Citrus Sinensis ID: 014751

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------42
Protein Sequence
MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPELEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEMVD
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHHHHHHccccHHHHHHccccccccccccccccccccEEEEEEccccEEEEEEEccEEEEEcccccEEEEEccccccccccccccccccccEEEEEEEEccccEEEEEEEEEEccEEcccccHHHHHHHHHHHHcccccccccccccccEEEEcccccccHHHHHHHHHcccccccEEEEEEEccccccccccccEEEEccccccccEEccccccccccccEEEEEEEccccEEEcccccEEEEEccccHHccccccccccEEEEEccccEEEEccEEEEcccEEccccccccccccHHHHHHHHHHHHHccccHHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHccccccccHHcccccccccHHHHHHcccccccHHHHHHHcHHHHHHcccccccccEEEEEcccccEEEEEEEccEEEEEEcccEEEEEccccccccccccccccccccEEEEEEEEEccccEEEEEEEEEEccccccccccHHHHHHHHcHHcHcccccccccccccEEEEcccccccHHHHHHHHHccccccccEEEEEEcccccccccccEEEEEEcccccEEEEEcccccccccccEEEEEEEcccEEEEcccccEEEEEccHHHHHHcccccccEEEEEEccccEEEEcccEEEEEEEEcccccHHcccccHHHHHHHHHHHHcccccHHHHHHHHccccccccccccEEccc
Coil and Loop (DISEMBL)
mappdlrrpfkrtaisDQQRRRELSLQRQSQNRRDAQQQARCLASSVLslqsqypdpvpeleiepesqpqqeagpltkdldirqasklrgpEVRKWFASQLmlpewmidvpdrlshdwyvfarpagkrcivvssngttvsrerngsilhhfpsalpsgartkdpsgsaqsyCILDCIFHELDQTYYVIDMVcwrgyslydctAEFRFFWLNSKlaetgacdapshyykfrfstvpvyncdqrglysAYIEsvpyakdgllfynkhahyqtgntplalvwkdekcsqyvidtdskgqvLSQQQVVLELQedgklstsddppvifgcldgefiqksglqsgsLLKFAigngglsfvdgkleksdlnylgksnrarmfaDSYSKVIFQYMVRhtplkfddllasvspsddeenkpcdvemvd
Flexible Loop (DISEMBL)
mappdlrrpfkrtaisdqqrrrELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPELEIepesqpqqeagpltKDLDIRqasklrgpeVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLAsvspsddeenkpcdvemvd
Low Complexity Region (SEG)
MAPPDLRRPFKRTAISDqqrrrelslqrqsqnrrDAQQQARCLASSVLSLQSQYPDPVPELEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGqvlsqqqvvlelqeDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEMVD
Disordered region (IsUnstruct)
*******************************************************************************************EVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNG*********************************SYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLE*************PVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLL********************
Disordered Region (DISOPRED)
************************************QQQARCLAS**************************************************WFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGA********AQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLA**********YYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEF*******SGSLLKFAIGNGGLSFVDGKLEKSDLN************DSYSKVIFQYMVRHTPLKFDDLL********************
Disordered Region (DISEMBL)
MAPPDLRRPFKRTAI***************************LASSVLSLQ***********************PLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPS**********AQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASV*****************
Disordered Region (DISPRO)
*******************RRRELSLQRQSQNRRDAQQQARCLASSV******************************************GPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTK***GSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSP***************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPELEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEMVD
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	419	2.2.26 [Sep-21-2011]
Q5ZI43	365	Snurportin-1 OS=Gallus ga	yes	no	0.439	0.504	0.424	8e-43
Q2TBK8	362	Snurportin-1 OS=Bos tauru	yes	no	0.441	0.511	0.433	2e-42
Q68FP5	358	Snurportin-1 OS=Rattus no	yes	no	0.429	0.502	0.434	4e-42
Q80W37	358	Snurportin-1 OS=Mus muscu	yes	no	0.579	0.678	0.364	1e-41
O95149	360	Snurportin-1 OS=Homo sapi	yes	no	0.575	0.669	0.353	1e-41

>sp|Q5ZI43|SPN1_CHICK Snurportin-1 OS=Gallus gallus GN=SNUPN PE=2 SV=1

 Score =  174 bits (442), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 79/186 (42%), Positives = 116/186 (62%), Gaps = 2/186 (1%)

Query: 90  GPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH 149
           G  + K +A+QLML EW++DVP  L  +W V   P GKR +VV+S G+T +  ++G  ++
Sbjct: 93  GRRLPKRYANQLMLSEWLVDVPVDLEQEWIVVVCPVGKRALVVASRGSTAAYTKSGFCVN 152

Query: 150 HFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFW 209
            FPS LP G R    + + + YCILDCI++E +QTYY++D++CWRG+ +YDC  +FRFFW
Sbjct: 153 RFPSLLPGGNRHN--TMNEKVYCILDCIYNEAEQTYYILDVMCWRGHPVYDCQTDFRFFW 210

Query: 210 LNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQ 269
           L+SK+ E       S    ++F  +  + C    L      + P+  DGLLFY+K  HY 
Sbjct: 211 LSSKIQEEEGLGEKSRINPYKFVGLQNFPCTSESLCEVLTTNFPFEVDGLLFYHKQTHYT 270

Query: 270 TGNTPL 275
            G+TPL
Sbjct: 271 PGSTPL 276

Functions as an U snRNP-specific nuclear import adapter. Involved in the trimethylguanosine (m3G)-cap-dependent nuclear import of U snRNPs. Binds specifically to the terminal m3G-cap U snRNAs.
Gallus gallus (taxid: 9031)

>sp|Q2TBK8|SPN1_BOVIN Snurportin-1 OS=Bos taurus GN=SNUPN PE=2 SV=1

 Score =  174 bits (440), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/187 (43%), Positives = 113/187 (60%), Gaps = 2/187 (1%)

Query: 90  GPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH 149
           G E+ K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G T +  ++G  ++
Sbjct: 92  GKELPKRYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRSLIVASQGLTSAYTKSGYCVN 151

Query: 150 HFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFW 209
            FPS LP G R    S + + Y ILDCI+ E++QTYYV+D++CWRG+  YDC  +FRF+W
Sbjct: 152 TFPSLLPGGNRRN--STTEKDYTILDCIYSEVNQTYYVLDVMCWRGHPFYDCQTDFRFYW 209

Query: 210 LNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQ 269
           L+SKL E       +    F+F  +  + C    L        P+  DGLLFY+K  HY 
Sbjct: 210 LHSKLPEEEGLGEKTKRNPFKFVGLKNFPCTPESLCKVLSMDFPFEVDGLLFYHKQTHYS 269

Query: 270 TGNTPLA 276
            G+TPL 
Sbjct: 270 PGSTPLV 276

Functions as an U snRNP-specific nuclear import adapter. Involved in the trimethylguanosine (m3G)-cap-dependent nuclear import of U snRNPs. Binds specifically to the terminal m3G-cap U snRNAs.

Bos taurus (taxid: 9913)

>sp|Q68FP5|SPN1_RAT Snurportin-1 OS=Rattus norvegicus GN=Snupn PE=2 SV=1

 Score =  172 bits (437), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 79/182 (43%), Positives = 111/182 (60%), Gaps = 2/182 (1%)

Query: 95  KWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSA 154
           K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+T +  ++G  ++ F S 
Sbjct: 97  KRYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSL 156

Query: 155 LPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKL 214
           LP G R    S +A+ Y ILDCI+ E++QTYYV+D++CWRG+  YDC  +FRF+W+NSKL
Sbjct: 157 LPGGNRRN--STTAKDYTILDCIYSEVNQTYYVLDVMCWRGHPFYDCQTDFRFYWMNSKL 214

Query: 215 AETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTP 274
            E       +    F+F  +  + C    L        P+  DGLLFY+K  HY  G+TP
Sbjct: 215 PEEEGLGEKTKINPFKFVGLKNFPCTPESLCKVLSMDFPFEVDGLLFYHKQTHYSPGSTP 274

Query: 275 LA 276
           L 
Sbjct: 275 LV 276

Functions as an U snRNP-specific nuclear import adapter. Involved in the trimethylguanosine (m3G)-cap-dependent nuclear import of U snRNPs. Binds specifically to the terminal m3G-cap U snRNAs.

Rattus norvegicus (taxid: 10116)

>sp|Q80W37|SPN1_MOUSE Snurportin-1 OS=Mus musculus GN=Snupn PE=2 SV=1

 Score =  171 bits (433), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 97/266 (36%), Positives = 143/266 (53%), Gaps = 23/266 (8%)

Query: 11  KRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPELEIEPESQPQ 70
           K +++   +RRR+L L+ Q   R D    AR LA               E +       +
Sbjct: 34  KYSSLEQSERRRQL-LELQKSKRLDYVNHARRLA---------------EDDWTGMESGE 77

Query: 71  QEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCI 130
           +E     +++DI  + KL      K +A+QLML EW+IDVP  L  +W V   P GKR +
Sbjct: 78  EENKKDEEEMDIDPSKKLP-----KRYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRAL 132

Query: 131 VVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDM 190
           +V+S G+T +  ++G  ++ F S LP G R    S +A+ Y ILDCI+ E++QTYYV+D+
Sbjct: 133 IVASRGSTSAYTKSGYCVNRFSSLLPGGNRRN--STTAKDYTILDCIYSEVNQTYYVLDV 190

Query: 191 VCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIE 250
           +CWRG+  YDC  +FRF+W++SKL E       +    F+F  +  + C    L      
Sbjct: 191 MCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKINPFKFVGLKNFPCTPESLCEVLSM 250

Query: 251 SVPYAKDGLLFYNKHAHYQTGNTPLA 276
             P+  DGLLFY+K  HY  G+TPL 
Sbjct: 251 DFPFEVDGLLFYHKQTHYSPGSTPLV 276

Functions as an U snRNP-specific nuclear import adapter. Involved in the trimethylguanosine (m3G)-cap-dependent nuclear import of U snRNPs. Binds specifically to the terminal m3G-cap U snRNAs.

Mus musculus (taxid: 10090)

>sp|O95149|SPN1_HUMAN Snurportin-1 OS=Homo sapiens GN=SNUPN PE=1 SV=1

 Score =  171 bits (432), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 94/266 (35%), Positives = 142/266 (53%), Gaps = 25/266 (9%)

Query: 11  KRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPELEIEPESQPQ 70
           K +++   +RRR L L+ Q   R D    AR LA    +                ES+ +
Sbjct: 34  KYSSLEQSERRRRL-LELQKSKRLDYVNHARRLAEDDWTGM--------------ESEEE 78

Query: 71  QEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCI 130
            +      D+D  +       ++ K +A+QLML EW+IDVP  L  +W V   P GKR +
Sbjct: 79  NKKDDEEMDIDTVK-------KLPKHYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRAL 131

Query: 131 VVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDM 190
           +V+S G+T +  ++G  ++ F S LP G R    + +A+ Y ILDCI++E++QTYYV+D+
Sbjct: 132 IVASRGSTSAYTKSGYCVNRFSSLLPGGNRR---NSTAKDYTILDCIYNEVNQTYYVLDV 188

Query: 191 VCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIE 250
           +CWRG+  YDC  +FRF+W++SKL E       +    F+F  +  + C    L      
Sbjct: 189 MCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSM 248

Query: 251 SVPYAKDGLLFYNKHAHYQTGNTPLA 276
             P+  DGLLFY+K  HY  G+TPL 
Sbjct: 249 DFPFEVDGLLFYHKQTHYSPGSTPLV 274

Functions as an U snRNP-specific nuclear import adapter. Involved in the trimethylguanosine (m3G)-cap-dependent nuclear import of U snRNPs. Binds specifically to the terminal m3G-cap U snRNAs.

Homo sapiens (taxid: 9606)

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	419
225456315	419	PREDICTED: snurportin-1 [Vitis vinifera]	0.997	0.997	0.763	0.0
224133956	420	predicted protein [Populus trichocarpa]	0.995	0.992	0.771	0.0
255540251	415	conserved hypothetical protein [Ricinus	0.985	0.995	0.757	0.0
297803634	416	hypothetical protein ARALYDRAFT_492350 [	0.992	1.0	0.713	1e-173
449440556	432	PREDICTED: uncharacterized protein LOC10	0.992	0.962	0.692	1e-170
18416444	417	snurportin-1 [Arabidopsis thaliana] gi|1	0.990	0.995	0.705	1e-170
356518893	413	PREDICTED: snurportin-1-like [Glycine ma	0.978	0.992	0.696	1e-165
356507357	404	PREDICTED: snurportin-1-like [Glycine ma	0.959	0.995	0.678	1e-163
115433968	407	Os01g0101300 [Oryza sativa Japonica Grou	0.966	0.995	0.633	1e-148
357127386	416	PREDICTED: uncharacterized protein LOC10	0.988	0.995	0.612	1e-143

>gi|225456315|ref|XP_002283742.1| PREDICTED: snurportin-1 [Vitis vinifera] gi|297734416|emb|CBI15663.3| unnamed protein product [Vitis vinifera]

 Score =  689 bits (1779), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 319/418 (76%), Positives = 368/418 (88%)

Query: 1   MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPE 60
           MAP ++RRPFKR AISDQQ+RRELSL RQ+QNRRDAQ  ARCLAS+V+SLQ+  P+P+ E
Sbjct: 1   MAPHEVRRPFKRPAISDQQKRRELSLLRQAQNRRDAQHHARCLASTVVSLQAPNPEPISE 60

Query: 61  LEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYV 120
            EI  E   + E+  + +D+D+RQASKL+G E R+WFA QLMLPEWMIDVPDRLSHDWYV
Sbjct: 61  PEIADEPSVESESQSIPRDIDVRQASKLKGYEARRWFARQLMLPEWMIDVPDRLSHDWYV 120

Query: 121 FARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE 180
            ARP GKRC VVSS+GTTVSR RNGS+LHHFPSALP+GART+D SGSAQSYCILDCIFHE
Sbjct: 121 LARPTGKRCFVVSSDGTTVSRLRNGSVLHHFPSALPNGARTRDISGSAQSYCILDCIFHE 180

Query: 181 LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD 240
           LDQTYYVIDMVCWRGYSLYDCTAEFRFFW+NSKLAETGACD PS Y+++RFS VP+YNCD
Sbjct: 181 LDQTYYVIDMVCWRGYSLYDCTAEFRFFWVNSKLAETGACDPPSPYHRYRFSVVPIYNCD 240

Query: 241 QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQ 300
           Q GLY+AY  + PY KDGLLFYN+HAHYQTGNTPL LVWKDE CSQYVIDTDSKGQV SQ
Sbjct: 241 QNGLYTAYTGAAPYVKDGLLFYNRHAHYQTGNTPLTLVWKDENCSQYVIDTDSKGQVPSQ 300

Query: 301 QQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEK 360
           QQVVLELQ+DG L+TSDDPPV+FG LDG+FIQKSGL SG+LL+FA+ +GGLSFVDGKLE+
Sbjct: 301 QQVVLELQDDGNLTTSDDPPVVFGSLDGDFIQKSGLCSGNLLRFAVSDGGLSFVDGKLER 360

Query: 361 SDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEMV 418
           +DL+YLGK NRAR FADSYSKV+FQ+ VRH+PL  DDLLAS++ ++D+E + CDVEM 
Sbjct: 361 ADLHYLGKVNRARAFADSYSKVMFQHSVRHSPLSIDDLLASITSTNDQEKEACDVEMA 418

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133956|ref|XP_002321701.1| predicted protein [Populus trichocarpa] gi|222868697|gb|EEF05828.1| predicted protein [Populus trichocarpa]

 Score =  677 bits (1747), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 324/420 (77%), Positives = 366/420 (87%), Gaps = 3/420 (0%)

Query: 1   MAPP-DLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVP 59
           MAPP D RRPFKR AISDQQRRR++SLQRQ+Q+RRDAQ QARCLAS+VLSLQ Q   P P
Sbjct: 1   MAPPQDTRRPFKRLAISDQQRRRDISLQRQAQSRRDAQHQARCLASTVLSLQHQ-TTPEP 59

Query: 60  ELEIEPESQPQ-QEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDW 118
           E  IE E  P+ +E+G  ++DLD+R A++L+G E RKWFA QLML EWMIDVPDRLS DW
Sbjct: 60  ESNIELELVPESEESGASSQDLDVRHAARLKGAEARKWFAKQLMLHEWMIDVPDRLSDDW 119

Query: 119 YVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIF 178
           YVFARPAGKRC VVS+NGTTVSR+RNGSILH FPSALP+GA+ +D SG  QSYCILDCIF
Sbjct: 120 YVFARPAGKRCFVVSTNGTTVSRQRNGSILHRFPSALPNGAKKRDGSGPNQSYCILDCIF 179

Query: 179 HELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYN 238
           HELDQTYYVIDMVCWRGYSLYDC AEFRFFWLNSKL ETGACD PS Y+K+RFSTVPVYN
Sbjct: 180 HELDQTYYVIDMVCWRGYSLYDCAAEFRFFWLNSKLGETGACDPPSFYHKYRFSTVPVYN 239

Query: 239 CDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVL 298
           CDQ GL+SAY   VPY KDGLLFYNKHAHYQTGNTPLALVWKD+ CSQYVIDTD+KG+V 
Sbjct: 240 CDQNGLFSAYSGDVPYVKDGLLFYNKHAHYQTGNTPLALVWKDQNCSQYVIDTDNKGEVP 299

Query: 299 SQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKL 358
           +QQQVVLELQ+DGKL TSDDPPV+FGCLD +FIQKSGL SG+LL+FAI +GGLS VDGKL
Sbjct: 300 TQQQVVLELQDDGKLVTSDDPPVVFGCLDSDFIQKSGLCSGNLLRFAISDGGLSSVDGKL 359

Query: 359 EKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEMV 418
            K+DL+YL K NRAR FADSYSK++FQ+ VRH PLK DDLLAS+S  DD++N+PCD+EMV
Sbjct: 360 VKADLHYLEKPNRARAFADSYSKIMFQHTVRHCPLKIDDLLASISSPDDQQNRPCDIEMV 419

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540251|ref|XP_002511190.1| conserved hypothetical protein [Ricinus communis] gi|223550305|gb|EEF51792.1| conserved hypothetical protein [Ricinus communis]

 Score =  665 bits (1717), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 316/417 (75%), Positives = 360/417 (86%), Gaps = 4/417 (0%)

Query: 1   MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPE 60
           MAP D+RRPFKR AISDQQRRR+L+LQRQ+Q+RRDAQQQARC+A++VLSLQ Q   P PE
Sbjct: 1   MAPNDVRRPFKRAAISDQQRRRDLTLQRQAQSRRDAQQQARCVATTVLSLQYQNTQPEPE 60

Query: 61  LEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYV 120
           L  + E    ++ G  + +LD+RQA K++G E RKWFA QLMLPEWMIDVPD L+ DWYV
Sbjct: 61  LLPDQE----EDGGGPSIELDVRQAYKVKGAEARKWFAKQLMLPEWMIDVPDSLAQDWYV 116

Query: 121 FARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE 180
           FARPAGKRC VVS NGTTVSR+RNGSILH FPSALP+GA+T+D SGS+QSY ILDCIFHE
Sbjct: 117 FARPAGKRCFVVSCNGTTVSRQRNGSILHRFPSALPNGAKTRDLSGSSQSYSILDCIFHE 176

Query: 181 LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD 240
           LDQTYYVIDMVCWRGYSLYDC+AEFRFFWLNSKL ETGAC+ PS Y+K+RFS VPVYNCD
Sbjct: 177 LDQTYYVIDMVCWRGYSLYDCSAEFRFFWLNSKLGETGACNPPSVYHKYRFSIVPVYNCD 236

Query: 241 QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQ 300
           Q GL+SAY  SVPY KDGLLFYNKHAHYQ GNTPLALVWKDE CSQYVIDTDSKGQV SQ
Sbjct: 237 QSGLWSAYTGSVPYTKDGLLFYNKHAHYQMGNTPLALVWKDENCSQYVIDTDSKGQVPSQ 296

Query: 301 QQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEK 360
           QQVVLELQ+DG L +SDDPPV+FGCLD  F+QK  L SG+L++FAI +GGL F DGKLEK
Sbjct: 297 QQVVLELQDDGSLISSDDPPVVFGCLDLGFVQKEVLHSGNLVRFAINDGGLRFADGKLEK 356

Query: 361 SDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEM 417
           +DL+YLGK NRAR  ADSYSKV+FQ+ VRH+PLK DDLLASV  SDD++N+PCD+EM
Sbjct: 357 ADLHYLGKPNRARASADSYSKVVFQHTVRHSPLKIDDLLASVCSSDDQQNRPCDIEM 413

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297803634|ref|XP_002869701.1| hypothetical protein ARALYDRAFT_492350 [Arabidopsis lyrata subsp. lyrata] gi|297315537|gb|EFH45960.1| hypothetical protein ARALYDRAFT_492350 [Arabidopsis lyrata subsp. lyrata]

 Score =  615 bits (1585), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 299/419 (71%), Positives = 344/419 (82%), Gaps = 3/419 (0%)

Query: 1   MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPE 60
           MAP ++RRPFKR  ISDQQ+RRELSL RQ+Q+R DAQQ+AR LASSV+SLQS  PD  PE
Sbjct: 1   MAPHEIRRPFKRRPISDQQKRRELSLLRQTQHRSDAQQRARNLASSVISLQSSSPDVDPE 60

Query: 61  LEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYV 120
           +  E E     E    +   D+RQAS+LRGPE RKWFA QLMLPEWMIDVPD LS DWYV
Sbjct: 61  ILSEAELNEGTELE--SSSFDVRQASRLRGPEARKWFAKQLMLPEWMIDVPDNLSQDWYV 118

Query: 121 FARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE 180
            ARPAGKRC VVSS+GTTVSR RNGSILHHFPSALP GAR K  SG A SY ILDCIFHE
Sbjct: 119 LARPAGKRCFVVSSDGTTVSRVRNGSILHHFPSALPGGARKKGASGPANSYSILDCIFHE 178

Query: 181 LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD 240
            DQTYYVIDMVCWRGYSLY+CTAEFRFFW+ SKLAETGACD PS Y+KFRFS VP YNCD
Sbjct: 179 SDQTYYVIDMVCWRGYSLYECTAEFRFFWMQSKLAETGACDPPSFYHKFRFSAVPFYNCD 238

Query: 241 QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQ 300
           Q GL+SAY  S+PY KDGLLFYNKHAHY TGNTPL L+WKDE CSQYVIDTD+ G+V  Q
Sbjct: 239 QSGLHSAYTGSLPYVKDGLLFYNKHAHYHTGNTPLVLIWKDESCSQYVIDTDNNGEVPHQ 298

Query: 301 QQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEK 360
           Q +VLELQE+GKL TSDDPPV F CL+ +F+++SGL SGSL++FAIGNGGL  VDG+ EK
Sbjct: 299 QHIVLELQEEGKLVTSDDPPVPFSCLNADFVKQSGLSSGSLIRFAIGNGGLKCVDGRFEK 358

Query: 361 SDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEMVD 419
           +DL Y+  SNRAR FADSYSK++FQYM RH+PLK +DL +++S  +++++KP +VEM D
Sbjct: 359 ADLQYISVSNRARAFADSYSKIMFQYMARHSPLKVEDLASTIS-HENQQDKPPEVEMSD 416

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440556|ref|XP_004138050.1| PREDICTED: uncharacterized protein LOC101214543 [Cucumis sativus]

 Score =  605 bits (1560), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 300/433 (69%), Positives = 350/433 (80%), Gaps = 17/433 (3%)

Query: 1   MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPV-- 58
           MAP D+RRP KR AISDQQ+RRELSLQRQ QNRRDAQQQAR LAS++LSL S + +P   
Sbjct: 1   MAPHDIRRPHKRPAISDQQKRRELSLQRQQQNRRDAQQQARSLASTLLSLSSSFDEPSTS 60

Query: 59  -PELEIE-PESQPQQEAG-----------PLTKDLDIRQASKLRGPEVRKWFASQLMLPE 105
            P LEIE  E +   E             P  K+LD+RQASKL+  E RKWF+ QL+LPE
Sbjct: 61  EPVLEIELNELESGTECSLEILSEREFNEPALKELDVRQASKLKSSEARKWFSKQLLLPE 120

Query: 106 WMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPS 165
           WMIDVPDRLS +WYVFARP+GKRC VVSSNGTT+SR RNGSILH FPS+LP+GA+TK  S
Sbjct: 121 WMIDVPDRLSDEWYVFARPSGKRCFVVSSNGTTISRLRNGSILHRFPSSLPNGAKTKKAS 180

Query: 166 GSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSH 225
           GS Q+Y ILDCIFHE DQTYYVIDM+CWRGYSLYDC AEFRFFWLNSKLAE+GAC+ PS+
Sbjct: 181 GSGQTYSILDCIFHETDQTYYVIDMICWRGYSLYDCAAEFRFFWLNSKLAESGACELPSY 240

Query: 226 YYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCS 285
           Y+K++FS VPVY+CDQ GL++AY  + P+ KDGLLFYNKH+HYQ GNTPLALVWKDE CS
Sbjct: 241 YHKYKFSLVPVYSCDQNGLHAAYAGAAPFVKDGLLFYNKHSHYQPGNTPLALVWKDENCS 300

Query: 286 QYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFA 345
           QYVIDTDS GQV SQQQ+VLELQ DGK++TSDDPPV FGCLDG+F+ K GL SG+LL+F 
Sbjct: 301 QYVIDTDSNGQVPSQQQLVLELQSDGKVATSDDPPVYFGCLDGDFLGKLGLSSGNLLRFT 360

Query: 346 IGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPS 405
           IG+GGL+ VDG+++ +DL Y GK NRAR FADSYSKV+FQY  R +PLK DDLLAS++ S
Sbjct: 361 IGDGGLTIVDGRIQGADLQYSGKVNRARAFADSYSKVMFQYAARRSPLKIDDLLASINSS 420

Query: 406 DDEENKPCDVEMV 418
           +D      D EMV
Sbjct: 421 NDGGGH--DSEMV 431

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18416444|ref|NP_567711.1| snurportin-1 [Arabidopsis thaliana] gi|16209705|gb|AAL14409.1| AT4g24880/F13M23_20 [Arabidopsis thaliana] gi|115311481|gb|ABI93921.1| At4g24880 [Arabidopsis thaliana] gi|332659572|gb|AEE84972.1| snurportin-1 [Arabidopsis thaliana]

 Score =  604 bits (1557), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 297/421 (70%), Positives = 346/421 (82%), Gaps = 6/421 (1%)

Query: 1   MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPE 60
           MAP ++RRPFKR  ISDQQ+RRELSL RQ+Q+R DAQQ+AR LASS++SLQS  PD  PE
Sbjct: 1   MAPHEIRRPFKRRPISDQQKRRELSLIRQTQHRSDAQQRARNLASSLISLQSSSPDVDPE 60

Query: 61  L--EIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDW 118
           +  E  PE    +     +   D+RQAS+LRGPE RKWFA QLMLPEWMIDVPD LS DW
Sbjct: 61  ILSEAVPELVGTESE---SSSFDVRQASRLRGPEARKWFAKQLMLPEWMIDVPDNLSQDW 117

Query: 119 YVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIF 178
           YV ARPAGKRC VVSS+GTTVSR RNGS LH FPSALP GAR K  SG A SY ILDCIF
Sbjct: 118 YVLARPAGKRCFVVSSDGTTVSRVRNGSTLHLFPSALPGGARKKGASGPANSYSILDCIF 177

Query: 179 HELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYN 238
           HE DQTYYVIDMVCWRGYSLY+CT+EFRFFWL SKLAETGACD PS Y+KFRFS VP YN
Sbjct: 178 HESDQTYYVIDMVCWRGYSLYECTSEFRFFWLQSKLAETGACDPPSVYHKFRFSVVPFYN 237

Query: 239 CDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVL 298
           CDQ GL+SAY  S+PY +DGLLFYNKHAHY TGNTPL L+WKDE CSQYVIDTD+ G+V 
Sbjct: 238 CDQSGLHSAYTGSLPYVRDGLLFYNKHAHYHTGNTPLVLIWKDESCSQYVIDTDNNGEVP 297

Query: 299 SQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKL 358
           +QQ +VLELQE+GKL TSDDPPV F CL+ +F+++SGL SGSL++FAIG+GGL  VDG+ 
Sbjct: 298 NQQHIVLELQEEGKLVTSDDPPVPFSCLNADFVKQSGLSSGSLIRFAIGDGGLKCVDGRF 357

Query: 359 EKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEMV 418
           EK+DL Y+G SNRAR FADSYSK++FQYM RH+PLK +DL +++SP +D+++KP +VEM 
Sbjct: 358 EKADLQYIGVSNRARAFADSYSKIMFQYMARHSPLKVEDLASTISP-EDQQDKPPEVEMS 416

Query: 419 D 419
           D
Sbjct: 417 D 417

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356518893|ref|XP_003528111.1| PREDICTED: snurportin-1-like [Glycine max]

 Score =  586 bits (1510), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 291/418 (69%), Positives = 338/418 (80%), Gaps = 8/418 (1%)

Query: 1   MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPE 60
           MAP DLRRPFKR AISDQ+RRRE SL RQ+Q+R+DAQ+ AR LAS+ LSL  + P+P  E
Sbjct: 1   MAPHDLRRPFKRPAISDQERRREQSLLRQAQSRQDAQRHARFLASAALSLPPKTPEPESE 60

Query: 61  LEIE-PESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWY 119
            + E  E++   ++G   + LDI  AS L   E RKWFA QLM PEWMID+P+ L+ DW+
Sbjct: 61  PKPELAETEASSDSG--YESLDIVGASTLSAAEARKWFAKQLMHPEWMIDIPNNLAQDWF 118

Query: 120 VFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFH 179
           VFARP+GKRC VVS NGTT+SR RNG+ILH FPSALPSGAR KDPS     Y ILDCIFH
Sbjct: 119 VFARPSGKRCFVVSCNGTTISRLRNGAILHRFPSALPSGARKKDPS-----YSILDCIFH 173

Query: 180 ELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC 239
           E+DQTYYVIDMVCWR Y L DCTAEFRFFWL SKLAETGA D PS+Y+K+RFS VPVY+C
Sbjct: 174 EVDQTYYVIDMVCWRDYPLSDCTAEFRFFWLTSKLAETGAFDPPSYYHKYRFSLVPVYSC 233

Query: 240 DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLS 299
           D  GLY+AY   VPY KDGLLFYNKH+HYQ G TPLALVWKDE CSQYV+DTDSKGQV +
Sbjct: 234 DSSGLYAAYSAPVPYVKDGLLFYNKHSHYQAGITPLALVWKDENCSQYVLDTDSKGQVPN 293

Query: 300 QQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLE 359
           QQQVVLELQEDGKL+TSDDPPV+FGCLDG FIQ+SGL SG LL+F+IG GG   +DGKLE
Sbjct: 294 QQQVVLELQEDGKLTTSDDPPVVFGCLDGSFIQQSGLHSGCLLRFSIGEGGFVLMDGKLE 353

Query: 360 KSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEM 417
           K+DL+YLGK+NRAR  ADS+SKV+FQ+ VRH+PL+ + LL SV    D+E+K CDVEM
Sbjct: 354 KADLHYLGKANRARASADSFSKVMFQHSVRHSPLRIEGLLESVGLPVDQESKACDVEM 411

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507357|ref|XP_003522434.1| PREDICTED: snurportin-1-like [Glycine max]

 Score =  581 bits (1498), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 283/417 (67%), Positives = 327/417 (78%), Gaps = 15/417 (3%)

Query: 1   MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPE 60
           MAP DL RPFKR AISDQ+RRRE SL RQ+QNR+DAQ+ AR LAS+ LSL        P+
Sbjct: 1   MAPHDLHRPFKRPAISDQERRREQSLLRQAQNRQDAQRHARFLASAALSLP-------PQ 53

Query: 61  LEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYV 120
                     +    L    +   ASKL+  E RKWFA QLMLPEWMID+P+ L+ DW+V
Sbjct: 54  SSEPESEPKPEPEFELA---EFEAASKLKAVEARKWFAKQLMLPEWMIDIPNNLAQDWFV 110

Query: 121 FARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE 180
           FARP+GKRC VVS NG T+SR RNG++LH FPS LPSGAR KDPS     Y ILDCIFHE
Sbjct: 111 FARPSGKRCFVVSCNGATISRLRNGAVLHRFPSGLPSGARKKDPS-----YSILDCIFHE 165

Query: 181 LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD 240
            DQTYYVIDMVCWRGY L DCTAEFRFFWL SKLAET A + PSHY+K+RFS VPV+NCD
Sbjct: 166 ADQTYYVIDMVCWRGYPLSDCTAEFRFFWLTSKLAETDAFEPPSHYHKYRFSLVPVFNCD 225

Query: 241 QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQ 300
             GLY+AY   VPY KDGLLFYNKHAHYQ G TPLALVWKDE CSQYV+DTDSKGQV +Q
Sbjct: 226 SNGLYAAYSAPVPYVKDGLLFYNKHAHYQAGITPLALVWKDENCSQYVLDTDSKGQVPNQ 285

Query: 301 QQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEK 360
           QQVVLELQ+DGKL+TSDDPP++FGCLDG FIQ+SGL SG LL+F+IG GGL  +DGKL+K
Sbjct: 286 QQVVLELQDDGKLTTSDDPPMVFGCLDGSFIQQSGLHSGCLLRFSIGEGGLVLMDGKLDK 345

Query: 361 SDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEM 417
           +DL+YLGK+NRAR  ADS+SKV+FQ+ VRH+PL+ D LL SVS   D+E+K CD+EM
Sbjct: 346 ADLHYLGKANRARASADSFSKVMFQHSVRHSPLRIDGLLESVSLPVDQESKACDIEM 402

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115433968|ref|NP_001041742.1| Os01g0101300 [Oryza sativa Japonica Group] gi|113531273|dbj|BAF03656.1| Os01g0101300 [Oryza sativa Japonica Group]

 Score =  529 bits (1363), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 264/417 (63%), Positives = 318/417 (76%), Gaps = 12/417 (2%)

Query: 1   MAPPDLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPE 60
           MAPP   RP+KR AISDQQRRR+L+LQ QS  R DAQ +AR LA+S+LS  S   D   E
Sbjct: 1   MAPPPPHRPYKRPAISDQQRRRDLALQAQSARRADAQARARSLANSLLSPSSAAADTAVE 60

Query: 61  LEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYV 120
            + E + +P               ASKLRG + R+WFA Q+MLPEWM D P  L+ DW+V
Sbjct: 61  GDSERDHEPTVAEA----------ASKLRGSDARRWFARQIMLPEWMADAPPHLATDWHV 110

Query: 121 FARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE 180
           FARPAGKRC+VVS NG T+SR RNGSILH FPSALP+G++ +D SG A SY ILDCIFHE
Sbjct: 111 FARPAGKRCLVVSCNGITISRLRNGSILHRFPSALPNGSK-RDISGPASSYSILDCIFHE 169

Query: 181 LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD 240
            D+TYY+IDM+CWRGYSLYDCTAEFRFFW+NSKL ET A D PS Y+++RFS VP+Y C 
Sbjct: 170 PDETYYIIDMICWRGYSLYDCTAEFRFFWVNSKLMETTAGDPPSTYHRYRFSAVPIYECT 229

Query: 241 QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVLSQ 300
            +GL +AY  S PY KDGLLFYNKHAHY  G TPLALVWKDE CSQYVIDTDSKGQV S+
Sbjct: 230 LQGLQAAYSGSTPYVKDGLLFYNKHAHYLAGITPLALVWKDEACSQYVIDTDSKGQVPSE 289

Query: 301 QQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKLEK 360
           Q +VL+LQEDGKL+TSDDPPV+FG LD EFIQKS L+ G+LL+FA+ +  +  VDGK+E 
Sbjct: 290 QHIVLDLQEDGKLTTSDDPPVVFGSLDNEFIQKSNLRPGNLLRFAVKDERVKLVDGKMEI 349

Query: 361 SDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEM 417
           S+L ++GK NRAR FADS+SK +FQY  RH PL+ +DL+AS+  S++ E +  DVEM
Sbjct: 350 SELQFVGKPNRARAFADSHSKALFQYAARHAPLRIEDLVASIQ-SNNMELESTDVEM 405

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357127386|ref|XP_003565362.1| PREDICTED: uncharacterized protein LOC100828275 [Brachypodium distachyon]

 Score =  513 bits (1321), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 258/421 (61%), Positives = 317/421 (75%), Gaps = 7/421 (1%)

Query: 1   MAPP--DLRRPFKRTAISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPV 58
           MAPP  D RRP+KR AISDQQRRR+ +LQ QS  R DAQ +AR LA+S+LS    YP PV
Sbjct: 1   MAPPQHDPRRPYKRAAISDQQRRRDFALQTQSARRADAQARARSLANSLLS--PSYP-PV 57

Query: 59  PELEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDW 118
            +    PE+     +     +     A+KLRGPE R+WFA Q+MLPEWM+D P  L+ DW
Sbjct: 58  DQAPASPEANHDDRSHEPAVNEVATAAAKLRGPEGRRWFACQIMLPEWMVDAPPHLARDW 117

Query: 119 YVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIF 178
            V ARPAG+RC+VVS+NG TVSR RNG++LH FPSALP+G++ +  SG A SY ILDCIF
Sbjct: 118 NVCARPAGQRCLVVSTNGITVSRLRNGTVLHRFPSALPNGSK-RGISGPASSYSILDCIF 176

Query: 179 HELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYN 238
           HE D+TYY++DM+CWRGYSLYDCTAEFRFFW+NSKL ET A D PS Y+++RF  VP+Y 
Sbjct: 177 HEPDETYYIVDMICWRGYSLYDCTAEFRFFWINSKLTETSAGDPPSTYHRYRFCAVPMYE 236

Query: 239 CDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGQVL 298
               GL +AY  S PY KDGLLFYNKHAHYQTG TPL LVWKDE CSQYV+DTDS+GQV 
Sbjct: 237 STLEGLQAAYSGSTPYVKDGLLFYNKHAHYQTGITPLTLVWKDEACSQYVLDTDSEGQVP 296

Query: 299 SQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKL 358
           ++Q VVLELQEDGKL TSDDPP+IFG L+ EFIQKS L+ G+L++F++ +  +  VDGK+
Sbjct: 297 TEQHVVLELQEDGKLITSDDPPIIFGTLNSEFIQKSNLRPGNLVRFSVRDESVKLVDGKM 356

Query: 359 EKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEMV 418
           E  +L + GK NR+R FADS+SKV+FQY  RH PL+ +DL+ASV  S+  E +  DVEM 
Sbjct: 357 EIGELQFAGKLNRSRTFADSHSKVLFQYAARHAPLRIEDLVASVQ-SNSMELESTDVEMQ 415

Query: 419 D 419
           D
Sbjct: 416 D 416

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	419
TAIR|locus:2117348	417	AT4G24880 [Arabidopsis thalian	0.990	0.995	0.655	3.8e-149
ZFIN|ZDB-GENE-030131-3464	365	snupn "snurportin 1" [Danio re	0.505	0.580	0.413	5.7e-43
UNIPROTKB|Q5ZI43	365	SNUPN "Snurportin-1" [Gallus g	0.439	0.504	0.424	1.1e-41
UNIPROTKB|Q2TBK8	362	SNUPN "Snurportin-1" [Bos taur	0.439	0.508	0.435	7.5e-41
UNIPROTKB|E2RL29	358	SNUPN "Uncharacterized protein	0.482	0.564	0.404	7.5e-41
UNIPROTKB|F1SJ72	363	SNUPN "Uncharacterized protein	0.482	0.556	0.409	7.5e-41
RGD|1303191	358	Snupn "snurportin 1" [Rattus n	0.455	0.533	0.419	9.6e-41
MGI|MGI:1913319	358	Snupn "snurportin 1" [Mus musc	0.455	0.533	0.419	1.6e-40
UNIPROTKB|C9K0X5	402	SNUPN "Snurportin-1" [Homo sap	0.453	0.472	0.414	2e-40
UNIPROTKB|O95149	360	SNUPN "Snurportin-1" [Homo sap	0.453	0.527	0.414	2e-40

TAIR|locus:2117348 AT4G24880 [Arabidopsis thaliana (taxid:3702)]

 Score = 1456 (517.6 bits), Expect = 3.8e-149, P = 3.8e-149
 Identities = 276/421 (65%), Positives = 319/421 (75%)

Query:     1 MAPPDLRRPFKRTAISDXXXXXXXXXXXXXXXXXDAQQQARCLASSVLSLQSQYPDPVPE 60
             MAP ++RRPFKR  ISD                 DAQQ+AR LASS++SLQS  PD  PE
Sbjct:     1 MAPHEIRRPFKRRPISDQQKRRELSLIRQTQHRSDAQQRARNLASSLISLQSSSPDVDPE 60

Query:    61 L--EIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDW 118
             +  E  PE    +     +   D+RQAS+LRGPE RKWFA QLMLPEWMIDVPD LS DW
Sbjct:    61 ILSEAVPELVGTESE---SSSFDVRQASRLRGPEARKWFAKQLMLPEWMIDVPDNLSQDW 117

Query:   119 YVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIF 178
             YV ARPAGKRC VVSS+GTTVSR RNGS LH FPSALP GAR K  SG A SY ILDCIF
Sbjct:   118 YVLARPAGKRCFVVSSDGTTVSRVRNGSTLHLFPSALPGGARKKGASGPANSYSILDCIF 177

Query:   179 HELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYN 238
             HE DQTYYVIDMVCWRGYSLY+CT+EFRFFWL SKLAETGACD PS Y+KFRFS VP YN
Sbjct:   178 HESDQTYYVIDMVCWRGYSLYECTSEFRFFWLQSKLAETGACDPPSVYHKFRFSVVPFYN 237

Query:   239 CDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVIDTDSKGXXX 298
             CDQ GL+SAY  S+PY +DGLLFYNKHAHY TGNTPL L+WKDE CSQYVIDTD+ G   
Sbjct:   238 CDQSGLHSAYTGSLPYVRDGLLFYNKHAHYHTGNTPLVLIWKDESCSQYVIDTDNNGEVP 297

Query:   299 XXXXXXXXXXXDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLLKFAIGNGGLSFVDGKL 358
                        +GKL TSDDPPV F CL+ +F+++SGL SGSL++FAIG+GGL  VDG+ 
Sbjct:   298 NQQHIVLELQEEGKLVTSDDPPVPFSCLNADFVKQSGLSSGSLIRFAIGDGGLKCVDGRF 357

Query:   359 EKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASVSPSDDEENKPCDVEMV 418
             EK+DL Y+G SNRAR FADSYSK++FQYM RH+PLK +DL +++SP +D+++KP +VEM 
Sbjct:   358 EKADLQYIGVSNRARAFADSYSKIMFQYMARHSPLKVEDLASTISP-EDQQDKPPEVEMS 416

Query:   419 D 419
             D
Sbjct:   417 D 417

GO:0005634 "nucleus" evidence=ISM

ZFIN|ZDB-GENE-030131-3464 snupn "snurportin 1" [Danio rerio (taxid:7955)]

 Score = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 91/220 (41%), Positives = 129/220 (58%)

Query:    56 DPVPELEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLS 115
             D   E E E +S  Q E G   + +++    KL  P   K +A+QLML EW++DVP  LS
Sbjct:    74 DSEDEEEAEKKSL-QTENGADEEGMEVEPRKKL--P---KHYANQLMLSEWLVDVPADLS 127

Query:   116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILD 175
              DW +   P GKR +VV+S G+T S  ++G  ++ FPS +P G R     G  + Y ILD
Sbjct:   128 SDWLMVVCPVGKRSLVVASKGSTTSYTKSGYCVNRFPSLIPGGNRHNSALG--KDYTILD 185

Query:   176 CIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVP 235
             CI+ ++D+TYY++D++CWRG+ +YDC+ EFRF+WL SK+ E  +    S    FRF  + 
Sbjct:   186 CIYSDVDRTYYILDVMCWRGHPVYDCSTEFRFYWLQSKVDEVESLSEISKINPFRFVALS 245

Query:   236 VYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPL 275
               +C    +  A      Y  DGLLFY+K  HY  G+TPL
Sbjct:   246 SISCSTESIQMALAHEYSYKVDGLLFYHKETHYTPGSTPL 285

GO:0005634 "nucleus" evidence=IEA

GO:0006370 "7-methylguanosine mRNA capping" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0004484 "mRNA guanylyltransferase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0061015 "snRNA import into nucleus" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

UNIPROTKB|Q5ZI43 SNUPN "Snurportin-1" [Gallus gallus (taxid:9031)]

 Score = 442 (160.7 bits), Expect = 1.1e-41, P = 1.1e-41
 Identities = 79/186 (42%), Positives = 116/186 (62%)

Query:    90 GPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH 149
             G  + K +A+QLML EW++DVP  L  +W V   P GKR +VV+S G+T +  ++G  ++
Sbjct:    93 GRRLPKRYANQLMLSEWLVDVPVDLEQEWIVVVCPVGKRALVVASRGSTAAYTKSGFCVN 152

Query:   150 HFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFW 209
              FPS LP G R    + + + YCILDCI++E +QTYY++D++CWRG+ +YDC  +FRFFW
Sbjct:   153 RFPSLLPGGNRHN--TMNEKVYCILDCIYNEAEQTYYILDVMCWRGHPVYDCQTDFRFFW 210

Query:   210 LNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQ 269
             L+SK+ E       S    ++F  +  + C    L      + P+  DGLLFY+K  HY 
Sbjct:   211 LSSKIQEEEGLGEKSRINPYKFVGLQNFPCTSESLCEVLTTNFPFEVDGLLFYHKQTHYT 270

Query:   270 TGNTPL 275
              G+TPL
Sbjct:   271 PGSTPL 276

GO:0004484 "mRNA guanylyltransferase activity" evidence=IEA

GO:0006370 "7-methylguanosine mRNA capping" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0061015 "snRNA import into nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|Q2TBK8 SNUPN "Snurportin-1" [Bos taurus (taxid:9913)]

 Score = 434 (157.8 bits), Expect = 7.5e-41, P = 7.5e-41
 Identities = 81/186 (43%), Positives = 113/186 (60%)

Query:    90 GPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH 149
             G E+ K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G T +  ++G  ++
Sbjct:    92 GKELPKRYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRSLIVASQGLTSAYTKSGYCVN 151

Query:   150 HFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFW 209
              FPS LP G R    S + + Y ILDCI+ E++QTYYV+D++CWRG+  YDC  +FRF+W
Sbjct:   152 TFPSLLPGGNRRN--STTEKDYTILDCIYSEVNQTYYVLDVMCWRGHPFYDCQTDFRFYW 209

Query:   210 LNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQ 269
             L+SKL E       +    F+F  +  + C    L        P+  DGLLFY+K  HY 
Sbjct:   210 LHSKLPEEEGLGEKTKRNPFKFVGLKNFPCTPESLCKVLSMDFPFEVDGLLFYHKQTHYS 269

Query:   270 TGNTPL 275
              G+TPL
Sbjct:   270 PGSTPL 275

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0061015 "snRNA import into nucleus" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

UNIPROTKB|E2RL29 SNUPN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 434 (157.8 bits), Expect = 7.5e-41, P = 7.5e-41
 Identities = 85/210 (40%), Positives = 126/210 (60%)

Query:    66 ESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPA 125
             ES+ +++     +++DI    KL  P   K +A+QLML EW+IDVP  L  +W V   P 
Sbjct:    74 ESEEEEDKKD-DEEMDIDAVKKL--P---KRYANQLMLSEWLIDVPSDLGQEWIVVVCPV 127

Query:   126 GKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTY 185
             GKR ++V+S G+T +  ++G  ++ F S LP G   K  S +A+ Y ILDCI+ E++QTY
Sbjct:   128 GKRALIVASRGSTSAYTKSGYCVNRFSSLLPGG--NKRNSTTAKDYTILDCIYSEVNQTY 185

Query:   186 YVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLY 245
             YV+D++CWRG+  YDC  +FRF+W++SKL E    +  +    F+F  +  + C    L 
Sbjct:   186 YVLDVMCWRGHPFYDCQTDFRFYWMHSKLPEEEGLEEKTKLNPFKFVGLKNFPCTPESLC 245

Query:   246 SAYIESVPYAKDGLLFYNKHAHYQTGNTPL 275
                    P+  DGLLFY+K  HY  G+TPL
Sbjct:   246 KVLSMDFPFEVDGLLFYHKQTHYSPGSTPL 275

GO:0061015 "snRNA import into nucleus" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1SJ72 SNUPN "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 434 (157.8 bits), Expect = 7.5e-41, P = 7.5e-41
 Identities = 86/210 (40%), Positives = 125/210 (59%)

Query:    66 ESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPA 125
             ES+ ++E     +++DI    KL  P   K +A+QLML EW+IDVP  L  +W V   P 
Sbjct:    75 ESEEEEEKKD-DEEMDIDIGKKL--P---KHYANQLMLSEWLIDVPSDLGQEWIVVVCPV 128

Query:   126 GKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTY 185
             GKR ++V+S G+T +  ++G  ++ F S LP G R    S +A+ Y ILDCI+ E++QTY
Sbjct:   129 GKRALIVASRGSTSAYTKSGYCVNRFSSLLPGGNRRN--STTAKDYTILDCIYSEVNQTY 186

Query:   186 YVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLY 245
             YV+D++CWRG+  YDC  +FRF+W++SKL E       +    F+F  +  + C    L 
Sbjct:   187 YVLDVMCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCTPESLC 246

Query:   246 SAYIESVPYAKDGLLFYNKHAHYQTGNTPL 275
                    P+  DGLLFY+K  HY  G+TPL
Sbjct:   247 EVLSMDFPFEVDGLLFYHKQTHYSPGSTPL 276

GO:0061015 "snRNA import into nucleus" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

RGD|1303191 Snupn "snurportin 1" [Rattus norvegicus (taxid:10116)]

 Score = 433 (157.5 bits), Expect = 9.6e-41, P = 9.6e-41
 Identities = 83/198 (41%), Positives = 119/198 (60%)

Query:    78 KDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGT 137
             +++D+    KL  P   K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+
Sbjct:    85 EEMDLDPVKKL--P---KRYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGS 139

Query:   138 TVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYS 197
             T +  ++G  ++ F S LP G R    S +A+ Y ILDCI+ E++QTYYV+D++CWRG+ 
Sbjct:   140 TSAYTKSGYCVNRFSSLLPGGNRRN--STTAKDYTILDCIYSEVNQTYYVLDVMCWRGHP 197

Query:   198 LYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKD 257
              YDC  +FRF+W+NSKL E       +    F+F  +  + C    L        P+  D
Sbjct:   198 FYDCQTDFRFYWMNSKLPEEEGLGEKTKINPFKFVGLKNFPCTPESLCKVLSMDFPFEVD 257

Query:   258 GLLFYNKHAHYQTGNTPL 275
             GLLFY+K  HY  G+TPL
Sbjct:   258 GLLFYHKQTHYSPGSTPL 275

GO:0000339 "RNA cap binding" evidence=TAS

GO:0005643 "nuclear pore" evidence=TAS

GO:0005737 "cytoplasm" evidence=IEA

GO:0005846 "nuclear cap binding complex" evidence=TAS

GO:0006606 "protein import into nucleus" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0061015 "snRNA import into nucleus" evidence=IEA

MGI|MGI:1913319 Snupn "snurportin 1" [Mus musculus (taxid:10090)]

 Score = 431 (156.8 bits), Expect = 1.6e-40, P = 1.6e-40
 Identities = 83/198 (41%), Positives = 120/198 (60%)

Query:    78 KDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGT 137
             +++DI  + KL  P   K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+
Sbjct:    85 EEMDIDPSKKL--P---KRYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGS 139

Query:   138 TVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYS 197
             T +  ++G  ++ F S LP G R    S +A+ Y ILDCI+ E++QTYYV+D++CWRG+ 
Sbjct:   140 TSAYTKSGYCVNRFSSLLPGGNRRN--STTAKDYTILDCIYSEVNQTYYVLDVMCWRGHP 197

Query:   198 LYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKD 257
              YDC  +FRF+W++SKL E       +    F+F  +  + C    L        P+  D
Sbjct:   198 FYDCQTDFRFYWMHSKLPEEEGLGEKTKINPFKFVGLKNFPCTPESLCEVLSMDFPFEVD 257

Query:   258 GLLFYNKHAHYQTGNTPL 275
             GLLFY+K  HY  G+TPL
Sbjct:   258 GLLFYHKQTHYSPGSTPL 275

GO:0003674 "molecular_function" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0061015 "snRNA import into nucleus" evidence=IEA

UNIPROTKB|C9K0X5 SNUPN "Snurportin-1" [Homo sapiens (taxid:9606)]

 Score = 430 (156.4 bits), Expect = 2.0e-40, P = 2.0e-40
 Identities = 82/198 (41%), Positives = 120/198 (60%)

Query:    78 KDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGT 137
             +++DI    KL  P   K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+
Sbjct:   126 EEMDIDTVKKL--P---KHYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGS 180

Query:   138 TVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYS 197
             T +  ++G  ++ F S LP G R    + +A+ Y ILDCI++E++QTYYV+D++CWRG+ 
Sbjct:   181 TSAYTKSGYCVNRFSSLLPGGNRR---NSTAKDYTILDCIYNEVNQTYYVLDVMCWRGHP 237

Query:   198 LYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKD 257
              YDC  +FRF+W++SKL E       +    F+F  +  + C    L        P+  D
Sbjct:   238 FYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFEVD 297

Query:   258 GLLFYNKHAHYQTGNTPL 275
             GLLFY+K  HY  G+TPL
Sbjct:   298 GLLFYHKQTHYSPGSTPL 315

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0061015 "snRNA import into nucleus" evidence=IEA

UNIPROTKB|O95149 SNUPN "Snurportin-1" [Homo sapiens (taxid:9606)]

 Score = 430 (156.4 bits), Expect = 2.0e-40, P = 2.0e-40
 Identities = 82/198 (41%), Positives = 120/198 (60%)

Query:    78 KDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGT 137
             +++DI    KL  P   K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+
Sbjct:    84 EEMDIDTVKKL--P---KHYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGS 138

Query:   138 TVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYS 197
             T +  ++G  ++ F S LP G R    + +A+ Y ILDCI++E++QTYYV+D++CWRG+ 
Sbjct:   139 TSAYTKSGYCVNRFSSLLPGGNRR---NSTAKDYTILDCIYNEVNQTYYVLDVMCWRGHP 195

Query:   198 LYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKD 257
              YDC  +FRF+W++SKL E       +    F+F  +  + C    L        P+  D
Sbjct:   196 FYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFEVD 255

Query:   258 GLLFYNKHAHYQTGNTPL 275
             GLLFY+K  HY  G+TPL
Sbjct:   256 GLLFYHKQTHYSPGSTPL 273

GO:0006606 "protein import into nucleus" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0061015 "snRNA import into nucleus" evidence=IEA

GO:0000339 "RNA cap binding" evidence=TAS

GO:0005643 "nuclear pore" evidence=TAS

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0034660 "ncRNA metabolic process" evidence=TAS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00017939001	SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (419 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00037236001	SubName- Full=Chromosome chr16 scaffold_86, whole genome shotgun sequence; (869 aa)					•	•			0.839
	GSVIVG00001303001	SubName- Full=Chromosome chr8 scaffold_115, whole genome shotgun sequence; (872 aa)					•	•			0.838
	GSVIVG00014046001	SubName- Full=Putative uncharacterized protein (Chromosome chr16 scaffold_10, whole genome shot [...] (1076 aa)					•		•		0.632

---

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	419
cd09232	186	cd09232, Snurportin-1_C, C-terminal m3G cap-bindin	4e-90
cd06846	182	cd06846, Adenylation_DNA_ligase_like, Adenylation	1e-13

>gnl|CDD|185717 cd09232, Snurportin-1_C, C-terminal m3G cap-binding domain of nuclear import adaptor snurportin-1

 Score =  270 bits (692), Expect = 4e-90
 Identities = 101/190 (53%), Positives = 125/190 (65%), Gaps = 7/190 (3%)

Query: 96  WFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSAL 155
            +A+QLML EWM++VPD LS +W V   P GKRC+VV+S G TV+R +NG  LH F SAL
Sbjct: 1   LYANQLMLSEWMVEVPDDLSEEWLVVPCPVGKRCLVVASKGKTVARSKNGRTLHRFSSAL 60

Query: 156 PSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLA 215
           P G+R    SG    Y ILDCI++E D+TYYV+D++CW G+ LYDC  EFRFFWL SKL 
Sbjct: 61  PGGSRKTSNSG----YTILDCIYNEDDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLE 116

Query: 216 ETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAY---IESVPYAKDGLLFYNKHAHYQTGN 272
           E    D PS    FRF  +P + C +  L SAY   +   PY  DGLLFY+K +HY  G+
Sbjct: 117 ELPELDEPSEKNPFRFVPLPYFPCTKESLQSAYSGPLNDDPYELDGLLFYHKESHYTPGS 176

Query: 273 TPLALVWKDE 282
           TPL L  KD 
Sbjct: 177 TPLVLWLKDY 186

Snurportin-1 (SPN1 or SNUPN) is a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs), which are assembled in the cytoplasm. After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1), which also transports the non-capped U snRNPs. The U snRNPs are essential elements of the spliceosome, which catalyzes the excision of introns and the ligation of exons to form a mature mRNA. SPN1 contains two domains, an N-terminal importin beta-binding (IBB) domain and a C-terminal m3G cap-binding domain. Length = 186

>gnl|CDD|185704 cd06846, Adenylation_DNA_ligase_like, Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases

 Score = 69.0 bits (169), Expect = 1e-13
 Identities = 45/194 (23%), Positives = 68/194 (35%), Gaps = 26/194 (13%)

Query: 100 QLMLPEWMIDVPDR--LSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPS 157
             +L   + +         ++YV  +  GKR ++V+ NG   +  R G         LPS
Sbjct: 1   PQLLNPILEEALSEYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTG-----LEVPLPS 55

Query: 158 -GARTKDPSGSAQSYCILDCI-------FHELDQTYYVIDMVCWRGYSLYDCTAEFRFFW 209
                ++       + ILD               TYY  D+V   G  L D     RF +
Sbjct: 56  ILIPGRELLTLKPGF-ILDGELVVENREVANPKPTYYAFDVVPLSGVGLRDLPYSDRFAY 114

Query: 210 LNSKLAETGACDAPSHYYKFRFST-VPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHY 268
           L S L E    D      K       P Y+     L     +     K+GL+F +  A Y
Sbjct: 115 LKSLLKEFEGLD----PVKLVPLENAPSYDETLDDLLE---KLKKKGKEGLVFKHPDAPY 167

Query: 269 QT--GNTPLALVWK 280
           +   G++   L  K
Sbjct: 168 KGRPGSSGNQLKLK 181

ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity. Length = 182

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	419
KOG3132	325	consensus m3G-cap-specific nuclear import receptor	100.0
cd09232	186	Snurportin-1_C C-terminal m3G cap-binding domain o	100.0
cd06846	182	Adenylation_DNA_ligase_like Adenylation domain of	99.68
PF01331	192	mRNA_cap_enzyme: mRNA capping enzyme, catalytic do	99.47
PF11538	40	Snurportin1: Snurportin1; InterPro: IPR024721 Snur	99.3
cd07895	215	Adenylation_mRNA_capping Adenylation domain of GTP	98.67
cd07906	190	Adenylation_DNA_ligase_LigD_LigC Adenylation domai	98.65
cd07897	207	Adenylation_DNA_ligase_Bac1 Adenylation domain of	98.18
cd07905	194	Adenylation_DNA_ligase_LigC Adenylation domain of	98.12
cd07903	225	Adenylation_DNA_ligase_IV Adenylation domain of DN	97.97
TIGR02779	298	NHEJ_ligase_lig DNA polymerase LigD, ligase domain	97.95
PRK08224	350	ligC ATP-dependent DNA ligase; Reviewed	97.93
cd07902	213	Adenylation_DNA_ligase_III Adenylation domain of D	97.91
PRK05972	860	ligD ATP-dependent DNA ligase; Reviewed	97.82
PF01068	202	DNA_ligase_A_M: ATP dependent DNA ligase domain; I	97.76
PRK07636	275	ligB ATP-dependent DNA ligase; Reviewed	97.74
TIGR00574	514	dnl1 DNA ligase I, ATP-dependent (dnl1). All prote	97.55
PRK09632	764	ATP-dependent DNA ligase; Reviewed	97.53
cd07901	207	Adenylation_DNA_ligase_Arch_LigB Adenylation domai	97.52
cd07898	201	Adenylation_DNA_ligase Adenylation domain of ATP-d	97.48
PLN03113	744	DNA ligase 1; Provisional	97.26
PRK09633	610	ligD ATP-dependent DNA ligase; Reviewed	97.21
cd07900	219	Adenylation_DNA_ligase_I_Euk Adenylation domain of	97.19
cd08039	235	Adenylation_DNA_ligase_Fungal Adenylation domain o	97.18
PRK09247	539	ATP-dependent DNA ligase; Validated	97.15
PRK01109	590	ATP-dependent DNA ligase; Provisional	97.08
PRK03180	508	ligB ATP-dependent DNA ligase; Reviewed	96.91
PHA00454	315	ATP-dependent DNA ligase	96.64
PHA02587	488	30 DNA ligase; Provisional	96.57
cd07896	174	Adenylation_kDNA_ligase_like Adenylation domain of	96.11
COG1793	444	CDC9 ATP-dependent DNA ligase [DNA replication, re	96.01
PRK09125	282	DNA ligase; Provisional	95.06
KOG0966	881	consensus ATP-dependent DNA ligase IV [Replication	86.0
TIGR02776	552	NHEJ_ligase_prk DNA ligase D. Members of this prot	85.89
KOG3132	325	consensus m3G-cap-specific nuclear import receptor	80.25

>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]

Probab=100.00  E-value=1.1e-96  Score=702.62  Aligned_cols=259  Identities=56%  Similarity=0.973  Sum_probs=238.8

Q ss_pred             CCCCCCCcCCCCC-CchHHH-HHHHHHHHHHHhHHHHHHHHhhhhhhhccccCCCCCCCCCCCCCCCCCccccCCCCccc
Q 014751            2 APPDLRRPFKRTA-ISDQQR-RRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPELEIEPESQPQQEAGPLTKD   79 (419)
Q Consensus         2 aph~~~~~~k~~~-~~~Q~~-RR~~~Le~Qk~~R~d~~~~aR~La~~~~~~~~~~~~~~~e~~~~~~~~e~~~~~~~~~~   79 (419)
                      +||||.+|||.+. ..+|++ ||+.+|++||.+|.|+++|+|+||.++|+    +        +  |++|      +  .
T Consensus        22 ~~hpR~sQykn~~s~aeQ~arrr~~llelQks~r~D~~~~~r~lA~dd~t----g--------~--Esee------~--k   79 (325)
T KOG3132|consen   22 LSHPRQSQYKNLTSDAEQRARRRASLLELQKSSRPDVDPEIRSLAVDDLT----G--------T--ESEE------S--K   79 (325)
T ss_pred             ccCchhhhhhhhhhHHHHHHHHHHHHHHhhhcCCCCccHHHHhhcccccc----c--------c--cchh------h--h
Confidence            7999999999986 445554 55569999999999999999999999886    2        1  1101      1  3


Q ss_pred             hhhhhhhhccCCcchhhhhhhcccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCC
Q 014751           80 LDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGA  159 (419)
Q Consensus        80 ~d~~~~~k~~gk~~rk~ya~qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~  159 (419)
                      .|++++++.+||+.+||||+||||||||+|||++|+++|+||+||+|||||||||+|+|++|+|+|+++++|+|+||||+
T Consensus        80 ~d~~~a~~~tgk~~~K~yA~qlMLsEWliDvP~~LsqdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~~v~rF~S~LPGGn  159 (325)
T KOG3132|consen   80 FDVRQASRLTGKEARKWYAKQLMLSEWLIDVPDNLSQDWYVVARPVGKRCLVVASRGTTVAYVKNGSTVHRFPSALPGGN  159 (325)
T ss_pred             hhhhHHhhhcchhHHHHHHHHhhhHHHhccCccccCcceEEEEeecCceEEEEecCCceEEEecCCeeEeeccccCCCCC
Confidence            56678888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCcEEEeeeEecCCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccC
Q 014751          160 RTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC  239 (419)
Q Consensus       160 ~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c  239 (419)
                      ++   .+.+++||||||||+|.|+|||||||||||||++|+|++|||||||+|||+|.+++++++.+|+|+|+++|+|||
T Consensus       160 rr---~~~a~~ytILDCIy~esnQTYYVlD~~cWrgh~~yec~~dFRffwl~SKL~E~~~l~~~t~~~~f~Fs~vp~~pC  236 (325)
T KOG3132|consen  160 RR---KGPANSYTILDCIYHESNQTYYVLDMVCWRGHSLYECTSDFRFFWLQSKLAETGALDPPTVYHKFRFSVVPFYPC  236 (325)
T ss_pred             cC---CCCcccceeeeeeecccCceEEEEEEEeecCcccccCchHHHHHHHhhhccccccCCCCCcCccceecccCCCCC
Confidence            85   467899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccCCCc
Q 014751          240 DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCS  285 (419)
Q Consensus       240 ~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s  285 (419)
                      ++++|..+|++++||.+||||||||..+|+||.||||||+|....+
T Consensus       237 ~q~~l~~~~~~~~pf~~DGLLFYhks~~yqpgqsplvgwlkp~ml~  282 (325)
T KOG3132|consen  237 DQSGLHSAYTGSLPFVRDGLLFYHKSVVYQPGQSPLVGWLKPWMLP  282 (325)
T ss_pred             CHHHHHHHHcCCCceeeeeEEEeecceeeCCCCCccccccchhhhH
Confidence            9999999999999999999999999999999999999999965544

>cd09232 Snurportin-1_C C-terminal m3G cap-binding domain of nuclear import adaptor snurportin-1

Probab=100.00  E-value=2e-69  Score=502.82  Aligned_cols=182  Identities=55%  Similarity=1.061  Sum_probs=175.6

Q ss_pred             hhhhcccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEee
Q 014751           97 FASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDC  176 (419)
Q Consensus        97 ya~qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDC  176 (419)
                      ||||||+||||+++|+||+++|+|+|||+||||||||++|.|++|+|+|++++.|+|.||||+..+    ..+++|||||
T Consensus         2 ~~~~lml~Ewm~~~p~~l~~~w~~~~~P~G~R~lvv~~~g~t~~~~r~g~~~~~f~s~lP~g~~~~----~~~g~tILDc   77 (186)
T cd09232           2 YANQLMLSEWMVEVPDDLSEEWLVVPCPVGKRCLVVASKGKTVARSKNGRTLHRFSSALPGGSRKT----SNSGYTILDC   77 (186)
T ss_pred             cccceechhhcccCCCccCcceEEEECcCceEEEEEEeCCEEEEEeCCCCEEEecccCCCCCCcCC----CCCCCEEEEE
Confidence            899999999999999999999999999999999999999999999999999999999999998642    5689999999


Q ss_pred             eEecCCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcCC---C
Q 014751          177 IFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESV---P  253 (419)
Q Consensus       177 Iy~e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~~~~---p  253 (419)
                      ||++.+.||||||||||||++++||+||||||||+|||+|.+.....+..|+|+|+.+|+|+|+.++|.++|+...   +
T Consensus        78 i~~~~~~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~~~~~~~~~f~~~p~~~~~~~~l~~~~~~~~~~~~  157 (186)
T cd09232          78 IYNEDDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDEPSEKNPFRFVPLPYFPCTKESLQSAYSGPLNDDP  157 (186)
T ss_pred             ecCCCCCEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCccccccccccCCceEEecCcccCcHHHHHHHHhcccccCC
Confidence            9999999999999999999999999999999999999999887777788999999999999999999999999998   9


Q ss_pred             CCcccEEeEeccccccCCCCcCeeeeccC
Q 014751          254 YAKDGLLFYNKHAHYQTGNTPLALVWKDE  282 (419)
Q Consensus       254 ~~~DGLLFYHKea~Y~~G~TPLv~~wkD~  282 (419)
                      +++||||||||+++|++|.||||+||||+
T Consensus       158 ~e~DGLlFyhk~~~Y~~G~tPlvl~wKp~  186 (186)
T cd09232         158 YELDGLLFYHKESHYTPGSTPLVLWLKDY  186 (186)
T ss_pred             CCCceEEEEeCCCcccCcCCCcEEEecCC
Confidence            99999999999999999999999999985

Snurportin-1 (SPN1 or SNUPN) is a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs), which are assembled in the cytoplasm. After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1), which also transports the non-capped U snRNPs. The U snRNPs are essential elements of the spliceosome, which catalyzes the excision of introns and the ligation of exons to form a mature mRNA. SPN1 contains two domains, an N-terminal importin beta-binding (IBB) domain and a C-terminal m3G cap-binding domain.

>cd06846 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases

Probab=99.68  E-value=5.4e-16  Score=141.71  Aligned_cols=170  Identities=23%  Similarity=0.264  Sum_probs=141.2

Q ss_pred             cccccccccCCC--CCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeE
Q 014751          101 LMLPEWMIDVPD--RLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIF  178 (419)
Q Consensus       101 LMlsEWl~dvP~--dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy  178 (419)
                      .|++.|+...+.  ....+|++-+..-|.||+++..+|.+.+++|+|..+..+...+|....     ......|||||-+
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~e~K~DG~R~~~~~~~~~v~~~sR~g~~~~~~~~~~~~~~~-----~~~~~~~ilDGEl   76 (182)
T cd06846           2 QLLNPILEEALSEYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPGREL-----LTLKPGFILDGEL   76 (182)
T ss_pred             CccchhhhHHHhhccccCcEEEEEccCceEEEEEEcCCeEEEEeCCCCEEecccccccchHH-----hccCCCeeEEEEE
Confidence            378888887654  457899999999999999999999999999999988876666764110     1123469999998


Q ss_pred             ecCC-------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcC
Q 014751          179 HELD-------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIES  251 (419)
Q Consensus       179 ~e~~-------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~~~  251 (419)
                      .-.+       -+|||.|||+|+|..+.+++..-|+-+|++.+.+....      .++.+..++.++|+.+.+.+++...
T Consensus        77 v~~~~~~~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~------~~~~i~~~~~~~~~~~~~~~~~~~~  150 (182)
T cd06846          77 VVENREVANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGL------DPVKLVPLENAPSYDETLDDLLEKL  150 (182)
T ss_pred             EeccCCCccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccC------CceeEEEeecccccchHHHHHHHHh
Confidence            7654       38999999999999999999999999999999775321      3577788888898877788888777


Q ss_pred             CCCCcccEEeEeccccc--cCCCCcCeeeecc
Q 014751          252 VPYAKDGLLFYNKHAHY--QTGNTPLALVWKD  281 (419)
Q Consensus       252 ~p~~~DGLLFYHKea~Y--~~G~TPLv~~wkD  281 (419)
                      ...-.||++|-+.++.|  .+|.++.++.||.
T Consensus       151 ~~~g~EGvi~K~~~s~Y~~~~gr~~~wlK~Kp  182 (182)
T cd06846         151 KKKGKEGLVFKHPDAPYKGRPGSSGNQLKLKP  182 (182)
T ss_pred             hhcCCceEEEEcCCCCccccCCCCCceEeecC
Confidence            77889999999999999  9999999999984

ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved seq

>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate

Probab=99.47  E-value=3.2e-13  Score=124.95  Aligned_cols=159  Identities=21%  Similarity=0.397  Sum_probs=109.3

Q ss_pred             CceEEEEecCCcEEEEEeeCCeEEEEcCCCcE--EE--eeccCCCCCCCCCCCCCCCCCcEEEeeeEecC------CcEE
Q 014751          116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSI--LH--HFPSALPSGARTKDPSGSAQSYCILDCIFHEL------DQTY  185 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~--l~--~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~------~~ty  185 (419)
                      .+++|..=.-|.|+|+...++.+-..+++-..  +.  .|+....+.      .+.....||||+.+..+      .-+|
T Consensus        16 ~~Y~V~eKaDG~Ryll~i~~~~~ylidr~~~~~~v~~~~~p~~~~~~------~~~~~~~TLLDGElV~d~~~~~~~~~f   89 (192)
T PF01331_consen   16 KDYFVCEKADGTRYLLLITDNGVYLIDRKNNVFKVDNLHFPSKKDSS------DGRHHQDTLLDGELVLDKDPGEKKPRF   89 (192)
T ss_dssp             S-EEEEEEESSEEEEEEEEEEEEEEEETTS-EEEESSST-ECTTC--------TTCEGCSEEEEEEEEEEECTTCEEEEE
T ss_pred             CCcEEEECCCCcEEEEEEecceEEEEeCCCcEEEecCcccccccccc------cccccCCEEEEEEEEcccCCCCCceEE
Confidence            47788888999999999999877666666543  22  455544321      12235579999966533      4699


Q ss_pred             EEEEEEeeCCcccccccchhhHHHhhhhccccCCC-----C-CCCCCCCCceeccccccCChHhH--HHHHhcCCCCCcc
Q 014751          186 YVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGAC-----D-APSHYYKFRFSTVPVYNCDQRGL--YSAYIESVPYAKD  257 (419)
Q Consensus       186 YVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~-----~-~~s~~n~~~F~~lp~~~c~~~~L--~~~~~~~~p~~~D  257 (419)
                      ||.|+|+|+|..+.+++...|+.||+..+.+....     . ...+..||.+..-+.++......  ...+....+++.|
T Consensus        90 lifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~~~~~~~~~~~~pf~i~~K~~~~~~~~~~~~~~~~~~~l~h~~D  169 (192)
T PF01331_consen   90 LIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAELKSGIIKKKKEPFSIRIKDFFPIYQIEKLLFEEFIPKLPHETD  169 (192)
T ss_dssp             EEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHHCHTTSCTCTTSSSEEEE---EEGGGHHHHCHHCCCCCTTSTEE
T ss_pred             EEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhccccccccccccceeeeccccHHHHhhHHHHHHHhhccCCCCCC
Confidence            99999999999999999999999999887763211     1 11223566666667776643322  3344567889999


Q ss_pred             cEEeEeccccccCCCCcCeeeec
Q 014751          258 GLLFYNKHAHYQTGNTPLALVWK  280 (419)
Q Consensus       258 GLLFYHKea~Y~~G~TPLv~~wk  280 (419)
                      ||+|.+.+..|.+|..+-++=||
T Consensus       170 GLIFtp~~~pY~~Gt~~~llKWK  192 (192)
T PF01331_consen  170 GLIFTPVNTPYVPGTCPNLLKWK  192 (192)
T ss_dssp             EEEEEESSSB--SEEEEEEEEE-
T ss_pred             EEEEecCCCCccCCCCCccEeeC
Confidence            99999999999999999999997

X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.

>PF11538 Snurportin1: Snurportin1; InterPro: IPR024721 Snurportin-1 is a nuclear import receptor that contains an N-terminal importin beta binding domain which is essential for its function as an snRNP-specific nuclear import receptor []

Probab=99.30  E-value=1.9e-12  Score=93.51  Aligned_cols=39  Identities=31%  Similarity=0.330  Sum_probs=35.3

Q ss_pred             CCCCCcCCCCC-CchHHHHHHHHHHHHHHhHHHHHHHHhh
Q 014751            4 PDLRRPFKRTA-ISDQQRRRELSLQRQSQNRRDAQQQARC   42 (419)
Q Consensus         4 h~~~~~~k~~~-~~~Q~~RR~~~Le~Qk~~R~d~~~~aR~   42 (419)
                      |||+++||.+. +.+|++||+++|++||++|+|++||||+
T Consensus         1 HPR~sqYK~~~~~~~Q~eRR~~~Le~QK~kR~d~~~~aR~   40 (40)
T PF11538_consen    1 HPRLSQYKNKGSALDQEERRREFLERQKNKRLDYVNHARR   40 (40)
T ss_dssp             -TTCSCTT-TTTSCSHHHHHHHHHHHHHSHHSHHHHHHHH
T ss_pred             CccHHHhhcccchHhHHHHHHHHHHHHHHHhHHHHHhccC
Confidence            89999999996 7799999999999999999999999995

Snurportin-1 interacts with m3G-cap where it enhances the m3G-cap dependent nuclear import of U snRNPs in Xenopus laevis oocytes and digitonin-permeabilized HeLa cells []. This entry represents the snurportin-1 N-terminal importin beta binding domain (IBB). The essential role of the IBB domain for snurportin-1 function suggests that snurportin-1 cooperates with importin beta in mediating nuclear import of snRNPs.; GO: 0005515 protein binding; PDB: 3LWW_D 3NC0_E 3NBZ_E 2Q5D_C 3NBY_B 3GB8_B 3GJX_B 2QNA_B 2P8Q_B.

>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes

Probab=98.67  E-value=4.5e-07  Score=85.52  Aligned_cols=162  Identities=17%  Similarity=0.293  Sum_probs=113.4

Q ss_pred             CceEEEEecCCcEEEEEeeC-CeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEecCCc------EEEEE
Q 014751          116 HDWYVFARPAGKRCIVVSSN-GTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQ------TYYVI  188 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas~-G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~~------tyYVL  188 (419)
                      .+|++-.=--|-||+++..+ |.+..++++|..+....-.+|.....    .....-||||+=+.....      +|||.
T Consensus        41 ~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~~~~~~~~~~~~~~~~~~----~~~~~~~ilDGElv~~~~~~~~~~~~~vF  116 (215)
T cd07895          41 NDYFVCEKSDGVRYLLLITGRGEVYLIDRKNDVFKVPGLFFPRRKNL----EPHHQGTLLDGELVIDKVPGKKRPRYLIF  116 (215)
T ss_pred             CCeEEEEeEcCeEEEEEEecCCcEEEEeCCCCeEEeccccCCCcccc----cccccCeeeEEEEEEEcCCCceEEEEEEE
Confidence            57777777789999999998 99999999998766433344421110    111345999997775443      69999


Q ss_pred             EEEeeCCcccccccchhhHHHhhhhccccCCCC----C-CCCCCCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeE
Q 014751          189 DMVCWRGYSLYDCTAEFRFFWLNSKLAETGACD----A-PSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFY  262 (419)
Q Consensus       189 Dvl~W~g~~l~dceteFRffWl~SKl~E~~~~~----~-~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFY  262 (419)
                      |+|+++|.++.+.+..=|.-.|+.-+.+...-.    . .....++.+..-++++++ .+.+...+....+...|||+|-
T Consensus       117 DiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~k~~~~~~~~~~~~~~~~~~~~~~~EGlIfk  196 (215)
T cd07895         117 DILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRLKDFFPLYKIEKLFEKIIPKLPHENDGLIFT  196 (215)
T ss_pred             EEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEecceEeHHhHHHHHHhccccCCCCCCCEEEc
Confidence            999999999999999999988888776532100    0 011223455556677763 2333333322357889999999


Q ss_pred             eccccccCCCCcCeeeecc
Q 014751          263 NKHAHYQTGNTPLALVWKD  281 (419)
Q Consensus       263 HKea~Y~~G~TPLv~~wkD  281 (419)
                      ..++.|.+|.++.++=||.
T Consensus       197 ~~~~~Y~~Gr~~~~lKwKp  215 (215)
T cd07895         197 PNDEPYVPGTDKNLLKWKP  215 (215)
T ss_pred             cCCCCccCccCCcceeeCC
Confidence            9999999999998888873

RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.

>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases

Probab=98.65  E-value=3e-07  Score=85.14  Aligned_cols=156  Identities=20%  Similarity=0.245  Sum_probs=110.5

Q ss_pred             cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEe-eccCCCCCCCCCCCCCCCCCcEEEeeeEe
Q 014751          101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHH-FPSALPSGARTKDPSGSAQSYCILDCIFH  179 (419)
Q Consensus       101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~-F~S~LPgG~~~~~~~~~~~~ytILDCIy~  179 (419)
                      -||+.=.-.+|+  +++|++=+---|-||+|+...|...++||+|..+.. |+....-...      ....-|||||-+.
T Consensus         3 pmLa~~~~~~~~--~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~t~~~p~l~~~~~~------~~~~~~iLDGElv   74 (190)
T cd07906           3 PMLATLVDEPPD--GEDWLYEIKWDGYRALARVDGGRVRLYSRNGLDWTARFPELAEALAA------LPVRDAVLDGEIV   74 (190)
T ss_pred             CeECCcCCCCCC--CCCeEEEEeEceEEEEEEEECCEEEEEcCCCCcchhhhHHHHHHHHh------cCCCCEEEEeEEE
Confidence            366666655555  469999999999999999999999999999987642 4321100000      0122399999554


Q ss_pred             c-------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceecc
Q 014751          180 E-------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTV  234 (419)
Q Consensus       180 e-------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~l  234 (419)
                      -                         ..-+|||.|||..+|.++.+=+..=|+-.|.+-+...          +-++...
T Consensus        75 ~~~~~~~~~F~~l~~~~~~~~~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~----------~~~i~~~  144 (190)
T cd07906          75 VLDEGGRPDFQALQNRLRLRRRLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAG----------SPRLRVS  144 (190)
T ss_pred             EECCCCCCCHHHHHHhhcccchhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccC----------CCcEEEC
Confidence            2                         1246999999999999988888888999888877653          2245667


Q ss_pred             ccccCChHhHHHHHhcCCCCCcccEEeEeccccccCCC-CcCee
Q 014751          235 PVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGN-TPLAL  277 (419)
Q Consensus       235 p~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~-TPLv~  277 (419)
                      |++....+.+   +.....--.+|+++-+.++.|.+|. |+.++
T Consensus       145 ~~~~~~~~~~---~~~~~~~g~EGiv~K~~~s~Y~~g~rs~~wl  185 (190)
T cd07906         145 EHFEGGGAAL---FAAACELGLEGIVAKRADSPYRSGRRSRDWL  185 (190)
T ss_pred             ceEcCCHHHH---HHHHHHcCCcEEEEecCCCCcCCCCCCCccE
Confidence            7777664332   3222233579999999999999999 87543

Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic cor

>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases

Probab=98.18  E-value=2.3e-05  Score=73.97  Aligned_cols=163  Identities=20%  Similarity=0.275  Sum_probs=113.9

Q ss_pred             cccccccccCCCCC--CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeee
Q 014751          101 LMLPEWMIDVPDRL--SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCI  177 (419)
Q Consensus       101 LMlsEWl~dvP~dL--~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCI  177 (419)
                      -||++=.-.+|+.+  ..+|++=+==-|-||++....|....+||+|..+. .|+....--.       .-..-||||+=
T Consensus         7 pmLA~~~~~~~~~~~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~-------~l~~~~iLDGE   79 (207)
T cd07897           7 FMLAHPLEDDPEDLGDPSDWQAEWKWDGIRGQLIRRGGEVFLWSRGEELITGSFPELLAAAE-------ALPDGTVLDGE   79 (207)
T ss_pred             ceeCCcCCCchhhhcCcccEEEEEeEceEEEEEEEcCCEEEEEeCCCCcccccchHHHHHHH-------hCCCCeEEEeE
Confidence            35666555555532  34788888788999999999999999999998765 3543211000       00124999984


Q ss_pred             Ee---cC-------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCC
Q 014751          178 FH---EL-------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKF  229 (419)
Q Consensus       178 y~---e~-------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~  229 (419)
                      ..   ..                         .-+|+|.|||..+|.++.+.+..=|.--|.+-+.+.+         .-
T Consensus        80 lv~~~~~~~~~F~~l~~r~~~~~~~~~~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~~~---------~~  150 (207)
T cd07897          80 LLVWRDGRPLPFNDLQQRLGRKTVGKKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLP---------PP  150 (207)
T ss_pred             EEEecCCCccCHHHHHHHhcccccchhhHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhhcC---------CC
Confidence            32   10                         1279999999999999999998888888888665421         13


Q ss_pred             ceeccccccCC-hHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeec
Q 014751          230 RFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK  280 (419)
Q Consensus       230 ~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wk  280 (419)
                      .+.+.|+..|+ .+.+.++|......-..|+++-..++.|.+|..- -.|||
T Consensus       151 ~i~~~~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Grr~-~~W~K  201 (207)
T cd07897         151 RLDLSPLIAFADWEELAALRAQSRERGAEGLMLKRRDSPYLVGRKK-GDWWK  201 (207)
T ss_pred             ceeecceEecCCHHHHHHHHHHHHHcCCeEEEEeCCCCCcCCCCcC-CCeeE
Confidence            55667777774 4667777765555568999999999999999643 23565

Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.

>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases

Probab=98.12  E-value=4.9e-05  Score=70.96  Aligned_cols=160  Identities=19%  Similarity=0.229  Sum_probs=111.7

Q ss_pred             cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeEe
Q 014751          101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFH  179 (419)
Q Consensus       101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~  179 (419)
                      -||+.-...+|+  ..+|++=+==-|-||+++...|.+..+|++|..+. .||....-- ..     ....-+||||=.-
T Consensus         3 PmLa~~~~~~~~--~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~~~~~~-~~-----~~~~~~iLDGElv   74 (194)
T cd07905           3 PMLARAVDALPE--PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAA-RA-----LLPPGCVLDGELV   74 (194)
T ss_pred             ceeCCccCCCCC--CCceEEEeeeceEEEEEEEeCCEEEEEeCCCCchhhhhHHHHHHH-Hh-----hCCCCEEEEeEEE
Confidence            367666666665  56899988889999999999999999999998765 344321100 00     0011389998543


Q ss_pred             c----------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCce
Q 014751          180 E----------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRF  231 (419)
Q Consensus       180 e----------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F  231 (419)
                      -                            ..-+|+|.|||..+|.++.+.+..=|.--|.+-+.+.          .-.+
T Consensus        75 ~~~~~~~~F~~l~~r~~~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~----------~~~i  144 (194)
T cd07905          75 VWRGGRLDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGW----------GPPL  144 (194)
T ss_pred             EEcCCCCCHHHHHHHhcccccchhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhccc----------CCCe
Confidence            1                            1137999999999999999999998888888777543          1234


Q ss_pred             eccccccCChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751          232 STVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE  282 (419)
Q Consensus       232 ~~lp~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~  282 (419)
                      ..+|... +.+.+.+++.....--..|+++-..++.|++|. .  .|||=.
T Consensus       145 ~~~~~~~-~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Gr-~--~WlK~K  191 (194)
T cd07905         145 HLSPATT-DRAEAREWLEEFEGAGLEGVVAKRLDGPYRPGE-R--AMLKVK  191 (194)
T ss_pred             EECCccC-CHHHHHHHHHHHHHCCCceEEEeCCCCCcCCCC-C--cEEEEe
Confidence            5556432 334455555544445578999999999999998 3  688743

Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is

>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV

Probab=97.97  E-value=6e-05  Score=71.49  Aligned_cols=156  Identities=17%  Similarity=0.231  Sum_probs=106.7

Q ss_pred             CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCC-CC--CCCCCCCCCcEEEeee---EecC-------
Q 014751          116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGA-RT--KDPSGSAQSYCILDCI---FHEL-------  181 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~-~~--~~~~~~~~~ytILDCI---y~e~-------  181 (419)
                      .+|++=.==-|-||+|...+|....+||+|..+. .|+-..=... ..  ...-.....-+||||=   ++..       
T Consensus        33 ~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~~~~l~~~~~~~~~~~iLDGElv~~~~~~~~~~~f  112 (225)
T cd07903          33 KPFYIETKLDGERIQLHKDGNEFKYFSRNGNDYTYLYGASLTPGSLTPYIHLAFNPKVKSCILDGEMVVWDKETKRFLPF  112 (225)
T ss_pred             CeEEEEEeeCceEEEEEecCCEEEEEeCCCccccccccccccccccchhhhhhccccCcEEEeceEEEEEEcCcCeeccc
Confidence            4666666667999999999999999999998765 3442210000 00  0000011234899973   3221       


Q ss_pred             -----------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCCh-Hh
Q 014751          182 -----------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQ-RG  243 (419)
Q Consensus       182 -----------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~-~~  243 (419)
                                       .-+|+|.|||..+|.++.+.+..=|.-=|.+-+.+.          +.++..+|.+.++. +.
T Consensus       113 ~~l~~~~~~~~~~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~~~~~----------~~~i~~~~~~~~~~~~~  182 (225)
T cd07903         113 GTLKDVAKLREVEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITPI----------PGRLEVVKRTEASTKEE  182 (225)
T ss_pred             hHHHHHHhhcccccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHhcCCC----------CCeEEEEEEEeCCCHHH
Confidence                             136999999999999999988888877777665432          13566778887754 66


Q ss_pred             HHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeecc
Q 014751          244 LYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKD  281 (419)
Q Consensus       244 L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD  281 (419)
                      +.+++.....--..|+++-..++.|.+| .|..++=||.
T Consensus       183 ~~~~~~~~~~~g~EGlv~K~~~s~Y~~g~Rs~~wlK~K~  221 (225)
T cd07903         183 IEEALNEAIDNREEGIVVKDLDSKYKPGKRGGGWIKIKP  221 (225)
T ss_pred             HHHHHHHHHHcCCceEEEecCCCCCccCCcCCCcEEech
Confidence            7777665555568999999999999999 6777766663

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more di

>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain

Probab=97.95  E-value=0.00038  Score=69.39  Aligned_cols=164  Identities=19%  Similarity=0.229  Sum_probs=109.3

Q ss_pred             cCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeEec---C---
Q 014751          109 DVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFHE---L---  181 (419)
Q Consensus       109 dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e---~---  181 (419)
                      +.|.+ +.+|++=+==-|-||++....|....+||+|..+. .|+... ....     .....-+||||=+.-   .   
T Consensus         6 ~~~~~-~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~-~~~~-----~~~~~~~iLDGElv~~d~~g~~   78 (298)
T TIGR02779         6 TTPPT-GDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPILA-AALA-----ALPILPAVLDGEIVVLDESGRS   78 (298)
T ss_pred             CCCCC-CCCEEEEEEEceEEEEEEEeCCEEEEEeCCCCchHhHhHHHH-HHHH-----hCCCCcEEEEeEEEEECCCCCC
Confidence            44433 46899888888999999999999999999998764 453211 0000     000123999984432   1   


Q ss_pred             ---------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccC-ChHhHH
Q 014751          182 ---------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC-DQRGLY  245 (419)
Q Consensus       182 ---------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c-~~~~L~  245 (419)
                                     .-+|+|.|||..+|.++.+-+..=|.--|.+-+.+.+.        +..+.  +. .+ +.+.+.
T Consensus        79 ~F~~l~~r~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~~--------~~~~~--~~-~~~~~~~~~  147 (298)
T TIGR02779        79 DFSALQNRLRAGRDRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKG--------PLAPD--RY-SVHFEGDGQ  147 (298)
T ss_pred             CHHHHHhhhhcCCCCceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccCC--------CceeE--ec-ccCchhHHH
Confidence                           12799999999999999888888888777776654321        11111  11 22 234455


Q ss_pred             HHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccCCCccceee
Q 014751          246 SAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVID  290 (419)
Q Consensus       246 ~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~~d  290 (419)
                      +++......-..|+++-+.++.|++|.|.-++=+|.....-++|-
T Consensus       148 ~~~~~~~~~g~EGiv~K~~ds~Y~~Grs~~WlK~K~~~~~d~vV~  192 (298)
T TIGR02779       148 ALLEAACRLGLEGVVAKRRDSPYRSGRSADWLKLKCRRRQEFVIG  192 (298)
T ss_pred             HHHHHHHHcCCceEEEeCCCCCCCCCCCCCcEEEccCCCCEEEEE
Confidence            555544455689999999999999999888777776555444443

DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.

>PRK08224 ligC ATP-dependent DNA ligase; Reviewed

Probab=97.93  E-value=0.00037  Score=71.40  Aligned_cols=168  Identities=19%  Similarity=0.213  Sum_probs=110.4

Q ss_pred             cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeEe
Q 014751          101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFH  179 (419)
Q Consensus       101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~  179 (419)
                      -||+.....+|+.  .+|++=+==-|-||++....|.+..+|+||.-+. +||-...-...      ....-+|||+=..
T Consensus        11 PMLA~~~~~~~~~--~~w~~E~K~DG~R~~~~~~~~~v~l~SRng~d~t~~fPel~~~~~~------~~~~~~vLDGEiV   82 (350)
T PRK08224         11 PMLAKSVDAIPPG--DGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRA------ELPERCVLDGEIV   82 (350)
T ss_pred             CccCCccCCCCCC--CcEEEEEeECeeEEEEEEECCEEEEEeCCCCCchhhhHHHHHHHHh------hCCCCEEEeeEEE
Confidence            5777766555553  5799988889999999999999999999998875 57652111000      0011389997432


Q ss_pred             c--C--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCce
Q 014751          180 E--L--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRF  231 (419)
Q Consensus       180 e--~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F  231 (419)
                      -  .                          .-+|||.|+|.++|.++.+-+..=|.=.|.+-+...         .  .+
T Consensus        83 v~~~~~~~F~~Lq~r~~~~~~~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~~~~---------~--~i  151 (350)
T PRK08224         83 VARDGGLDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAGS---------G--PV  151 (350)
T ss_pred             EeCCCCCCHHHHHhhhhccccchhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhcCCC---------C--cE
Confidence            1  1                          127999999999999999888777777777766321         1  24


Q ss_pred             eccccccCChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccCCCcccee
Q 014751          232 STVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVI  289 (419)
Q Consensus       232 ~~lp~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~~  289 (419)
                      .+.|.+.. .+...+++......-..|++.-..++.|.+|..- ++=+|-.....++|
T Consensus       152 ~~~~~~~~-~~~~~~~~~~a~~~G~EGIV~Kr~dS~Y~~Grr~-WlKiK~~~~~d~vI  207 (350)
T PRK08224        152 HLTPATTD-PATARRWFEEFEGAGLDGVIAKPLDGPYQPGKRA-MFKVKHERTADCVV  207 (350)
T ss_pred             EEecccCC-HHHHHHHHHHHHhCCCcEEEEeCCCCCcCCCCcC-EEEEccCCcEEEEE
Confidence            44554432 2344444543344568999999999999999765 44444433333433

>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III

Probab=97.91  E-value=7.8e-05  Score=70.71  Aligned_cols=145  Identities=17%  Similarity=0.166  Sum_probs=99.1

Q ss_pred             CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEe--ec---cCCCCCCCCCCCCCCCCCcEEEeee---Eec-------
Q 014751          116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHH--FP---SALPSGARTKDPSGSAQSYCILDCI---FHE-------  180 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~--F~---S~LPgG~~~~~~~~~~~~ytILDCI---y~e-------  180 (419)
                      .+|++=+==-|-||+|+-..|....+||+|.-+..  |+   ..++..-+       ...-|||||=   +..       
T Consensus        34 ~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~~~~~~~~~~~~~~-------~~~~~iLDGEiv~~d~~~g~~~~  106 (213)
T cd07902          34 NGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPKAFP-------HGHSMILDSEVLLVDTKTGKPLP  106 (213)
T ss_pred             CceEEEeccCCEEEEEEEcCCEEEEEcCCCcccccchhHHHHHHHHHhcc-------cccceeeeeEEEEEECCCCcccc
Confidence            35766666679999999888999999999976432  22   21221110       0123888863   322       


Q ss_pred             --------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHH
Q 014751          181 --------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLY  245 (419)
Q Consensus       181 --------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~  245 (419)
                                    ..-+|||.|||.++|.++.+.+..=|.-=|.+-+.+..          -++.+.|...++ .+.+.
T Consensus       107 F~~l~~~~~~~~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~----------~~~~~~~~~~~~~~~~l~  176 (213)
T cd07902         107 FGTLGIHKKSAFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIP----------NRIMLSEMKFVKKADDLS  176 (213)
T ss_pred             cchhhhhhccccccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCC----------CeEEEEEEEEcCCHHHHH
Confidence                          12479999999999999999888877766666553321          135666766663 45666


Q ss_pred             HHHhcCCCCCcccEEeEeccccccCCCCcCeeeec
Q 014751          246 SAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK  280 (419)
Q Consensus       246 ~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wk  280 (419)
                      +++.....--..|+++-+.++.|.+|..   .|||
T Consensus       177 ~~~~~~~~~g~EGvV~K~~~s~Y~~G~r---~W~K  208 (213)
T cd07902         177 AMIARVIKEGLEGLVLKDLKSVYEPGKR---HWLK  208 (213)
T ss_pred             HHHHHHHHCCCCeEEEeCCCCCccCCCC---CceE
Confidence            6665544556899999999999999986   4777

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nuc

>PRK05972 ligD ATP-dependent DNA ligase; Reviewed

Probab=97.82  E-value=0.00069  Score=76.62  Aligned_cols=194  Identities=19%  Similarity=0.221  Sum_probs=128.5

Q ss_pred             hcccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeE
Q 014751          100 QLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIF  178 (419)
Q Consensus       100 qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy  178 (419)
                      .-||+.-....|++  .+|++=.==-|-||++...+|....+|+||.-+. +|+...-.-. .     ..-.-+|||+=.
T Consensus       235 ~PMLAt~~~~~p~g--~~W~~E~K~DG~R~~a~~~gg~vrL~SRnG~d~T~~fPel~~~~~-~-----l~~~~~ILDGEI  306 (860)
T PRK05972        235 APQLATLVDRPPSG--DGWIYEIKFDGYRILARIEGGEVRLFTRNGLDWTAKLPALAKAAA-A-----LGLPDAWLDGEI  306 (860)
T ss_pred             CcccCccCCCCCCc--CceEEEeeeCcEEEEEEEECCEEEEEeCCCCccccccHHHHHHHH-h-----cCCCceeEeEEE
Confidence            35777755566654  7999988889999999999999999999998754 4553211000 0     001137999844


Q ss_pred             ec---------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccc
Q 014751          179 HE---------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVY  237 (419)
Q Consensus       179 ~e---------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~  237 (419)
                      .-                     ..-+|||.|||..+|.++.+.+..=|.--|++-+.+..        ++ .+...+++
T Consensus       307 Vvld~~G~~~F~~Lq~r~~~~~~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~--------~~-~i~~s~~~  377 (860)
T PRK05972        307 VVLDEDGVPDFQALQNAFDEGRTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAAR--------SD-RIRFSEHF  377 (860)
T ss_pred             EEECCCCCCCHHHHHHHhhccCCCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcC--------CC-cEEEecee
Confidence            31                     11379999999999999999988888888877665421        11 45667777


Q ss_pred             cCChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccCCCccceee--cCCCCCccccceEEEEEecCCce
Q 014751          238 NCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYVID--TDSKGQVLSQQQVVLELQEDGKL  313 (419)
Q Consensus       238 ~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~~d--~d~~g~~~~~q~vvL~~~~~g~l  313 (419)
                      .++.+.+.+   .....-..|++.-..++.|.+|.|.-|+=+|-....-++|-  +..+|....--++.|-+.++|+|
T Consensus       378 ~~~g~~ll~---~a~~~GlEGIVaKr~dS~Y~~GRs~~WlKiK~~~~~E~VIgGy~~~~Gkr~g~gSLLlGvyd~~~L  452 (860)
T PRK05972        378 DAGGDAVLA---SACRLGLEGVIGKRADSPYVSGRSEDWIKLKCRARQEFVIGGYTDPKGSRSGFGSLLLGVHDDDHL  452 (860)
T ss_pred             cchHHHHHH---HHHHcCCceEEEeCCCCCCCCCCCCCcEEEecCCCceEEEEEEeCCCCccccceeEEEEEecCCEE
Confidence            776544333   22334588999999999999999988777776666666664  33334311112345554444443

>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose

Probab=97.76  E-value=7.7e-05  Score=68.62  Aligned_cols=145  Identities=23%  Similarity=0.310  Sum_probs=104.5

Q ss_pred             CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEe-eccC-------CCCCCCCCCCCCCCCCcEEEeeeEec------
Q 014751          115 SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHH-FPSA-------LPSGARTKDPSGSAQSYCILDCIFHE------  180 (419)
Q Consensus       115 ~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~-F~S~-------LPgG~~~~~~~~~~~~ytILDCIy~e------  180 (419)
                      ...|++=+==-|-||+|+...|....+||+|..+.. |+..       +..+.          .-+||||=..-      
T Consensus        18 ~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~~~~~~~l~~~l~~~~~~~~----------~~~vLDGElv~~d~~~~   87 (202)
T PF01068_consen   18 GGPWYVEPKYDGVRCQIHKDGGGVRLFSRNGKDITSQFPELAEALRELLFPDG----------PDFVLDGELVVLDPNTG   87 (202)
T ss_dssp             TSCEEEEEEESSEEEEEEEETTEEEEEETTSSB-GGGHHHHHHHHHHHBCTSC----------TEEEEEEEEEEBETTTS
T ss_pred             CCCeEEEEeEeeEEeeeeeccccceeecccccchhhHHHHHHHHHHHHhcCCC----------CceEEEEEEEEEecCCC
Confidence            567888888889999999999999999999998765 4422       22211          12899983331      


Q ss_pred             -----------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccc
Q 014751          181 -----------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVY  237 (419)
Q Consensus       181 -----------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~  237 (419)
                                             ..-+|||.|||..+|.++.+.+.+=|.--|..-+..          ..-.+..++++
T Consensus        88 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~----------~~~~i~~~~~~  157 (202)
T PF01068_consen   88 SPLPFQELSGRLNRRSKKIPEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEP----------PPPRIRIVESY  157 (202)
T ss_dssp             SBCCHHHHHHHHBHSSSCHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-----------BTSSEEEEEEE
T ss_pred             cchhHHHHhhhhhhhcccchhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhcc----------CCCceeEeeee
Confidence                                   245899999999999999888888888888777721          12456777888


Q ss_pred             cCCh-HhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeec
Q 014751          238 NCDQ-RGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK  280 (419)
Q Consensus       238 ~c~~-~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wk  280 (419)
                      .|+. +.+.+++.....--..|+++-..++.|++|.. --.|||
T Consensus       158 ~~~~~~~~~~~~~~~~~~g~EG~v~K~~~~~Y~~Gkr-s~~w~K  200 (202)
T PF01068_consen  158 VVNSKEELEELFEEAIDQGFEGLVLKDPDSPYEPGKR-SSGWLK  200 (202)
T ss_dssp             EESSHHHHHHHHHHHHHTTSSEEEEEETTSSC-TTEE-EEEEEE
T ss_pred             cCCCHHHHHHHHHHHHHcCCceEEEECCCCccCCCCc-CCCcEE
Confidence            8854 55666554433344789999999999999965 234665

It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This domain belongs to a more diverse superfamily, including catalytic domain of the mRNA capping enzyme (IPR001339 from INTERPRO) and NAD-dependent DNA ligase (IPR001679 from INTERPRO) []. ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 1X9N_A 2CFM_A 3QWU_B 3GDE_A 2Q2U_C 2Q2T_A 1FVI_A 1P8L_A 2VUG_A ....

>PRK07636 ligB ATP-dependent DNA ligase; Reviewed

Probab=97.74  E-value=0.00091  Score=66.24  Aligned_cols=154  Identities=17%  Similarity=0.140  Sum_probs=104.4

Q ss_pred             ccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeEec
Q 014751          102 MLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFHE  180 (419)
Q Consensus       102 MlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e  180 (419)
                      ||+.-....|++  .+|++=+==-|-||++....|....+|++|..++ +||..+.-.-         ..-+|||+=..-
T Consensus         6 mLa~~~~~~~~~--~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~fPe~~~~~~---------~~~~vLDGElv~   74 (275)
T PRK07636          6 MLLESAKEPFNS--ENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVTAKFPELLNLDI---------PDGTVLDGELIV   74 (275)
T ss_pred             ccCCcCCCCCCC--CcEEEEEEEceeEEEEEEeCCEEEEEeCCCCCchhhhhhHHhhhc---------CCCEEEEeEEEE
Confidence            666654444443  5898888889999999999999999999998765 5665432211         112899985431


Q ss_pred             ------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceecccc
Q 014751          181 ------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPV  236 (419)
Q Consensus       181 ------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~  236 (419)
                                              ..-+|||.|+|.++|.++.+-+..=|.=.|.+-+...          + .+..+|.
T Consensus        75 ~d~~g~~~F~~l~~r~~~~~~~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~----------~-~~~~~~~  143 (275)
T PRK07636         75 LGSTGAPDFEAVMERFQSKKSTKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPH----------P-NVKIIEG  143 (275)
T ss_pred             ECCCCCCCHHHHHHHhccccccccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCC----------C-CEEEccc
Confidence                                    1237999999999999998888777766665554321          1 2345555


Q ss_pred             ccCChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeec
Q 014751          237 YNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWK  280 (419)
Q Consensus       237 ~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wk  280 (419)
                      ...+.+.+.+..   ..--..|+++-..++.|.+| .|.-++=.|
T Consensus       144 ~~~~~~~~~~~~---~~~g~EGiV~K~~ds~Y~~g~Rs~~WlKiK  185 (275)
T PRK07636        144 IEGHGTAYFELV---EERELEGIVIKKANSPYEINKRSDNWLKVI  185 (275)
T ss_pred             ccccHHHHHHHH---HHcCCcEEEEeCCCCCCCCCCCCCCeEEEe
Confidence            554444433322   22347799999999999998 677654444

>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1)

Probab=97.55  E-value=0.00055  Score=73.11  Aligned_cols=161  Identities=21%  Similarity=0.224  Sum_probs=117.0

Q ss_pred             hcccccccccCCCC---CCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccC--------CCCCCCCCCCCCC
Q 014751          100 QLMLPEWMIDVPDR---LSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSA--------LPSGARTKDPSGS  167 (419)
Q Consensus       100 qLMlsEWl~dvP~d---L~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~--------LPgG~~~~~~~~~  167 (419)
                      +-||++....+|+.   +..+|++=.==-|-||+|...+|....+||+|.-+. .|+..        +|.+         
T Consensus       168 ~PMLA~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~v~l~SR~g~~~t~~~pei~~~~~~~~~~~~---------  238 (514)
T TIGR00574       168 KPMLAERAKSIEEALKKKGNKFYVEYKYDGERVQIHKDGDKFKIFSRRLENYTYAYPEIFTEFIKEAFPGI---------  238 (514)
T ss_pred             ccccCCccCCHHHHHHHhCCceEEEEeecceEEEEEEcCCEEEEEcCCCcccccccchhHHHHHHHhcCcc---------
Confidence            45777766555532   234788888888999999998899999999998765 56543        3321         


Q ss_pred             CCCcEEEeee---EecC--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccC
Q 014751          168 AQSYCILDCI---FHEL--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETG  218 (419)
Q Consensus       168 ~~~ytILDCI---y~e~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~  218 (419)
                        .-||||+=   ++..                          .-+|||.|||..+|.++.+-+..=|.=-|++-+.+.+
T Consensus       239 --~~~ILDGElv~~d~~~g~~~~F~~l~~r~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~  316 (514)
T TIGR00574       239 --KSCILDGEMVAIDPETGKILPFQTLLRRKRRYDIDSMEKKVPVCLFVFDILYLNGESLIDEPLIERREILESILKPIP  316 (514)
T ss_pred             --ceeeecceEEEEEcCCCCCcCcHhHHhhhhhccccccccccceEEEEEEEEEECCcchhcCcHHHHHHHHHHhccCCC
Confidence              13788863   3221                          1389999999999999999888888888877664421


Q ss_pred             CCCCCCCCCCCceeccccccC-ChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeecc
Q 014751          219 ACDAPSHYYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKD  281 (419)
Q Consensus       219 ~~~~~s~~n~~~F~~lp~~~c-~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD  281 (419)
                                -.+..+|...+ +.+.+.+++.....--..|+++-..++.|++| .++-|+=||.
T Consensus       317 ----------~~i~~~~~~~~~~~e~~~~~~~~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K~  371 (514)
T TIGR00574       317 ----------NRIEIAEMKITSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKFKP  371 (514)
T ss_pred             ----------CcEEEEEEEecCCHHHHHHHHHHHHHcCCceEEEecCCCcccCCCCCCcceeCch
Confidence                      24667788777 45667776665555568999999999999999 7877666664

All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK09632 ATP-dependent DNA ligase; Reviewed

Probab=97.53  E-value=0.0026  Score=71.32  Aligned_cols=149  Identities=18%  Similarity=0.237  Sum_probs=107.1

Q ss_pred             CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc------CCCCCCCCCCCCCCCCCcEEEeeeEe---c----
Q 014751          115 SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS------ALPSGARTKDPSGSAQSYCILDCIFH---E----  180 (419)
Q Consensus       115 ~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S------~LPgG~~~~~~~~~~~~ytILDCIy~---e----  180 (419)
                      +.+|++=+==-|-||++...+|....+|+||.-+. +|+.      .||+            .-+|||+=..   +    
T Consensus       476 ~~~w~~E~K~DG~R~~~~~~~g~vrL~SRnG~d~T~~fPel~~~~~~l~~------------~~~ILDGEiVvld~~G~~  543 (764)
T PRK09632        476 ASQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAALAEDLAD------------HHVVLDGEIVALDDSGVP  543 (764)
T ss_pred             CCCEEEEEEECceeEEEEEeCCEEEEEeCCCCCccccchhHHHHHhhCCC------------cceeeeeEEEEeCCCCCC
Confidence            35798888788999999999999999999998655 5663      3332            1389997543   2    


Q ss_pred             -----------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHh
Q 014751          181 -----------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYI  249 (419)
Q Consensus       181 -----------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~  249 (419)
                                 ..-+|||.|||..+|.++.+.+..=|.=.|.+-+.+.           -.+...+.+..+.+.+   +.
T Consensus       544 ~F~~Lq~r~~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~~-----------~~i~~s~~~~~~~~~~---l~  609 (764)
T PRK09632        544 SFGLLQNRGRDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSG-----------GSLTVPPLLPGDGAEA---LA  609 (764)
T ss_pred             CHHHHhhhhhcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCCC-----------CcEEecceecccHHHH---HH
Confidence                       1248999999999999999988888887777766421           1234455566554443   33


Q ss_pred             cCCCCCcccEEeEeccccccCCC-CcCeeeeccCCCcccee
Q 014751          250 ESVPYAKDGLLFYNKHAHYQTGN-TPLALVWKDEKCSQYVI  289 (419)
Q Consensus       250 ~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~wkD~~~s~y~~  289 (419)
                      .....-..|++.-..++.|.+|. |.-++=+|-.....++|
T Consensus       610 ~a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK~~~~~e~VI  650 (764)
T PRK09632        610 YSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWRTQEVVI  650 (764)
T ss_pred             HHHHcCCcEEEEeCCCCCCCCCCcCCCeEEEecCCceEEEE
Confidence            22334588999999999999996 88766666555555555

>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases

Probab=97.52  E-value=0.0011  Score=62.44  Aligned_cols=150  Identities=17%  Similarity=0.137  Sum_probs=102.9

Q ss_pred             CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeE---ec----------
Q 014751          115 SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIF---HE----------  180 (419)
Q Consensus       115 ~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy---~e----------  180 (419)
                      ...|++=+==-|-||+|....+....+||+|.-+. .|+...+-....     ....-+|||+=.   .+          
T Consensus        24 ~~~~~~E~K~DG~R~~~~~~~~~v~~~SR~~~~~t~~~pel~~~~~~~-----~~~~~~iLDGElv~~~~~g~~~~F~~l   98 (207)
T cd07901          24 GGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLEDITNALPEVVEAVREL-----VKAEDAILDGEAVAYDPDGRPLPFQET   98 (207)
T ss_pred             CCcEEEEEeEcceeEEEEEeCCEEEEEeCCCccccchhhHHHHHHHhc-----CCCCCEEEeCEEEEECCCCCccCHHHH
Confidence            56777777778999999999999999999997653 554321110000     000128888633   21          


Q ss_pred             ----------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHh
Q 014751          181 ----------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRG  243 (419)
Q Consensus       181 ----------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~  243 (419)
                                      ..-+|||.|||..+|.++.+-+..-|.--|.+-+...           -.+.++|...|+ .+.
T Consensus        99 ~~r~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-----------~~i~~~~~~~~~~~~~  167 (207)
T cd07901          99 LRRFRRKYDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-----------EAILLAPRIVTDDPEE  167 (207)
T ss_pred             HHHhccccchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-----------CcEEEEEEEecCCHHH
Confidence                            0136999999999999988888887877777666432           135566777774 456


Q ss_pred             HHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeec
Q 014751          244 LYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWK  280 (419)
Q Consensus       244 L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wk  280 (419)
                      +.+++......-..|+++-+.++.|.+| .|.-++=||
T Consensus       168 ~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~Rs~~wlK~K  205 (207)
T cd07901         168 AEEFFEEALEAGHEGVMVKSLDSPYQAGRRGKNWLKVK  205 (207)
T ss_pred             HHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCeEEec
Confidence            6666655555568999999999999999 676554444

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adeny

>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases

Probab=97.48  E-value=0.0011  Score=61.92  Aligned_cols=149  Identities=19%  Similarity=0.222  Sum_probs=99.8

Q ss_pred             CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeE---ecCC---------
Q 014751          116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIF---HELD---------  182 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy---~e~~---------  182 (419)
                      ..|++=.==-|-||+++...|....+||+|..+. .|+-...-..       ....-|||||=+   +...         
T Consensus        21 ~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~i~~~~~-------~~~~~~vLDGElv~~~~~~~~~f~~~~~   93 (201)
T cd07898          21 AAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPELAAAAK-------ALPHEFILDGEILAWDDNRGLPFSELFK   93 (201)
T ss_pred             CeEEEEEeeceEEEEEEEeCCEEEEEcCCChhchhhhhhHHHHHH-------hCCCCEEEEEEEEEEeCCCCCcHHHHHH
Confidence            3566655556999999999999999999998753 3332111000       012359999743   2211         


Q ss_pred             ----------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCCh-HhHH
Q 014751          183 ----------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQ-RGLY  245 (419)
Q Consensus       183 ----------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~-~~L~  245 (419)
                                      -+|||.|||..+|.++.+=+..=|.==|..-+...          +-++..+|...++. +.+.
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~----------~~~i~~~~~~~~~~~~~~~  163 (201)
T cd07898          94 RLGRKFRDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEI----------PGRIRIAPALPVESAEELE  163 (201)
T ss_pred             HhcccccchhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCC----------CCcEEEeeeEEcCCHHHHH
Confidence                            36999999999999888766555554444433221          23456677777764 4466


Q ss_pred             HHHhcCCCCCcccEEeEeccccccCCC-CcCeeeecc
Q 014751          246 SAYIESVPYAKDGLLFYNKHAHYQTGN-TPLALVWKD  281 (419)
Q Consensus       246 ~~~~~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~wkD  281 (419)
                      .++.....--.+|+++-..++.|.+|. |.-|+=||.
T Consensus       164 ~~~~~~~~~g~EGim~K~~~s~Y~~g~Rs~~wlK~K~  200 (201)
T cd07898         164 AAFARARARGNEGLMLKDPDSPYEPGRRGLAWLKLKK  200 (201)
T ss_pred             HHHHHHHHcCCceEEEeCCCCCcCCCCcCCCcEEeCC
Confidence            666555555689999999999999996 877766664

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-f

>PLN03113 DNA ligase 1; Provisional

Probab=97.26  E-value=0.0019  Score=72.16  Aligned_cols=168  Identities=18%  Similarity=0.222  Sum_probs=114.7

Q ss_pred             hcccccccccCCC---CC-CCceEEEEecCCcEEEEEe-eCCeEEEEcCCCcEE-EeeccCCCCCCCCCCCCCCCCCcEE
Q 014751          100 QLMLPEWMIDVPD---RL-SHDWYVFARPAGKRCIVVS-SNGTTVSRERNGSIL-HHFPSALPSGARTKDPSGSAQSYCI  173 (419)
Q Consensus       100 qLMlsEWl~dvP~---dL-~~~Wl~vpcPvGkRcLVVa-s~G~T~ay~k~G~~l-~~F~S~LPgG~~~~~~~~~~~~ytI  173 (419)
                      .-||++..-.+++   .+ +.+|++=.==-|-||.|+. .+|....|+|||.-+ .+||-.+--....   ...+-.-||
T Consensus       371 ~PMLA~~~~~~~eil~~~~g~~~~~E~KyDGeR~QiH~~~~g~v~lfSRn~ed~T~~fPel~~~~~~~---~~~~~~~~I  447 (744)
T PLN03113        371 GPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERNTGKYPDVVVAISRL---KKPSVKSFI  447 (744)
T ss_pred             CCccCCCCCChHHHhhccCCCCEEEEEeeccceEEEEEecCCEEEEEeCCCCcccccchhHHHHHHHh---ccccCCCEE
Confidence            3688886655533   23 3468777666799999985 688999999999764 4676443111000   000112399


Q ss_pred             Eeee---EecCC-------------------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCC
Q 014751          174 LDCI---FHELD-------------------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSH  225 (419)
Q Consensus       174 LDCI---y~e~~-------------------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~  225 (419)
                      |||=   |+..+                         -+|||.|+|.+||.++.+.+..-|---|++-|.+.        
T Consensus       448 LDGEiVa~d~~~~~~lpFq~Lq~R~rk~~~~~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~~~~~~~--------  519 (744)
T PLN03113        448 LDCELVAYDREKKKILPFQILSTRARKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFEED--------  519 (744)
T ss_pred             EEeEEEEEECCCCCcCCHHHHHhhhccccchhccccceEEEEEeccccCccChhcCCHHHHHHHHHHHhccC--------
Confidence            9984   33221                         26999999999999999999888888888777552        


Q ss_pred             CCCCceeccccccC-ChHhHHHHHhcCCCCCcccEEeEe--ccccccCC-CCcCeeeec
Q 014751          226 YYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYN--KHAHYQTG-NTPLALVWK  280 (419)
Q Consensus       226 ~n~~~F~~lp~~~c-~~~~L~~~~~~~~p~~~DGLLFYH--Kea~Y~~G-~TPLv~~wk  280 (419)
                        +-+|...+...+ +.+.+...+......-..||+.-.  .++.|++| .+.-|+=||
T Consensus       520 --~~~i~~~~~~~~~~~ee~~~~~~~ai~~g~EGlmvK~l~~dS~Y~pGkRs~~WlKlK  576 (744)
T PLN03113        520 --PGFFQFATAITSNDLEEIQKFLDAAVDASCEGLIIKTLNKDATYEPSKRSNNWLKLK  576 (744)
T ss_pred             --CCcEEEeeeeccCCHHHHHHHHHHHHHcCCceEEEeccCCCCCccCCCCCCCeEEEe
Confidence              124666777665 466777777666666789999996  58899999 566655555

>PRK09633 ligD ATP-dependent DNA ligase; Reviewed

Probab=97.21  E-value=0.0099  Score=65.28  Aligned_cols=175  Identities=18%  Similarity=0.214  Sum_probs=112.1

Q ss_pred             cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccC------CCCCCCCCCCCCCCCCcEE
Q 014751          101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSA------LPSGARTKDPSGSAQSYCI  173 (419)
Q Consensus       101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~------LPgG~~~~~~~~~~~~ytI  173 (419)
                      -||+..-...|++  .+|++=.==-|-||++...+|....||+||.-+. +|+..      +++..+       +..-+|
T Consensus         3 PMLa~~~~~~p~g--~~w~~E~K~DG~R~~~h~~~~~V~L~SRng~d~T~~fPel~~~~~~~~~~~~-------~~~~~I   73 (610)
T PRK09633          3 PMQPTLTTSIPIG--DEWRYEVKYDGFRCLLIIDETGITLISRNGRELTNTFPEIIEFCESNFEHLK-------EELPLT   73 (610)
T ss_pred             CCcCCcCCCCCCC--CcEEEEEeEcceEEEEEEECCEEEEEeCCCCcchhhhhHHHHHHHhhhhccc-------cCCcee
Confidence            3676666666654  7899888888999999999999999999998765 56652      111110       011279


Q ss_pred             EeeeE---ecC---------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCC
Q 014751          174 LDCIF---HEL---------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAP  223 (419)
Q Consensus       174 LDCIy---~e~---------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~  223 (419)
                      ||+=.   .+.                           .-+|||.|||..+|.++.+-+..=|.=-|.+=+.+.+.-.+.
T Consensus        74 LDGEiVvld~~g~~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~~~  153 (610)
T PRK09633         74 LDGELVCLVNPYRSDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPASP  153 (610)
T ss_pred             eeeEEEEecCCCCCCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhccccccc
Confidence            99743   211                           026999999999999999988888877777766543210000


Q ss_pred             CCCCCCceeccccccCChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeeccCCCccce
Q 014751          224 SHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKDEKCSQYV  288 (419)
Q Consensus       224 s~~n~~~F~~lp~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD~~~s~y~  288 (419)
                      .....-.+..++++.    ...+++......-..|++.-..++.|.+| .|.-|+=+|-.....++
T Consensus       154 ~~~~~~~i~~~~~~~----~~~~l~~~a~~~g~EGIV~Kr~dS~Y~~G~Rs~~WlKiK~~~~~d~v  215 (610)
T PRK09633        154 DPYAKARIQYIPSTT----DFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKNWRYVHVI  215 (610)
T ss_pred             ccccccceEEcCCHH----HHHHHHHHHHHcCCceEEEeCCCCCCCCCCCCCCeEEEeccCCceeE
Confidence            000111334444433    34444433333457999999999999988 78876666643333333

>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I

Probab=97.19  E-value=0.0026  Score=60.91  Aligned_cols=149  Identities=15%  Similarity=0.137  Sum_probs=94.2

Q ss_pred             ceEEEEecCCcEEEEEeeC-CeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeee---EecC----------
Q 014751          117 DWYVFARPAGKRCIVVSSN-GTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCI---FHEL----------  181 (419)
Q Consensus       117 ~Wl~vpcPvGkRcLVVas~-G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCI---y~e~----------  181 (419)
                      .|++=+==-|-||++.... |....+||+|.-++ +|+....-....  . .....-|||||=   +...          
T Consensus        32 ~~~~E~K~DG~R~~~h~~~~~~v~l~SR~g~~~t~~~pel~~~~~~~--~-~~~~~~~iLDGElv~~~~~~g~~~~F~~l  108 (219)
T cd07900          32 EFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKS--L-KPSVKSFILDSEIVAYDRETGKILPFQVL  108 (219)
T ss_pred             eEEEEEeecceEEEEEEcCCCeEEEECCCCccccchhhHHHHHHHHH--h-cccCccEEEeeEEEEEEcCCCCCcChHHH
Confidence            5666555669999998765 89999999998653 554322110000  0 000123899974   3321          


Q ss_pred             ---------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHH
Q 014751          182 ---------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLY  245 (419)
Q Consensus       182 ---------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~  245 (419)
                                     .-+|+|.|||..+|.++.+=+    |.-.+..|++.-.  +    .+-++.++++..++ .+.+.
T Consensus       109 ~~r~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~p----l~eRr~~L~~~~~--~----~~~~~~~~~~~~~~~~~~~~  178 (219)
T cd07900         109 STRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKP----LRERRELLHSLFK--E----VPGRFQFATSKDSEDTEEIQ  178 (219)
T ss_pred             hhhcccccccccCcccEEEEEEEEEEECCchhhcCC----HHHHHHHHHHhcC--C----CCCeEEEEEEEecCCHHHHH
Confidence                           125999999999998776644    4444444544311  1    12346677777764 55676


Q ss_pred             HHHhcCCCCCcccEEeEecc--ccccCC-CCcCeeeec
Q 014751          246 SAYIESVPYAKDGLLFYNKH--AHYQTG-NTPLALVWK  280 (419)
Q Consensus       246 ~~~~~~~p~~~DGLLFYHKe--a~Y~~G-~TPLv~~wk  280 (419)
                      +++......-..|++.-..+  +.|.+| .|.  .|||
T Consensus       179 ~~~~~~~~~g~EGiv~K~~~~~s~Y~~g~Rs~--~W~K  214 (219)
T cd07900         179 EFLEEAVKNNCEGLMVKTLDSDATYEPSKRSH--NWLK  214 (219)
T ss_pred             HHHHHHHHcCCceEEEecCCCCCccCCCCcCC--CceE
Confidence            77665555678999999999  999998 565  3555

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligo

>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins

Probab=97.18  E-value=0.005  Score=59.85  Aligned_cols=143  Identities=13%  Similarity=0.088  Sum_probs=91.0

Q ss_pred             ceEEEEecCCcEEEEEee----CCeEEEEcCCCcEE-EeeccC-------CCCCCCCCCCCCCCCCcEEEeeeE---ecC
Q 014751          117 DWYVFARPAGKRCIVVSS----NGTTVSRERNGSIL-HHFPSA-------LPSGARTKDPSGSAQSYCILDCIF---HEL  181 (419)
Q Consensus       117 ~Wl~vpcPvGkRcLVVas----~G~T~ay~k~G~~l-~~F~S~-------LPgG~~~~~~~~~~~~ytILDCIy---~e~  181 (419)
                      +|++=.==-|-||+|...    .|.+..+|++|.-+ +.|+-.       |..+..    ......-+||||=+   +..
T Consensus        23 ~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~----~~~~~~~~ILDGEiVv~d~~   98 (235)
T cd08039          23 RMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKP----GCKFSKNCILEGEMVVWSDR   98 (235)
T ss_pred             cEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhcccc----ccCCCccEEEEeEEEEEECC
Confidence            344444445999999876    78899999999875 456631       111100    00112348999844   431


Q ss_pred             C---------------------------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCC
Q 014751          182 D---------------------------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYK  228 (419)
Q Consensus       182 ~---------------------------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~  228 (419)
                      +                                 -+|||.|||.+||.++.+-+..-|---|.+=+...+        + 
T Consensus        99 ~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~--------~-  169 (235)
T cd08039          99 QGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIP--------G-  169 (235)
T ss_pred             CCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCC--------C-
Confidence            1                                 289999999999999998887776665555443211        1 


Q ss_pred             Cceecccccc------CChHhHHHHHhcCCCCCcccEEeEeccccccCCCC
Q 014751          229 FRFSTVPVYN------CDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNT  273 (419)
Q Consensus       229 ~~F~~lp~~~------c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~T  273 (419)
                       .+.+++...      .+.+.+.+++.....--..|++.-..++.|.+|.+
T Consensus       170 -~~~~~~~~~i~~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~~S~Y~pgr~  219 (235)
T cd08039         170 -YAGLSERFPIDFSRSSGYERLRQIFARAIAERWEGLVLKGDEEPYFDLFL  219 (235)
T ss_pred             -cEEEEEEEeecccCCCCHHHHHHHHHHHHHcCCceEEEecCCCCcccCcc
Confidence             122222222      24566777776555556889999999999999975

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site res

>PRK09247 ATP-dependent DNA ligase; Validated

Probab=97.15  E-value=0.0032  Score=67.93  Aligned_cols=166  Identities=17%  Similarity=0.170  Sum_probs=115.1

Q ss_pred             hcccccccccCCCCCC--CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEee
Q 014751          100 QLMLPEWMIDVPDRLS--HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDC  176 (419)
Q Consensus       100 qLMlsEWl~dvP~dL~--~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDC  176 (419)
                      ..||++...++.+.+.  .+|++=.==-|-||+++..+|....+||+|.-+. +||-..--...      . ..-|||||
T Consensus       207 ~pMLA~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~v~lfSR~g~d~t~~fPei~~~~~~------l-~~~~ILDG  279 (539)
T PRK09247        207 PFFLAHPLEDEDLTLGDPADWQAEWKWDGIRVQLVRRGGEVRLWSRGEELITERFPELAEAAEA------L-PDGTVLDG  279 (539)
T ss_pred             CCeeCCcCCCchhhhcCCCcEEEEEeEcceEEEEEEeCCEEEEEeCCCccchhhhHHHHHHHHh------C-CCCEEEEe
Confidence            3688888776554321  3688777778999999999999999999998754 45532211000      0 11389997


Q ss_pred             e---Eec-C--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCC
Q 014751          177 I---FHE-L--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHY  226 (419)
Q Consensus       177 I---y~e-~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~  226 (419)
                      =   +.. .                          .-+|+|.|||..+|.++.+-+..=|.=-|++-+.+.+        
T Consensus       280 Elv~~~~~~~~~~~F~~l~~R~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~~~~~--------  351 (539)
T PRK09247        280 ELLVWRPEDGRPQPFADLQQRIGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLP--------  351 (539)
T ss_pred             EEEEEECCCCCcCCHHHHHHHhcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHhcccC--------
Confidence            3   331 0                          1279999999999999999988888877777765432        


Q ss_pred             CCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751          227 YKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE  282 (419)
Q Consensus       227 n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~  282 (419)
                       .-+|...|...++ .+.+...+.....--..|+++-..++.|++|..-- .|||=.
T Consensus       352 -~~~i~~~~~~~~~~~~e~~~~~~~a~~~g~EGlm~K~~~s~Y~~Grr~~-~WlK~K  406 (539)
T PRK09247        352 -DPRLDLSPLVPFSDWDELAALRAAARERGVEGLMLKRRDSPYLVGRKKG-PWWKWK  406 (539)
T ss_pred             -CCeEEecCceecCCHHHHHHHHHHHHHCCCceEEEecCCCCcCCCCCcc-hhhccc
Confidence             1256677776663 45566666655556689999999999999996532 355533

>PRK01109 ATP-dependent DNA ligase; Provisional

Probab=97.08  E-value=0.0033  Score=68.51  Aligned_cols=165  Identities=16%  Similarity=0.179  Sum_probs=111.8

Q ss_pred             hcccccccccCCC---CCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEE-EeeccCCCCCCCCCCCCCCCCCcEEEe
Q 014751          100 QLMLPEWMIDVPD---RLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSIL-HHFPSALPSGARTKDPSGSAQSYCILD  175 (419)
Q Consensus       100 qLMlsEWl~dvP~---dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l-~~F~S~LPgG~~~~~~~~~~~~ytILD  175 (419)
                      +-||++....+|+   .++.+|++=.==-|-||+|....|....+||||.-+ +.||...+--...     -...-||||
T Consensus       229 ~PmLA~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~~pel~~~~~~~-----~~~~~~ILD  303 (590)
T PRK01109        229 RPMLAERLSSPKEILKKMGGEALVEYKYDGERAQIHKKGDKVKIFSRRLENITHQYPDVVEYAKEA-----IKAEEAIVE  303 (590)
T ss_pred             CcccCCccCCHHHHHHHcCCCeEEEecCCceEEEEEEcCCEEEEEeCCchhhccccchHHHHHHHh-----cCccceEEe
Confidence            4577776655442   245678766666899999999999999999999754 3565432211000     001238999


Q ss_pred             e---eEec-CC-------------------------cEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCC
Q 014751          176 C---IFHE-LD-------------------------QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHY  226 (419)
Q Consensus       176 C---Iy~e-~~-------------------------~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~  226 (419)
                      |   +|+. ..                         -+|||.|||.++|.++.+-+..-|.=-|++-+.+.+        
T Consensus       304 GElv~~d~~~g~~~~F~~l~~R~r~~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~--------  375 (590)
T PRK01109        304 GEIVAVDPETGEMRPFQELMHRKRKYDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKEND--------  375 (590)
T ss_pred             eeEEEEECCCCcccChHHHhhcccccchhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCCCC--------
Confidence            7   3441 11                         158999999999999999888888777777664421        


Q ss_pred             CCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEec--cccccCC-CCcCeeeec
Q 014751          227 YKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNK--HAHYQTG-NTPLALVWK  280 (419)
Q Consensus       227 n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHK--ea~Y~~G-~TPLv~~wk  280 (419)
                         .+...++..++ .+.+.+++.....--..|++.-..  ++.|.+| .+.-|+=+|
T Consensus       376 ---~~~~~~~~~~~~~~~~~~~~~~a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~WlK~K  430 (590)
T PRK01109        376 ---KVKLAERIITDDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYK  430 (590)
T ss_pred             ---ceEEeeeEecCCHHHHHHHHHHHHHcCCceEEEecCCCCCCcCCCCCCccHHHhh
Confidence               25566666653 456777776656566889999999  9999999 565443344

>PRK03180 ligB ATP-dependent DNA ligase; Reviewed

Probab=96.91  E-value=0.0067  Score=65.14  Aligned_cols=162  Identities=18%  Similarity=0.159  Sum_probs=111.8

Q ss_pred             hcccccccccCCCC---CCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEE-EeeccCCCCCCCCCCCCCCCCCcEEEe
Q 014751          100 QLMLPEWMIDVPDR---LSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSIL-HHFPSALPSGARTKDPSGSAQSYCILD  175 (419)
Q Consensus       100 qLMlsEWl~dvP~d---L~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l-~~F~S~LPgG~~~~~~~~~~~~ytILD  175 (419)
                      +.||+....++|+.   ++.+|++=.==-|-||+|+..+|....|||+|.-+ ++||..+-.- ..     ....-+|||
T Consensus       185 ~PMLA~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~fPei~~~~-~~-----~~~~~~ILD  258 (508)
T PRK03180        185 RPMLAQTATSVAEALARLGGPAAVEAKLDGARVQVHRDGDDVRVYTRTLDDITARLPEVVEAV-RA-----LPVRSLVLD  258 (508)
T ss_pred             CCccCCcCCChHHHHHHhCCCeEEEEEEceeEEEEEEECCEEEEEeCCCCcchhhhHHHHHHH-Hh-----CCCcceeec
Confidence            56888887766653   44678888878899999999999999999999865 4565332100 00     001238888


Q ss_pred             eeE---ecC--------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCC
Q 014751          176 CIF---HEL--------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHY  226 (419)
Q Consensus       176 CIy---~e~--------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~  226 (419)
                      |=.   ++.                          .-+||+.|+|.++|.++.+-+..=|.--|++-+.+.         
T Consensus       259 GElv~~d~~g~~~~F~~l~~R~~~k~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~---------  329 (508)
T PRK03180        259 GEAIALRPDGRPRPFQVTASRFGRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAA---------  329 (508)
T ss_pred             ceEEEECCCCCcCCHHHHHHHhccccchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhccc---------
Confidence            733   211                          137999999999999998888777766666655320         


Q ss_pred             CCCceeccccccC-ChHhHHHHHhcCCCCCcccEEeEeccccccCCC-CcCeeeecc
Q 014751          227 YKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGN-TPLALVWKD  281 (419)
Q Consensus       227 n~~~F~~lp~~~c-~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~-TPLv~~wkD  281 (419)
                           ..+|...+ +.+.+.+.+.....--..|++.-+.++.|.+|. +..|+=||-
T Consensus       330 -----~~~~~~~~~~~~~~~~~~~~a~~~g~EGlm~K~~ds~Y~~GrR~~~WlK~K~  381 (508)
T PRK03180        330 -----HRVPRLVTADPAAAAAFLAAALAAGHEGVMVKSLDAPYAAGRRGAGWLKVKP  381 (508)
T ss_pred             -----ccccceecCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCcEEEcC
Confidence                 11233333 466777777665666789999999999999995 666655663

>PHA00454 ATP-dependent DNA ligase

Probab=96.64  E-value=0.012  Score=59.42  Aligned_cols=149  Identities=14%  Similarity=0.108  Sum_probs=91.8

Q ss_pred             CCcEEEEEeeCCe-EEEEcCCCcEEEeeccCC------CCCCCCCCCCCCCCCcEEEeeeEecC----------------
Q 014751          125 AGKRCIVVSSNGT-TVSRERNGSILHHFPSAL------PSGARTKDPSGSAQSYCILDCIFHEL----------------  181 (419)
Q Consensus       125 vGkRcLVVas~G~-T~ay~k~G~~l~~F~S~L------PgG~~~~~~~~~~~~ytILDCIy~e~----------------  181 (419)
                      -|-||++....|. ...+|++|..+.......      +.--+.  ....-..-.|||+=..-.                
T Consensus        36 DG~R~~~~~~~~~~v~l~SR~g~~~p~l~~~~~~~~~~~~~~~~--~~~~l~~~~vLDGElv~~~~~f~~~~~~l~~k~~  113 (315)
T PHA00454         36 DGVRGNIVVDNTADHGWLSREGKTIPALEHLNGFDRRWAKLLND--DRCIFPDGFMLDGELMVKGVDFNTGSGLLRRKWK  113 (315)
T ss_pred             ceEEEEEEEcCCCeEEEEeCCCCcccchhhhhhhhhhhhhhhhh--hhhcCCCCeEEEEEEEecCCCHHHHHHHhccCcc
Confidence            3899999887775 999999997432211110      000000  000001136888643211                


Q ss_pred             --------CcEEEEEEEEeeCCccc-c--cccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccC-ChHhHHHHHh
Q 014751          182 --------DQTYYVIDMVCWRGYSL-Y--DCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNC-DQRGLYSAYI  249 (419)
Q Consensus       182 --------~~tyYVLDvl~W~g~~l-~--dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c-~~~~L~~~~~  249 (419)
                              .-+|||.|+|.++|..- .  ++....++-+.+..|++.-.  .   ...-.+...|++.| +.+.+.+++.
T Consensus       114 ~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr~~L~~l~~--~---~~~~~~~~~~~~~~~~~~~~~~~~~  188 (315)
T PHA00454        114 VLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVRAMVPLLME--Y---FPEIDWFLSESYEVYDMESLQELYE  188 (315)
T ss_pred             chhhhccCceEEEEEEeeEeccccCCccccccccccHHHHHHHHHHHHh--h---CCCcceEeeceEEcCCHHHHHHHHH
Confidence                    13799999999995421 1  22355677777777765421  0   11123778899988 4567777776


Q ss_pred             cCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751          250 ESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE  282 (419)
Q Consensus       250 ~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~  282 (419)
                      ....--..|++.-..++.|++|.+.  .|||=.
T Consensus       189 ~~~~~g~EGiv~K~~ds~Y~~Grr~--~~~K~K  219 (315)
T PHA00454        189 KKRAEGHEGLVVKDPSLIYRRGKKS--GWWKMK  219 (315)
T ss_pred             HHHhCCCceEEEeCCCCCCCCCCcc--CcEEEc
Confidence            6555668999999999999999764  367754

>PHA02587 30 DNA ligase; Provisional

Probab=96.57  E-value=0.017  Score=61.82  Aligned_cols=157  Identities=16%  Similarity=0.174  Sum_probs=101.2

Q ss_pred             ceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEe---c-------------
Q 014751          117 DWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFH---E-------------  180 (419)
Q Consensus       117 ~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~---e-------------  180 (419)
                      .|++=.==-|-||.++..+|....|||+|.-++.|+-..+.-......-.....-+|||+=..   .             
T Consensus       153 ~~~~E~K~DG~R~q~h~~~~~v~l~SR~g~~~~~~p~i~~~l~~~~~~~~~~~~~~VLDGElv~~~~~~~~~~~~~f~~~  232 (488)
T PHA02587        153 PAYAQLKADGARCFADIDADGIEIRSRNGNEYLGLDLLKEELKKMTAEARQRPGGVVIDGELVYVEVETKKPNGLSFLFD  232 (488)
T ss_pred             cEEEEEccCceEEEEEEeCCEEEEEecCCccccCChhHHHHHHHHhhhhcccCCcEEEEeEEEEEecccCCCccchhhcc
Confidence            566555567999999999999999999999876553221110000000000012378887331   1             


Q ss_pred             ----------------------------------CCcEEEEEEEEee---CCcccccccchhhHHHhhhhccccCCCCCC
Q 014751          181 ----------------------------------LDQTYYVIDMVCW---RGYSLYDCTAEFRFFWLNSKLAETGACDAP  223 (419)
Q Consensus       181 ----------------------------------~~~tyYVLDvl~W---~g~~l~dceteFRffWl~SKl~E~~~~~~~  223 (419)
                                                        ..-+|||.|+|-+   .|..+.+-+..=|.=.|++-+...+     
T Consensus       233 ~~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~pl~eRr~~L~~l~~~~~-----  307 (488)
T PHA02587        233 DSKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMPYDDRFSKLAQMFEDCG-----  307 (488)
T ss_pred             cccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCCHHHHHHHHHHHHhhcC-----
Confidence                                              1126999999953   2333556666667666666553111     


Q ss_pred             CCCCCCceeccccccC-ChHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751          224 SHYYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE  282 (419)
Q Consensus       224 s~~n~~~F~~lp~~~c-~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~  282 (419)
                          .-++.++|...| +.+.+.+.+.....--..|++.-+.++.|++|.+.-+++||..
T Consensus       308 ----~~~i~l~~~~~~~~~ee~~~~~~~a~~~G~EGimlK~~ds~Y~~GRs~~WlKiK~~  363 (488)
T PHA02587        308 ----YDRVELIENQVVNNLEEAKEIYKRYVDQGLEGIILKNTDGLWEDGRSKDQIKFKEV  363 (488)
T ss_pred             ----CCcEEEEeeEEcCCHHHHHHHHHHHHhCCCCeEEEECCCCCCCCCCCCCcEEecCC
Confidence                125566777666 4567777776666667899999999999999999988899854

>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins

Probab=96.11  E-value=0.023  Score=51.84  Aligned_cols=133  Identities=20%  Similarity=0.201  Sum_probs=81.9

Q ss_pred             CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEec---------------
Q 014751          116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE---------------  180 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e---------------  180 (419)
                      ..|++=+==-|-||++.   |. .++||+|..+..- ..+.-+-         .. +|||+=+.-               
T Consensus        16 ~~~~~e~K~DG~R~~~~---~~-~~~SR~g~~~t~~-~~~~~~l---------~~-~ilDGElv~~~~~f~~l~~~~~~~   80 (174)
T cd07896          16 SGYLVSEKLDGVRAYWD---GK-QLLSRSGKPIAAP-AWFTAGL---------PP-FPLDGELWIGRGQFEQTSSIVRSK   80 (174)
T ss_pred             HHeeechhhceEEEEEe---cc-EEEecCCcCCCCC-HHHHhhC---------CC-CccCceEEcCCCCHHHHHHHHhcC
Confidence            46666555569999763   33 8899999875421 1111010         11 788874432               


Q ss_pred             -------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHHhcCC
Q 014751          181 -------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESV  252 (419)
Q Consensus       181 -------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~  252 (419)
                             ..-.|||.|+|. .+.     +..=|.=-|.+-+.+.+         .-.|.++|++.|. .+.+..++....
T Consensus        81 ~~~~~~~~~~~f~vFDil~-~~~-----p~~eR~~~L~~~i~~~~---------~~~~~~~~~~~~~~~~~i~~~~~~~~  145 (174)
T cd07896          81 KPDDEDWRKVKFMVFDLPS-AKG-----PFEERLERLKNLLEKIP---------NPHIKIVPQIPVKSNEALDQYLDEVV  145 (174)
T ss_pred             CCChhhcccceEEEEeCCC-CCC-----CHHHHHHHHHHHHHhCC---------CCcEEEEeeeeeCCHHHHHHHHHHHH
Confidence                   124899999998 222     33334444444443321         2357788888884 455666665444


Q ss_pred             CCCcccEEeEeccccccCCCCcCeeeec
Q 014751          253 PYAKDGLLFYNKHAHYQTGNTPLALVWK  280 (419)
Q Consensus       253 p~~~DGLLFYHKea~Y~~G~TPLv~~wk  280 (419)
                      .--.+|+++-..++.|++|.+.  .|||
T Consensus       146 ~~g~EGlv~K~~ds~Y~~gR~~--~wlK  171 (174)
T cd07896         146 AAGGEGLMLRRPDAPYETGRSD--NLLK  171 (174)
T ss_pred             hcCCCeEEEecCCCcccCCcCC--Ccee
Confidence            4458999999999999999886  4555

The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most me

>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]

Probab=96.01  E-value=0.15  Score=54.14  Aligned_cols=159  Identities=19%  Similarity=0.260  Sum_probs=112.5

Q ss_pred             cCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc-------CCCCCCCCCCCCCCCCCcEEEee---e
Q 014751          109 DVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS-------ALPSGARTKDPSGSAQSYCILDC---I  177 (419)
Q Consensus       109 dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S-------~LPgG~~~~~~~~~~~~ytILDC---I  177 (419)
                      +.|.....+|.+=.==-|-||.+....|....|||+|.-+. +||.       .||..            -+|||+   +
T Consensus       126 ~~~~~~~~~w~~E~K~DG~R~q~h~~~~~vrl~SR~g~d~T~~fP~~~~~~~~~l~~~------------~~iiDGE~V~  193 (444)
T COG1793         126 EALPRDGGDWAYEEKFDGYRVQIHIDGGKVRLYSRNGEDWTGRFPDILEAAAEALPAD------------DFILDGEIVV  193 (444)
T ss_pred             ccCCCCCCCEEEEEeeceEEEEEEEcCCEEEEEeCCCccchhhChHHHHHHHhcCCCC------------ceEEeeeEEE
Confidence            33444455699888889999999999999999999997654 5662       23321            389996   3


Q ss_pred             Eec-------------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCcee
Q 014751          178 FHE-------------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFS  232 (419)
Q Consensus       178 y~e-------------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~  232 (419)
                      +++                         ..-+||+.|+|.-+|+++.+.+..=|--=|.+-+...+.         +...
T Consensus       194 ~~~~~~~~F~~Lq~r~~~k~~v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~~~---------~~~~  264 (444)
T COG1793         194 LDEEGRLDFQALQQRLRRKYDVAKLRRETPLVLFAFDLLYLDGEDLRGLPLEERRALLEELVKSSDK---------IEIA  264 (444)
T ss_pred             ECCCCCCCHHHHHHHhhhccchhhhccCCceEEEEEEEEeECCcccccCchHHHHHHHHHHhccccc---------cccc
Confidence            332                         135799999999999999999999998888888876411         1111


Q ss_pred             ccccccCChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeeccCCCcccee
Q 014751          233 TVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKDEKCSQYVI  289 (419)
Q Consensus       233 ~lp~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD~~~s~y~~  289 (419)
                      ..-.+ -+.+.....+.....--..|++=-++++.|++| .+-.|+=||-...-.++|
T Consensus       265 ~~i~~-~~~~~~~~~~~~a~~~g~EGvv~K~~ds~Y~~g~R~~~W~K~K~~~~~d~vv  321 (444)
T COG1793         265 ERIPF-SDAEEGEAFLEAAIELGLEGVVAKRPDSPYRAGGRSNKWLKVKRDETLDLVV  321 (444)
T ss_pred             cceec-cChhhHHHHHHHHHhcCceEEEEeCCCCCcCCCCCCCcceEeccCCcccEEE
Confidence            11112 334556666655555568999999999999954 698888888654444433

>PRK09125 DNA ligase; Provisional

Probab=95.06  E-value=0.17  Score=50.52  Aligned_cols=136  Identities=20%  Similarity=0.199  Sum_probs=87.8

Q ss_pred             CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEec---------------
Q 014751          116 HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE---------------  180 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e---------------  180 (419)
                      .+|++=+==-|-||.+   .| +..+||+|..+.. +..+-.+-         . -+|||+=..-               
T Consensus        43 ~~~~~E~K~DG~R~~~---~~-v~l~SR~g~~it~-p~~~~~~~---------~-~~vLDGElv~~~~~F~~l~~r~~~k  107 (282)
T PRK09125         43 SGYLVSEKLDGVRAYW---DG-KQLLTRQGNPIAA-PAWFTAGF---------P-PFPLDGELWAGRGQFEAISSIVRDK  107 (282)
T ss_pred             hhEEEEeeeeeEeEEE---CC-eEEEcCCCCcCCC-chhHHhcC---------C-CccEeEEEEeCCCCHHHHHHHHccC
Confidence            4787777667999963   34 6799999998643 11110000         0 2688875421               


Q ss_pred             -------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHHhcCC
Q 014751          181 -------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESV  252 (419)
Q Consensus       181 -------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~  252 (419)
                             ..-+|||.|++..+|      +..-|.=-|.+-+.+.+        + -.+..+|+..|+ .+.+.+++....
T Consensus       108 ~~~~~~~~~v~~~vFDll~~~g------pl~eRr~~L~~li~~~~--------~-~~i~~~~~~~~~~~~~~~~~~~~~~  172 (282)
T PRK09125        108 TPDDAAWRKVRFMVFDLPDAPG------DFEERLAVLKKLLAKLP--------S-PYIKIIEQIRVRSEAALQQFLDQIV  172 (282)
T ss_pred             CcchhhhcccEEEEEEcCCCCC------CHHHHHHHHHHHHhhCC--------C-CcEEEEeEEEcCCHHHHHHHHHHHH
Confidence                   123899999997765      44445555666554321        1 146778888884 455666665555


Q ss_pred             CCCcccEEeEeccccccCCCCcCeeeecc
Q 014751          253 PYAKDGLLFYNKHAHYQTGNTPLALVWKD  281 (419)
Q Consensus       253 p~~~DGLLFYHKea~Y~~G~TPLv~~wkD  281 (419)
                      .--..|+++-+.++.|++|.|.-++=+|.
T Consensus       173 ~~G~EGiV~K~~ds~Y~~GRs~~wlKiK~  201 (282)
T PRK09125        173 AAGGEGLMLHRPDAPYEAGRSDDLLKLKP  201 (282)
T ss_pred             HcCCCEEEEeCCCCCCcCCCCCCcEEEEe
Confidence            55689999999999999999875444443

>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]

Probab=86.00  E-value=3.3  Score=47.15  Aligned_cols=168  Identities=18%  Similarity=0.308  Sum_probs=113.2

Q ss_pred             hhhhcccccccccCCCCC-CCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCC-------
Q 014751           97 FASQLMLPEWMIDVPDRL-SHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGARTKDPSGS-------  167 (419)
Q Consensus        97 ya~qLMlsEWl~dvP~dL-~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~-------  167 (419)
                      .|+.-|+.+|  ++=+.+ +++.++=-==-|-|..+.-..|.-.-+++||.-.. .|     |.+..++...+       
T Consensus       232 La~~~~~~~~--~~~e~m~~~~f~lEtK~DGERiQlHk~g~~~~yfSRNg~dyT~~y-----g~s~~~g~lt~~i~~~f~  304 (881)
T KOG0966|consen  232 LAQKQKLGDW--AIIEKMGGQDFYLETKFDGERIQLHKDGGEYKYFSRNGNDYTYEY-----GASYAHGTLTQRIHGAFN  304 (881)
T ss_pred             HHhhhccchH--HHHHHhcCCceEEEeeccCceEEEEecCCEEEEEecCCcchhhhc-----CcccccccccHHHHhhhh
Confidence            4555677777  332333 33333333456999999999888888899997533 33     22221111110       


Q ss_pred             -CCCcEEEeeeE---ecC-----------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCC
Q 014751          168 -AQSYCILDCIF---HEL-----------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGAC  220 (419)
Q Consensus       168 -~~~ytILDCIy---~e~-----------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~  220 (419)
                       .=.-|||||=+   +..                       +-+|-|.|+|..||.++..-+-.-|.+-|++=+.+.+. 
T Consensus       305 ~~v~~cILDGEMm~wD~~~~~f~~~G~~~dik~~~~~~~~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~-  383 (881)
T KOG0966|consen  305 KEVESCILDGEMMTWDTKTKRFCPFGSNSDIKELSSRDGSQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSG-  383 (881)
T ss_pred             hcchheEecceEEEeecchhhhccCCchhhHHHhhccccCCCceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCC-
Confidence             12358999843   211                       25677889999999999999999999999887766432 


Q ss_pred             CCCCCCCCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccC
Q 014751          221 DAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDE  282 (419)
Q Consensus       221 ~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~  282 (419)
                               ++.++++-.|. .+.+.+.+...+.---.|++----++.|.+|.- -=+|.|..
T Consensus       384 ---------~iei~~~~~~~~~edi~~~f~~ai~~~~EGIVlK~~~S~Y~pg~R-~~gW~K~K  436 (881)
T KOG0966|consen  384 ---------RIEIVRSEVGSTKEDIEQFFEEAIDNGEEGIVLKKPDSSYVPGQR-SNGWIKLK  436 (881)
T ss_pred             ---------eeEEeehhhcccHHHHHHHHHHHHhcCCCceEEeccCcccCcccc-CCCcEeec
Confidence                     36778887774 677777776655555679999999999999976 45677654

>TIGR02776 NHEJ_ligase_prk DNA ligase D

Probab=85.89  E-value=2.8  Score=45.94  Aligned_cols=90  Identities=19%  Similarity=0.216  Sum_probs=62.0

Q ss_pred             CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcCCCCCcccEEe
Q 014751          182 DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLF  261 (419)
Q Consensus       182 ~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~~~~p~~~DGLLF  261 (419)
                      .-+|||.|+|..+|.++.+.+..-|.=-|++-|.+...        + .+...+.+..+.+   +++.....--..|++.
T Consensus        57 pv~~~vFDlL~l~G~dL~~~Pl~eRr~~L~~ll~~~~~--------~-~i~~~~~~~~~~~---~~~~~a~~~G~EGIV~  124 (552)
T TIGR02776        57 PLTYYAFDLLFLSGEDLRDLPLEERKKRLKQLLKAQDE--------P-AIRYSDHFESDGD---ALLESACRLGLEGVVS  124 (552)
T ss_pred             ceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCC--------C-cEEEeeeecccHH---HHHHHHHHCCCceEEE
Confidence            45899999999999999998888888888777654211        1 1233333444444   3333333345789999


Q ss_pred             EeccccccCCCCcCeeeeccCC
Q 014751          262 YNKHAHYQTGNTPLALVWKDEK  283 (419)
Q Consensus       262 YHKea~Y~~G~TPLv~~wkD~~  283 (419)
                      -+.++.|.+|.|.-|+=+|-..
T Consensus       125 K~~dS~Y~~GRs~~WlKlK~~~  146 (552)
T TIGR02776       125 KRLDSPYRSGRSKDWLKLKCRR  146 (552)
T ss_pred             eCCCCCCCCCCCcchhcccccc
Confidence            9999999999988765555433

Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.

>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]

Probab=80.25  E-value=0.78  Score=45.80  Aligned_cols=163  Identities=29%  Similarity=0.419  Sum_probs=91.2

Q ss_pred             CCCCCCcCCCCCCchHHHHHHHHHHHHHHhH---HHHHHHHhhhhhhhccccC-CCCCCCCCCCCCCCCCccccCCCCcc
Q 014751            3 PPDLRRPFKRTAISDQQRRRELSLQRQSQNR---RDAQQQARCLASSVLSLQS-QYPDPVPELEIEPESQPQQEAGPLTK   78 (419)
Q Consensus         3 ph~~~~~~k~~~~~~Q~~RR~~~Le~Qk~~R---~d~~~~aR~La~~~~~~~~-~~~~~~~e~~~~~~~~e~~~~~~~~~   78 (419)
                      ||..++|+|+..+.+|.+||+..+-||.|-|   .++...||++++. +.++. ..+|.++  +  -.+.-.+++-.++.
T Consensus         1 ~~el~~~l~s~f~vdql~~~~~~hpR~sQykn~~s~aeQ~arrr~~l-lelQks~r~D~~~--~--~r~lA~dd~tg~Es   75 (325)
T KOG3132|consen    1 PHELRRPLKSRFIVDQLKRRELSHPRQSQYKNLTSDAEQRARRRASL-LELQKSSRPDVDP--E--IRSLAVDDLTGTES   75 (325)
T ss_pred             ChhHhhhhhcccccchhhhhhccCchhhhhhhhhhHHHHHHHHHHHH-HHhhhcCCCCccH--H--HHhhcccccccccc
Confidence            7889999999999999999999999999988   8999999999973 33332 2233222  1  11222334433311


Q ss_pred             chhhhhhhhccCCcchhhhhhhcccccccccCCCCCCCceEE-EEecCCcEEEEEe-eCCe-EEEEcCCCcEEEeecc--
Q 014751           79 DLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYV-FARPAGKRCIVVS-SNGT-TVSRERNGSILHHFPS--  153 (419)
Q Consensus        79 ~~d~~~~~k~~gk~~rk~ya~qLMlsEWl~dvP~dL~~~Wl~-vpcPvGkRcLVVa-s~G~-T~ay~k~G~~l~~F~S--  153 (419)
                          + .+|...+...+.--+.  +..|..+- -.| .+|++ ||=-.|+--.||+ .-|+ |-+-.-.|..+..-.+  
T Consensus        76 ----e-e~k~d~~~a~~~tgk~--~~K~yA~q-lML-sEWliDvP~~LsqdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~  146 (325)
T KOG3132|consen   76 ----E-ESKFDVRQASRLTGKE--ARKWYAKQ-LML-SEWLIDVPDNLSQDWYVVARPVGKRCLVVASRGTTVAYVKNGS  146 (325)
T ss_pred             ----h-hhhhhhhHHhhhcchh--HHHHHHHH-hhh-HHHhccCccccCcceEEEEeecCceEEEEecCCceEEEecCCe
Confidence                1 1222221111111111  23343321 123 57875 5667777766665 4443 4455667887765542  


Q ss_pred             ---CCCCCCCCCCCCCCCCCcEEEeeeEecCCcEEEEEEEEe
Q 014751          154 ---ALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVC  192 (419)
Q Consensus       154 ---~LPgG~~~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~  192 (419)
                         ..|.--+    .|+.+.         ..++.|-|||+|.
T Consensus       147 ~v~rF~S~LP----GGnrr~---------~~a~~ytILDCIy  175 (325)
T KOG3132|consen  147 TVHRFPSALP----GGNRRK---------GPANSYTILDCIY  175 (325)
T ss_pred             eEeeccccCC----CCCcCC---------CCcccceeeeeee
Confidence               1222111    111111         3578999999986

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	419
3gjx_B	365	Crystal Structure Of The Nuclear Export Complex Crm		4e-42
3nbz_B	362	Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp		4e-42
3gb8_B	329	Crystal Structure Of Crm1SNURPORTIN-1 Complex Lengt		4e-42
3nby_B	361	Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclea		4e-42
1xk5_A	204	Crystal Structure Of The M3g-Cap-Binding Domain Of		5e-41

>pdb|3GJX|B Chain B, Crystal Structure Of The Nuclear Export Complex Crm1- Snurportin1-Rangtp Length = 365

Iteration: 1
 Score =  169 bits (427), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 81/197 (41%), Positives = 117/197 (59%), Gaps = 8/197 (4%)
Query: 80  LDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTV 139
           +DI    KL      K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+T 
Sbjct: 91  MDIDTVKKLP-----KHYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTS 145
Query: 140 SRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLY 199
           +  ++G  ++ F S LP G R    + +A+ Y ILDCI++E++QTYYV+D++CWRG+  Y
Sbjct: 146 AYTKSGYCVNRFSSLLPGGNRR---NSTAKDYTILDCIYNEVNQTYYVLDVMCWRGHPFY 202
Query: 200 DCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGL 259
           DC  +FRF+W++SKL E       +    F+F  +  + C    L        P+  DGL
Sbjct: 203 DCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFEVDGL 262
Query: 260 LFYNKHAHYQTGNTPLA 276
           LFY+K  HY  G+TPL 
Sbjct: 263 LFYHKQTHYSPGSTPLV 279

>pdb|3NBZ|B Chain B, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear Export Complex (Crystal I) Length = 362

Iteration: 1
 Score =  169 bits (427), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 81/197 (41%), Positives = 117/197 (59%), Gaps = 8/197 (4%)
Query: 80  LDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTV 139
           +DI    KL      K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+T 
Sbjct: 88  MDIDTVKKLP-----KHYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTS 142
Query: 140 SRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLY 199
           +  ++G  ++ F S LP G R    + +A+ Y ILDCI++E++QTYYV+D++CWRG+  Y
Sbjct: 143 AYTKSGYCVNRFSSLLPGGNRR---NSTAKDYTILDCIYNEVNQTYYVLDVMCWRGHPFY 199
Query: 200 DCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGL 259
           DC  +FRF+W++SKL E       +    F+F  +  + C    L        P+  DGL
Sbjct: 200 DCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFEVDGL 259
Query: 260 LFYNKHAHYQTGNTPLA 276
           LFY+K  HY  G+TPL 
Sbjct: 260 LFYHKQTHYSPGSTPLV 276

>pdb|3GB8|B Chain B, Crystal Structure Of Crm1SNURPORTIN-1 Complex Length = 329

Iteration: 1
 Score =  168 bits (426), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 77/182 (42%), Positives = 112/182 (61%), Gaps = 3/182 (1%)
Query: 95  KWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSA 154
           K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+T +  ++G  ++ F S 
Sbjct: 97  KHYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSL 156
Query: 155 LPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKL 214
           LP G R    + +A+ Y ILDCI++E++QTYYV+D++CWRG+  YDC  +FRF+W++SKL
Sbjct: 157 LPGGNRR---NSTAKDYTILDCIYNEVNQTYYVLDVMCWRGHPFYDCQTDFRFYWMHSKL 213
Query: 215 AETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTP 274
            E       +    F+F  +  + C    L        P+  DGLLFY+K  HY  G+TP
Sbjct: 214 PEEEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFEVDGLLFYHKQTHYSPGSTP 273
Query: 275 LA 276
           L 
Sbjct: 274 LV 275

>pdb|3NBY|B Chain B, Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclear Export Complex Length = 361

Iteration: 1
 Score =  168 bits (426), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 81/197 (41%), Positives = 117/197 (59%), Gaps = 8/197 (4%)
Query: 80  LDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTV 139
           +DI    KL      K +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+T 
Sbjct: 87  MDIDTVKKLP-----KHYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTS 141
Query: 140 SRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLY 199
           +  ++G  ++ F S LP G R    + +A+ Y ILDCI++E++QTYYV+D++CWRG+  Y
Sbjct: 142 AYTKSGYCVNRFSSLLPGGNRR---NSTAKDYTILDCIYNEVNQTYYVLDVMCWRGHPFY 198
Query: 200 DCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGL 259
           DC  +FRF+W++SKL E       +    F+F  +  + C    L        P+  DGL
Sbjct: 199 DCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFEVDGL 258
Query: 260 LFYNKHAHYQTGNTPLA 276
           LFY+K  HY  G+TPL 
Sbjct: 259 LFYHKQTHYSPGSTPLV 275

>pdb|1XK5|A Chain A, Crystal Structure Of The M3g-Cap-Binding Domain Of Snurportin1 In Complex With A M3gpppg-Cap Dinucleotide Length = 204

Iteration: 1
 Score =  165 bits (417), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 76/180 (42%), Positives = 111/180 (61%), Gaps = 3/180 (1%)
Query: 97  FASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALP 156
           +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+T +  ++G  ++ F S LP
Sbjct: 2   YANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSLLP 61
Query: 157 SGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAE 216
            G R    + +A+ Y ILDCI++E++QTYYV+D++CWRG+  YDC  +FRF+W++SKL E
Sbjct: 62  GGNRR---NSTAKDYTILDCIYNEVNQTYYVLDVMCWRGHPFYDCQTDFRFYWMHSKLPE 118
Query: 217 TGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLA 276
                  +    F+F  +  + C    L        P+  DGLLFY+K  HY  G+TPL 
Sbjct: 119 EEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFEVDGLLFYHKQTHYSPGSTPLV 178

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	419
3gjx_B	365	Snurportin-1; transport, cytoplasm, nucleus, RNA-b	3e-88
1xk5_A	204	Snurportin-1; protein-RNA-complex, transport prote	2e-82
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-08

>3gjx_B Snurportin-1; transport, cytoplasm, nucleus, RNA-binding, acetylation, GTP-binding, HOST-virus interaction, nucleotide-binding, phosphoprotein; HET: GTP; 2.50A {Homo sapiens} PDB: 3nby_B* 3nbz_B* 3nc0_B* 3gb8_B 2qna_B Length = 365

 Score =  271 bits (693), Expect = 3e-88
 Identities = 99/287 (34%), Positives = 143/287 (49%), Gaps = 25/287 (8%)

Query: 2   APPDLRRPFKRTAIS-DQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPE 60
           AP      +K    S +Q  RR   L+ Q   R D    AR LA      +  +     E
Sbjct: 28  APHPRLSQYKSKYSSLEQSERRRRLLELQKSKRLDYVNHARRLA------EDDWTGMESE 81

Query: 61  LEIEPESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYV 120
            E + + +            DI    KL      K +A+QLML EW+IDVP  L  +W V
Sbjct: 82  EENKKDDEEM----------DIDTVKKLP-----KHYANQLMLSEWLIDVPSDLGQEWIV 126

Query: 121 FARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE 180
              P GKR ++V+S G+T +  ++G  ++ F S LP G R    + +A+ Y ILDCI++E
Sbjct: 127 VVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSLLPGGNRR---NSTAKDYTILDCIYNE 183

Query: 181 LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD 240
           ++QTYYV+D++CWRG+  YDC  +FRF+W++SKL E       +    F+F  +  + C 
Sbjct: 184 VNQTYYVLDVMCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCT 243

Query: 241 QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQY 287
              L        P+  DGLLFY+K  HY  G+TPL    +    S  
Sbjct: 244 PESLCDVLSMDFPFEVDGLLFYHKQTHYSPGSTPLVGWLRPYMVSDV 290

>1xk5_A Snurportin-1; protein-RNA-complex, transport protein; HET: TPG; 2.40A {Homo sapiens} Length = 204

 Score =  250 bits (640), Expect = 2e-82
 Identities = 77/191 (40%), Positives = 113/191 (59%), Gaps = 3/191 (1%)

Query: 97  FASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALP 156
           +A+QLML EW+IDVP  L  +W V   P GKR ++V+S G+T +  ++G  ++ F S LP
Sbjct: 2   YANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSLLP 61

Query: 157 SGARTKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAE 216
            G R    + +A+ Y ILDCI++E++QTYYV+D++CWRG+  YDC  +FRF+W++SKL E
Sbjct: 62  GGNR---RNSTAKDYTILDCIYNEVNQTYYVLDVMCWRGHPFYDCQTDFRFYWMHSKLPE 118

Query: 217 TGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLA 276
                  +    F+F  +  + C    L        P+  DGLLFY+K  HY  G+TPL 
Sbjct: 119 EEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFEVDGLLFYHKQTHYSPGSTPLV 178

Query: 277 LVWKDEKCSQY 287
              +    S  
Sbjct: 179 GWLRPYMVSDV 189

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 56.4 bits (135), Expect = 1e-08
 Identities = 71/476 (14%), Positives = 136/476 (28%), Gaps = 137/476 (28%)

Query: 16  SDQQRRRELSLQRQSQ--NRRDAQQQAR----------------CLASSVLS---LQSQY 54
           +D Q   + ++ R       R A  + R                 +A  V     +Q + 
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKM 180

Query: 55  PDPV----------PELEIEP-ESQPQQEAGPLTKDLDIRQASKLRGPEVRKWFASQLML 103
              +          PE  +E  +    Q     T   D     KLR   ++      L  
Sbjct: 181 DFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS 240

Query: 104 PEW----MI--DVPDRLSHDWYVFARPAGKRC-IVVSSNGTTVSRERNGSILHHFPSALP 156
             +    ++  +V +  +  W  F       C I++++    V+   + +   H      
Sbjct: 241 KPYENCLLVLLNVQN--AKAWNAF----NLSCKILLTTRFKQVTDFLSAATTTHISLDHH 294

Query: 157 SGARTKDPSGSAQSYCILDCIFHEL-DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLA 215
           S   T D   S      LDC   +L  +             S+       R         
Sbjct: 295 SMTLTPDEVKSLLLKY-LDCRPQDLPREVLTTNPRRL----SI--IAESIR--------- 338

Query: 216 ETGACDAPSH--YYKFRFSTVPVYNCDQRGLYSAYIE-SVPYAKDGLLFYNKHAHYQT-- 270
                D  +    +K         NCD+    +  IE S+    + L        +    
Sbjct: 339 -----DGLATWDNWKH-------VNCDK---LTTIIESSL----NVLEPAEYRKMFDRLS 379

Query: 271 -----GNTP---LALVWKD----------EKCSQY-VIDTDSKGQVLS----QQQVVLEL 307
                 + P   L+L+W D           K  +Y +++   K   +S      ++ ++L
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL 439

Query: 308 QEDGKL-------------STSDDPPVIFGCLDGEFIQ------KSGLQSGSLLKFAIGN 348
           + +  L               SDD       LD  F        K+      +  F +  
Sbjct: 440 ENEYALHRSIVDHYNIPKTFDSDDLIPP--YLDQYFYSHIGHHLKNIEHPERMTLFRMVF 497

Query: 349 GGLSFVDGKLEKSDLNYLGKSNRARMFAD--SYSKVIFQYMVRHTPLKFDDLLASV 402
               F++ K+      +    +          Y      Y+  + P K++ L+ ++
Sbjct: 498 LDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKP----YICDNDP-KYERLVNAI 548

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	419
3gjx_B	365	Snurportin-1; transport, cytoplasm, nucleus, RNA-b	100.0
1xk5_A	204	Snurportin-1; protein-RNA-complex, transport prote	100.0
2p8q_B	40	Snurportin-1; heat repeat, IBB-domain, importin, k	99.22
1ckm_A	330	MRNA capping enzyme; nucleotidyltransferase; HET:	98.95
3rtx_A	343	MRNA-capping enzyme; guanylyltransferase, RNA poly	98.7
1p16_A	395	GTP--RNA, mRNA capping enzyme alpha subunit; guany	98.48
3kyh_C	461	MRNA-capping enzyme subunit alpha; 5' modification	98.48
1vs0_A	310	Putative DNA ligase-like protein RV0938/MT0965; OB	98.1
3l2p_A	579	DNA ligase 3; DNA ligase, DNA repair, ATP-binding,	97.78
2cfm_A	561	Thermostable DNA ligase; protein-nucleotide comple	97.72
3gde_A	558	DNA ligase; DNA-binding domain, adenylation domain	97.7
2hiv_A	621	Thermostable DNA ligase; ATP-dependent, open confo	97.61
1x9n_A	688	DNA ligase I; 5'-adenylated nicked DNA, protein-DN	97.57
3vnn_A	139	DNA ligase 4; non-homologous END joining, DNA repa	97.24
1a0i_A	348	DNA ligase; DNA replication; HET: DNA ATP; 2.60A {	96.69
1fvi_A	297	Chlorella virus DNA ligase-adenylate; adenylated D	96.68

>3gjx_B Snurportin-1; transport, cytoplasm, nucleus, RNA-binding, acetylation, GTP-binding, HOST-virus interaction, nucleotide-binding, phosphoprotein; HET: GTP; 2.50A {Homo sapiens} PDB: 3nby_B* 3nbz_B* 3nc0_B* 3gb8_B 2qna_B

Probab=100.00  E-value=3.9e-100  Score=759.88  Aligned_cols=263  Identities=37%  Similarity=0.691  Sum_probs=228.5

Q ss_pred             CCCCCCCcCCCCC-CchHHHHHHHHHHHHHHhHHHHHHHHhhhhhhhccccCCCCCCCCCCCCCCCCCccccCCCCccch
Q 014751            2 APPDLRRPFKRTA-ISDQQRRRELSLQRQSQNRRDAQQQARCLASSVLSLQSQYPDPVPELEIEPESQPQQEAGPLTKDL   80 (419)
Q Consensus         2 aph~~~~~~k~~~-~~~Q~~RR~~~Le~Qk~~R~d~~~~aR~La~~~~~~~~~~~~~~~e~~~~~~~~e~~~~~~~~~~~   80 (419)
                      |||||++|||+++ +.+|++||+++|++||++|+|++||||+||+++|+.    .+          ++||++++.+  +|
T Consensus        28 a~HPR~sqyK~k~~~~~Q~~RR~~~Le~QK~kR~d~~~haR~La~~~~~~----~~----------seeed~~~~e--em   91 (365)
T 3gjx_B           28 APHPRLSQYKSKYSSLEQSERRRRLLELQKSKRLDYVNHARRLAEDDWTG----ME----------SEEENKKDDE--EM   91 (365)
T ss_dssp             SCCGGGCC---CTTCCSCCHHHHHHHHHTCCCCSCHHHHHHHHHHTCCC-------------------------------
T ss_pred             CCCcchhhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcccccccccc----cc----------cccccccccc--hh
Confidence            8999999999998 558999999999999999999999999999999862    11          1122233333  57


Q ss_pred             hhhhhhhccCCcchhhhhhhcccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCC
Q 014751           81 DIRQASKLRGPEVRKWFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGAR  160 (419)
Q Consensus        81 d~~~~~k~~gk~~rk~ya~qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~  160 (419)
                      |++     .|++++++|||||||||||+++|+||+++|+|||||+||||||||++|+|++|+++|+++++|+|+||||++
T Consensus        92 d~~-----~~~k~~k~yanqlMlsEWl~dvP~dL~~~W~~vpcPvGkRcLVVas~G~T~aysk~G~~l~~F~S~LPGG~~  166 (365)
T 3gjx_B           92 DID-----TVKKLPKHYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSLLPGGNR  166 (365)
T ss_dssp             ----------CCCCCSSSSCSEEEEECCSCCTTHHHHEEEEEEESSEEEEEEEETTEEEEECTTCCEEEEECCSSTTTCC
T ss_pred             ccc-----ccccccHHHHhhHHHHHhcccCCcccccCeeEEeccCCcEEEEEecCceEEEECCCCCEEeeeCCCCCCCCc
Confidence            776     467888999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCcEEEeeeEecCCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC
Q 014751          161 TKDPSGSAQSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD  240 (419)
Q Consensus       161 ~~~~~~~~~~ytILDCIy~e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~  240 (419)
                      +  ++. +++||||||||++.++|||||||||||||++|||+||||||||+|||+|+++++++++.|||+|++||+|+|+
T Consensus       167 ~--~s~-~~~~TILDCIy~e~~~tyYVLDVL~W~g~~l~dCeteFRffWl~SKL~E~~~l~e~s~~np~~Fv~lp~~~C~  243 (365)
T 3gjx_B          167 R--NST-AKDYTILDCIYNEVNQTYYVLDVMCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCT  243 (365)
T ss_dssp             -------CCCCEEEEEEEETTTTEEEEEEEEEETTEECTTSCHHHHHHHHHHHGGGSTTTTSCCSSCCSEEEECCEEECC
T ss_pred             c--ccC-CCCCEEEEEEeecCCceEEEEEEeeeCCcccccCchHHHHHHHHHHhhhcccccccccCCCCceeccCCCCcC
Confidence            5  333 7899999999999999999999999999999999999999999999999988999999999999999999999


Q ss_pred             hHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeeccCCCccce
Q 014751          241 QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYV  288 (419)
Q Consensus       241 ~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~  288 (419)
                      +++|+.+++..+||++||||||||++||++|.||||+|||+.+++..+
T Consensus       244 ~esL~~~ls~~~pfe~DGLLFYHK~ahY~~G~TPLVgWLkPyMv~diL  291 (365)
T 3gjx_B          244 PESLCDVLSMDFPFEVDGLLFYHKQTHYSPGSTPLVGWLRPYMVSDVL  291 (365)
T ss_dssp             HHHHHHHTTCCCSSCEEEEEEEETTCCCCSEEEEEEEEECHHHHTTTT
T ss_pred             HHHHHHHhccCCCCccceEEEEeccccccCCCCccceecchhhhHHHh
Confidence            999999999999999999999999999999999999999987776654

>1xk5_A Snurportin-1; protein-RNA-complex, transport protein; HET: TPG; 2.40A {Homo sapiens}

Probab=100.00  E-value=2.1e-80  Score=581.55  Aligned_cols=190  Identities=41%  Similarity=0.862  Sum_probs=181.8

Q ss_pred             hhhhhcccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEe
Q 014751           96 WFASQLMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILD  175 (419)
Q Consensus        96 ~ya~qLMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILD  175 (419)
                      +|||||||||||+|||+||+++|+|||||+||||||||+||+|++|+|+|+++++|+|+||||+++  +++ +++|||||
T Consensus         1 ~ya~~lmlsEWl~diP~dl~~~Wl~vp~P~GkRcLvva~~G~T~~~~k~G~~~~~F~S~LPgG~~~--~~~-~~~~tILD   77 (204)
T 1xk5_A            1 HYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSLLPGGNRR--NST-AKDYTILD   77 (204)
T ss_dssp             CCSSCSEEEEECCSCCTTHHHHEEEEEEESSEEEEEEEETTEEEEECTTSCEEEEECCSSSSSCSS--SCC-TTCCEEEE
T ss_pred             CcccchhhhhhcccCCCccCCCeEEEECCCCcEEEEEecCCeEEEECCCCcEEEEEcccCCCCCcc--cCC-CCCCEEEE
Confidence            389999999999999999999999999999999999999999999999999999999999999975  222 68899999


Q ss_pred             eeEecCCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcCCCCC
Q 014751          176 CIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYA  255 (419)
Q Consensus       176 CIy~e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~~~~p~~  255 (419)
                      |||++.++|||||||||||||++|||+||||||||+|||+|+++++++++.|+|+|+++|+|+|+.++|+++++..+||+
T Consensus        78 CI~~e~~~tyYVLDvl~W~g~~l~dcetefRffWl~skl~E~~~l~~~s~~n~~~f~~lp~~~c~~~~l~~~~~~~~~~~  157 (204)
T 1xk5_A           78 CIYNEVNQTYYVLDVMCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCTPESLCDVLSMDFPFE  157 (204)
T ss_dssp             EEEEGGGTEEEEEEEEEETTEECTTSCHHHHHHHHHHHTTTSTTTTSCBTTBSSEEEECCEEECSHHHHHHHHTCCCSSC
T ss_pred             EEEecCCcEEEEEEEEEECCceeecCcHHHHHHHHHHHhccccccccccccCCcceEecccccCCHHHHHHHHccCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccEEeEeccccccCCCCcCeeeeccCCCccce
Q 014751          256 KDGLLFYNKHAHYQTGNTPLALVWKDEKCSQYV  288 (419)
Q Consensus       256 ~DGLLFYHKea~Y~~G~TPLv~~wkD~~~s~y~  288 (419)
                      +||||||||++||++|.||||+|+|+.+....+
T Consensus       158 ~DGlLFyHK~a~Y~~G~TPLv~WLkp~mlpeiL  190 (204)
T 1xk5_A          158 VDGLLFYHKQTHYSPGSTPLVGWLRPYMVSDVL  190 (204)
T ss_dssp             EEEEEEEESSCCCCSEEEEEEEEECGGGHHHHH
T ss_pred             cceEEEEeccccccCCCCChhhhcchhhchhhh
Confidence            999999999999999999999999987766554

>2p8q_B Snurportin-1; heat repeat, IBB-domain, importin, karyopherin, transport; 2.35A {Homo sapiens} PDB: 2q5d_C 3lww_B

Probab=99.22  E-value=3.4e-12  Score=90.97  Aligned_cols=39  Identities=26%  Similarity=0.212  Sum_probs=35.7

Q ss_pred             CCCCCcCCCCC-CchHHHHHHHHHHHHHHhHHHHHHHHhh
Q 014751            4 PDLRRPFKRTA-ISDQQRRRELSLQRQSQNRRDAQQQARC   42 (419)
Q Consensus         4 h~~~~~~k~~~-~~~Q~~RR~~~Le~Qk~~R~d~~~~aR~   42 (419)
                      |||+++||.++ +++|++||+++|++||++|+|++||||+
T Consensus         1 HPR~sqYK~k~~~~~q~~rRr~~L~~QK~~R~D~~nhaR~   40 (40)
T 2p8q_B            1 HPRLSQYKSKYSSLEQSERRRRLLELQKSKRLDYVNHARR   40 (40)
T ss_dssp             -CCGGGTTCCCCSCSTTHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             CccHHhhccccchhhHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            89999999996 7889998888999999999999999995

>1ckm_A MRNA capping enzyme; nucleotidyltransferase; HET: GTP; 2.50A {Paramecium bursaria chlorella virus 1} SCOP: b.40.4.6 d.142.2.3 PDB: 1ckn_A* 1cko_A* 1ckn_B*

Probab=98.95  E-value=3.8e-08  Score=97.74  Aligned_cols=240  Identities=15%  Similarity=0.145  Sum_probs=158.9

Q ss_pred             CceEEEEecCCcEEEEEee----CCeEEEEcCCCcEEE-eeccCCCCCCCCCCCCCCCCCcEEEeeeEecC--C--cEEE
Q 014751          116 HDWYVFARPAGKRCIVVSS----NGTTVSRERNGSILH-HFPSALPSGARTKDPSGSAQSYCILDCIFHEL--D--QTYY  186 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas----~G~T~ay~k~G~~l~-~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~--~--~tyY  186 (419)
                      .+|++-.=.-|-||+++..    .|.+..++++|..+. .|+. ++..         ...-||||+-+.-.  +  -+||
T Consensus        75 ~~y~ve~K~DG~R~ll~~~~~~g~g~v~L~sR~~~~~t~~fp~-~~~~---------~~~~~vLDGElv~~~~~~~~~f~  144 (330)
T 1ckm_A           75 NKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMTVYLLPFKN-IPRV---------LFQGSIFDGELCVDIVEKKFAFV  144 (330)
T ss_dssp             SCEEEEEEECSEEEEEEEEEETTEEEEEEECTTCCEEECCCSC-CCTT---------GGGCEEEEEEEEEETTTTEEEEE
T ss_pred             CCEEEEECcceEEEEEEEEecCCCCEEEEEeCCCCEEeccChh-hhhc---------cCCCeeEEEEEEEEcCCCeEEEE
Confidence            4799999999999999988    688999999998765 3432 2211         12359999966532  2  3899


Q ss_pred             EEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCChHhHHHHHhcCC--CCCcccEEeEec
Q 014751          187 VIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESV--PYAKDGLLFYNK  264 (419)
Q Consensus       187 VLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~~~L~~~~~~~~--p~~~DGLLFYHK  264 (419)
                      |.|+|.++|.++.+.+..=|.--|..-+....    .....++.+...+.++.+.+.+...+....  .|..|||+|-+.
T Consensus       145 vFDlL~~~G~dl~~~pl~eRr~~L~~~l~~~~----~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~yg~EGlI~K~~  220 (330)
T 1ckm_A          145 LFDAVVVSGVTVSQMDLASRFFAMKRSLKEFK----NVPEDPAILRYKEWIPLEHPTIIKDHLKKANAIYHTDGLIIMSV  220 (330)
T ss_dssp             EEEEEEETTEECTTSCHHHHHHHHHHHHTTCC----CCTTSSSEEEECCCEETTCHHHHHHHHHHHHHHSCEEEEEEEES
T ss_pred             EEeeeeeCCcccccCCHHHHHHHHHHHHhhhc----ccCCCCeEEEEEEEEehhHHHHHHHHHHHHhccCCCceEEEeeC
Confidence            99999999999999998888888887774210    011234555556666665444442111222  237999999999


Q ss_pred             cccccCCCCcCeeeecc--CCCccceeecCCCCCccccceEEEEEecCCceeccCCCceEEecccchhhhhcCCCCCCee
Q 014751          265 HAHYQTGNTPLALVWKD--EKCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSGLQSGSLL  342 (419)
Q Consensus       265 ea~Y~~G~TPLv~~wkD--~~~s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~T~D~~pv~~~~~~~~~i~~~~l~~g~L~  342 (419)
                      ++.|.+|.+.-++-||.  .++-.|+|-. ..|      .+-|-...+|.+       |-+|++.      ..+.+|.++
T Consensus       221 dspY~~Gr~~~~lKwK~~~~~tvDfvi~~-g~g------~~gl~~~~~~~~-------vp~~~~~------k~~~~g~Iv  280 (330)
T 1ckm_A          221 DEPVIYGRNFNLFKLKPGTHHTIDFIIMS-EDG------TIGIFDPNLRKN-------VPVGKLD------GYYNKGSIV  280 (330)
T ss_dssp             SSCCCCEEEEEEEEECSTTCCCEEEEECS-TTC------CEEEEETTTTEE-------EECCCCS------SCCCTTCEE
T ss_pred             CCcccCCCccCeEEEEeCCCceEEEEEEc-cCC------eEEEEeCCCCce-------eeeeeee------hhhcCCeEE
Confidence            99999999988899998  6777787762 233      233322112222       4445543      123577777


Q ss_pred             eEEEcCCceeeccCceeeeceEEeecCCccccCCchhhHHHHHHhhhcCCCchhHHHhhc
Q 014751          343 KFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASV  402 (419)
Q Consensus       343 Rf~i~~~~~~~~~~~~~~~~l~~~~~~~~~R~~aDs~sKIlfq~~~r~~p~~i~~~~~~~  402 (419)
                      =|+..       .|.|..--++..      +..||+++-+.-=...-..|||.++|+..+
T Consensus       281 E~~~~-------~G~wr~~R~R~D------K~~~n~~~t~~~v~~si~~~vt~eeL~~~~  327 (330)
T 1ckm_A          281 ECGFA-------DGTWKYIQGRSD------KNQANDRLTYEKTLLNIEENITIDELLDLF  327 (330)
T ss_dssp             EEEEE-------TTEEEEEEECTT------CSSCCBHHHHHHHHHHHHHCCCHHHHTTCC
T ss_pred             EEEEE-------CCceEEEEEeCC------CCCCCHHHHHHHHHHhhhcCCCHHHHHHhh
Confidence            77775       344444333322      336888877655555567899999999877

>3rtx_A MRNA-capping enzyme; guanylyltransferase, RNA polymerase II CTD, lysyl-N-GMP, NUC mRNA capping, transferase; HET: SEP GUN; 2.81A {Mus musculus} PDB: 3s24_A

Probab=98.70  E-value=9.3e-08  Score=95.82  Aligned_cols=254  Identities=16%  Similarity=0.272  Sum_probs=127.4

Q ss_pred             CceEEEEecCCcEEEEEee-CCeEEEEcCCCcEEE----eeccCCCCCCCCCCCCCCCCCcEEEeeeEec--CC----cE
Q 014751          116 HDWYVFARPAGKRCIVVSS-NGTTVSRERNGSILH----HFPSALPSGARTKDPSGSAQSYCILDCIFHE--LD----QT  184 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas-~G~T~ay~k~G~~l~----~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e--~~----~t  184 (419)
                      .+|++-.=.-|-|||+... .|.+..++++|..+.    +||..---.        ....-||||+-+.-  .+    -+
T Consensus        63 ~~y~v~~K~DG~R~ll~i~~~~~v~L~sR~~~~~~~~~~~FP~~~~~~--------~~~~~tvLDGElV~~~~~g~~~~~  134 (343)
T 3rtx_A           63 KPYKVSWKADGTRYMMLIDGTNEVFMIDRDNSVFHVSNLEFPFRKDLR--------MHLSNTLLDGEMIIDKVNGQAVPR  134 (343)
T ss_dssp             SCEEEEEECCCEEEEEEECSTTCEEEECTTCCEEEETTCCCEETTEEE--------EECCSEEEEEEEEEEESSSSEEEE
T ss_pred             CCEEEEECCCceEEEEEEEcCCEEEEEeCCCCeEEeccccCCcchhhh--------ccCCCeEEEEEEEEecCCCcEeeE
Confidence            5788888889999999888 899999999998763    576431100        01234999995542  22    38


Q ss_pred             EEEEEEEeeCCcccccccchhhHHHhhhhcccc-----CCCCCCCCCCCCceeccccccCCh-HhHH-HHHhcCCCCCcc
Q 014751          185 YYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAET-----GACDAPSHYYKFRFSTVPVYNCDQ-RGLY-SAYIESVPYAKD  257 (419)
Q Consensus       185 yYVLDvl~W~g~~l~dceteFRffWl~SKl~E~-----~~~~~~s~~n~~~F~~lp~~~c~~-~~L~-~~~~~~~p~~~D  257 (419)
                      |+|.|+|.++|.++.+++..=|.--|..-+-+-     ..........||.+..-++++.+. +.|. .-+........|
T Consensus       135 ~~~FDlL~~~G~dl~~~pl~eR~~~L~~~i~~p~~~~~~~~~~~~~~~pf~vr~K~~~~~~~~~~ll~~~~~~~l~~~~d  214 (343)
T 3rtx_A          135 YLIYDIIKFNAQPVGDCDFNIRLQCIEREIISPRHEKMKTGLIDKTQEPFSVRPKQFFDINISRKLLEGNFAKEVSHEMD  214 (343)
T ss_dssp             EEEEEEEEBTTBCGGGSCHHHHHHHHHHHTHHHHHHHHHHSSCCTTTSSSEEEECCCEEGGGHHHHSCC----------C
T ss_pred             EEEEEEEeECCcCcccCCHHHHHHHHHHHhhhHHHHHhhcccccccCCCcEEEEEEeEehhhHHHHHhhhhHhhcCCCCC
Confidence            999999999999999999999988876544320     000011234567666677777654 2222 122345667899


Q ss_pred             cEEeEeccccccCCCCcCeeeeccC--CCccceeecCCCCCccccceEEEEEecCCceeccCCCceEEecccchhhhhcC
Q 014751          258 GLLFYNKHAHYQTGNTPLALVWKDE--KCSQYVIDTDSKGQVLSQQQVVLELQEDGKLSTSDDPPVIFGCLDGEFIQKSG  335 (419)
Q Consensus       258 GLLFYHKea~Y~~G~TPLv~~wkD~--~~s~y~~d~d~~g~~~~~q~vvL~~~~~g~l~T~D~~pv~~~~~~~~~i~~~~  335 (419)
                      ||+|.+.+ .|.+|.++-++=||.+  ++..|.+--...+...    + |- ...|.|+. +|.-+.++.+..   .. .
T Consensus       215 GlIf~~~~-~Y~~G~~~~~lKwKp~~~~tvDF~l~~~~~~~~g----~-~~-~~~~~l~~-~g~~~~f~~~~~---t~-~  282 (343)
T 3rtx_A          215 GLIFQPIG-KYKPGRCDDILKWKPPSLNSVDFRLKITRMGGEG----L-LP-QNVGLLYV-GGYERPFAQIKV---TK-E  282 (343)
T ss_dssp             EEEEEESS-CCCCEEEEEEEEECCSTTCC---------------------------------------------------
T ss_pred             eEEEEECc-cCcCCCCcceEEEecCcceEEEEEEEecccCCCC----c-cc-cccceEEE-CCeeeecceeec---cc-c
Confidence            99999999 9999999999999995  7778877432211100    0 00 01122222 111234443310   00 0


Q ss_pred             CC--CCCeeeEEEcCCceeeccCceeeeceEEeecCCccccCCchhhHHHHHHhhhcCCCchhHHHhhc
Q 014751          336 LQ--SGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQYMVRHTPLKFDDLLASV  402 (419)
Q Consensus       336 l~--~g~L~Rf~i~~~~~~~~~~~~~~~~l~~~~~~~~~R~~aDs~sKIlfq~~~r~~p~~i~~~~~~~  402 (419)
                      ++  .|.++=|+..       +|.+..     + |-+.=+..|-++|-+.-=...=..|||.++|+..+
T Consensus       283 l~~ld~~IvEC~~~-------~~~W~~-----~-R~R~DK~~pN~~~tv~~v~~SI~d~Vt~e~L~~~i  338 (343)
T 3rtx_A          283 LKQYDNKIIECKFE-------NNSWVF-----M-RQRIDKSFPNAYNTAMAVCNSISNPVTKEMLFEFI  338 (343)
T ss_dssp             --------------------------------------------CHHHHHHHHHHHHSCCCHHHHHHHH
T ss_pred             chhcCCEEEEEEEE-------CCEEEE-----E-EEcCCCCCCchHHHHHHHHHHHHccCCHHHHHHHH
Confidence            11  2333333322       122211     1 22222456777777666555558899999999876

>1p16_A GTP--RNA, mRNA capping enzyme alpha subunit; guanylyltransferase, transcription, capping, CTD, mRNA; HET: SEP G GTP; 2.70A {Candida albicans} SCOP: b.40.4.6 d.142.2.3

Probab=98.48  E-value=4.7e-07  Score=91.77  Aligned_cols=265  Identities=15%  Similarity=0.231  Sum_probs=153.4

Q ss_pred             CceEEEEecCCcEEEEEe-----eCCeEEEEcCCCcEEE----eeccCCCCCCCCCCCCCCCCCcEEEeeeEecCC----
Q 014751          116 HDWYVFARPAGKRCIVVS-----SNGTTVSRERNGSILH----HFPSALPSGARTKDPSGSAQSYCILDCIFHELD----  182 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVa-----s~G~T~ay~k~G~~l~----~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~----  182 (419)
                      .+|++-+=--|-||+++.     ..|.+..++++|..+.    +||...--. ++   ......-||||+-+.-.+    
T Consensus        60 ~~~~ve~K~DG~R~ll~~~~~~~~g~~v~L~sR~~~~~~i~~~~FP~~~~~~-~~---~~~~~~~~vLDGElV~~~~~~~  135 (395)
T 1p16_A           60 KDYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRENDYYFIPNIHFPLSVNET-RE---KPTYHHGTLLDGELVLENRNVS  135 (395)
T ss_dssp             SCEEEEEEECSEEEEEEEEEETTTEEEEEEEETTCCEEECCSCCCCSCTTCC-SS---SCCCCSSEEEEEEEEEECCSSS
T ss_pred             CCEEEEECccceEEEEEEeecccCCCEEEEEeCCCceEEeccccCCcccccc-cc---hhccCCcceeeeEEEEeccCCC
Confidence            478888888999999988     4467889999999864    676532111 00   000122499998655322    


Q ss_pred             ---cEEEEEEEEeeCCcccccccchhhHHHhhhhcccc-CC-C---C--CCCCCCCCceeccccccCChHhHHHHHhc--
Q 014751          183 ---QTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAET-GA-C---D--APSHYYKFRFSTVPVYNCDQRGLYSAYIE--  250 (419)
Q Consensus       183 ---~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~-~~-~---~--~~s~~n~~~F~~lp~~~c~~~~L~~~~~~--  250 (419)
                         -+|+|.|+|.++|.++.+.+..=|.--|..-+.+. .. .   .  ..+...+|.+..-++++...  +..++..  
T Consensus       136 ~~~~~f~~FDlL~~~G~dl~~~pl~eR~~~L~~~i~~~~~~~~~~~~~~~~~~~~pf~v~~~~~~~~~~--~~~~~~~~~  213 (395)
T 1p16_A          136 EPVLRYVIFDALAIHGKCIIDRPLPKRLGYITENVMKPFDNFKKHNPDIVNSPEFPFKVGFKTMLTSYH--ADDVLSKMD  213 (395)
T ss_dssp             CCEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHTHHHHHHHHHHCHHHHSCTTSCCEEEECCCEEGGG--THHHHTTGG
T ss_pred             cceeEEEEEEEEEECCeEcccCCHHHHHHHHHHHhhcccHhhhhcCccccccccCceEEEEecchhHHH--HHHHHHHHH
Confidence               37999999999999999999988888887744221 00 0   0  01122334444444454432  2333322  


Q ss_pred             CCCCCcccEEeEeccccccCCCCcCeeeecc--CCCccceeec------C----CCCC------ccccce-EEEEEecCC
Q 014751          251 SVPYAKDGLLFYNKHAHYQTGNTPLALVWKD--EKCSQYVIDT------D----SKGQ------VLSQQQ-VVLELQEDG  311 (419)
Q Consensus       251 ~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD--~~~s~y~~d~------d----~~g~------~~~~q~-vvL~~~~~g  311 (419)
                      ......|||+|-..++.|.+|.+..++=||-  .++-.|++-.      +    ..|.      +.+... +.|-+...|
T Consensus       214 ~~~~g~EGlI~K~~ds~Y~~Gr~~~wlKwK~~~~~TvDfvl~~~~~~~~~~~~~g~G~~~~~~dy~~~p~~~~l~v~~~~  293 (395)
T 1p16_A          214 KLFHASDGLIYTCAETPYVFGTDQTLLKWKPAEENTVDFQLEFVFNEVQDPDLDERDPTSTYLDYDAKPNLIKLRVWQGS  293 (395)
T ss_dssp             GCSSCEEEEEEEESSSCCCSEEEEEEEEECCGGGCCEEEEEEEECEEEECTTSCTTSTTCEEEECSSCCSEEEEEEECST
T ss_pred             hcCCCCCeEEEEeCCCCcCCCCccceEEEecCCCeEEEEEEEEEecccccccccccCccccccccccccceeEEEEEeCC
Confidence            3457799999999999999999988888886  6777777651      1    1221      000111 333332221


Q ss_pred             ceeccCCCceEEecc---cchhhh--hc-CCCCCCeeeEEEcCCceeeccCceeeeceEEeecCCccccCCchhhHHHHH
Q 014751          312 KLSTSDDPPVIFGCL---DGEFIQ--KS-GLQSGSLLKFAIGNGGLSFVDGKLEKSDLNYLGKSNRARMFADSYSKVIFQ  385 (419)
Q Consensus       312 ~l~T~D~~pv~~~~~---~~~~i~--~~-~l~~g~L~Rf~i~~~~~~~~~~~~~~~~l~~~~~~~~~R~~aDs~sKIlfq  385 (419)
                      +-      =+.++++   ++++-.  +. .--+|.++=|+..+.    ..|.|..--++.      =+..|++++-+.-=
T Consensus       294 ~~------~~~f~~~~ltd~e~~~l~~~~~~~~~~IvEc~~~~~----~~g~wr~~R~R~------DK~~pN~~~t~~~v  357 (395)
T 1p16_A          294 NV------HTDFAKLDLSDDDWERLKALEQPLQGRIAECRQSTT----KKGYWEMLRFRN------DKSNGNHISVVEKI  357 (395)
T ss_dssp             TC------EEEEEEECCCHHHHHHHHHSSSCCTTCEEEEEECSS----STTEEEEEEECT------TCSSCCBHHHHHHH
T ss_pred             cc------cceeeEEEeCHHHHHHhHhhcccCCCEEEEEEeecC----CCCccEEEEEeC------CCCCcChHHHHHHH
Confidence            10      1233432   222221  11 122567766666420    234344332222      23357877765444


Q ss_pred             HhhhcCCCchhHHHhhc
Q 014751          386 YMVRHTPLKFDDLLASV  402 (419)
Q Consensus       386 ~~~r~~p~~i~~~~~~~  402 (419)
                      ...=..|||.++|+..+
T Consensus       358 l~si~~~vt~eeL~~~~  374 (395)
T 1p16_A          358 LVSIKDGVKEKEVIEWC  374 (395)
T ss_dssp             HHHHHHSCCHHHHHHHH
T ss_pred             HHHHHccCCHHHHHHHH
Confidence            44446899999999875

>3kyh_C MRNA-capping enzyme subunit alpha; 5' modification, triphosphatase, guanylyltransferase, complex, hydrolase, mRNA processing, nucleus; 3.00A {Saccharomyces cerevisiae}

Probab=98.48  E-value=1.5e-06  Score=90.25  Aligned_cols=172  Identities=19%  Similarity=0.296  Sum_probs=114.8

Q ss_pred             CceEEEEecCCcEEEEEee------CCeEEEEcCCCcEEE----eeccCCCCCCCCCCCCCCCCCcEEEeeeEecC----
Q 014751          116 HDWYVFARPAGKRCIVVSS------NGTTVSRERNGSILH----HFPSALPSGARTKDPSGSAQSYCILDCIFHEL----  181 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas------~G~T~ay~k~G~~l~----~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~----  181 (419)
                      .+|++-.=.-|.|||+...      .|.+..++++|....    +||..-......  .-.....-||||+-+.-.    
T Consensus        65 ~dY~V~eK~DGiR~Ll~i~~~~~~g~g~v~LidR~~~~~~v~~~~FP~~~~~~~~~--~l~~~~~~TlLDGElV~d~~~~  142 (461)
T 3kyh_C           65 HDYYVCEKTDGLRVLMFIVINPVTGEQGCFMIDRENNYYLVNGFRFPRLPQKKKEE--LLETLQDGTLLDGELVIQTNPM  142 (461)
T ss_dssp             SCEEEEEEECSEEEEEEEEECTTTCCEEEEEECSSSCEEEECCCCCCCCSSCCSSG--GGTCCCCSEEEEEEEEEEECTT
T ss_pred             CCEEEEEcccceEEEEEEeccccCCCceEEEEeCCCCeEEcccccCCcccccchhh--hhhccCCCeEEEEEEEeccCCC
Confidence            5788888888999998876      378888999998763    676432110000  000123459999944421    


Q ss_pred             ----CcEEEEEEEEeeCCcccccccchhhHHHhhhhcccc--CCC--C-CCCCCCCCceeccccccC-ChHhHHHHHhcC
Q 014751          182 ----DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAET--GAC--D-APSHYYKFRFSTVPVYNC-DQRGLYSAYIES  251 (419)
Q Consensus       182 ----~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~--~~~--~-~~s~~n~~~F~~lp~~~c-~~~~L~~~~~~~  251 (419)
                          .-+|+|.|+|.++|.++.+++..=|.-.|..-+.+.  ..+  . ......||.+..-.++++ ..+.|.. ....
T Consensus       143 ~~~~~~~y~~FDlL~~~G~dl~~~pl~eR~~~Le~~I~~P~~~~~~~~p~~~~~~pF~V~~K~~~~~~~~~~l~~-~~~~  221 (461)
T 3kyh_C          143 TKLQELRYLMFDCLAINGRCLTQSPTSSRLAHLGKEFFKPYFDLRAAYPNRCTTFPFKISMKHMDFSYQLVKVAK-SLDK  221 (461)
T ss_dssp             TCCEEEEEEEEEEEEETTEECSSSBHHHHHHHHHHTTHHHHHHHHHHCSTTCSCCCSEEEECCCEEGGGHHHHHH-HHTT
T ss_pred             CCccceEEEEEEEEeECCcCcccCCHHHHHHHHHHHhcccchhhhhccccccccCCcEEEeccchhhhhHHHHHH-hhhh
Confidence                127999999999999999999999998887665321  000  0 011234454444445454 2333333 2345


Q ss_pred             CCCCcccEEeEeccccccC-CCCcCeeeeccC--CCccceee
Q 014751          252 VPYAKDGLLFYNKHAHYQT-GNTPLALVWKDE--KCSQYVID  290 (419)
Q Consensus       252 ~p~~~DGLLFYHKea~Y~~-G~TPLv~~wkD~--~~s~y~~d  290 (419)
                      .....|||+|.+.++.|.+ |.+.-++=||.+  ++-.|++-
T Consensus       222 l~~~~EGLv~k~~~spY~~Ggr~~~~lKwKp~~~nTVDF~L~  263 (461)
T 3kyh_C          222 LPHLSDGLIFTPVKAPYTAGGKDSLLLKWKPEQENTVDFKLI  263 (461)
T ss_dssp             CSSCEEEEEEEESSSBCCSSSEEEEEEECCCTTTCCCEEEEE
T ss_pred             ccCCCCeEEEEeCCCCCcCCCcCCCeEEEEcCCCeeEEEEEE
Confidence            7788999999999999999 688999999985  77777664

>1vs0_A Putative DNA ligase-like protein RV0938/MT0965; OB fold, nucleotidyl transferase, structural genomic protein structure initiative; HET: APK MSE; 2.40A {Mycobacterium tuberculosis}

Probab=98.10  E-value=1.4e-05  Score=78.37  Aligned_cols=155  Identities=19%  Similarity=0.217  Sum_probs=111.9

Q ss_pred             cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc------CCCCCCCCCCCCCCCCCcEE
Q 014751          101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS------ALPSGARTKDPSGSAQSYCI  173 (419)
Q Consensus       101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S------~LPgG~~~~~~~~~~~~ytI  173 (419)
                      .||+.-. ++|.-...+|++=.==-|-||++....|....+|++|..+. +||.      .||.            .-+|
T Consensus        11 PmLA~~~-~~~~~~~~~~~~E~K~DG~R~~~~~~~g~v~l~SR~g~~~t~~fPel~~~~~~l~~------------~~~i   77 (310)
T 1vs0_A           11 PMLATHG-TVAGLKASQWAFEGXWDGYRLLVEADHGAVRLRSRSGRDVTAEYPQLRALAEDLAD------------HHVV   77 (310)
T ss_dssp             CCEEEEC-CCTTCCTTTEEEEEECCSEEEEEEEETTEEEEEETTCCBCGGGCGGGHHHHHHTTT------------CEEE
T ss_pred             CeECCCc-CCCccCCCCEEEEEccCcEEEEEEEECCEEEEEcCCCCCchhhchhHHHHHHhCCC------------ccEE
Confidence            5777766 46653356899988889999999999999999999998764 4542      2342            1389


Q ss_pred             EeeeEecC------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccc
Q 014751          174 LDCIFHEL------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVP  235 (419)
Q Consensus       174 LDCIy~e~------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp  235 (419)
                      |||=..-.                  .-+|||.|+|.++|.++.+-+..=|.--|.+-+.+.            ++...|
T Consensus        78 LDGElv~~d~~g~~~F~~l~~r~~~~~~~~~vFDll~~~g~~l~~~pl~eRr~~L~~~~~~~------------~i~~~~  145 (310)
T 1vs0_A           78 LDGEAVVLDSSGVPSFSQMQNRGRDTRVEFWAFDLLYLDGRALLGTRYQDRRKLLETLANAT------------SLTVPE  145 (310)
T ss_dssp             EEEEEECBCTTSCBCHHHHHTCCTTSCCEEEEEEEEEETTEECTTSCHHHHHHHHHHHHHHS------------CCCCCC
T ss_pred             EeeEEEEECCCCCcCHHHHHhhccCCcEEEEEEEeEEECCcCcccCCHHHHHHHHHHhccCC------------cEEECc
Confidence            99844321                  127999999999999999988888877776665431            333445


Q ss_pred             cccCChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeeccCC
Q 014751          236 VYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKDEK  283 (419)
Q Consensus       236 ~~~c~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD~~  283 (419)
                      .+..+   +.+.+.....--.+|+++-..++.|++| .|.-++=||-..
T Consensus       146 ~~~~~---~~~~~~~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K~~~  191 (310)
T 1vs0_A          146 LLPGD---GAQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDKHWN  191 (310)
T ss_dssp             CCCSS---HHHHHHHHHHTTCCEEEEEETTCCCCTTCEEEEEEEEESSE
T ss_pred             cCchH---HHHHHHHHHHcCCceEEEeCCCCCcCCCCcChHHhccchhe
Confidence            55544   3444433334558999999999999999 887777777654

>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell divisi damage; HET: DNA AMP; 3.00A {Homo sapiens}

Probab=97.78  E-value=8e-05  Score=79.22  Aligned_cols=155  Identities=19%  Similarity=0.223  Sum_probs=108.5

Q ss_pred             cccccccccCCC---CCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccC-----------CCCCCCCCCCCC
Q 014751          101 LMLPEWMIDVPD---RLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSA-----------LPSGARTKDPSG  166 (419)
Q Consensus       101 LMlsEWl~dvP~---dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~-----------LPgG~~~~~~~~  166 (419)
                      -||++-..+++.   .+..+|++=+==-|-||+|+...|....+||+|..+  |+..           +|++        
T Consensus       229 PMLA~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~l~SR~g~~~--~p~~~~~l~~~l~~~~~~~--------  298 (579)
T 3l2p_A          229 PMLAEACKSVEYAMKKCPNGMFSEIKYDGERVQVHKNGDHFSYFSRSLKPV--LPHKVAHFKDYIPQAFPGG--------  298 (579)
T ss_dssp             CCEEEECCCHHHHHHHCTTCEEEEECCCSEEEEEEEETTEEEEECTTSCBC--CGGGTTTGGGTHHHHSTTC--------
T ss_pred             CccCCcCCCHHHHHhhCCCCeEEEEccCcEEEEEEEECCEEEEECCCCCcc--ChhHHHHHHHHHHHhcCcC--------
Confidence            366666544433   234578766666699999999999999999999875  4431           2322        


Q ss_pred             CCCCcEEEee---eEec---------------------CCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCC
Q 014751          167 SAQSYCILDC---IFHE---------------------LDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDA  222 (419)
Q Consensus       167 ~~~~ytILDC---Iy~e---------------------~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~  222 (419)
                         .-+||||   +++.                     ..-+|||.|+|.++|.++.+-+..=|.--|.+=+.+.+    
T Consensus       299 ---~~~iLDGElv~~d~~~g~~~~F~~L~~~~~~~~~~~~v~~~vFDlL~l~G~~L~~~Pl~eRr~~L~~~~~~~~----  371 (579)
T 3l2p_A          299 ---HSMILDSEVLLIDNKTGKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIP----  371 (579)
T ss_dssp             ---SEEEEEEEEEEBCTTTCCBCCGGGGSHHHHHHCSSCCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHCCCBT----
T ss_pred             ---CceEEEeEEEEEeCCCCcccCHHHHHHHhhhhcccCCeEEEEEEeeccCCCccccCCHHHHHHHHHHHhhcCC----
Confidence               1389998   2221                     13479999999999999999888888777766654421    


Q ss_pred             CCCCCCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEeccccccCCCCcCeeeecc
Q 014751          223 PSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWKD  281 (419)
Q Consensus       223 ~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TPLv~~wkD  281 (419)
                            -+|...|...++ .+.+.+.+.....--..|++.-+.++.|++|..   .|||=
T Consensus       372 ------~~i~~~~~~~~~~~~~~~~~~~~a~~~g~EGlv~K~~ds~Y~~Grr---~WlK~  422 (579)
T 3l2p_A          372 ------NRIMFSEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKR---HWLKV  422 (579)
T ss_dssp             ------TTEEECCEEEECSHHHHHHHHHHHHHTTCCCEEEEESSCCCCTTCE---EEEEE
T ss_pred             ------CeEEEeeeEEcCCHHHHHHHHHHHHHhCCCceEEecCcCCCCCCCe---eeEEE
Confidence                  245666655554 455666665544456899999999999999997   46663

>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle, cell division, DNA damage, DNA recombination, DNA repair, DNA replication; HET: AMP; 1.8A {Pyrococcus furiosus} PDB: 3rr5_A*

Probab=97.72  E-value=7.7e-05  Score=78.86  Aligned_cols=160  Identities=16%  Similarity=0.128  Sum_probs=117.8

Q ss_pred             cccccccccCCCC---CCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc-------CCCCCCCCCCCCCCCC
Q 014751          101 LMLPEWMIDVPDR---LSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS-------ALPSGARTKDPSGSAQ  169 (419)
Q Consensus       101 LMlsEWl~dvP~d---L~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S-------~LPgG~~~~~~~~~~~  169 (419)
                      .||+.-..++|+.   +..+|++=.==-|-||+++..+|....+||+|..+. +||.       .||.            
T Consensus       224 PmLA~~~~~~~~~~~~~~~~~~~E~K~DG~R~~i~~~~g~v~l~SR~g~~~t~~fPel~~~~~~~l~~------------  291 (561)
T 2cfm_A          224 PMLAQQAASIRDALLEMGGEAEFEIKYDGARVQVHKDGSKIIVYSRRLENVTRAIPEIVEALKEAIIP------------  291 (561)
T ss_dssp             CCEEEEESCHHHHHHHTTSCEEEEEECCSEEEEEEEETTEEEEECTTCCBCGGGCHHHHHHHHHHBCS------------
T ss_pred             CeeCCcCCChhHHHhhcCCcEEEEEeEceEEEEEEEECCEEEEEeCCCCCchhhhhhHHHHHHHhCCC------------
Confidence            3676665555442   344899888889999999999999999999998765 4554       3442            


Q ss_pred             CcEEEeeeEecC-----------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCC
Q 014751          170 SYCILDCIFHEL-----------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGAC  220 (419)
Q Consensus       170 ~ytILDCIy~e~-----------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~  220 (419)
                      .-|||||=..-.                             .-.|||.|+|.++|.++.+.+..=|.--|.+-+.+.   
T Consensus       292 ~~~iLDGElv~~d~~g~~~~F~~L~~r~~~~~~~~~~~~~~~~~~~vFDlL~l~g~~l~~~pl~eRr~~L~~~~~~~---  368 (561)
T 2cfm_A          292 EKAIVEGELVAIGENGRPLPFQYVLRRFRRKHNIEEMMEKIPLELNLFDVLYVDGQSLIDTKFIDRRRTLEEIIKQN---  368 (561)
T ss_dssp             SEEEEEEEEEEBCTTSSBCCTHHHHHHHHCCSCHHHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCC---
T ss_pred             cceEeeeEEEEEcCCCcccCHHHHHHHhhcccchhhhcccCceEEEEEEEEeECCcCcccCCHHHHHHHHHHHhCcC---
Confidence            138999833211                             126999999999999999988888887777666431   


Q ss_pred             CCCCCCCCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeeccCC
Q 014751          221 DAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWKDEK  283 (419)
Q Consensus       221 ~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wkD~~  283 (419)
                              -++...|.+.++ .+.+.+.+.....--.+|+++-..++.|++| .+.-|+=||...
T Consensus       369 --------~~i~~~~~~~~~~~~~~~~~~~~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K~~~  425 (561)
T 2cfm_A          369 --------EKIKVAENLITKKVEEAEAFYKRALEMGHEGLMAKRLDAVYEPGNRGKKWLKIKPTM  425 (561)
T ss_dssp             --------SSEEECCEEEESCHHHHHHHHHHHHHTTCCEEEEECTTCCCCTTCEEEEEEEECSSC
T ss_pred             --------CcEEEeeeEEcCCHHHHHHHHHHHHHcCCceeEEeCCCCCCCCCCcCCCeEEEcccC
Confidence                    246677877774 5566666655555668999999999999999 677777777554

>3gde_A DNA ligase; DNA-binding domain, adenylation domain, OB-fold domain, ATP-binding, cell cycle, cell division, DNA damage, DNA recombination; HET: DNA; 2.30A {Archaeoglobus fulgidus}

Probab=97.70  E-value=5.3e-05  Score=80.21  Aligned_cols=155  Identities=17%  Similarity=0.125  Sum_probs=112.7

Q ss_pred             cccccccccCCCCCC--CceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eeccC-------CCCCCCCCCCCCCCCC
Q 014751          101 LMLPEWMIDVPDRLS--HDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPSA-------LPSGARTKDPSGSAQS  170 (419)
Q Consensus       101 LMlsEWl~dvP~dL~--~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S~-------LPgG~~~~~~~~~~~~  170 (419)
                      -||++-...+|+.+.  .+|++=+==-|-||+|+...|....+||+|..+. +||..       ||.            +
T Consensus       228 PmLA~~~~~~~~~~~~~~~~~~E~K~DG~R~qi~~~g~~v~l~SR~g~d~t~~fPel~~~~~~~l~~------------~  295 (558)
T 3gde_A          228 MMLAQVAESLESAVREMRTAAVEWKFDGSRVQVHWDGSRVTIYSRRLENVTNALPDIVEEIKKSVKP------------G  295 (558)
T ss_dssp             CCEEEECSCHHHHHHHSSSEEEEEECSSEEEEEEECSSCCEEEETTCCBCGGGCHHHHHHHHHHBCS------------S
T ss_pred             CeeCCcCCChHHHhhhccceEEEEeEeeEEEEEEEeCCEEEEEcCCCCcccccchHHHHHHHhhCCC------------C
Confidence            477766555665432  5788777777999999999999999999998765 34432       442            2


Q ss_pred             cEEEee---eEecC-------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCC
Q 014751          171 YCILDC---IFHEL-------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDA  222 (419)
Q Consensus       171 ytILDC---Iy~e~-------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~  222 (419)
                       +||||   ++...                         .-+|||.|+|.++| ++.+.+..=|.--|.+-+.+      
T Consensus       296 -~iLDGElv~~~~g~~~~F~~L~~r~~~~~~~~~~~~~~pv~~~vFDlL~l~G-~l~~~pl~eRr~~L~~~~~~------  367 (558)
T 3gde_A          296 -VILDGEVIAVKEGKPMPFQHVLRRFRRKHDVAKMVEKIPLEAHFFDILYHDG-ECIDLPLRERRKLLESAVNE------  367 (558)
T ss_dssp             -EEEEEEEEEEETTEEECHHHHHHHHHC--CTHHHHHHSCEEEEEEEEEEESS-BCTTSBHHHHHHHHHHHBCC------
T ss_pred             -eEEEeEEEEcCCCcCCCHHHHHHHhccccchhhHhhcCCeEEEEEEEEeeCC-CccCCCHHHHHHHHHHhcCC------
Confidence             99998   22110                         12699999999999 99999888888877766642      


Q ss_pred             CCCCCCCceeccccccC-ChHhHHHHHhcCCCCCcccEEeEeccccccCC-CCcCeeeec
Q 014751          223 PSHYYKFRFSTVPVYNC-DQRGLYSAYIESVPYAKDGLLFYNKHAHYQTG-NTPLALVWK  280 (419)
Q Consensus       223 ~s~~n~~~F~~lp~~~c-~~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G-~TPLv~~wk  280 (419)
                           +-++...|.+.+ +.+.+...+.....--.+|+++-+.++.|++| .+.-|+=||
T Consensus       368 -----~~~i~~~~~~~~~~~~~~~~~~~~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K  422 (558)
T 3gde_A          368 -----SEKIKLAKQIVTDSVDEVRKMYDEAISAGHEGVMIKLPSSPYIPGKRGKNWLKVK  422 (558)
T ss_dssp             -----CSSEEECCEEEESCHHHHHHHHHHHHHTTCCEEEEECTTCBCCTTCEEEEEEEEE
T ss_pred             -----CCeEEEeeeEecCCHHHHHHHHHHHHHcCCceeEEecCCCCCCCCCcCCceEEEe
Confidence                 124666777776 45666666655554568999999999999999 677666666

>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A*

Probab=97.61  E-value=0.00015  Score=77.63  Aligned_cols=161  Identities=14%  Similarity=0.153  Sum_probs=119.7

Q ss_pred             cccccccccCCCC---CCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEE-eecc-------CCCCCCCCCCCCCCCC
Q 014751          101 LMLPEWMIDVPDR---LSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILH-HFPS-------ALPSGARTKDPSGSAQ  169 (419)
Q Consensus       101 LMlsEWl~dvP~d---L~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~-~F~S-------~LPgG~~~~~~~~~~~  169 (419)
                      .||+.-...+|+.   +..+|++=.==-|-||+++...|....++|+|..+. +||.       .||.            
T Consensus       255 PmLA~~~~~~~~~l~~~~~~~~~E~K~DG~R~qi~~~g~~v~l~SR~g~~~t~~fP~l~~~~~~~l~~------------  322 (621)
T 2hiv_A          255 PMLAERLSNPEEILKKMGGNAIVDYKYDGERAQIHKKEDKIFIFSRRLENITSQYPDVVDYVSKYIEG------------  322 (621)
T ss_dssp             CCEEEECSCHHHHHHHTTTCEEEEEECSSEEEEEEEETTEEEEECTTCCBCGGGCHHHHHHHHHHBCC------------
T ss_pred             CeeCCccCchhHHHhhcCCcEEEEEEEcceeEEEEEcCCEEEEEcCCCcCcHhhhhhHHHHHHHhCCC------------
Confidence            4777766555543   344798888778999999999999999999998765 4654       4552            


Q ss_pred             CcEEEeeeEecC-----------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCC
Q 014751          170 SYCILDCIFHEL-----------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGAC  220 (419)
Q Consensus       170 ~ytILDCIy~e~-----------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~  220 (419)
                      .-+||||=..-.                             .-+|||.|+|.++|.++.+-+..=|.--|.+-+.+.   
T Consensus       323 ~~~iLDGElv~~d~~~g~~l~F~~L~~r~~~~~~~~~~~~~~v~~~vFDlL~l~G~~l~~~pl~eRr~~L~~~~~~~---  399 (621)
T 2hiv_A          323 KEFIIEGEIVAIDPESGEMRPFQELMHRKRKSDIYEAIKEYPVNVFLFDLMYYEDVDYTTKPLEARRKLLESIVKPN---  399 (621)
T ss_dssp             SSEEEEEEEEEBCTTTCCBCCTHHHHHHHHCSCHHHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCC---
T ss_pred             cCeEEeEEEEEeecCCCCcCCHHHHhhhccccchhhhcccCceEEEEEeccccCCCccccCCHHHHHHHHHHHhCcC---
Confidence            128999833211                             125999999999999999988888888777766541   


Q ss_pred             CCCCCCCCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEec--cccccCC-CCcCeeeeccCCC
Q 014751          221 DAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNK--HAHYQTG-NTPLALVWKDEKC  284 (419)
Q Consensus       221 ~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHK--ea~Y~~G-~TPLv~~wkD~~~  284 (419)
                              -++...|.+.++ .+.+.+.+.....--.+|+++-..  ++.|++| .+.-|+=||....
T Consensus       400 --------~~i~~~~~~~~~~~~~~~~~~~~~~~~g~EGlv~K~~~~ds~Y~~G~Rs~~WlK~K~~~~  459 (621)
T 2hiv_A          400 --------DYVKIAHHIQANNVEDLKSFFYRAISEGGEGVMVKAIGKDAIYQAGARGWLWIKLKRDYQ  459 (621)
T ss_dssp             --------SSEEECCEEEESSHHHHHHHHHHHHHTTCCEEEEECCSTTCCCCTTCEEEEEEEEETTCT
T ss_pred             --------CcEEEeeeEEeCCHHHHHHHHHHHHhcCCceEEEEecCCCCCccCCCcCCCeEEEechhc
Confidence                    245667777774 556777665555566899999999  9999999 6778878886653

>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP: a.235.1.1 b.40.4.6 d.142.2.1

Probab=97.57  E-value=0.00021  Score=77.52  Aligned_cols=165  Identities=18%  Similarity=0.172  Sum_probs=113.6

Q ss_pred             cccccccccCCCC---C-CCceEEEEecCCcEEEEEe-eCCeEEEEcCCCcEEE-eecc---CCCCCCCCCCCCCCCCCc
Q 014751          101 LMLPEWMIDVPDR---L-SHDWYVFARPAGKRCIVVS-SNGTTVSRERNGSILH-HFPS---ALPSGARTKDPSGSAQSY  171 (419)
Q Consensus       101 LMlsEWl~dvP~d---L-~~~Wl~vpcPvGkRcLVVa-s~G~T~ay~k~G~~l~-~F~S---~LPgG~~~~~~~~~~~~y  171 (419)
                      .||+.-..++|+.   + ..+|++=.==-|-||+|+. .+|....+||+|..+. +|+-   .++.--.      .+..-
T Consensus       311 PMLA~~~~~~~~~l~~~~~~~~~~E~K~DG~R~qih~~~~g~v~l~SR~g~d~t~~fPel~~~l~~~~~------~~~~~  384 (688)
T 1x9n_A          311 PMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKL------PSVTS  384 (688)
T ss_dssp             CCEEEEESSHHHHHHHTTTSCEEEEEEESSEEEEEEECTTSCEEEECTTSCBCTTTCHHHHHTSGGGBC------TTCCC
T ss_pred             CccCCccCCHHHHHhhcCCCeEEEEEccccEeEEEEEcCCCeEEEEeCCCCcccccchHHHHHHHHhhc------cCCCC
Confidence            5676655444332   2 2478888877899999999 5788999999998765 4542   1221000      00123


Q ss_pred             EEEeeeE---ecC-------------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCC
Q 014751          172 CILDCIF---HEL-------------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAP  223 (419)
Q Consensus       172 tILDCIy---~e~-------------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~  223 (419)
                      +||||=.   +..                         .-+|||.|+|.++|.++.+-+..=|.--|..-+.+.+     
T Consensus       385 ~ILDGElV~~d~~~g~~~~F~~L~~r~r~~~~~~~~~~~v~~~vFDlL~l~G~~l~~~Pl~eRr~~L~~~~~~~~-----  459 (688)
T 1x9n_A          385 FILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETE-----  459 (688)
T ss_dssp             EEEEEEEEEECTTTCSBCCHHHHTTSCSSCCCGGGCCSEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCBT-----
T ss_pred             eEEeEEEEEEeCCCCCcCCHHHHHHHhhcccchhhcccceEEEEEechhhcCCccccCCHHHHHHHHHHhhccCC-----
Confidence            8999733   221                         1379999999999999999888888777776665421     


Q ss_pred             CCCCCCceeccccccCC-hHhHHHHHhcCCCCCcccEEeEec--cccccCC-CCcCeeeecc
Q 014751          224 SHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAKDGLLFYNK--HAHYQTG-NTPLALVWKD  281 (419)
Q Consensus       224 s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~DGLLFYHK--ea~Y~~G-~TPLv~~wkD  281 (419)
                           -++...+.+.++ .+.+...+.....--.+||++-+.  ++.|++| .+.-|+=||-
T Consensus       460 -----~~i~~~~~~~~~~~~~~~~~~~~a~~~g~EGlV~K~~~~ds~Y~~GkRs~~WlK~K~  516 (688)
T 1x9n_A          460 -----GEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKK  516 (688)
T ss_dssp             -----TTEEECCEECCCCHHHHHHHHHHHHHTSEEEEEEEESSSSCSSCTTTCSEEEEEEEH
T ss_pred             -----CcEEEEeeEecCCHHHHHHHHHHHHhcCCceeEEeecccCCCCCCCCcCchHheeeh
Confidence                 246667777764 556666665555566899999999  9999998 6777666664

>3vnn_A DNA ligase 4; non-homologous END joining, DNA repair, XRCC4; HET: DNA; 2.90A {Homo sapiens}

Probab=97.24  E-value=0.0012  Score=57.71  Aligned_cols=93  Identities=20%  Similarity=0.242  Sum_probs=61.9

Q ss_pred             CCcEEEEEeeCCeEEEEcCCCcEEE-eeccCCCCCCC---CCCCCCCCCCcEEEee---eEecC----------------
Q 014751          125 AGKRCIVVSSNGTTVSRERNGSILH-HFPSALPSGAR---TKDPSGSAQSYCILDC---IFHEL----------------  181 (419)
Q Consensus       125 vGkRcLVVas~G~T~ay~k~G~~l~-~F~S~LPgG~~---~~~~~~~~~~ytILDC---Iy~e~----------------  181 (419)
                      -|-||++....|....+|++|.-+. +||-..-.|.-   -...-..+-.-+||||   ++++.                
T Consensus         8 DG~R~q~~~~g~~v~l~SR~g~d~t~~fPel~~~~~l~~~i~~~~~~~~~~~iLDGEiv~~d~~~~~f~~~~~~~~~~~~   87 (139)
T 3vnn_A            8 DGERMQMHKDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTFMQKGTKFDIKRM   87 (139)
T ss_dssp             CCEEEEEEEETTEEEEECSSCCBCTTTSCSSTTC--CCSGGGSCCCTTCCEEEEEEEEEEEETTTTEECCC---------
T ss_pred             CeEEEEEEEECCEEEEEeCCCCCchhhccchhhhcchhHHHHHHHhccCCceEeeeEEEEecCCCCCHHHHHhhhhhhhh
Confidence            3899999999999999999998764 46532100000   0000000113489998   22221                


Q ss_pred             ------CcEEEEEEEEeeCCcccccccchhhHHHhhhhcccc
Q 014751          182 ------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAET  217 (419)
Q Consensus       182 ------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~  217 (419)
                            .-+|||.|+|.++|.++.+.+..=|---|.+-+.+.
T Consensus        88 ~~~~~~~~~~~vFDlL~l~G~~L~~~pl~eRr~~L~~l~~~~  129 (139)
T 3vnn_A           88 VEDSDLQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPI  129 (139)
T ss_dssp             ----CCEEEEEEEEEEEETTEECSSSCHHHHHHHHHHHCCCB
T ss_pred             hhccCceEEEEEEEEEeECCcCcccCCHHHHHHHHHHHhhcC
Confidence                  127899999999999999999888887777766553

>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria phage T7} SCOP: b.40.4.6 d.142.2.1

Probab=96.69  E-value=0.0041  Score=61.48  Aligned_cols=91  Identities=13%  Similarity=0.062  Sum_probs=63.0

Q ss_pred             EEEEEEEEeeC----Cccc---ccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHHhcCCCCC
Q 014751          184 TYYVIDMVCWR----GYSL---YDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYA  255 (419)
Q Consensus       184 tyYVLDvl~W~----g~~l---~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~  255 (419)
                      +|||.|||..+    |.++   .+-+..=|.--|.+-+...+         .-.+...|.+.++ .+.+.+++.....--
T Consensus       144 ~~~vFDll~l~~~~~G~~l~~~~~~pl~eRr~~L~~l~~~~~---------~~~i~~~~~~~~~~~~~~~~~~~~~~~~g  214 (348)
T 1a0i_A          144 HIKLYAILPLHIVESGEDCDVMTLLMQEHVKNMLPLLQEYFP---------EIEWQAAESYEVYDMVELQQLYEQKRAEG  214 (348)
T ss_dssp             EEEEEEEEEHHHHHHCCCEEEEHHHHHHHHHHHHHHHHHHCT---------TSEEEECCEEEESSHHHHHHHHHHHHTTT
T ss_pred             EEEEEeeEeeCCCCCCccchhhccCCHHHHHHHHHHHhhhCC---------CCeEEEeccEecCCHHHHHHHHHHHHHcC
Confidence            69999999999    8877   55555556555555433211         1256778888875 466777776655566


Q ss_pred             cccEEeEeccccccCCCCcCeeeeccCC
Q 014751          256 KDGLLFYNKHAHYQTGNTPLALVWKDEK  283 (419)
Q Consensus       256 ~DGLLFYHKea~Y~~G~TPLv~~wkD~~  283 (419)
                      .+|+++-..++.|++|.+.-++=||...
T Consensus       215 ~EGlv~K~~ds~Y~~Grr~~wlK~K~~~  242 (348)
T 1a0i_A          215 HEGLIVKDPMCIYKRGKKSGWWKMKPEN  242 (348)
T ss_dssp             CCCEEEECTTCEECSEEEEEEEEESCCE
T ss_pred             CceEEEeCCCCCCCCCCccCcEEEeecc
Confidence            8999999999999999765333444333

>1fvi_A Chlorella virus DNA ligase-adenylate; adenylated DNA ligase; HET: AMP; 2.00A {Chlorella virus} SCOP: b.40.4.6 d.142.2.1 PDB: 2q2t_A* 2q2u_A* 1p8l_A*

Probab=96.68  E-value=0.0017  Score=63.24  Aligned_cols=153  Identities=14%  Similarity=0.084  Sum_probs=99.1

Q ss_pred             cccccccccCCCCCCCceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeec------cCCCCCCCCCCCCCCCCCcEEE
Q 014751          101 LMLPEWMIDVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFP------SALPSGARTKDPSGSAQSYCIL  174 (419)
Q Consensus       101 LMlsEWl~dvP~dL~~~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~------S~LPgG~~~~~~~~~~~~ytIL  174 (419)
                      -||+.-...+|+ ...+|++=+==-|-||++   +|  ..+|++|..+.. |      ..++              -+||
T Consensus         5 PmLA~~~~~~~~-~~~~~~~E~K~DG~R~~~---~g--~l~SR~g~~~t~-p~l~~~~~~~~--------------~~iL   63 (297)
T 1fvi_A            5 PLLAATLENIED-VQFPCLATPKIAGIRSVK---QT--QMLSRTFKPIRN-SVMNRLLTELL--------------PEGS   63 (297)
T ss_dssp             CCBCEECCCGGG-CCSSEEEEECCCSEEEEE---SS--SEECTTSCBCSC-HHHHHHHHHHS--------------CTTE
T ss_pred             ceeCCccCcCcC-CCCcEEEEeeEeeeeEEe---cC--EEECCCCcccCc-HHHHHHHHhcC--------------CeeE
Confidence            467766655544 236788877778999998   77  899999998652 2      1111              2788


Q ss_pred             eeeEe--------------------cCCcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceecc
Q 014751          175 DCIFH--------------------ELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTV  234 (419)
Q Consensus       175 DCIy~--------------------e~~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~l  234 (419)
                      |+=..                    ...-+|||.|+|..+    .+-+..=|.--|.+-+.+.+.     ....-.+..+
T Consensus        64 DGElv~~~~~F~~l~~~~~~~~~~~~~~~~~~vFDll~l~----~~~pl~eRr~~L~~~~~~~~~-----~~~~~~i~~~  134 (297)
T 1fvi_A           64 DGEISIEGATFQDTTSAVMTGHKMYNAKFSYYWFDYVTDD----PLKKYIDRVEDMKNYITVHPH-----ILEHAQVKII  134 (297)
T ss_dssp             EEEEECTTSCHHHHHHHHHSCC----CCEEEEEEEECSSC----TTSCHHHHHHHHHHHHHHCGG-----GGGCSSEEEE
T ss_pred             EEEEEECCCCHHHHHHHhccCCCCCccceEEEEEeccCCC----CCCCHHHHHHHHHHHHhhcCC-----ccccceEEEc
Confidence            98443                    123479999999776    333444455555544433211     0000145566


Q ss_pred             c--cccCC-hHhHHHHHhcCCCCCcccEEeEeccccccCCCCc----CeeeeccCC
Q 014751          235 P--VYNCD-QRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTP----LALVWKDEK  283 (419)
Q Consensus       235 p--~~~c~-~~~L~~~~~~~~p~~~DGLLFYHKea~Y~~G~TP----Lv~~wkD~~  283 (419)
                      |  .+.++ .+.+.+.+.....--.+|+++-..++.|++|.+.    -++=||...
T Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~g~EGlv~K~~ds~Y~~GRs~~~~g~wlK~K~~~  190 (297)
T 1fvi_A          135 PLIPVEINNITELLQYERDVLSKGFEGVMIRKPDGKYKFGRSTLKEGILLKMKQFK  190 (297)
T ss_dssp             ECCCEEECSHHHHHHHHHHHHHTTCCSEEEECTTCCCCSSBCCTTTTSSEEECCCE
T ss_pred             CcceEecCCHHHHHHHHHHHHHCCCcEEEEECCCCCcCCCCCCCCCCCeEEECCCC
Confidence            6  77764 5667766655555568999999999999999888    777777543

---

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	419
d1ckma2	228	d.142.2.3 (A:11-238) RNA guanylyltransferase (mRNA	1e-05
d1p16a2	245	d.142.2.3 (A:1-245) mRNA capping enzyme alpha subu	3e-05

>d1ckma2 d.142.2.3 (A:11-238) RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]} Length = 228

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: mRNA capping enzyme
domain: RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain
species: Chlorella virus PBCV-1 [TaxId: 10506]

 Score = 43.6 bits (102), Expect = 1e-05
 Identities = 24/172 (13%), Positives = 41/172 (23%), Gaps = 3/172 (1%)

Query: 109 DVPDRLSHDWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSA 168
           D      + + V  +  G R ++  +                    LP     +     +
Sbjct: 58  DFEKLKQNKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDR-AMTVYLLPFKNIPRVLFQGS 116

Query: 169 QSYCILDCIFHELDQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYK 228
                L     E    + + D V   G ++       RFF +   L E      P     
Sbjct: 117 IFDGELCVDIVEKKFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNV--PEDPAI 174

Query: 229 FRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPLALVWK 280
            R+                   +  Y  DGL+  +       G        K
Sbjct: 175 LRYKEWIPLEHPTIIKDHLKKANAIYHTDGLIIMSVDEPVIYGRNFNLFKLK 226

>d1p16a2 d.142.2.3 (A:1-245) mRNA capping enzyme alpha subunit {Yeast (Candida albicans) [TaxId: 5476]} Length = 245

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: mRNA capping enzyme
domain: mRNA capping enzyme alpha subunit
species: Yeast (Candida albicans) [TaxId: 5476]

 Score = 42.9 bits (100), Expect = 3e-05
 Identities = 25/185 (13%), Positives = 46/185 (24%), Gaps = 19/185 (10%)

Query: 115 SHDWYVFARPAGKRCIVVSSNGTTVSRE-----RNGSILHHFPSALPSGARTKDPSGSAQ 169
             D++V  +  G RC++   N            R            P          +  
Sbjct: 59  QKDYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRENDYYFIPNIHFPLSVNETREKPTYH 118

Query: 170 SYCILDCIF-------HELDQTYYVIDMVCWRGYSL-------YDCTAEFRFFWLNSKLA 215
              +LD           E    Y + D +   G  +                        
Sbjct: 119 HGTLLDGELVLENRNVSEPVLRYVIFDALAIHGKCIIDRPLPKRLGYITENVMKPFDNFK 178

Query: 216 ETGACDAPSHYYKFRFSTVPVYNCDQRGLYSAYIESVPYAKDGLLFYNKHAHYQTGNTPL 275
           +       S  + F+     +          + ++ + +A DGL++      Y  G    
Sbjct: 179 KHNPDIVNSPEFPFKVGFKTMLTSYHADDVLSKMDKLFHASDGLIYTCAETPYVFGTDQT 238

Query: 276 ALVWK 280
            L WK
Sbjct: 239 LLKWK 243

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	419
d1ckma2	228	RNA guanylyltransferase (mRNA capping enzyme), N-t	98.68
d1p16a2	245	mRNA capping enzyme alpha subunit {Yeast (Candida	98.56
d1x9na3	220	DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId:	97.96
d1a0ia2	239	ATP-dependent DNA ligase, N-terminal domain {Bacte	97.07
d1fvia2	188	ATP-dependent DNA ligase, N-terminal domain {Chlor	85.95

>d1ckma2 d.142.2.3 (A:11-238) RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: mRNA capping enzyme
domain: RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain
species: Chlorella virus PBCV-1 [TaxId: 10506]

Probab=98.68  E-value=8.4e-08  Score=87.24  Aligned_cols=154  Identities=14%  Similarity=0.091  Sum_probs=111.0

Q ss_pred             CceEEEEecCCcEEEEEeeC----CeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEec----CCcEEEE
Q 014751          116 HDWYVFARPAGKRCIVVSSN----GTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHE----LDQTYYV  187 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas~----G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e----~~~tyYV  187 (419)
                      .+|++-.==-|.|+|+...+    +.+...++++.....=...+|...         -.-||||+=+.-    .+.+|+|
T Consensus        65 ~~Y~vseK~DG~R~ll~~~~~~~~~~~~li~r~~~~~~~~~~~~~~~~---------~~~ti~DGEli~~~~~~~~~f~i  135 (228)
T d1ckma2          65 NKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMTVYLLPFKNIPRVL---------FQGSIFDGELCVDIVEKKFAFVL  135 (228)
T ss_dssp             SCEEEEEEECSEEEEEEEEEETTEEEEEEECTTCCEEECCCSCCCTTG---------GGCEEEEEEEEEETTTTEEEEEE
T ss_pred             CCeEEEEeecCEEEEEEEEecCCceEEEEEeCCCceEEcccccCchhh---------cCCceEeEEEEeecccccceEEE
Confidence            36888888889999987653    456677888876431111233321         123999986542    3357999


Q ss_pred             EEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHH-hcCCCCCcccEEeEecc
Q 014751          188 IDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAY-IESVPYAKDGLLFYNKH  265 (419)
Q Consensus       188 LDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~-~~~~p~~~DGLLFYHKe  265 (419)
                      .|++.|+|.++.+++..-|+..|+.=+.+...    ....++.+..-+.++.+ ...+.+.+ ....+|..|||+|..++
T Consensus       136 fD~l~~~g~~~~~~pf~~Rl~~L~~~l~~~~~----~~~~~~~i~~k~~~~~~~~~~l~~~~~~~~~~y~~DGLIf~p~~  211 (228)
T d1ckma2         136 FDAVVVSGVTVSQMDLASRFFAMKRSLKEFKN----VPEDPAILRYKEWIPLEHPTIIKDHLKKANAIYHTDGLIIMSVD  211 (228)
T ss_dssp             EEEEEETTEECTTSCHHHHHHHHHHHHTTCCC----CTTSSSEEEECCCEETTCHHHHHHHHHHHHHHSCEEEEEEEESS
T ss_pred             eeEEEEcCcchhcCChHHHHHHHHHHHhhhhc----cccCceeEEeeeeeehhhHHHHHHHHhhhccCCCCceEEEEeCC
Confidence            99999999999999999999999877766432    12345666677777775 34455544 44678999999999999


Q ss_pred             ccccCCCCcCeeeeccC
Q 014751          266 AHYQTGNTPLALVWKDE  282 (419)
Q Consensus       266 a~Y~~G~TPLv~~wkD~  282 (419)
                      +.|.+|.+-.++=||++
T Consensus       212 ~pY~~Gr~~~~~KWKP~  228 (228)
T d1ckma2         212 EPVIYGRNFNLFKLKPG  228 (228)
T ss_dssp             SCCCCEEEEEEEEECST
T ss_pred             CCEeCCCCCCeEEeCCC
Confidence            99999988778888864

>d1p16a2 d.142.2.3 (A:1-245) mRNA capping enzyme alpha subunit {Yeast (Candida albicans) [TaxId: 5476]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: mRNA capping enzyme
domain: mRNA capping enzyme alpha subunit
species: Yeast (Candida albicans) [TaxId: 5476]

Probab=98.56  E-value=2.4e-07  Score=83.99  Aligned_cols=166  Identities=16%  Similarity=0.235  Sum_probs=105.4

Q ss_pred             CceEEEEecCCcEEEEEee-----CCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEecCC-------c
Q 014751          116 HDWYVFARPAGKRCIVVSS-----NGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHELD-------Q  183 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVVas-----~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~~-------~  183 (419)
                      .+|++-.=--|.|||++..     ++.+..+++++.........+|...............||||+-+.-.+       -
T Consensus        60 ~~Y~v~eK~DG~R~lL~i~~~~~~~~~~~li~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~tilDGElv~~~~~~~~~~~  139 (245)
T d1p16a2          60 KDYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRENDYYFIPNIHFPLSVNETREKPTYHHGTLLDGELVLENRNVSEPVL  139 (245)
T ss_dssp             SCEEEEEEECSEEEEEEEEEETTTEEEEEEEETTCCEEECCSCCCCSCTTCCSSSCCCCSSEEEEEEEEEECCSSSCCEE
T ss_pred             CCEEEEECcCCeEEEEEEEEcCCCceEEEEEeCCCCeEEccccccccccccccccccccCCeeEEEEEEeecccCCcceE
Confidence            3688888789999999874     344557788887765433344433221111112234599999765332       2


Q ss_pred             EEEEEEEEeeCCcccccccchhhHHHhhhhccccCC-------CCCCCCCCCCceeccccccCCh-HhHHHHHhcCCCCC
Q 014751          184 TYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGA-------CDAPSHYYKFRFSTVPVYNCDQ-RGLYSAYIESVPYA  255 (419)
Q Consensus       184 tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~-------~~~~s~~n~~~F~~lp~~~c~~-~~L~~~~~~~~p~~  255 (419)
                      .|+|.|+++++|.++.+.+..-|.--++..+.+...       ........++.+..-+.+..+. +.+.. .....+|.
T Consensus       140 ~~~ifDil~~~g~~l~~~~l~~R~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~l~~-~~~~~~~~  218 (245)
T d1p16a2         140 RYVIFDALAIHGKCIIDRPLPKRLGYITENVMKPFDNFKKHNPDIVNSPEFPFKVGFKTMLTSYHADDVLS-KMDKLFHA  218 (245)
T ss_dssp             EEEEEEEEEETTEECTTSCHHHHHHHHHHHTHHHHHHHHHHCHHHHSCTTSCCEEEECCCEEGGGTHHHHT-TGGGCSSC
T ss_pred             EEEEeeehhhCCceeeeccHHHHHHHHHHHHHHhhhhhhhcccccccchhhhhhhhhhhhhhHHHHHHHHH-HhhhcCCC
Confidence            699999999999999999988888766655433210       0000111223333333333321 22222 23457899


Q ss_pred             cccEEeEeccccccCCCCcCeeeeccC
Q 014751          256 KDGLLFYNKHAHYQTGNTPLALVWKDE  282 (419)
Q Consensus       256 ~DGLLFYHKea~Y~~G~TPLv~~wkD~  282 (419)
                      .|||+|...++-|.+|.+..++=||.+
T Consensus       219 ~DGLIf~p~~~pY~~Gr~~~~lKWKP~  245 (245)
T d1p16a2         219 SDGLIYTCAETPYVFGTDQTLLKWKPA  245 (245)
T ss_dssp             EEEEEEEESSSCCCSEEEEEEEEECCG
T ss_pred             CCeEEEEcCCCCEeCCCCCCeEEeCCC
Confidence            999999999999999998888889863

>d1x9na3 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: ATP-dependent DNA ligase catalytic domain
domain: DNA ligase I (LIG1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.96  E-value=1.3e-05  Score=71.84  Aligned_cols=149  Identities=19%  Similarity=0.167  Sum_probs=101.5

Q ss_pred             CceEEEEecCCcEEEEE-eeCCeEEEEcCCCcEE-Eeecc---CCCCCCCCCCCCCCCCCcEEEeeeEe---cC------
Q 014751          116 HDWYVFARPAGKRCIVV-SSNGTTVSRERNGSIL-HHFPS---ALPSGARTKDPSGSAQSYCILDCIFH---EL------  181 (419)
Q Consensus       116 ~~Wl~vpcPvGkRcLVV-as~G~T~ay~k~G~~l-~~F~S---~LPgG~~~~~~~~~~~~ytILDCIy~---e~------  181 (419)
                      .+|++=+==-|-||+++ ..+|....+|++|..+ ..|+-   .++....      .+..-+|||+=..   ..      
T Consensus        28 ~~~~~e~K~DG~R~~i~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~~~~~------~~~~~~iLDGEl~~~d~~~~~~~~  101 (220)
T d1x9na3          28 AAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKL------PSVTSFILDTEAVAWDREKKQIQP  101 (220)
T ss_dssp             SCEEEEEEESSEEEEEEECTTSCEEEECTTSCBCTTTCHHHHHTSGGGBC------TTCCCEEEEEEEEEECTTTCSBCC
T ss_pred             CcEEEEEeECcEEEEEEEECCCEEEEEeCCCccccccchhHHHHHHHhhc------CCCcceeeeeeeEEecCCCCccch
Confidence            56877666679999875 5788889999999876 34432   2221100      0112379998542   11      


Q ss_pred             -------------------CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-h
Q 014751          182 -------------------DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-Q  241 (419)
Q Consensus       182 -------------------~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~  241 (419)
                                         .-.|||.|+|.++|.++.+.+..=|.--|+.-+.+..          -++..++.+.++ .
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~~~~~p~~eR~~~L~~~~~~~~----------~~~~~~~~~~~~~~  171 (220)
T d1x9na3         102 FQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETE----------GEFVFATSLDTKDI  171 (220)
T ss_dssp             HHHHTTSCSSCCCGGGCCSEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCBT----------TTEEECCEECCCCH
T ss_pred             HHHHhhhhhcccchhhhccccceEEEEEEEECCcchhhhhHHHHHHHHHHHhccCC----------CeEEEEEeeccCCH
Confidence                               1369999999999999999988888887877665432          246778888886 4


Q ss_pred             HhHHHHHhcCCCCCcccEEeE--eccccccCC-CCcCeeeec
Q 014751          242 RGLYSAYIESVPYAKDGLLFY--NKHAHYQTG-NTPLALVWK  280 (419)
Q Consensus       242 ~~L~~~~~~~~p~~~DGLLFY--HKea~Y~~G-~TPLv~~wk  280 (419)
                      +.+..++.....--..|++.-  +.++.|.+| .|.-++=||
T Consensus       172 ~~~~~~~~~~~~~g~EGim~K~~~~~s~Y~~GkRs~~w~K~K  213 (220)
T d1x9na3         172 EQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLK  213 (220)
T ss_dssp             HHHHHHHHHHHHTSEEEEEEEESSSSCSSCTTTCSEEEEEEE
T ss_pred             HHHHHHHHHHHHCCCceEEEeccCCCCCeecCCcCCCeEEEc
Confidence            556666644333346899996  578999999 575544445

>d1a0ia2 d.142.2.1 (A:2-240) ATP-dependent DNA ligase, N-terminal domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: ATP-dependent DNA ligase catalytic domain
domain: ATP-dependent DNA ligase, N-terminal domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=97.07  E-value=0.0006  Score=60.43  Aligned_cols=87  Identities=13%  Similarity=0.102  Sum_probs=56.9

Q ss_pred             EEEEEEEEeeCCccccc------ccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCC-hHhHHHHHhcCCCCCc
Q 014751          184 TYYVIDMVCWRGYSLYD------CTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCD-QRGLYSAYIESVPYAK  256 (419)
Q Consensus       184 tyYVLDvl~W~g~~l~d------ceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~-~~~L~~~~~~~~p~~~  256 (419)
                      .|+|.|++.+++....+      ....-|.-=|.+.+.+..        .+..+...+.+.|+ .+.+..++.....--.
T Consensus       144 ~~~vfD~l~l~~~~~~~~~~~~~~~~~~r~~~l~~~~~~~~--------~~~~~~~~~~~~~~~~~el~~~~~~~~~~g~  215 (239)
T d1a0ia2         144 HIKLYAILPLHIVESGEDCDVMTLLMQEHVKNMLPLLQEYF--------PEIEWQAAESYEVYDMVELQQLYEQKRAEGH  215 (239)
T ss_dssp             EEEEEEEEEHHHHHHCCCEEEEHHHHHHHHHHHHHHHHHHC--------TTSEEEECCEEEESSHHHHHHHHHHHHTTTC
T ss_pred             eEEEEEEeeccccccccchhhccccHHHHHHHHHHHHhhcC--------CCccEEEeeeEecCCHHHHHHHHHHHHHCCC
Confidence            58999999997643222      222223333344444432        23567778888775 4567776655444456


Q ss_pred             ccEEeEeccccccCCCCcCeeeec
Q 014751          257 DGLLFYNKHAHYQTGNTPLALVWK  280 (419)
Q Consensus       257 DGLLFYHKea~Y~~G~TPLv~~wk  280 (419)
                      .|++-=+.++.|++|.+-  .|||
T Consensus       216 EGlmiK~~~s~Y~~GR~~--~w~K  237 (239)
T d1a0ia2         216 EGLIVKDPMCIYKRGKKS--GWWK  237 (239)
T ss_dssp             CCEEEECTTCEECSEEEE--EEEE
T ss_pred             cEEEEeCCCCccCCCCCC--CcEE
Confidence            799999999999999884  6887

>d1fvia2 d.142.2.1 (A:2-189) ATP-dependent DNA ligase, N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: ATP-dependent DNA ligase catalytic domain
domain: ATP-dependent DNA ligase, N-terminal domain
species: Chlorella virus PBCV-1 [TaxId: 10506]

Probab=85.95  E-value=0.25  Score=41.63  Aligned_cols=138  Identities=11%  Similarity=-0.013  Sum_probs=85.8

Q ss_pred             ceEEEEecCCcEEEEEeeCCeEEEEcCCCcEEEeeccCCCCCCCCCCCCCCCCCcEEEeeeEecC---------------
Q 014751          117 DWYVFARPAGKRCIVVSSNGTTVSRERNGSILHHFPSALPSGARTKDPSGSAQSYCILDCIFHEL---------------  181 (419)
Q Consensus       117 ~Wl~vpcPvGkRcLVVas~G~T~ay~k~G~~l~~F~S~LPgG~~~~~~~~~~~~ytILDCIy~e~---------------  181 (419)
                      -+++=+==-|-||+.   ++  ..+|++|..+....   |--.      ......++|||=+.-.               
T Consensus        20 p~~~e~K~DG~R~~~---~~--~l~SR~g~~~~~~~---~~~~------~~~~~~~~lDGEl~~~~~~~~~~~~~~~~~~   85 (188)
T d1fvia2          20 PCLATPKIAGIRSVK---QT--QMLSRTFKPIRNSV---MNRL------LTELLPEGSDGEISIEGATFQDTTSAVMTGH   85 (188)
T ss_dssp             SEEEEECCCSEEEEE---SS--SEECTTSCBCSCHH---HHHH------HHHHSCTTEEEEEECTTSCHHHHHHHHHSCC
T ss_pred             cEEEEeccccEeEEe---EE--EEEecCCCccCCcC---hHHH------HhhCccccccceeeccCCchhhhHHHHhhcc
Confidence            344555556899973   22  48899997664221   1000      0011235688866522               


Q ss_pred             -----CcEEEEEEEEeeCCcccccccchhhHHHhhhhccccCCCCCCCCCCCCceeccccccCCh-HhHHHHHhcCCCCC
Q 014751          182 -----DQTYYVIDMVCWRGYSLYDCTAEFRFFWLNSKLAETGACDAPSHYYKFRFSTVPVYNCDQ-RGLYSAYIESVPYA  255 (419)
Q Consensus       182 -----~~tyYVLDvl~W~g~~l~dceteFRffWl~SKl~E~~~~~~~s~~n~~~F~~lp~~~c~~-~~L~~~~~~~~p~~  255 (419)
                           .-.|+|.|++.+++    ++...=|.-.|+..+.+....   .......++.++.+.|+. +.+...+.....--
T Consensus        86 ~~~~~~~~~~vfD~~~~~~----~~~~~~r~~~l~~~l~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G  158 (188)
T d1fvia2          86 KMYNAKFSYYWFDYVTDDP----LKKYIDRVEDMKNYITVHPHI---LEHAQVKIIPLIPVEINNITELLQYERDVLSKG  158 (188)
T ss_dssp             ----CCEEEEEEEECSSCT----TSCHHHHHHHHHHHHHHCGGG---GGCSSEEEEECCCEEECSHHHHHHHHHHHHHTT
T ss_pred             cccccccEEEEEEEecCcc----cccHHHHHHHHHHHHHhcccc---cccCceEEEeeeeEecCCHHHHHHHHHHHHHCC
Confidence                 25699999988775    355555778888888775432   112445667777777754 55665554433334


Q ss_pred             cccEEeEeccccccCCCCcC
Q 014751          256 KDGLLFYNKHAHYQTGNTPL  275 (419)
Q Consensus       256 ~DGLLFYHKea~Y~~G~TPL  275 (419)
                      ..|++.=+.++.|++|.+.-
T Consensus       159 ~EGlmiK~~ds~Y~~gr~s~  178 (188)
T d1fvia2         159 FEGVMIRKPDGKYKFGRSTL  178 (188)
T ss_dssp             CCSEEEECTTCCCCSSBCCT
T ss_pred             CcEEEEECCCCccCCCCcCC
Confidence            68999999999999998754