Phosphoesterase; InterPro: I	99.04
TIGR03223	228	Phn_opern_protn putative phosphonate metabolism pr	98.76
PLN00108	257	unknown protein; Provisional	98.73
PF02834	87	LigT_PEase: LigT like Phosphoesterase; InterPro: I	98.38
PF09749	239	HVSL: Uncharacterised conserved protein; InterPro:	98.07
PHA02977	201	hypothetical protein; Provisional	97.8
PF06299	160	DUF1045: Protein of unknown function (DUF1045); In	97.6
PF05213	248	Corona_NS2A: Coronavirus NS2A protein; InterPro: I	96.87
COG5255	239	Uncharacterized protein conserved in bacteria [Fun	95.39
PF08302	257	tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase	93.98
PRK13679	168	hypothetical protein; Provisional	93.61
PF06299	160	DUF1045: Protein of unknown function (DUF1045); In	91.27
PHA02574	149	57B hypothetical protein; Provisional	90.46
COG1514	180	LigT 2'-5' RNA ligase [Translation, ribosomal stru	90.19
PF13563	153	2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB	87.2
TIGR02258	179	2_5_ligase 2'-5' RNA ligase. This protein family c	87.04
PF07823	196	CPDase: Cyclic phosphodiesterase-like protein; Int	86.66
TIGR03223	228	Phn_opern_protn putative phosphonate metabolism pr	86.32

>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=100.00  E-value=2.4e-32  Score=212.71  Aligned_cols=169  Identities=38%  Similarity=0.704  Sum_probs=117.1

Q ss_pred             eEEEEEeCCh--hHHHHHHHHHHHHHhhcCC--CCCCCeEEeecCCcC-ChhHHHHHHHHHhccCCce-----eEEEcee
Q 029664           16 FYSVWAIPPD--EVRARVKKLMEGLRSEFGG--PQFDPHVTVVGAMSL-TADDALEKFKSACNGLKAY-----NCTVNRV   85 (190)
Q Consensus        16 ~~slwl~P~~--~~~~~l~~~~~~l~~~~~~--~~~~pHiTL~g~~~~-~~~~~~~~l~~~~~~~~pf-----~l~~~~v   85 (190)
                      .||||++|++  +.+++|..+|+.|+..+.+  |.|.|||||.|.+.. ..+++.+.|+.++.+.+++     .++++++
T Consensus         2 ~~SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~~p~F~PHiTL~s~i~~~~~~~~~~~L~~~~~~~~~~~~~~~~v~~~~v   81 (196)
T PF07823_consen    2 PYSLWLVPPPGSPLYERLKTLISSLASLFPGSPPPFEPHITLTSGISLDSSDDVQKVLDSAAAALKPLPKNHFTVRFDKV   81 (196)
T ss_dssp             -EEEEEEE-T--TTHHHHHHHHHHHHHHST---------EEEEEEEEE--HHHHHHHHHHHHHH-B-E-----EEEEEEE
T ss_pred             eEEEEEcCCCCccHHHHHHHHHHHHHHHCCCCCCCcCCeEEEeCCCccCCHHHHHHHHHHHHHhccCcccceeEEEeeeE
Confidence            4999999999  8999999999999999985  899999999988875 5778888898888889999     9999999


Q ss_pred             eeccceeeEEEEEeeCCccccchHHHHhhhh----------CCCCCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccc--
Q 029664           86 ATGTFFYQCVFLLLHPTPEVAEPSSHCCGHF----------GYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDES--  153 (190)
Q Consensus        86 ~~~~~~~~vv~l~v~~~~~L~~L~~~l~~~~----------g~~~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~--  153 (190)
                      ..++.|+|+||+.++++++|.+|++.+++.+          +.....+|+|||||+|+++...+++.+..........  
T Consensus        82 ~~g~~yfq~vyl~v~~t~~L~~l~~~~r~~~~~~~~~~~~~~~~~~~~y~PHlSLlY~d~~~~e~~~~~~~~~~i~~~l~  161 (196)
T PF07823_consen   82 ASGDKYFQCVYLEVEKTPELMSLAQIARELFVEGPPDEVKAAEWPREPYMPHLSLLYGDLPPEEKAEAAEIAQRIDDALG  161 (196)
T ss_dssp             EEEEETTEEEEEEE---HHHHHHHCHHHHCT----------T----S----EEEEE-----HHHHHHHHHHHHHH-TT--
T ss_pred             eeCCeEEEEEEEEecCChhHHHHHHHHHHHhhhccccccccccccCCCCCCeEEEEEcCCCcccHHHHHHHHHHhccccc
Confidence            9999999999999999999999999999987          2335679999999999999877665544444443333  


Q ss_pred             ----cCCccEEeceEEEEEecCCCCCcCCceEeEEEcC
Q 029664          154 ----IGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNL  187 (190)
Q Consensus       154 ----~~~~~~~v~~l~L~~s~~~~~~~~~w~~l~~~~L  187 (190)
                          ..+.+|.+++|.||++++   ++..|++|++++|
T Consensus       162 ~~~~~~~~~~~~~~l~lv~t~g---~v~~W~~l~~~~l  196 (196)
T PF07823_consen  162 VDSGISGLGWEGGELKLVRTDG---PVEEWEVLASVDL  196 (196)
T ss_dssp             ----GTT-EEEEEEEEEEE--T---T-TT-EEEEEEE-
T ss_pred             ccccCCCCCEeccEEEEEEcCC---CCCcEEEEEEEeC
Confidence                345699999999999988   4789999999986

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=99.96  E-value=1.7e-27  Score=182.76  Aligned_cols=166  Identities=16%  Similarity=0.225  Sum_probs=133.4

Q ss_pred             eEEEEEeCChhHHHHHHHHHHHHHhhc---CCCCCCCeEEee--cCCcC-ChhHHHHHHHHHhccCCceeEEEceeeecc
Q 029664           16 FYSVWAIPPDEVRARVKKLMEGLRSEF---GGPQFDPHVTVV--GAMSL-TADDALEKFKSACNGLKAYNCTVNRVATGT   89 (190)
Q Consensus        16 ~~slwl~P~~~~~~~l~~~~~~l~~~~---~~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~   89 (190)
                      .|.+.+.||+++++.+.++++.++...   +..+.++||||+  |+++. ..+++.+.|..+.... +|+++++|+|+|+
T Consensus         2 RlFiAl~~p~~i~~~i~~~~~~~~~~~~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i~~~~-~f~i~l~g~g~F~   80 (180)
T COG1514           2 RLFIALDPPAEIAERLARIRARLKGARAIKWVEPENLHITLKFLGEVDEDKADELIEALARIAAPE-PFPITLDGAGSFP   80 (180)
T ss_pred             eeEEEecCCHHHHHHHHHHHHhcCcccccccccccCceEEEEccCCcCchHHHHHHHHHHHhhcCC-ceEEEEeeEcccC
Confidence            466777799999999999999998876   355679999999  99986 5677888888888777 9999999999865


Q ss_pred             --ceeeEEEEEeeCCccccchHHHHhhh---hCCC-CCCCCcceeEeeeCCCCHHHHHHHHHHHHhcc-cccCCccEEec
Q 029664           90 --FFYQCVFLLLHPTPEVAEPSSHCCGH---FGYK-SSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLD-ESIGSLSFPIT  162 (190)
Q Consensus        90 --~~~~vv~l~v~~~~~L~~L~~~l~~~---~g~~-~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~-~~~~~~~~~v~  162 (190)
                        .+++++|+++++++.|.+|++.+.+.   .|+. +.++|+|||||+|.+.. .   .+.+.+..+. ..+ + ++.|+
T Consensus        81 ~~~~~rvi~~~v~~~~~L~~L~~~l~~~~~~~g~~~~~r~F~PHvTl~r~k~~-~---~~~~~~~~~~~~~~-~-~~~vd  154 (180)
T COG1514          81 NPRRPRVIWVGVEETEELRALAEELERALARLGLRPEERPFVPHVTLARVKSK-D---KLVEALGEFKNVEF-G-EMEVD  154 (180)
T ss_pred             CCCCCcEEEEcCCCcHHHHHHHHHHHHHHHhcCCCCCCCCcCCCEEEEeeccc-c---hhhhhhhhhccccc-c-ceEee
Confidence              47899999999989999999999974   4664 78999999999998761 1   2222222211 111 2 67899


Q ss_pred             eEEEEEecCCCCCcCCceEeEEEcCCC
Q 029664          163 RLQLWKTDTEDTTLKSWEMVAECNLSP  189 (190)
Q Consensus       163 ~l~L~~s~~~~~~~~~w~~l~~~~L~~  189 (190)
                      +|.||+|..++ .|+.|+.+.+|+|.+
T Consensus       155 ~~~L~~S~l~~-~gp~Y~~~~~~~L~~  180 (180)
T COG1514         155 RFSLYSSTLTP-GGPIYETLKEFPLSG  180 (180)
T ss_pred             EEEEEEEeeCC-CCCEEEEEEEEecCC
Confidence            99999998876 589999999999975

>PRK15124 2'-5' RNA ligase; Provisional

Probab=99.94  E-value=3e-26  Score=175.83  Aligned_cols=159  Identities=16%  Similarity=0.232  Sum_probs=119.7

Q ss_pred             CCceEEEEEeCChhHHHHHHHHHHHHHhh---cCCCCCCCeEEee--cCCcCChhHHHHHHHHHhc--cCCceeEEEcee
Q 029664           13 KKGFYSVWAIPPDEVRARVKKLMEGLRSE---FGGPQFDPHVTVV--GAMSLTADDALEKFKSACN--GLKAYNCTVNRV   85 (190)
Q Consensus        13 ~~~~~slwl~P~~~~~~~l~~~~~~l~~~---~~~~~~~pHiTL~--g~~~~~~~~~~~~l~~~~~--~~~pf~l~~~~v   85 (190)
                      ++.+++|+  +|+++++.|.++++.+...   .+.++.+.||||+  |+++.   +.++.+.++++  ..+||+++++|+
T Consensus         5 ~RlFiAl~--~p~~~~~~l~~~~~~~~~~~~~rwv~~~nlHiTL~FlG~v~~---~~~~~l~~~l~~~~~~pF~l~l~~~   79 (176)
T PRK15124          5 KRLFFAID--LPDEIRQQIIHWRATHFPPEAGRPVAAANLHLTLAFLGEVSA---EKQQALSQLAGRIRQPGFTLTLDDA   79 (176)
T ss_pred             eEEEEEeC--CCHHHHHHHHHHHHHhccccCcccccccccEEEEEecCCCCH---HHHHHHHHHHHhcccCCeEEEECcc
Confidence            34455544  8889999999999887543   2345678999999  99863   34444444444  478999999999


Q ss_pred             eeccceeeEEEEEeeC-CccccchHHHHhhh---hCC-CCCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEE
Q 029664           86 ATGTFFYQCVFLLLHP-TPEVAEPSSHCCGH---FGY-KSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFP  160 (190)
Q Consensus        86 ~~~~~~~~vv~l~v~~-~~~L~~L~~~l~~~---~g~-~~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~  160 (190)
                      |+|+ .|++||+++++ .+.|.+||+++++.   +|+ .+.++|+|||||||......   .    +..  . .....|.
T Consensus        80 g~Fp-~prvlwlg~~~~~~~L~~L~~~l~~~l~~~G~~~e~r~f~PHiTLaR~~~~~~---~----~~~--~-~~~~~~~  148 (176)
T PRK15124         80 GQWP-RSRVVWLGMRQPPRGLLQLANMLRSQAARSGCYQSPQPFHPHITLLRDASRPV---A----IPP--P-GFNWSFP  148 (176)
T ss_pred             cCcC-CCCEEEEEcCCCCHHHHHHHHHHHHHHHHcCCCCCCCCCCCCEeeccCCCCcc---c----ccC--C-CCCCceE
Confidence            9976 58999999975 67999999999874   577 47899999999999643211   1    111  1 1133689


Q ss_pred             eceEEEEEecCCCCCcCCceEeEEEcCC
Q 029664          161 ITRLQLWKTDTEDTTLKSWEMVAECNLS  188 (190)
Q Consensus       161 v~~l~L~~s~~~~~~~~~w~~l~~~~L~  188 (190)
                      |++|.||+|...+ .|+.|+++++|+|.
T Consensus       149 v~~~~L~~S~l~~-~g~~Y~~l~~~~L~  175 (176)
T PRK15124        149 VTEFTLYASSFAR-GRTRYTPLQRWPLT  175 (176)
T ss_pred             cCEEEEEEEeccC-CCCEEEEEEEEeCC
Confidence            9999999998765 57899999999996

>PRK13679 hypothetical protein; Provisional

Probab=99.93  E-value=9.7e-25  Score=166.30  Aligned_cols=163  Identities=16%  Similarity=0.203  Sum_probs=126.5

Q ss_pred             eEEEEEeCChhHHHHHHHHHHHHHhhcCCCCCCCeEEee--cCCcC-ChhHHHHHHHHHhccCCceeEEEceeeecccee
Q 029664           16 FYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVV--GAMSL-TADDALEKFKSACNGLKAYNCTVNRVATGTFFY   92 (190)
Q Consensus        16 ~~slwl~P~~~~~~~l~~~~~~l~~~~~~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~~~~   92 (190)
                      .|+|.+.|+.++++.+.++++.+...  ...++|||||.  |+++. ..+++.+.+++++....||+++++++++++..+
T Consensus         2 ~~~iai~~p~~~~~~l~~~~~~~~~~--~~~v~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~F~~~~   79 (168)
T PRK13679          2 KYGIVLFPSKKIQDFANSYRKRYDPH--YALIPPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSSFAPTN   79 (168)
T ss_pred             eeEEEEcCCHHHHHHHHHHHHhhCcc--cccCCCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEeccccCCCCC
Confidence            67888889998888888888777543  23467899998  66754 456788888888888999999999999876556


Q ss_pred             eEEEEEeeCCccccchHHHHhhhh-CCCCCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEecC
Q 029664           93 QCVFLLLHPTPEVAEPSSHCCGHF-GYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDT  171 (190)
Q Consensus        93 ~vv~l~v~~~~~L~~L~~~l~~~~-g~~~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~  171 (190)
                      ++||++++++++|.+||+++++.+ +..+.++|+|||||||... .++...+.+.++..   -....|.|++|.||....
T Consensus        80 ~vl~l~~~~~~~L~~L~~~l~~~~~~~~~~~~f~PHiTlar~~~-~~~~~~~~~~l~~~---~~~~~~~v~~i~L~~~~~  155 (168)
T PRK13679         80 NVIYFKVEKTEELEELHERLHSGDFYGEAEYAFVPHITIGQGLS-DDEHEDVLGQLKMA---DVDHEETIDRFHLLYQLE  155 (168)
T ss_pred             CEEEEEccCCHHHHHHHHHHHhcccccccCCCCCCeEEeeCCCC-cHHHHHHHHHHhcC---CcceeEEECeEEEEEECC
Confidence            999999999899999999998743 3346788999999998643 34445555555431   223378999999996544


Q ss_pred             CCCCcCCceEeEEEcCC
Q 029664          172 EDTTLKSWEMVAECNLS  188 (190)
Q Consensus       172 ~~~~~~~w~~l~~~~L~  188 (190)
                      +    ..|+.+.+|.|+
T Consensus       156 ~----~~w~~~~~~~~~  168 (168)
T PRK13679        156 N----GSWTVYETFRLG  168 (168)
T ss_pred             C----CeEEEEEEeeCC
Confidence            3    499999999986

>TIGR02258 2_5_ligase 2'-5' RNA ligase

Probab=99.93  E-value=9e-25  Score=167.78  Aligned_cols=164  Identities=14%  Similarity=0.221  Sum_probs=122.6

Q ss_pred             ceEEEEEeCChhHHHHHHHHHHHHHhhc----CCCCCCCeEEee--cCCcC-ChhHHHHHHHHHhccCCceeEEEceeee
Q 029664           15 GFYSVWAIPPDEVRARVKKLMEGLRSEF----GGPQFDPHVTVV--GAMSL-TADDALEKFKSACNGLKAYNCTVNRVAT   87 (190)
Q Consensus        15 ~~~slwl~P~~~~~~~l~~~~~~l~~~~----~~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~   87 (190)
                      .+++|+  |+.++++.|.++++.++...    +.++.++||||.  |+++. ..+++.+.|.+++  .++|+++++|+|+
T Consensus         3 ~FiAl~--~p~~~~~~l~~~~~~l~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~--~~~f~l~l~~~~~   78 (179)
T TIGR02258         3 LFIAID--LPPEIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIA--EPPFTLKLEGIGV   78 (179)
T ss_pred             EEEEec--CCHHHHHHHHHHHHHhhccCCCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHhc--CCCeEEEEeeeee
Confidence            445555  88899999999999987432    234567899998  87763 3445666666654  3669999999998


Q ss_pred             ccc--eeeEEEEEeeCCccccchHHHHhhhh---CCC-CCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEe
Q 029664           88 GTF--FYQCVFLLLHPTPEVAEPSSHCCGHF---GYK-SSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPI  161 (190)
Q Consensus        88 ~~~--~~~vv~l~v~~~~~L~~L~~~l~~~~---g~~-~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v  161 (190)
                      ++.  .++++|++++.++.|.+|++.+.+.+   |+. +.++|+|||||||......   .+.+.+.... ...+..|.|
T Consensus        79 F~~~~~~~vl~l~~~~~~~L~~L~~~l~~~~~~~g~~~~~~~f~PHiTlar~~~~~~---~~~~~~~~~~-~~~~~~~~v  154 (179)
T TIGR02258        79 FGNPKRPRVLWAGVEQSEELTQLHADLERELAKLGFSKEERPFTPHITLARKKSGKP---GVPEFLQEFA-NEEFGSFHV  154 (179)
T ss_pred             CCCCCCCeEEEEeeCCCHHHHHHHHHHHHHHHHcCCCCCCCCcCCCEEEEEecCCcH---hHHHHHHHhC-CCCCCceEe
Confidence            643  47899999998889999999998753   553 6789999999999765432   2223333222 144679999


Q ss_pred             ceEEEEEecCCCCCcCCceEeEEEcC
Q 029664          162 TRLQLWKTDTEDTTLKSWEMVAECNL  187 (190)
Q Consensus       162 ~~l~L~~s~~~~~~~~~w~~l~~~~L  187 (190)
                      ++|.||+|.... .|+.|+++++|+|
T Consensus       155 ~~i~L~~S~~~~-~g~~Y~~l~~~~l  179 (179)
T TIGR02258       155 DEFHLYSSTLTP-GGPIYEPLARFQL  179 (179)
T ss_pred             eEEEEEEeeccC-CCCcceEEEEEcC
Confidence            999999987765 4789999999997

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.

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

Probab=99.81  E-value=2.3e-20  Score=139.10  Aligned_cols=143  Identities=22%  Similarity=0.397  Sum_probs=79.5

Q ss_pred             CChhHHHHHHHHHHHHHhhcC--CCCCCCeEEeecCCcC--ChhHHHHHHHHHhccCCceeEEEceeeeccceeeEEEEE
Q 029664           23 PPDEVRARVKKLMEGLRSEFG--GPQFDPHVTVVGAMSL--TADDALEKFKSACNGLKAYNCTVNRVATGTFFYQCVFLL   98 (190)
Q Consensus        23 P~~~~~~~l~~~~~~l~~~~~--~~~~~pHiTL~g~~~~--~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~~~~~vv~l~   98 (190)
                      ||+++.+++.++.   +..+.  ....+|||||.+....  ..+++.+.|..++.+.++|+++++++++++...++||+.
T Consensus         1 pp~~~~~~i~~lr---~~~~~~~~~~~~pHITL~~~~~~~~~~~~~~~~l~~~~~~~~~f~l~l~~~~~F~~~~~vi~l~   77 (153)
T PF13563_consen    1 PPDELAEEIEALR---RQKGDKRYPRWPPHITLAFPFDIDDSLDELVEALARLAAGFPPFELRLDGFGSFPGKGRVIFLN   77 (153)
T ss_dssp             ------------G---T-TTEEE--GGG-EEEEEEEEE--GGGHHHHHHHHHHHHHS--EEEEEEEEEEESSSSSSEEEE
T ss_pred             Ccccccccchhhh---cccCCCCCCCCCCEeEEEecCcccccHHHHHHHHHHHHccCCCeEEEEccEEEcCCCCCEEEEE
Confidence            5665666655554   12222  4556799999954443  337899999999999999999999999865445699999


Q ss_pred             eeCCccccchHHHHhhhhC---CC-CC-CCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEecCC
Q 029664           99 LHPTPEVAEPSSHCCGHFG---YK-SS-TPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTE  172 (190)
Q Consensus        99 v~~~~~L~~L~~~l~~~~g---~~-~~-~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~~  172 (190)
                      ++.++.|.+||+++.+.+.   .. +. ++|+|||||||....... ..+.+.+   .....+.+|.|++|.|++++..
T Consensus        78 ~~~~~~L~~L~~~l~~~~~~~~~~~~~~~~~~PHiTia~~~~~~~~-~~~~~~~---~~~~~~~~~~v~~l~L~~~~~~  152 (153)
T PF13563_consen   78 VEPSPELEALHRALREALRPFGFKQDSYRPFRPHITIARRLSPKQA-AEAIEKL---QSEFPPISFTVDELALVRSDGN  152 (153)
T ss_dssp             EEE-HHHHHHHHHHHHHHHHHHGGGGGGS----EEEEEEESS---------------------EEEEE-EEEEEEEE--
T ss_pred             cCCCHHHHHHHHHHHHHHHHcCCccccCCCcceEEEEeccCCcchh-HHHHHHH---hCcCCCcEEEEeEEEEEEECCc
Confidence            9999999999999998643   22 22 899999999997655332 3333333   2235567999999999997653

>PHA02574 57B hypothetical protein; Provisional

Probab=99.79  E-value=4.7e-19  Score=131.50  Aligned_cols=113  Identities=12%  Similarity=0.074  Sum_probs=90.0

Q ss_pred             eCCCCceEEEEEeCChhHHHHHHHHHHHHHhhcCCCCCCCeEEeecCCcCChhHHHHHHHHHhccCCceeEEEceeeecc
Q 029664           10 DKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGT   89 (190)
Q Consensus        10 ~~~~~~~~slwl~P~~~~~~~l~~~~~~l~~~~~~~~~~pHiTL~g~~~~~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~   89 (190)
                      ....+.+++||  ++++++++|.++++++......++.++|+||+-+     ++.++.+..   +.++|.++++|+|.++
T Consensus         6 ~~~~RlF~Al~--~~~~~r~~L~~lq~~l~~~r~V~~enLHlTL~F~-----~~~v~~l~~---~~~~F~l~l~glG~F~   75 (149)
T PHA02574          6 EFSQGTYVAAK--FSEATLDALERLQRTLRIPNPVPRDKLHSTIVYS-----RVYVPFIPA---SGSTEVASSGHLEVWE   75 (149)
T ss_pred             cccceEEEEEc--CCHHHHHHHHHHHHhccCCcccCHHHCEEEEecC-----HHHhHHHhc---cCCCeEEEeccccccC
Confidence            33567888888  8889999999999997553345677899999861     233333433   6799999999999975


Q ss_pred             c-eeeEEEEEeeCCccccchHHHHhhhhCCCCCCCCcceeEeeeC
Q 029664           90 F-FYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYG  133 (190)
Q Consensus        90 ~-~~~vv~l~v~~~~~L~~L~~~l~~~~g~~~~~~f~PHlTLar~  133 (190)
                      . .+|+||++++ +++|.+|++++++.+.-.+.++|+|||||+|.
T Consensus        76 ~~~~rvlWlg~~-~~~L~~L~~~l~~~l~~~~~r~F~PHITLaR~  119 (149)
T PHA02574         76 TQDKNALVLVLE-SEYLQCRHKYARALGATHDFDDYTPHITLSYD  119 (149)
T ss_pred             CCCCCEEEEEeC-CHHHHHHHHHHHHHhhcCCCCCcCCcEEEeec
Confidence            3 5899999998 99999999999997544556789999999994

>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=99.39  E-value=2.2e-11  Score=95.75  Aligned_cols=170  Identities=15%  Similarity=0.161  Sum_probs=109.6

Q ss_pred             EEEEEeC-ChhHHHHHHHHHHHHHhhcC-------CCCCCCeEEee--cCCcC-ChhHHHHHHHHH---hcc----CCce
Q 029664           17 YSVWAIP-PDEVRARVKKLMEGLRSEFG-------GPQFDPHVTVV--GAMSL-TADDALEKFKSA---CNG----LKAY   78 (190)
Q Consensus        17 ~slwl~P-~~~~~~~l~~~~~~l~~~~~-------~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~---~~~----~~pf   78 (190)
                      |.|.+.- .+++.+.+.++++.+.....       .++..+||||.  +-.+. ..+...+.|+.+   +..    ..++
T Consensus         3 hFl~ipl~~~~i~~~~~~fq~~v~~~~~~~~~~~~i~~~~lHlTL~vl~L~~~~~i~~a~~~L~~~~~~i~~~~~~~~~~   82 (209)
T PF10469_consen    3 HFLCIPLNSPEIQEKFKEFQNEVLSKDPGLDESAFIPPEKLHLTLGVLSLDTDEEIEKAKEALKSLKQEIKDQLQNPPPL   82 (209)
T ss_pred             eEEEEECCCHHHHHHHHHHHHHHHhhcCCCCHHHcCCcccceEEEEEeeCCCHHHHHHHHHHHHHHHHHHhhhccCCCCc
Confidence            5555544 36788999999998876543       23457899998  22221 233344444433   222    4999


Q ss_pred             eEEEceeeecc---ceeeEEEEEeeC---CccccchHHHHhhhh---CCC---CCC-CCcceeEeeeCCCC--HHHH--H
Q 029664           79 NCTVNRVATGT---FFYQCVFLLLHP---TPEVAEPSSHCCGHF---GYK---SST-PYMPHLSLLYGDLT--DDEK--K  141 (190)
Q Consensus        79 ~l~~~~v~~~~---~~~~vv~l~v~~---~~~L~~L~~~l~~~~---g~~---~~~-~f~PHlTLar~~~~--~~~~--~  141 (190)
                      .+++.|++++.   ...+|+|+++++   ...|.++.+.+.+.|   |+.   +.+ +|.||+||++....  ...+  .
T Consensus        83 ~i~l~Gl~~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~~~~~~H~Tl~n~~~~~~~~~~~~~  162 (209)
T PF10469_consen   83 KITLKGLGYFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDDRRFSFKPHITLMNTSYRKKKKRRQGN  162 (209)
T ss_pred             eEEeeechhhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccccCCCcceEEEEEeccccccccccccC
Confidence            99999999832   245999999986   378999999998754   653   234 38999999996541  0010  1


Q ss_pred             --HHHHHHHhcccccCCccEEeceEEEEEecCCCCCcCCceEeEEEcC
Q 029664          142 --IAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNL  187 (190)
Q Consensus       142 --~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~~~~~~~~w~~l~~~~L  187 (190)
                        ...+.++.+.. ...+.+.|++|+|.+....+....-|..+++++|
T Consensus       163 ~~d~~~~~~~~~~-~~fG~~~v~~i~Lc~m~~~~~~dg~Y~~~~~i~l  209 (209)
T PF10469_consen  163 KFDASELLEKYKD-FDFGEQPVEEIQLCSMGSTKPSDGYYQCIASIPL  209 (209)
T ss_pred             ccccHHHHHHcCC-CccceEEECEEEEEeCCCCCCCCCeEEEEEEecC
Confidence              11223333322 3335789999999885222223679999999987

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.

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

Probab=99.04  E-value=5.7e-10  Score=75.58  Aligned_cols=75  Identities=19%  Similarity=0.358  Sum_probs=59.6

Q ss_pred             eCChhHHHHHHHHHHHHHhhcC------CCCCCCeEEee--cCCcC-ChhHHHHHHHHHhccCCceeEEEceeeeccc--
Q 029664           22 IPPDEVRARVKKLMEGLRSEFG------GPQFDPHVTVV--GAMSL-TADDALEKFKSACNGLKAYNCTVNRVATGTF--   90 (190)
Q Consensus        22 ~P~~~~~~~l~~~~~~l~~~~~------~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~~--   90 (190)
                      .|+++++++|.++++.++....      ..++++||||.  |+++. ..+++.+.+..++....+|++++++++.+++  
T Consensus         2 ~~p~~~~~~L~~l~~~l~~~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~f~~~~~~~~~f~s~~   81 (87)
T PF02834_consen    2 DLPEEIKEQLNQLQERLRQALPPLGIRWVRPFNPHITLAFLGEVPPDQLPELIEALANIASRFPPFTLTVDGFGLFPSRL   81 (87)
T ss_dssp             E-THHHHHHHHHHHHHHHHHCCSCTEEEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHCCCB-EEEEEEEEEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHHHhhhccccCCcccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhccCCCeEEEEeEEEEeCCCC
Confidence            3788899999999999995542      35789999999  88863 4566788888888899999999999997543  


Q ss_pred             eeeEEE
Q 029664           91 FYQCVF   96 (190)
Q Consensus        91 ~~~vv~   96 (190)
                      .++++|
T Consensus        82 ~~rvi~   87 (87)
T PF02834_consen   82 RPRVIW   87 (87)
T ss_dssp             TCEEEE
T ss_pred             CCCCcC
Confidence            678888

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.

>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein

Probab=98.76  E-value=1.7e-07  Score=74.13  Aligned_cols=134  Identities=13%  Similarity=0.232  Sum_probs=94.0

Q ss_pred             CCCeEEeecCCcC----ChhHHHHHHHHHhccCCceeEE---EceeeeccceeeEEEEEeeCCccccchHHHHhhhhC-C
Q 029664           47 FDPHVTVVGAMSL----TADDALEKFKSACNGLKAYNCT---VNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFG-Y  118 (190)
Q Consensus        47 ~~pHiTL~g~~~~----~~~~~~~~l~~~~~~~~pf~l~---~~~v~~~~~~~~vv~l~v~~~~~L~~L~~~l~~~~g-~  118 (190)
                      .-.|+||+-+|..    +.+++.++++..+....||++.   +..+|.  +   .-+..+.++++|.+|+.++.+.|. +
T Consensus        56 YGfHaTLKaPFrLa~g~~~a~L~~al~~fA~~~~pf~i~~L~l~~Lg~--F---lAL~P~~~~~~L~~LAa~~V~~~d~f  130 (228)
T TIGR03223        56 YGFHATLKAPFRLAPGVTEAELLAAVAAFAATRAPFALPPLRVALLGG--F---LALRPAAPCPALQALAAACVRELDPF  130 (228)
T ss_pred             cccceeecCCcccCCCCCHHHHHHHHHHHHhcCCCccCCcceeeeeCC--E---EEEeeCCCCHHHHHHHHHHHHhhhhc
Confidence            4579999988864    4678999999999999999865   333332  1   112234568999999999987542 1


Q ss_pred             ----C---------------------------CCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEE
Q 029664          119 ----K---------------------------SSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLW  167 (190)
Q Consensus       119 ----~---------------------------~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~  167 (190)
                          .                           --..|+-||||-- .+.......+.+.+...-..+.+..+.|+.|.|+
T Consensus       131 RAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~deFrFHmTLTg-~l~~~~~~~~~~~l~~~~~~~l~~p~~id~laLf  209 (228)
T TIGR03223       131 RAPLTEAELARRRPDQLTPRQRALLERWGYPYVLEEFRFHMTLTG-RLDEEERAAVLARLEARFAPLLADPLAVDGLALF  209 (228)
T ss_pred             cCCCCHHHHhhcCccCCCHHHHHHHHHcCCCceecceEEEEEecC-CCChHHHHHHHHHHHHHhhhccCCCeeeeeEEEE
Confidence                0                           1247999999984 4555555555555554322344568999999999


Q ss_pred             EecCCCCCcCCceEeEEEcCCC
Q 029664          168 KTDTEDTTLKSWEMVAECNLSP  189 (190)
Q Consensus       168 ~s~~~~~~~~~w~~l~~~~L~~  189 (190)
                      .-..   .|.....+..++|++
T Consensus       210 ~e~~---~g~pF~~~~~~~l~~  228 (228)
T TIGR03223       210 VEPE---PGAPFRLIARVALAG  228 (228)
T ss_pred             eccC---CCCCcEEEEeecCCC
Confidence            6444   356799999999975

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.

>PLN00108 unknown protein; Provisional

Probab=98.73  E-value=9.7e-07  Score=70.96  Aligned_cols=175  Identities=11%  Similarity=0.058  Sum_probs=106.7

Q ss_pred             CCceEEEEEeC--ChhHHHHHHHHHHHHHhh--------------cC------CCCCCCeEEee-cCCcC--ChhHHHHH
Q 029664           13 KKGFYSVWAIP--PDEVRARVKKLMEGLRSE--------------FG------GPQFDPHVTVV-GAMSL--TADDALEK   67 (190)
Q Consensus        13 ~~~~~slwl~P--~~~~~~~l~~~~~~l~~~--------------~~------~~~~~pHiTL~-g~~~~--~~~~~~~~   67 (190)
                      .+..|.|.+..  .+++.+.+.++++.+-..              ++      ..+..+||||. -.+..  ..+...+.
T Consensus        34 ~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~~~~~~f~~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~  113 (257)
T PLN00108         34 EVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDKDPLKFQSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNI  113 (257)
T ss_pred             CCCCeEEEEEcCCCHHHHHHHHHHHHHHHhccccccccccccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHH
Confidence            34566777666  378999999988886542              11      12346899997 22221  12222222


Q ss_pred             HHHH---hc---cCCceeEEEceeeec---cceeeEEEEEeeCC---ccccchHHHHhhhh---CCC--C-CCCCcceeE
Q 029664           68 FKSA---CN---GLKAYNCTVNRVATG---TFFYQCVFLLLHPT---PEVAEPSSHCCGHF---GYK--S-STPYMPHLS  129 (190)
Q Consensus        68 l~~~---~~---~~~pf~l~~~~v~~~---~~~~~vv~l~v~~~---~~L~~L~~~l~~~~---g~~--~-~~~f~PHlT  129 (190)
                      |++.   +.   +.+|+.+++.|++..   +..-+|||+.|+..   +.|..+.+.+.+.|   |+.  + .+++.+|+|
T Consensus       114 L~s~~~~i~~~l~~~pl~I~lkGL~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~d~~~~vKLH~T  193 (257)
T PLN00108        114 LKSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKDAKSRLKLHAT  193 (257)
T ss_pred             HHHHHHHHHHhhCCCCeEEEEEeehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCcccccCcceeeEeE
Confidence            3222   21   359999999999983   22358999999863   56777777887754   763  3 368999999


Q ss_pred             eeeCCCCHH---HHH--HHHHHHHhcccccCCccEEeceEEEEEecCCCCCcCCceEeEEEcCCC
Q 029664          130 LLYGDLTDD---EKK--IAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSP  189 (190)
Q Consensus       130 Lar~~~~~~---~~~--~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~~~~~~~~w~~l~~~~L~~  189 (190)
                      |........   .+.  .+-+.++.+.. ...+.+.|++++|-+....+ .-.=|+..++++|.+
T Consensus       194 lmNt~~rk~k~~k~~sFDA~~Il~~f~d-~~FG~~~i~~vhls~r~s~~-~dGyY~~~~sl~~~~  256 (257)
T PLN00108        194 LMNASYRKDKSKKMDTFDAREIHKEFEN-KDWGTYLIREAHISQRYKYD-PNGYFHCCASLPFPH  256 (257)
T ss_pred             EechhhhhcccCccccccHHHHHHhccC-cccceEEecEEEEEeecccC-CCCCEEEEEEeecCC
Confidence            997521110   000  11123443322 33468899999995422122 234899999999864

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

Probab=98.38  E-value=2.3e-07  Score=62.70  Aligned_cols=76  Identities=12%  Similarity=0.293  Sum_probs=53.5

Q ss_pred             CccccchHHHHhhh---hCCCCCCCCcceeEeeeC-CCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEecCCCCCcC
Q 029664          102 TPEVAEPSSHCCGH---FGYKSSTPYMPHLSLLYG-DLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLK  177 (190)
Q Consensus       102 ~~~L~~L~~~l~~~---~g~~~~~~f~PHlTLar~-~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~~~~~~~  177 (190)
                      .+.|.+|++.+.+.   +|+...++|.|||||++. +...+....+.+.++.......+.+++++++.+|.+...  ++.
T Consensus         8 ~~~L~~l~~~l~~~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~~~~~f~~~~~~~~~f~s~~~--~rv   85 (87)
T PF02834_consen    8 KEQLNQLQERLRQALPPLGIRWVRPFNPHITLAFLGEVPPDQLPELIEALANIASRFPPFTLTVDGFGLFPSRLR--PRV   85 (87)
T ss_dssp             HHHHHHHHHHHHHHCCSCTEEEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHCCCB-EEEEEEEEEEEEEEET--CEE
T ss_pred             HHHHHHHHHHHhhhccccCCcccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhccCCCeEEEEeEEEEeCCCCC--CCC
Confidence            36789999999854   355444899999999994 445555666666666543335566899999999998764  344


Q ss_pred             Cc
Q 029664          178 SW  179 (190)
Q Consensus       178 ~w  179 (190)
                      .|
T Consensus        86 i~   87 (87)
T PF02834_consen   86 IW   87 (87)
T ss_dssp             EE
T ss_pred             cC
Confidence            55

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.

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

Probab=98.07  E-value=0.0004  Score=55.81  Aligned_cols=117  Identities=14%  Similarity=0.179  Sum_probs=80.9

Q ss_pred             EEEeCChhHHHHHHHHHHHHHhhcC--------------CCCCCCeEEeecCCcC---ChhHHHHHHHHHh--ccCCcee
Q 029664           19 VWAIPPDEVRARVKKLMEGLRSEFG--------------GPQFDPHVTVVGAMSL---TADDALEKFKSAC--NGLKAYN   79 (190)
Q Consensus        19 lwl~P~~~~~~~l~~~~~~l~~~~~--------------~~~~~pHiTL~g~~~~---~~~~~~~~l~~~~--~~~~pf~   79 (190)
                      |=..|+.+..+.|..+++.+.+...              +.+.++||+|.-.+..   ..+...+.|++.+  ....+|.
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            3334556677788888888776543              1235799999977765   3566888999999  7999999


Q ss_pred             EEEceeee--ccceeeEEEEE--eeC-Ccc-ccchHHHHhhh---hCCCC-C-CCCcceeEeeeCCCC
Q 029664           80 CTVNRVAT--GTFFYQCVFLL--LHP-TPE-VAEPSSHCCGH---FGYKS-S-TPYMPHLSLLYGDLT  136 (190)
Q Consensus        80 l~~~~v~~--~~~~~~vv~l~--v~~-~~~-L~~L~~~l~~~---~g~~~-~-~~f~PHlTLar~~~~  136 (190)
                      +.++++..  +....| .|++  |.. ... |..|-+.+.+.   +|... . .+..||||||.....
T Consensus       126 v~f~~~~~~~N~e~TR-~FL~l~V~~~~~~~l~~l~~~i~~~l~~~~lp~~Y~~~~~fHvSIAw~~~~  192 (239)
T PF09749_consen  126 VSFSGLDVYTNDEKTR-SFLALRVSEGSNNELKRLLDRINEVLKEFGLPPFYDEDPSFHVSIAWTLGD  192 (239)
T ss_pred             EEeCceEEEecCCCCe-EEEEEEecccccHHHHHHHHHHHHHHHHhCCCcccCCCCCCEEEEEEECCC
Confidence            99999886  322333 3333  333 233 88888888764   56643 3 578999999996444

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

>PHA02977 hypothetical protein; Provisional

Probab=97.80  E-value=0.00048  Score=50.58  Aligned_cols=57  Identities=25%  Similarity=0.350  Sum_probs=42.9

Q ss_pred             eEEEEEeeCCccccchHHHHhhh-------hCC-CCCCCCcceeEeeeCCCCHH-HHHHHHHHHHh
Q 029664           93 QCVFLLLHPTPEVAEPSSHCCGH-------FGY-KSSTPYMPHLSLLYGDLTDD-EKKIAQEKAHK  149 (190)
Q Consensus        93 ~vv~l~v~~~~~L~~L~~~l~~~-------~g~-~~~~~f~PHlTLar~~~~~~-~~~~~~~~l~~  149 (190)
                      +.+.+.++.++.|.+|+..+-++       ||- ....+|.||||++|....++ .+.++.+.++.
T Consensus       124 ~avvmkle~sddlkalrnvl~n~vp~pkdifg~i~~d~~w~phitigyv~~dd~dnk~r~ie~~~~  189 (201)
T PHA02977        124 CAVVMKLEASDDLKALRNVLFNAVPCPKDIFGDILSDNPWCPHITIGYVKADDEDNKKRFIECAEA  189 (201)
T ss_pred             cEEEEEEEechHHHHHHHHhhcccCCcHHhhcccccCCCCCCceEEEeecccchhhHHHHHHHHHH
Confidence            56888888899999999999774       342 24679999999999755543 55677666654

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

Probab=97.60  E-value=0.001  Score=50.02  Aligned_cols=113  Identities=17%  Similarity=0.278  Sum_probs=74.5

Q ss_pred             EeecCCcC----ChhHHHHHHHHHhccCCceeEE---EceeeeccceeeEEEEEe-eCCccccchHHHHhhhhC-C----
Q 029664           52 TVVGAMSL----TADDALEKFKSACNGLKAYNCT---VNRVATGTFFYQCVFLLL-HPTPEVAEPSSHCCGHFG-Y----  118 (190)
Q Consensus        52 TL~g~~~~----~~~~~~~~l~~~~~~~~pf~l~---~~~v~~~~~~~~vv~l~v-~~~~~L~~L~~~l~~~~g-~----  118 (190)
                      ||+-++..    +.+++..++...+....||.+.   +..+|.  +    +-+.. .++++|.+|+..+.+.|. +    
T Consensus         1 TLKaPF~La~g~~~~~L~~a~~~~a~~~~pf~l~~L~v~~lg~--F----lALvp~~~~~~L~~LAa~cV~~~d~fRAPl   74 (160)
T PF06299_consen    1 TLKAPFRLAEGASEADLLAALAAFAARFAPFELPGLEVARLGG--F----LALVPAGPCPALQALAAACVRAFDPFRAPL   74 (160)
T ss_pred             CCCCCcccCCCCCHHHHHHHHHHHhccCCCccCCceeEeeECC--E----EEEeeCCCCHHHHHHHHHHHHhhhhccCCC
Confidence            56655543    4578999999999999998744   455442  1    22222 347899999999876431 1    


Q ss_pred             --------------------------C-CCCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEecC
Q 029664          119 --------------------------K-SSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDT  171 (190)
Q Consensus       119 --------------------------~-~~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s~~  171 (190)
                                                . --..|+.||||-.. +...+...+.+.+...-..+....+.|+++.|+.-..
T Consensus        75 s~aelaRR~~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg~-l~~~~~~~~~~~l~~~f~~~l~~p~~id~laLf~e~~  153 (160)
T PF06299_consen   75 SEAELARRRPAGLSPRQRANLERWGYPYVMDEFRFHMTLTGR-LDPAERARVEAALEAHFAPLLPEPLRIDSLALFGEPE  153 (160)
T ss_pred             ChHHHhhcCcccCCHHHHHHHHHhCCCceeCcCEeeEEeCCC-CCHHHHHHHHHHHHHHHHhhcCCCeeecceEEEeccC
Confidence                                      0 12589999999854 5555566666666553233445688999999996443

The function of this family is unknown.

>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=96.87  E-value=0.003  Score=49.35  Aligned_cols=102  Identities=17%  Similarity=0.176  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHHHHhh-cCCC-CCCCeEEee-cCCc-CChhHHHHHHHHHhccC--CceeEEEceeeeccceeeEEEEEee
Q 029664           27 VRARVKKLMEGLRSE-FGGP-QFDPHVTVV-GAMS-LTADDALEKFKSACNGL--KAYNCTVNRVATGTFFYQCVFLLLH  100 (190)
Q Consensus        27 ~~~~l~~~~~~l~~~-~~~~-~~~pHiTL~-g~~~-~~~~~~~~~l~~~~~~~--~pf~l~~~~v~~~~~~~~vv~l~v~  100 (190)
                      .-....+++.++-+. ++.. --.|||||. =.+. ....+|...|+++.+..  .-..+++++---   --+++-+.| 
T Consensus        20 f~~~~~~LQ~~~~~eG~d~k~QkaPHlSl~mL~Isd~~i~~V~~~iq~ViddM~~~~~~it~tnp~M---Lg~~yV~nV-   95 (248)
T PF05213_consen   20 FMLNFKDLQFQLLEEGVDCKLQKAPHLSLGMLDISDEDIPDVETAIQKVIDDMVWFEGDITFTNPHM---LGRCYVANV-   95 (248)
T ss_pred             HHHHHHHHHHHHHHcCCCccccccCeeEEEEEEcChhhhhhHHHHHHHHHHHhhcccceEEecCcee---eccEEEEec-
Confidence            334556666665433 3332 246999997 2232 23556776777777654  333555554321   114444444 


Q ss_pred             CCccccchHHHHhhhh---CC--CCCCCCcceeEeeeCC
Q 029664          101 PTPEVAEPSSHCCGHF---GY--KSSTPYMPHLSLLYGD  134 (190)
Q Consensus       101 ~~~~L~~L~~~l~~~~---g~--~~~~~f~PHlTLar~~  134 (190)
                        ..+.+||..+.+.+   |.  ...|.|.||+||+...
T Consensus        96 --~Gv~slh~ki~n~~~~kgit~gQSRmwIPHiTia~~~  132 (248)
T PF05213_consen   96 --KGVLSLHDKIVNVFRKKGITFGQSRMWIPHITIAQLN  132 (248)
T ss_pred             --ccHHHHHHHHHHHHHHhCcCcCcccccccceehhhhh
Confidence              67889999998743   33  4589999999999964

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.

>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.39  E-value=0.068  Score=41.61  Aligned_cols=116  Identities=16%  Similarity=0.149  Sum_probs=70.7

Q ss_pred             CceEEEEEeCCh-hHHHHHHHHHHHHHhhc-----C-CCCCCCeEEee-cCCcC---------------ChhHHHHHHHH
Q 029664           14 KGFYSVWAIPPD-EVRARVKKLMEGLRSEF-----G-GPQFDPHVTVV-GAMSL---------------TADDALEKFKS   70 (190)
Q Consensus        14 ~~~~slwl~P~~-~~~~~l~~~~~~l~~~~-----~-~~~~~pHiTL~-g~~~~---------------~~~~~~~~l~~   70 (190)
                      +.+.=++=++.. +..+.+-.+.+++...-     . .|....|+|+. |-++.               ..+++.+...+
T Consensus        40 pGNTVVchl~~gs~t~~vvl~i~~r~~~mpfadklt~tP~sSlHMTvfqg~~e~~R~~~~WpqdlPLDtpi~~~~~~~~e  119 (239)
T COG5255          40 PGNTVVCHLVTGSDTEEVVLIIRSRYLEMPFADKLTFTPVSSLHMTVFQGLIEERRELPYWPQDLPLDTPIDAITDYYAE  119 (239)
T ss_pred             CCCeEEEeccCCCchHHHHHHHHHHhhccchhhhhccCCcchhhHHHHHHHhhhcccCCCCCccCCCCCcHHHHHHHHHH
Confidence            344555555553 45666777777766431     1 34556899998 43321               12344444455


Q ss_pred             HhccC----CceeEEEceeeeccceeeEEEEEeeC--CccccchHHHHhhhhCC--CCCCCCcceeEeeeC
Q 029664           71 ACNGL----KAYNCTVNRVATGTFFYQCVFLLLHP--TPEVAEPSSHCCGHFGY--KSSTPYMPHLSLLYG  133 (190)
Q Consensus        71 ~~~~~----~pf~l~~~~v~~~~~~~~vv~l~v~~--~~~L~~L~~~l~~~~g~--~~~~~f~PHlTLar~  133 (190)
                      .++.+    .+|.+++.+++    .-.++..++.+  ...|.++++.+...||+  .+...|.=||||+|.
T Consensus       120 rLk~F~l~~~~~~mrvte~r----p~~i~v~paddad~~~l~~~Rd~ls~~~g~r~P~HDaY~FHITlgYl  186 (239)
T COG5255         120 RLKIFPLLDEEFNMRVTEMR----PQGILVEPADDADAKILEEWRDYLSEKFGYRHPDHDAYQFHITLGYL  186 (239)
T ss_pred             HHhcccCCchhhcchhhccc----ccceEeccCCHHHHHHHHHHHHHHhhhhcccCCCCcceEEEEEeeeE
Confidence            44433    25666666654    12334444433  35688999999888887  467789999999995

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

Probab=93.98  E-value=1.5  Score=35.70  Aligned_cols=113  Identities=14%  Similarity=0.272  Sum_probs=57.7

Q ss_pred             CCceEEEEEeCChhHHHHHHHHHHH--------HHhhcCCCC--CCCeEEee--cCCcCCh-hHHHHHHHHHhc----c-
Q 029664           13 KKGFYSVWAIPPDEVRARVKKLMEG--------LRSEFGGPQ--FDPHVTVV--GAMSLTA-DDALEKFKSACN----G-   74 (190)
Q Consensus        13 ~~~~~slwl~P~~~~~~~l~~~~~~--------l~~~~~~~~--~~pHiTL~--g~~~~~~-~~~~~~l~~~~~----~-   74 (190)
                      .+..||+-+ |..++...|..+...        +.......+  -.+||||.  ......+ .++.+.......    . 
T Consensus        71 ~p~Yf~i~i-~~~~i~~~l~~~f~~~~~~~~~~~~~L~~~~RvQ~~FHVTL~H~as~k~~~~k~lW~~y~~~~~~~~~~~  149 (257)
T PF08302_consen   71 KPEYFGISI-PTQDIKSLLEKLFEDSPPETARFYNQLKNSRRVQPEFHVTLIHRASSKEQPAKELWKRYTKLYKSALKKN  149 (257)
T ss_pred             CCeEEEEEC-CHHHHHHHHHHHhccCCHHHHHHHHHHHhCCCCCCCCeEEEEecccCCcCcchHHHHHHHHHHHhhcccc
Confidence            346677765 666777777666643        222222222  25899999  2222222 244444433322    1 


Q ss_pred             ----------CCceeEEEceeeeccceeeEEEEEeeCCccccchHHHHhhhhCCCCCCCCcceeEeeeCC
Q 029664           75 ----------LKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGD  134 (190)
Q Consensus        75 ----------~~pf~l~~~~v~~~~~~~~vv~l~v~~~~~L~~L~~~l~~~~g~~~~~~f~PHlTLar~~  134 (190)
                                ...+++++.++.+   ..|++-+.|+-.+.-..-..    .-++. -..=.||||++-.+
T Consensus       150 ~~~~~~~~~~~~~~~v~L~rlvw---d~rimai~V~~~~~~~~~~~----~~~~~-c~N~~~HITVGT~~  211 (257)
T PF08302_consen  150 PKQEPTQTPTLGSCDVRLERLVW---DDRIMAIVVRIVPPEDEEDE----VPEWE-CTNKIPHITVGTRD  211 (257)
T ss_pred             cccccccccccceEEEEEEEEEE---CCcEEEEEEEccCccccccc----cCCcc-cCCCCCEEEEEcCC
Confidence                      2458899988884   33566666553211000000    11222 23458999999853

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

>PRK13679 hypothetical protein; Provisional

Probab=93.61  E-value=0.18  Score=38.10  Aligned_cols=71  Identities=11%  Similarity=0.230  Sum_probs=40.6

Q ss_pred             EEEEeeCCccccchHHHHhhhhCCCCCCCCcceeEeee-CCCCHHHHHHHHHHHHhcccccCCccEEeceEEE
Q 029664           95 VFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLY-GDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQL  166 (190)
Q Consensus        95 v~l~v~~~~~L~~L~~~l~~~~g~~~~~~f~PHlTLar-~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L  166 (190)
                      ..+++...+.+.+.-+++++.++.. .+...|||||.. ++...+..+.+.+.+........+.+..++.+.-
T Consensus         3 ~~iai~~p~~~~~~l~~~~~~~~~~-~~~v~pHITL~f~g~~~~~~~~~l~~~l~~~~~~~~pf~l~l~~~~~   74 (168)
T PRK13679          3 YGIVLFPSKKIQDFANSYRKRYDPH-YALIPPHITLKEPFEISDEQLDSIVEELRAIASETKPFTLHVTKVSS   74 (168)
T ss_pred             eEEEEcCCHHHHHHHHHHHHhhCcc-cccCCCceEEecCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEecccc
Confidence            3566766666666666666655432 345678999997 4555555555666555432223334445544433

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

Probab=91.27  E-value=0.27  Score=37.07  Aligned_cols=41  Identities=15%  Similarity=0.190  Sum_probs=29.3

Q ss_pred             CCCeEEeecCCcC-ChhHHHHHHHHHhccCCceeEEEceeee
Q 029664           47 FDPHVTVVGAMSL-TADDALEKFKSACNGLKAYNCTVNRVAT   87 (190)
Q Consensus        47 ~~pHiTL~g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~   87 (190)
                      |..|+||.|.++. ..+.+...++.......+=.+.++++.-
T Consensus       107 FRFHmTLTg~l~~~~~~~~~~~l~~~f~~~l~~p~~id~laL  148 (160)
T PF06299_consen  107 FRFHMTLTGRLDPAERARVEAALEAHFAPLLPEPLRIDSLAL  148 (160)
T ss_pred             CEeeEEeCCCCCHHHHHHHHHHHHHHHHhhcCCCeeecceEE
Confidence            6789999999964 2444667777766666556677788773

The function of this family is unknown.

>PHA02574 57B hypothetical protein; Provisional

Probab=90.46  E-value=0.69  Score=34.49  Aligned_cols=35  Identities=11%  Similarity=0.117  Sum_probs=22.0

Q ss_pred             EEEEEeCChhHHHHHHHHHHHHHhh---cCCCCCCCeEEee
Q 029664           17 YSVWAIPPDEVRARVKKLMEGLRSE---FGGPQFDPHVTVV   54 (190)
Q Consensus        17 ~slwl~P~~~~~~~l~~~~~~l~~~---~~~~~~~pHiTL~   54 (190)
                      -.+|+-+.   .+.|..+.+.++..   .+..+|.|||||.
T Consensus        80 rvlWlg~~---~~~L~~L~~~l~~~l~~~~~r~F~PHITLa  117 (149)
T PHA02574         80 NALVLVLE---SEYLQCRHKYARALGATHDFDDYTPHITLS  117 (149)
T ss_pred             CEEEEEeC---CHHHHHHHHHHHHHhhcCCCCCcCCcEEEe
Confidence            45887775   23344444444433   4456799999999

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

Probab=90.19  E-value=1.2  Score=34.23  Aligned_cols=74  Identities=18%  Similarity=0.324  Sum_probs=45.9

Q ss_pred             EEEEeeCCccccchHHHHhhhhC----CCCCCCCcceeEeee-CCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEe
Q 029664           95 VFLLLHPTPEVAEPSSHCCGHFG----YKSSTPYMPHLSLLY-GDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKT  169 (190)
Q Consensus        95 v~l~v~~~~~L~~L~~~l~~~~g----~~~~~~f~PHlTLar-~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s  169 (190)
                      +++++..++++.+.-.++.+.+.    ..-..+-.+||||.. ++......+.+.+.+......+ +...+++.+..|..
T Consensus         3 lFiAl~~p~~i~~~i~~~~~~~~~~~~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i~~~~-~f~i~l~g~g~F~~   81 (180)
T COG1514           3 LFIALDPPAEIAERLARIRARLKGARAIKWVEPENLHITLKFLGEVDEDKADELIEALARIAAPE-PFPITLDGAGSFPN   81 (180)
T ss_pred             eEEEecCCHHHHHHHHHHHHhcCcccccccccccCceEEEEccCCcCchHHHHHHHHHHHhhcCC-ceEEEEeeEcccCC
Confidence            56777776655555444444322    123567889999998 5666555566666666544333 56777777777753

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

Probab=87.20  E-value=0.34  Score=35.25  Aligned_cols=49  Identities=14%  Similarity=0.209  Sum_probs=23.6

Q ss_pred             CCCCcceeEeeeCCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEEe
Q 029664          121 STPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKT  169 (190)
Q Consensus       121 ~~~f~PHlTLar~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~s  169 (190)
                      .....|||||.+........+.+.+.+...-....+....++.+..+..
T Consensus        21 ~~~~~pHITL~~~~~~~~~~~~~~~~l~~~~~~~~~f~l~l~~~~~F~~   69 (153)
T PF13563_consen   21 YPRWPPHITLAFPFDIDDSLDELVEALARLAAGFPPFELRLDGFGSFPG   69 (153)
T ss_dssp             --GGG-EEEEEEEEE--GGGHHHHHHHHHHHHHS--EEEEEEEEEEESS
T ss_pred             CCCCCCEeEEEecCcccccHHHHHHHHHHHHccCCCeEEEEccEEEcCC
Confidence            3455699999985333221123333333322234556778888888754

>TIGR02258 2_5_ligase 2'-5' RNA ligase

Probab=87.04  E-value=3.1  Score=31.34  Aligned_cols=72  Identities=14%  Similarity=0.379  Sum_probs=36.3

Q ss_pred             EEEEeeCCccccchHHHHhhhhC-CCCCCCCcc----eeEeee-CCCCHHHHHHHHHHHHhcccccCCccEEeceEEEEE
Q 029664           95 VFLLLHPTPEVAEPSSHCCGHFG-YKSSTPYMP----HLSLLY-GDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWK  168 (190)
Q Consensus        95 v~l~v~~~~~L~~L~~~l~~~~g-~~~~~~f~P----HlTLar-~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~L~~  168 (190)
                      +|+++...+++.+.-.++.+.+. ......+.|    ||||+. ++......+.+.+.+....  ..+.++.++.+..|.
T Consensus         3 ~FiAl~~p~~~~~~l~~~~~~l~~~~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~--~~~f~l~l~~~~~F~   80 (179)
T TIGR02258         3 LFIAIDLPPEIREQLSRIQRKLKSPLDGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIA--EPPFTLKLEGIGVFG   80 (179)
T ss_pred             EEEEecCCHHHHHHHHHHHHHhhccCCCcEECChHHCEEEEEEccCCCHHHHHHHHHHHHHhc--CCCeEEEEeeeeeCC
Confidence            56777654433333333333222 111223333    999986 4555555555655555432  223466677776664

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=86.66  E-value=0.71  Score=35.91  Aligned_cols=39  Identities=23%  Similarity=0.466  Sum_probs=17.2

Q ss_pred             EEEEEeeC-CccccchHHHH---hhhhCCCCCCCCcceeEeeeC
Q 029664           94 CVFLLLHP-TPEVAEPSSHC---CGHFGYKSSTPYMPHLSLLYG  133 (190)
Q Consensus        94 vv~l~v~~-~~~L~~L~~~l---~~~~g~~~~~~f~PHlTLar~  133 (190)
                      +||+...+ ++.-..|+..+   ...++-. ...|-|||||.-+
T Consensus         4 SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~-~p~F~PHiTL~s~   46 (196)
T PF07823_consen    4 SLWLVPPPGSPLYERLKTLISSLASLFPGS-PPPFEPHITLTSG   46 (196)
T ss_dssp             EEEEEE-T--TTHHHHHHHHHHHHHHST----------EEEEEE
T ss_pred             EEEEcCCCCccHHHHHHHHHHHHHHHCCCC-CCCcCCeEEEeCC
Confidence            68999876 33344444444   3334411 3689999999974

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.

>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein

Probab=86.32  E-value=1  Score=35.97  Aligned_cols=41  Identities=22%  Similarity=0.286  Sum_probs=28.5

Q ss_pred             CCCeEEeecCCcC-ChhHHHHHHHHHhccCCceeEEEceeee
Q 029664           47 FDPHVTVVGAMSL-TADDALEKFKSACNGLKAYNCTVNRVAT   87 (190)
Q Consensus        47 ~~pHiTL~g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~   87 (190)
                      |..|+||.|.++. ..+.+...|+......-+-.+.++++.-
T Consensus       167 FrFHmTLTg~l~~~~~~~~~~~l~~~~~~~l~~p~~id~laL  208 (228)
T TIGR03223       167 FRFHMTLTGRLDEEERAAVLARLEARFAPLLADPLAVDGLAL  208 (228)
T ss_pred             eEEEEEecCCCChHHHHHHHHHHHHHhhhccCCCeeeeeEEE
Confidence            5789999999974 2345667777766555545677788773

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	190
1fsi_A	189	Crystal Structure Of Cyclic Nucleotide Phosphodiest		1e-62

>pdb|1FSI|A Chain A, Crystal Structure Of Cyclic Nucleotide Phosphodiesterase Of Appr>p From Arabidopsis Thaliana Length = 189

Iteration: 1
 Score =  235 bits (600), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 113/181 (62%), Positives = 138/181 (76%)
Query: 9   VDKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKF 68
           +++ KK  YSVWA+P +E   R KKLME LRSEF GP+F PHVTV  +  LTAD+A + F
Sbjct: 1   MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMF 60
Query: 69  KSACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHL 128
           +SAC+GLKAY  TV+RV+TGTFF+QCVFLLL  TPEV E   HC  HF   ++TPYMPHL
Sbjct: 61  ESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHL 120
Query: 129 SLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLS 188
           SLLY +LT++EKK AQEKA+ LD S+  LSF + RL L KTDTED TL++WE VA CNL+
Sbjct: 121 SLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLN 180
Query: 189 P 189
           P
Sbjct: 181 P 181

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	190
1jh6_A	189	Cyclic phosphodiesterase; ADP-ribose 1'',2''-cycli	8e-60
2d4g_A	171	Hypothetical protein BSU11850; beta barrel, alpha	1e-11
1vgj_A	184	Hypothetical protein PH0099; alpha+beta, LIGT-like	6e-05
1iuh_A	198	2'-5' RNA ligase; riken structural genomics/proteo	3e-04

>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* Length = 189

 Score =  184 bits (467), Expect = 8e-60
 Identities = 113/180 (62%), Positives = 137/180 (76%)

Query: 10  DKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFK 69
           ++ KK  YSVWA+P +E   R KKLME LRSEF GP+F PHVTV  +  LTAD+A + F+
Sbjct: 2   EEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFE 61

Query: 70  SACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLS 129
           SAC+GLKAY  TV+RV+TGTFF+QCVFLLL  TPEV E   HC  HF   ++TPYMPHLS
Sbjct: 62  SACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHLS 121

Query: 130 LLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSP 189
           LLY +LT++EKK AQEKA+ LD S+  LSF + RL L KTDTED TL++WE VA CNL+P
Sbjct: 122 LLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP 181

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

 Score = 59.1 bits (143), Expect = 1e-11
 Identities = 26/178 (14%), Positives = 59/178 (33%), Gaps = 20/178 (11%)

Query: 17  YSVWAIPPDEVRARVKKLMEGLRSEFGGPQFD---PHVTVVGAMSLT---ADDALEKFKS 70
           Y +   P  +++          R  +  P +    PH+T+  +       AD  +   ++
Sbjct: 3   YGIVLFPSKKLQDLA----NSYRKRY-DPSYSLIPPHLTLRASFECAEEKADQLVSHLRN 57

Query: 71  ACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCC-GHFGYKSSTPYMPHLS 129
                      + + ++       +++   PT E+   +     G    +    ++PH++
Sbjct: 58  IAKESHPLVLKMTKYSSFAPVNNVIYIKAEPTEELKTLNEKLYTGVLAGEQEYNFVPHVT 117

Query: 130 LLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNL 187
           +   +L+DDE     +   +L     S    + R  L           SW +     L
Sbjct: 118 VGQ-NLSDDE---HSDVLGQLKMQEVSHEEIVDRFHLLYQLENG----SWTVYETFLL 167

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

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 26/167 (15%), Positives = 61/167 (36%), Gaps = 20/167 (11%)

Query: 16  FYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDP----HVTVV--GAMSL-TADDALEKF 68
           F ++     + VR  + +  + + S+    +F      H+T+   G ++   A++     
Sbjct: 4   FIAID--VNESVRDSLVRAQDYIGSKEAKIKFVERENLHITLKFLGEITEEQAEEIKNIL 61

Query: 69  KSACNGLKAYNCTVNRVATGTF----FYQCVFLLLHPTPEV---AEPSSHCCGHFGYKSS 121
           K      K +   V  +  G F    + + ++  +     +   A          G+K  
Sbjct: 62  KKIAEKYKKHEVKVKGI--GVFPNPNYIRVIWAGIENDEIIREMAREIEDELAKLGFKKE 119

Query: 122 TPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWK 168
             ++ H++L       D+  +  +     +E  G  SF +  ++L K
Sbjct: 120 GNFVAHITLGRVKFVKDKLGLTMKLKELANEDFG--SFVVDAIELKK 164

>1iuh_A 2'-5' RNA ligase; riken structural genomics/proteomics initiative, RSGI, structural genomics; 2.50A {Thermus thermophilus} SCOP: d.61.1.2 Length = 198

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 29/170 (17%), Positives = 52/170 (30%), Gaps = 29/170 (17%)

Query: 16  FYSVWAIPPDEVRARVKKLMEGLRSEFGG---PQFDPHVTVV--GAMSLTADDALEK--- 67
           FY+V+   P+EVRA + +    +R   G    P    H+T++  G               
Sbjct: 4   FYAVF--LPEEVRAALVEAQTKVRPFRGWKPVPPHQLHLTLLFLGERPEEELPDYLALGH 61

Query: 68  --------FKSACNGLKAY-NCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGY 118
                   F++   G   + N    RV       +    L        E           
Sbjct: 62  RLARLEAPFRARLRGTGYFPNEGTPRVWFAKAEAEGFLRLAEGLRAGVEELLGEEAVRIP 121

Query: 119 KSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWK 168
               P+ PH++L             +  A ++   +  L +P+    L +
Sbjct: 122 GWDKPFKPHITLAR----------RKAPAPRVPPVLFGLEWPVEGFALVR 161

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

---

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	190
d1jh6a_	181	d.61.1.1 (A:) tRNA splicing product Appr>p cyclic	1e-47
d1iuha_	183	d.61.1.2 (A:) 2'-5' RNA ligase LigT {Thermus therm	1e-04

>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 =  151 bits (382), Expect = 1e-47
 Identities = 113/180 (62%), Positives = 137/180 (76%)

Query: 10  DKNKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFK 69
           ++ KK  YSVWA+P +E   R KKLME LRSEF GP+F PHVTV  +  LTAD+A + F+
Sbjct: 2   EEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFE 61

Query: 70  SACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLS 129
           SAC+GLKAY  TV+RV+TGTFF+QCVFLLL  TPEV E   HC  HF   ++TPYMPHLS
Sbjct: 62  SACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHLS 121

Query: 130 LLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAECNLSP 189
           LLY +LT++EKK AQEKA+ LD S+  LSF + RL L KTDTED TL++WE VA CNL+P
Sbjct: 122 LLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP 181

>d1iuha_ d.61.1.2 (A:) 2'-5' RNA ligase LigT {Thermus thermophilus [TaxId: 274]} Length = 183

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]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 25/170 (14%), Positives = 43/170 (25%), Gaps = 29/170 (17%)

Query: 16  FYSVWAIPPDEVRARVKKLMEGLRSEFGG---PQFDPHVTV--VGAMSL-TADDALEKFK 69
           FY+V+   P+EVRA + +    +R   G    P    H+T+  +G        D L    
Sbjct: 4   FYAVF--LPEEVRAALVEAQTKVRPFRGWKPVPPHQLHLTLLFLGERPEEELPDYLALGH 61

Query: 70  SACNGLKAYNCTVNRVATGTFFYQCVFLLLHPTPE--------VAEPSSHCCGHFGY--- 118
                   +   +                     E        +        G       
Sbjct: 62  RLARLEAPFRARLRGTGYFPNEGTPRVWFAKAEAEGFLRLAEGLRAGVEELLGEEAVRIP 121

Query: 119 KSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWK 168
               P+ PH++L                          L +P+    L +
Sbjct: 122 GWDKPFKPHITLARRKAPAPRVPPVLF----------GLEWPVEGFALVR 161

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	190
d1jh6a_	181	tRNA splicing product Appr>p cyclic nucleotide pho	100.0
d1iuha_	183	2'-5' RNA ligase LigT {Thermus thermophilus [TaxId	99.94
d2fsqa1	232	Putative phosphoesterase Atu0111 {Agrobacterium tu	98.44
d1jh6a_	181	tRNA splicing product Appr>p cyclic nucleotide pho	96.02

>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=100.00  E-value=1.3e-38  Score=214.82  Aligned_cols=178  Identities=63%  Similarity=1.031  Sum_probs=157.7

Q ss_pred             CCCCEEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEECEEEECCCE
Q ss_conf             98823799993995489999999998874219999999078516876894689999999861498416997226524600
Q 029664           12 NKKGFYSVWAIPPDEVRARVKKLMEGLRSEFGGPQFDPHVTVVGAMSLTADDALEKFKSACNGLKAYNCTVNRVATGTFF   91 (190)
Q Consensus        12 ~~~~~~slwl~P~~~~~~~l~~~~~~l~~~~~~~~~~pHiTL~g~~~~~~~~~~~~l~~~~~~~~pf~l~~~~v~~~~~~   91 (190)
                      .++..||||++|+++...+|+++++.++..++.+.++|||||.+.++.+.+++.+.+..++...+||.++++|+++|..+
T Consensus         4 ~~~~~yslwl~P~~~~~~~l~~l~~~l~~~~~~~~~~pHiTL~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~~~   83 (181)
T d1jh6a_           4 VKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFF   83 (181)
T ss_dssp             CCCEEEEEEEEECTTTHHHHHHHHHHHHHHHTCCCCCCCEEEEEEEEECHHHHHHHHHHHHHTCBCEEEEEEEEEEEEET
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCC
T ss_conf             67773899998988999999999999888618988897278860676898999999999885089837983465458987


Q ss_pred             EEEEEEEEECCCCCCCHHHHHHHHHCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCEEECEEEEEEECC
Q ss_conf             01899983089141134788851308999999842257431789978999999999730333598627933699998469
Q 029664           92 YQCVFLLLHPTPEVAEPSSHCCGHFGYKSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGSLSFPITRLQLWKTDT  171 (190)
Q Consensus        92 ~~vi~l~v~~~~~L~~L~~~~~~~~g~~~~~~f~PHiTLa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~L~~~~~  171 (190)
                      ++++|+.++.++.|.+|++.+.+.++..+.++|+|||||+|++...++++.+...+......+.+..|.++++.||++.+
T Consensus        84 ~~~v~~~~~~~~~L~~l~~~l~~~~~~~~~~~f~PHiTLa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vd~i~L~~s~~  163 (181)
T d1jh6a_          84 FQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDT  163 (181)
T ss_dssp             TEEEEEEECCCHHHHHHHHHHHHHTTCCCCSCCCCEEEEECCCCCHHHHHHHHHHHHHHCTTCTTCEEEEEEEEEEECCT
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECC
T ss_conf             41899826899899999999887448666777787288883577705689999999874055777637974899999878


Q ss_pred             CCCCCCCCEEEEEECCCC
Q ss_conf             888767814867770789
Q 029664          172 EDTTLKSWEMVAECNLSP  189 (190)
Q Consensus       172 ~~~~~~~w~~l~~~~L~~  189 (190)
                      .++.+..|+++++|+|++
T Consensus       164 ~~~~v~~W~~l~~~~L~~  181 (181)
T d1jh6a_         164 EDKTLETWETVAVCNLNP  181 (181)
T ss_dssp             TCTTCTTCEEEEEEECBC
T ss_pred             CCCCCCCEEEEEEEECCC
T ss_conf             789877678999995979

>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=99.94  E-value=7e-27  Score=154.55  Aligned_cols=164  Identities=15%  Similarity=0.193  Sum_probs=120.1

Q ss_pred             CCEEEEEEECCHHHHHHHHHHHHHHHHHCC---CCCCCCEEEEE--CCCCC-CHHHHHHHHHHHHCCCCCEEEEECEEEE
Q ss_conf             823799993995489999999998874219---99999907851--68768-9468999999986149841699722652
Q 029664           14 KGFYSVWAIPPDEVRARVKKLMEGLRSEFG---GPQFDPHVTVV--GAMSL-TADDALEKFKSACNGLKAYNCTVNRVAT   87 (190)
Q Consensus        14 ~~~~slwl~P~~~~~~~l~~~~~~l~~~~~---~~~~~pHiTL~--g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~~   87 (190)
                      +.+++|+  |++++.+.+.++.+.+...+.   .++.+.||||.  |+++. ..+++.+.+++++....||.++++++++
T Consensus         2 RlFial~--~p~~~~~~l~~~~~~l~~~~~~r~~~~~~lHiTL~flg~~~~~~~~~l~~~l~~~~~~~~pf~l~~~~~~~   79 (183)
T d1iuha_           2 RLFYAVF--LPEEVRAALVEAQTKVRPFRGWKPVPPHQLHLTLLFLGERPEEELPDYLALGHRLARLEAPFRARLRGTGY   79 (183)
T ss_dssp             EEEEEEE--CCHHHHHHHHHHHGGGTTCTTEEECCGGGCEEEEEEEEECCGGGHHHHHHHHHHHHHHSCCEEEEEEEEEE
T ss_pred             EEEEEEC--CCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf             0999970--99999999999998705002656378503789997088899899999999999997048983898266113


Q ss_pred             CCC-EEEEEEEEEECCCCCCCHHHHHHHH---------HCC-CCCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCCCCC
Q ss_conf             460-0018999830891411347888513---------089-99999842257431789978999999999730333598
Q 029664           88 GTF-FYQCVFLLLHPTPEVAEPSSHCCGH---------FGY-KSSTPYMPHLSLLYGDLTDDEKKIAQEKAHKLDESIGS  156 (190)
Q Consensus        88 ~~~-~~~vi~l~v~~~~~L~~L~~~~~~~---------~g~-~~~~~f~PHiTLa~~~~~~~~~~~~~~~~~~~~~~~~~  156 (190)
                      +.. ...+||+.+.+++.+.+|+++++..         .|+ .+.++|+|||||||.+.....          ......+
T Consensus        80 f~~~~~~~v~~~~~~~~~~~~L~~~l~~~l~~~~~~~~~~~~~~~r~f~PHITlar~~~~~~~----------~~~~~~~  149 (183)
T d1iuha_          80 FPNEGTPRVWFAKAEAEGFLRLAEGLRAGVEELLGEEAVRIPGWDKPFKPHITLARRKAPAPR----------VPPVLFG  149 (183)
T ss_dssp             ESSSSSCSEEEEEEECHHHHHHHHHHHHHHHHHHGGGGGGSTTTTSCCCCEEEEEEESSCCCC----------CCCCCCC
T ss_pred             CCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCHH----------HHCCCCC
T ss_conf             799987689998338859999999999999987666414888667782787877857587323----------4313678


Q ss_pred             CCEEECEEEEEEECCCCCCCCCCEEEEEECCCCC
Q ss_conf             6279336999984698887678148677707899
Q 029664          157 LSFPITRLQLWKTDTEDTTLKSWEMVAECNLSPD  190 (190)
Q Consensus       157 ~~~~v~~l~L~~~~~~~~~~~~w~~l~~~~L~~~  190 (190)
                      .+|+|++|.||+|...+ .|+.|+++++|+|+|+
T Consensus       150 ~~~~v~~~~L~~S~~~~-~g~~Y~~l~~~~L~g~  182 (183)
T d1iuha_         150 LEWPVEGFALVRSELKP-KGPVYTVLEKFSLRGE  182 (183)
T ss_dssp             EEEEECEEEEEEEEECS-SSEEEEEEEEEECCCC
T ss_pred             CEEEEEEEEEEEEECCC-CCCCCEEEEEEECCCC
T ss_conf             52894379999986369-8981319899948898

>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=98.44  E-value=1.9e-06  Score=49.51  Aligned_cols=161  Identities=14%  Similarity=0.114  Sum_probs=89.4

Q ss_pred             CEEEEEEECCH--HHHHHHHHHHHHHHHHCC------CCCCCCEEEEE-CCCCC---------------CHHHHHHHHHH
Q ss_conf             23799993995--489999999998874219------99999907851-68768---------------94689999999
Q 029664           15 GFYSVWAIPPD--EVRARVKKLMEGLRSEFG------GPQFDPHVTVV-GAMSL---------------TADDALEKFKS   70 (190)
Q Consensus        15 ~~~slwl~P~~--~~~~~l~~~~~~l~~~~~------~~~~~pHiTL~-g~~~~---------------~~~~~~~~l~~   70 (190)
                      .|+.|.-.+++  +....+..+++.+.+...      -|+--.|+||. |-.+.               ..+++...+..
T Consensus        34 pGnTiI~~i~~~s~~~~~l~~~q~~l~~~~~~~~~~~LP~sSfHMTLfd~~n~~~r~~~~wP~~l~~d~~~~~~~~~~~~  113 (232)
T d2fsqa1          34 PGNTVVCHLVEGSQTESAIVSTRQRFLDMPEASQLAFTPVSSLHMTVFQGVIESRRALPYWPQTLPLDTPIDAVTDYYRD  113 (232)
T ss_dssp             CEEEEEEEBCTTSHHHHHHHHHHHHHHTSGGGGGEEECCGGGCEEEEEEEEETTCCSTTSSCTTSCTTCCHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             99779871288866999999999999720720024668704424787464334645677897557855489999999999


Q ss_pred             HHCC---CCCEEEEECEEEECCCEEEEEEEEEEC--CCCCCCHHHHHHHHHCCC--CCCCCCCEEEEEECC--CCHHHHH
Q ss_conf             8614---984169972265246000189998308--914113478885130899--999984225743178--9978999
Q 029664           71 ACNG---LKAYNCTVNRVATGTFFYQCVFLLLHP--TPEVAEPSSHCCGHFGYK--SSTPYMPHLSLLYGD--LTDDEKK  141 (190)
Q Consensus        71 ~~~~---~~pf~l~~~~v~~~~~~~~vi~l~v~~--~~~L~~L~~~~~~~~g~~--~~~~f~PHiTLa~~~--~~~~~~~  141 (190)
                      .+..   ..+|.+++.+.+    ...++..+..+  ...|.++++.+.+.+|..  ....|.+||||||.-  .+..+..
T Consensus       114 rl~~~~~~~~~~~~~~~~~----~~~v~L~p~~e~d~~~L~~~R~~l~~l~gi~~~~h~~Y~fHITLaY~l~~l~~~e~~  189 (232)
T d2fsqa1         114 RLSTFPTLPAFNMRVTGLR----PVGMVMKGATAEDDSIVALWRDTFADFFGYRHPDHDTYEFHITLSYIVSWFEPECLP  189 (232)
T ss_dssp             HGGGCCCCCCCCEEEEEEE----TTEEEEEESSHHHHHHHHHHHHHHHHHHTCCCTTGGGCCEEEECEEESSCBCGGGHH
T ss_pred             HHHCCCCCCCEEEEEECCC----CCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCCCCHHHHH
T ss_conf             9854898754689996354----527999608889999999999999999666787775067788888516779858899


Q ss_pred             HHHHHHHHC----CCCCCCCCEEECEEEEEEECCCCCCCCCCEEEEEE
Q ss_conf             999999730----33359862793369999846988876781486777
Q 029664          142 IAQEKAHKL----DESIGSLSFPITRLQLWKTDTEDTTLKSWEMVAEC  185 (190)
Q Consensus       142 ~~~~~~~~~----~~~~~~~~~~v~~l~L~~~~~~~~~~~~w~~l~~~  185 (190)
                      .+.+.+..+    .... | .+++++..+-.-.    .+..|+.+-.+
T Consensus       190 ~~~~~l~~~~~~~~~~~-p-~i~l~~~e~c~Fe----dM~~F~~i~~~  231 (232)
T d2fsqa1         190 RWQAMLDEELEKLRVAA-P-VIQMRPPAFCEFK----DMNHFKELVVF  231 (232)
T ss_dssp             HHHHHHHHHHHHHHHHC-S-SCCBCCCEEEEES----STTCCEEEEEC
T ss_pred             HHHHHHHHHHHHHHHHC-C-EEEECCCCEEEEC----CCCCCCEEECC
T ss_conf             99999999999998559-8-5651796267605----61047324405

>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=96.02  E-value=0.0094  Score=30.48  Aligned_cols=57  Identities=21%  Similarity=0.338  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHCC---CCCCCCEEEEE-CCCCC-CHHHHHHHHHHHHCCCCCEEEEECEEE
Q ss_conf             99999998874219---99999907851-68768-946899999998614984169972265
Q 029664           30 RVKKLMEGLRSEFG---GPQFDPHVTVV-GAMSL-TADDALEKFKSACNGLKAYNCTVNRVA   86 (190)
Q Consensus        30 ~l~~~~~~l~~~~~---~~~~~pHiTL~-g~~~~-~~~~~~~~l~~~~~~~~pf~l~~~~v~   86 (190)
                      .|..+.+.++..+.   ...|.|||||. |.... ..+.+...+........++...++++.
T Consensus        96 ~L~~l~~~l~~~~~~~~~~~f~PHiTLa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vd~i~  157 (181)
T d1jh6a_          96 EVMEAGEHCKNHFNCSTTTPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLA  157 (181)
T ss_dssp             HHHHHHHHHHHHTTCCCCSCCCCEEEEECCCCCHHHHHHHHHHHHHHCTTCTTCEEEEEEEE
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEEE
T ss_conf             99999999887448666777787288883577705689999999874055777637974899