Citrus Sinensis ID: 026445

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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-------24
Protein Sequence
MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEVNL
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccEEEEccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccEEEEccEEEEEccEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEccc
Secondary Structure Prediction (SSPRO)
cccHHHcccccccccEEEEccccccEccccccccccccccccccccccEEEEEEEEEEccccccHHcccccccccccccccccccEccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccEEEccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccEEEEccccEEcccEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEHHEEEEcc
Coil and Loop (DISEMBL)
magkvasgftpqaqrvfavpvqkpaaalapfpsssrahsnsntqfngrqftvrrrsfvlpskattdqqgqvegdevvDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYegkavmsneEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYvagkpimsdeEYDKLKQKLKMEgseivvegprcslrsrkvysDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEVNL
Flexible Loop (DISEMBL)
magkvasgftpqaqrVFAVPVQKPAAALAPfpsssrahsnsntqfngrqftvRRRSFVLpskattdqqgqvegdevvdSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKmegseivvegprcslrsrkVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEVNL
Low Complexity Region (SEG)
MAGKVASGFTPQAQRVFAVPVQKpaaalapfpsssraHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEVNL
Disordered region (IsUnstruct)
********************************************************************************ILQY*****************FLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGK********************EIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEV**
Disordered Region (DISOPRED)
*********TPQAQRV**************************************************************SKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEVNL
Disordered Region (DISEMBL)
********FTPQAQRVFAVPVQKPAAALAP*************QFNGRQFTVRRRSFVLPS*************EVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEVNL
Disordered Region (DISPRO)
******S*FTPQAQRVFAVPVQKPAAA*****************FNGRQFTVRRRSFVLPSK**********GDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEVNL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHoooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEVNL
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	238	2.2.26 [Sep-21-2011]
Q8H112	324	PGR5-like protein 1A, chl	yes	no	0.794	0.583	0.778	1e-85
Q8GYC7	313	PGR5-like protein 1B, chl	no	no	0.848	0.645	0.769	9e-84

>sp|Q8H112|PGL1A_ARATH PGR5-like protein 1A, chloroplastic OS=Arabidopsis thaliana GN=PGRL1A PE=1 SV=1

 Score =  316 bits (809), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 148/190 (77%), Positives = 174/190 (91%), Gaps = 1/190 (0%)

Query: 47  GRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQAL 106
           G+  ++RRR F+LP+KATT+Q G V GD V DS +L YCSI+K EKK++GE+EQEFLQAL
Sbjct: 45  GKSISLRRRVFLLPAKATTEQSGPVGGDNV-DSNVLPYCSINKAEKKTIGEMEQEFLQAL 103

Query: 107 QAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYD 166
           Q+FYY+GKA+MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI++DEEYD
Sbjct: 104 QSFYYDGKAIMSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILNDEEYD 163

Query: 167 KLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDIT 226
           KLK KLK++GS+IV EGPRCSLRS+KVYSDL+VDY KMLLLNVPATVVALGLFFFLDDIT
Sbjct: 164 KLKLKLKIDGSDIVSEGPRCSLRSKKVYSDLAVDYFKMLLLNVPATVVALGLFFFLDDIT 223

Query: 227 GFEITYLLEV 236
           GFEITY++E+
Sbjct: 224 GFEITYIMEL 233

Involved in cyclic electron flow (CEF) around photosystem I.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8GYC7|PGL1B_ARATH PGR5-like protein 1B, chloroplastic OS=Arabidopsis thaliana GN=PGRL1B PE=1 SV=1

 Score =  309 bits (792), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 157/204 (76%), Positives = 180/204 (88%), Gaps = 2/204 (0%)

Query: 33  SSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEK 92
           SSSR    +    +GR  ++RRR  +LP KA+TDQ GQV G+EV DSKIL YCSI+K EK
Sbjct: 21  SSSRTQCPAPFT-HGRSISLRRRLTLLPLKASTDQSGQVGGEEV-DSKILPYCSINKNEK 78

Query: 93  KSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMA 152
           +++GE+EQEFLQA+Q+FYYEGKA+MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMA
Sbjct: 79  RTIGEMEQEFLQAMQSFYYEGKAIMSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMA 138

Query: 153 YVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPAT 212
           YV+G PI+SDEEYDKLK KLKM+GSEIV EGPRCSLRS+KVYSDL++DY KM LLNVPAT
Sbjct: 139 YVSGNPILSDEEYDKLKMKLKMDGSEIVCEGPRCSLRSKKVYSDLAIDYFKMFLLNVPAT 198

Query: 213 VVALGLFFFLDDITGFEITYLLEV 236
           VVALGLFFFLDDITGFEITYLLE+
Sbjct: 199 VVALGLFFFLDDITGFEITYLLEL 222

Involved in cyclic electron flow (CEF) around photosystem I.

Arabidopsis thaliana (taxid: 3702)

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	238
224071670	327	predicted protein [Populus trichocarpa]	0.983	0.715	0.735	5e-91
255537217	320	conserved hypothetical protein [Ricinus	0.957	0.712	0.729	6e-91
356514103	321	PREDICTED: PGR5-like protein 1A, chlorop	0.945	0.700	0.741	7e-91
255645443	321	unknown [Glycine max]	0.945	0.700	0.741	8e-91
225426724	331	PREDICTED: PGR5-like protein 1A, chlorop	0.987	0.709	0.728	1e-90
118487360	323	unknown [Populus trichocarpa]	0.970	0.715	0.738	2e-90
297742627	326	unnamed protein product [Vitis vinifera]	0.987	0.720	0.728	2e-90
449460457	321	PREDICTED: PGR5-like protein 1A, chlorop	0.890	0.660	0.781	6e-89
224058627	327	predicted protein [Populus trichocarpa]	0.970	0.706	0.701	3e-88
356497195	316	PREDICTED: PGR5-like protein 1A, chlorop	0.810	0.610	0.803	8e-86

>gi|224071670|ref|XP_002303553.1| predicted protein [Populus trichocarpa] gi|222840985|gb|EEE78532.1| predicted protein [Populus trichocarpa]

 Score =  339 bits (870), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 175/238 (73%), Positives = 200/238 (84%), Gaps = 4/238 (1%)

Query: 1   MAGKVASGFTPQAQRVFAVPVQKPA-AALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVL 59
           MA K+A  F   + RVF  P+QKP  ++ +  PS S    ++  Q NG+QF++R R   L
Sbjct: 1   MASKLA--FNLTSPRVFTAPIQKPIISSSSSLPSLSSPSCSTRVQLNGKQFSLRGRMLFL 58

Query: 60  PSKATTDQQ-GQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMS 118
           P+KAT DQQ  QV+ D++ D KILQYCSIDKK KKSLGE+EQ+FLQALQAFYYEGKA+MS
Sbjct: 59  PTKATADQQTDQVQEDDMDDGKILQYCSIDKKGKKSLGEMEQDFLQALQAFYYEGKAIMS 118

Query: 119 NEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSE 178
           NEEFDNLKEELMW+GSSVVMLSS EQKFLEAS+AYV+G PIM+DEE+DKLK KLK EGSE
Sbjct: 119 NEEFDNLKEELMWQGSSVVMLSSDEQKFLEASLAYVSGNPIMNDEEFDKLKIKLKTEGSE 178

Query: 179 IVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEV 236
           IVVEGPRCSLRSRKVYSDLSVDYLKM LLNVPATVVALGLFFFLDD+TGFEITYLLE+
Sbjct: 179 IVVEGPRCSLRSRKVYSDLSVDYLKMFLLNVPATVVALGLFFFLDDLTGFEITYLLEL 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255537217|ref|XP_002509675.1| conserved hypothetical protein [Ricinus communis] gi|223549574|gb|EEF51062.1| conserved hypothetical protein [Ricinus communis]

 Score =  339 bits (870), Expect = 6e-91,   Method: Compositional matrix adjust.
 Identities = 173/237 (72%), Positives = 197/237 (83%), Gaps = 9/237 (3%)

Query: 1   MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLP 60
           MA K+A  F+    RV++ P+ KP  +       S +    ++  +G+  +VRRR  +LP
Sbjct: 1   MASKLA--FSLTFPRVYSAPILKPLIS------LSSSSRIHSSHLHGKHLSVRRRILLLP 52

Query: 61  SKATTDQQ-GQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSN 119
            KAT DQQ G+VEGDEVVD KILQYCSIDKK+KKS+GE+EQEFLQALQAFYYEGKA+MSN
Sbjct: 53  IKATADQQQGKVEGDEVVDGKILQYCSIDKKDKKSIGEMEQEFLQALQAFYYEGKAIMSN 112

Query: 120 EEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEI 179
           EEFDNLKEELMWEGSSVVMLS  EQKFLEASMAYV+G PIMSDEE+D+LK +LK EGSEI
Sbjct: 113 EEFDNLKEELMWEGSSVVMLSCDEQKFLEASMAYVSGNPIMSDEEFDQLKLRLKQEGSEI 172

Query: 180 VVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEV 236
           VVEGPRCSLRSRKVYSDLSVDYLKM LLNVPA VVALGLFFFLDD+TGFEITYLLE+
Sbjct: 173 VVEGPRCSLRSRKVYSDLSVDYLKMFLLNVPAAVVALGLFFFLDDLTGFEITYLLEL 229

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356514103|ref|XP_003525746.1| PREDICTED: PGR5-like protein 1A, chloroplastic-like [Glycine max]

 Score =  339 bits (869), Expect = 7e-91,   Method: Compositional matrix adjust.
 Identities = 172/232 (74%), Positives = 189/232 (81%), Gaps = 7/232 (3%)

Query: 9   FTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQ 68
           FT         P +   A L P  S+S  H     QFNGR   +R+R F+L   AT DQQ
Sbjct: 2   FTASKLAFTLTPPRPCTAPLTPISSASGVHL---IQFNGRHLCLRQRLFLLSPMATADQQ 58

Query: 69  GQVEGDE----VVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDN 124
           G+VE  E     VDSKIL YCSIDKKEKKS+GELEQEFLQALQAFYYEGKA+MSNEEFDN
Sbjct: 59  GKVEEFEDDSNTVDSKILPYCSIDKKEKKSIGELEQEFLQALQAFYYEGKAIMSNEEFDN 118

Query: 125 LKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGP 184
           LKEELMWEGSSVVMLSS EQKFLEASMAYV+GKPIMSD+E+D+LK +LK+EGSEIV EGP
Sbjct: 119 LKEELMWEGSSVVMLSSDEQKFLEASMAYVSGKPIMSDKEFDELKLRLKIEGSEIVAEGP 178

Query: 185 RCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEV 236
           RCSLRSRKVYSDLSVDYLKMLLLNVPATV+ALGLFFFLDD+TGFEITYLLE+
Sbjct: 179 RCSLRSRKVYSDLSVDYLKMLLLNVPATVIALGLFFFLDDLTGFEITYLLEL 230

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255645443|gb|ACU23217.1| unknown [Glycine max]

 Score =  338 bits (868), Expect = 8e-91,   Method: Compositional matrix adjust.
 Identities = 172/232 (74%), Positives = 189/232 (81%), Gaps = 7/232 (3%)

Query: 9   FTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQ 68
           FT         P +   A L P  S+S  H     QFNGR   +R+R F+L   AT DQQ
Sbjct: 2   FTASKLAFTLTPPRPCTAPLTPISSASGVHL---IQFNGRHLCLRQRLFLLSPMATADQQ 58

Query: 69  GQVEGDE----VVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDN 124
           G+VE  E     VDSKIL YCSIDKKEKKS+GELEQEFLQALQAFYYEGKA+MSNEEFDN
Sbjct: 59  GKVEEFEDDSNTVDSKILPYCSIDKKEKKSIGELEQEFLQALQAFYYEGKAIMSNEEFDN 118

Query: 125 LKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGP 184
           LKEELMWEGSSVVMLSS EQKFLEASMAYV+GKPIMSD+E+D+LK +LK+EGSEIV EGP
Sbjct: 119 LKEELMWEGSSVVMLSSDEQKFLEASMAYVSGKPIMSDKEFDELKLRLKIEGSEIVAEGP 178

Query: 185 RCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEV 236
           RCSLRSRKVYSDLSVDYLKMLLLNVPATV+ALGLFFFLDD+TGFEITYLLE+
Sbjct: 179 RCSLRSRKVYSDLSVDYLKMLLLNVPATVIALGLFFFLDDLTGFEITYLLEL 230

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225426724|ref|XP_002282120.1| PREDICTED: PGR5-like protein 1A, chloroplastic-like [Vitis vinifera]

 Score =  338 bits (866), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 172/236 (72%), Positives = 195/236 (82%), Gaps = 1/236 (0%)

Query: 1   MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLP 60
           MA K+    T  A R+FA   +KP  + A   S+S      + Q  GRQ  + RR F++ 
Sbjct: 6   MATKLGFALT-TAPRLFASSSRKPLISPASLSSASSCSRVESFQLVGRQLRLSRRLFIIS 64

Query: 61  SKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNE 120
            KAT DQQGQV+GD+VVDSKIL YCSIDKKEK+S+GE+EQ+FLQALQ+FYYEGKA+MSNE
Sbjct: 65  PKATADQQGQVQGDDVVDSKILPYCSIDKKEKRSIGEMEQDFLQALQSFYYEGKAIMSNE 124

Query: 121 EFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIV 180
           EFDNLKEELMWEGSSVVMLSS EQKFLEASMAYVAG PIMSDEE+D LK KLK+EGSEIV
Sbjct: 125 EFDNLKEELMWEGSSVVMLSSDEQKFLEASMAYVAGNPIMSDEEFDDLKIKLKIEGSEIV 184

Query: 181 VEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEV 236
           VEGPRCSLRS+KVYSDLSVDYLKM LLNVPA VVAL LFFFLDD+TGFEIT+LLE+
Sbjct: 185 VEGPRCSLRSKKVYSDLSVDYLKMFLLNVPAAVVALSLFFFLDDVTGFEITFLLEL 240

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118487360|gb|ABK95508.1| unknown [Populus trichocarpa]

 Score =  338 bits (866), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 175/237 (73%), Positives = 200/237 (84%), Gaps = 6/237 (2%)

Query: 1   MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLP 60
           MA K+A  F   + RVF  P+QKP  + +   SS  + S++  Q NG+QF++R R   LP
Sbjct: 1   MASKLA--FNLTSPRVFTAPIQKPIISSS---SSLPSLSSTRVQLNGKQFSLRGRMLFLP 55

Query: 61  SKATTDQQ-GQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSN 119
           +KAT DQQ  QV+ D++ D KILQYCSIDKK KKSLGE+EQ+FLQALQAFYYEGKA+MSN
Sbjct: 56  TKATADQQTDQVQEDDMDDGKILQYCSIDKKGKKSLGEMEQDFLQALQAFYYEGKAIMSN 115

Query: 120 EEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEI 179
           EEFDNLKEELMW+GSSVVMLSS EQKFLEAS+AYV+G PIM+DEE+DKLK KLK EGSEI
Sbjct: 116 EEFDNLKEELMWQGSSVVMLSSDEQKFLEASLAYVSGNPIMNDEEFDKLKIKLKTEGSEI 175

Query: 180 VVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEV 236
           VVEGPRCSLRSRKVYSDLSVDYLKM LLNVPATVVALGLFFFLDD+TGFEITYLLE+
Sbjct: 176 VVEGPRCSLRSRKVYSDLSVDYLKMFLLNVPATVVALGLFFFLDDLTGFEITYLLEL 232

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742627|emb|CBI34776.3| unnamed protein product [Vitis vinifera]

 Score =  337 bits (865), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 172/236 (72%), Positives = 195/236 (82%), Gaps = 1/236 (0%)

Query: 1   MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLP 60
           MA K+    T  A R+FA   +KP  + A   S+S      + Q  GRQ  + RR F++ 
Sbjct: 1   MATKLGFALT-TAPRLFASSSRKPLISPASLSSASSCSRVESFQLVGRQLRLSRRLFIIS 59

Query: 61  SKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNE 120
            KAT DQQGQV+GD+VVDSKIL YCSIDKKEK+S+GE+EQ+FLQALQ+FYYEGKA+MSNE
Sbjct: 60  PKATADQQGQVQGDDVVDSKILPYCSIDKKEKRSIGEMEQDFLQALQSFYYEGKAIMSNE 119

Query: 121 EFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIV 180
           EFDNLKEELMWEGSSVVMLSS EQKFLEASMAYVAG PIMSDEE+D LK KLK+EGSEIV
Sbjct: 120 EFDNLKEELMWEGSSVVMLSSDEQKFLEASMAYVAGNPIMSDEEFDDLKIKLKIEGSEIV 179

Query: 181 VEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEV 236
           VEGPRCSLRS+KVYSDLSVDYLKM LLNVPA VVAL LFFFLDD+TGFEIT+LLE+
Sbjct: 180 VEGPRCSLRSKKVYSDLSVDYLKMFLLNVPAAVVALSLFFFLDDVTGFEITFLLEL 235

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460457|ref|XP_004147962.1| PREDICTED: PGR5-like protein 1A, chloroplastic-like [Cucumis sativus] gi|449494267|ref|XP_004159497.1| PREDICTED: PGR5-like protein 1A, chloroplastic-like [Cucumis sativus]

 Score =  332 bits (852), Expect = 6e-89,   Method: Compositional matrix adjust.
 Identities = 168/215 (78%), Positives = 187/215 (86%), Gaps = 3/215 (1%)

Query: 22  QKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKI 81
           QKPAA+L     SS   S+   + + R+  +RR+  + P +ATTDQ GQVEGDEVVDS +
Sbjct: 22  QKPAASLL---PSSSRSSSQLIRVSSRRLFLRRKLVLPPPRATTDQPGQVEGDEVVDSNV 78

Query: 82  LQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSS 141
           LQYCSIDKKEKK++GELEQEFLQALQAFYYEGKA+MSNEEFDNLKEELMWEGSSVVMLSS
Sbjct: 79  LQYCSIDKKEKKTIGELEQEFLQALQAFYYEGKAIMSNEEFDNLKEELMWEGSSVVMLSS 138

Query: 142 AEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDY 201
            EQKFLEASMAYV+G PI+SD+E+D LK +LK EGSEIVVEGPRCSLRSRKVYSDLSVDY
Sbjct: 139 DEQKFLEASMAYVSGNPILSDKEFDDLKLRLKTEGSEIVVEGPRCSLRSRKVYSDLSVDY 198

Query: 202 LKMLLLNVPATVVALGLFFFLDDITGFEITYLLEV 236
            KM LLNVPATVVALGLFFFLDDITGFEITYLLE+
Sbjct: 199 FKMFLLNVPATVVALGLFFFLDDITGFEITYLLEL 233

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224058627|ref|XP_002299573.1| predicted protein [Populus trichocarpa] gi|222846831|gb|EEE84378.1| predicted protein [Populus trichocarpa]

 Score =  330 bits (846), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 169/241 (70%), Positives = 193/241 (80%), Gaps = 10/241 (4%)

Query: 1   MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLP 60
           MAGK+A  FT  + RV   P+QKP  + +         S++   FN +QF++RRR  + P
Sbjct: 1   MAGKLA--FTLTSPRVLIAPIQKPFISSSSSLPPPSCSSSTRVHFNVKQFSLRRRMLLPP 58

Query: 61  SKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNE 120
           +KAT DQQ +   DE+VD KILQYCSIDK+ KKS+GE+EQEFLQALQAFYYEGKA+MSNE
Sbjct: 59  TKATADQQAE---DEMVDGKILQYCSIDKRGKKSIGEMEQEFLQALQAFYYEGKAIMSNE 115

Query: 121 EFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG---- 176
           EFDNLKEELMWEGSSVVMLSS EQKFLEASMAYV+  PIMSD+EYD+LK KLK+      
Sbjct: 116 EFDNLKEELMWEGSSVVMLSSDEQKFLEASMAYVSENPIMSDKEYDELKMKLKVSAWLFS 175

Query: 177 -SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLE 235
            SEIVVEGPRCSLRSRKVYSDL VDYLKM LLNVPATV ALGLFFFLDD+TGFEITYLLE
Sbjct: 176 RSEIVVEGPRCSLRSRKVYSDLYVDYLKMFLLNVPATVTALGLFFFLDDLTGFEITYLLE 235

Query: 236 V 236
           +
Sbjct: 236 L 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356497195|ref|XP_003517448.1| PREDICTED: PGR5-like protein 1A, chloroplastic-like [Glycine max]

 Score =  322 bits (825), Expect = 8e-86,   Method: Compositional matrix adjust.
 Identities = 155/193 (80%), Positives = 172/193 (89%)

Query: 44  QFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFL 103
           QFNGR   +R R F+    AT DQ    E   VVDSKILQYCSIDKKEKKS+GE+EQEFL
Sbjct: 33  QFNGRHICLRPRLFLFSPMATADQDKVEEDAAVVDSKILQYCSIDKKEKKSVGEMEQEFL 92

Query: 104 QALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDE 163
           QALQAFYYEGKA+MSNEEFDNLKEELMWEGS+VVMLSS EQKFLEASMAYV+GKPI+SD+
Sbjct: 93  QALQAFYYEGKAIMSNEEFDNLKEELMWEGSTVVMLSSDEQKFLEASMAYVSGKPILSDK 152

Query: 164 EYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLD 223
           E+D+LK +LKMEGSEIV EGPRCSLRSRKVYSDLSVDYLKM LLNVPATVVALGLFFFLD
Sbjct: 153 EFDELKLRLKMEGSEIVAEGPRCSLRSRKVYSDLSVDYLKMFLLNVPATVVALGLFFFLD 212

Query: 224 DITGFEITYLLEV 236
           D+TGFEI+YL+++
Sbjct: 213 DVTGFEISYLIKI 225

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	238
TAIR|locus:2118031	313	PGRL1B "AT4G11960" [Arabidopsi	0.827	0.629	0.778	4.2e-79
TAIR|locus:2127233	324	PGR5-LIKE A "AT4G22890" [Arabi	0.810	0.595	0.769	2.1e-77
TAIR|locus:2148338	301	AT5G59400 "AT5G59400" [Arabido	0.315	0.249	0.392	2.9e-06

TAIR|locus:2118031 PGRL1B "AT4G11960" [Arabidopsis thaliana (taxid:3702)]

 Score = 795 (284.9 bits), Expect = 4.2e-79, P = 4.2e-79
 Identities = 158/203 (77%), Positives = 181/203 (89%)

Query:    39 SNSNTQ----F-NGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKK 93
             S+S TQ    F +GR  ++RRR  +LP KA+TDQ GQV G+EV DSKIL YCSI+K EK+
Sbjct:    21 SSSRTQCPAPFTHGRSISLRRRLTLLPLKASTDQSGQVGGEEV-DSKILPYCSINKNEKR 79

Query:    94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAY 153
             ++GE+EQEFLQA+Q+FYYEGKA+MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAY
Sbjct:    80 TIGEMEQEFLQAMQSFYYEGKAIMSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAY 139

Query:   154 VAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATV 213
             V+G PI+SDEEYDKLK KLKM+GSEIV EGPRCSLRS+KVYSDL++DY KM LLNVPATV
Sbjct:   140 VSGNPILSDEEYDKLKMKLKMDGSEIVCEGPRCSLRSKKVYSDLAIDYFKMFLLNVPATV 199

Query:   214 VALGLFFFLDDITGFEITYLLEV 236
             VALGLFFFLDDITGFEITYLLE+
Sbjct:   200 VALGLFFFLDDITGFEITYLLEL 222

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009773 "photosynthetic electron transport in photosystem I" evidence=IGI;RCA

GO:0015979 "photosynthesis" evidence=IGI

GO:0015996 "chlorophyll catabolic process" evidence=RCA

TAIR|locus:2127233 PGR5-LIKE A "AT4G22890" [Arabidopsis thaliana (taxid:3702)]

 Score = 779 (279.3 bits), Expect = 2.1e-77, P = 2.1e-77
 Identities = 150/195 (76%), Positives = 177/195 (90%)

Query:    43 TQFN-GRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQE 101
             TQ + G+  ++RRR F+LP+KATT+Q G V GD V DS +L YCSI+K EKK++GE+EQE
Sbjct:    40 TQLSPGKSISLRRRVFLLPAKATTEQSGPVGGDNV-DSNVLPYCSINKAEKKTIGEMEQE 98

Query:   102 FLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMS 161
             FLQALQ+FYY+GKA+MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI++
Sbjct:    99 FLQALQSFYYDGKAIMSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILN 158

Query:   162 DEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFF 221
             DEEYDKLK KLK++GS+IV EGPRCSLRS+KVYSDL+VDY KMLLLNVPATVVALGLFFF
Sbjct:   159 DEEYDKLKLKLKIDGSDIVSEGPRCSLRSKKVYSDLAVDYFKMLLLNVPATVVALGLFFF 218

Query:   222 LDDITGFEITYLLEV 236
             LDDITGFEITY++E+
Sbjct:   219 LDDITGFEITYIMEL 233

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009773 "photosynthetic electron transport in photosystem I" evidence=IGI;RCA

GO:0015979 "photosynthesis" evidence=IGI

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009637 "response to blue light" evidence=RCA

GO:0009657 "plastid organization" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010114 "response to red light" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0010304 "PSII associated light-harvesting complex II catabolic process" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

GO:0043085 "positive regulation of catalytic activity" evidence=RCA

TAIR|locus:2148338 AT5G59400 "AT5G59400" [Arabidopsis thaliana (taxid:3702)]

 Score = 129 (50.5 bits), Expect = 2.9e-06, P = 2.9e-06
 Identities = 31/79 (39%), Positives = 49/79 (62%)

Query:   143 EQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYL 202
             E  + +A  AY  GKP++ D+ +D+++ KL+  GS+ VV+ PRCSL  +  Y+D   D  
Sbjct:    75 EALYRQAKDAYYNGKPLIVDDMFDRVELKLRWYGSKSVVKYPRCSLLRQSTYADAEDDAS 134

Query:   203 KMLLLNVPATVVALGLFFF 221
             ++LLL   ATV  + +F F
Sbjct:   135 QVLLL---ATVWIM-IFLF 149


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.132   0.362    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      238       224   0.00099  112 3  11 22  0.41    33
                                                     32  0.40    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  3
  No. of states in DFA:  589 (63 KB)
  Total size of DFA:  154 KB (2093 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.40u 0.13s 22.53t   Elapsed:  00:00:01
  Total cpu time:  22.40u 0.13s 22.53t   Elapsed:  00:00:01
  Start:  Mon May 20 15:41:09 2013   End:  Mon May 20 15:41:10 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8H112	PGL1A_ARATH	No assigned EC number	0.7789	0.7941	0.5833	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	238
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	94.89
cd00114	307	LIGANc NAD+ dependent DNA ligase adenylation domai	94.31
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	93.93
PF01653	315	DNA_ligase_aden: NAD-dependent DNA ligase adenylat	93.55
smart00532	441	LIGANc Ligase N family.	92.67
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	92.4
cd00114	307	LIGANc NAD+ dependent DNA ligase adenylation domai	91.85
PF01653	315	DNA_ligase_aden: NAD-dependent DNA ligase adenylat	90.95
smart00532	441	LIGANc Ligase N family.	90.67
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	89.07
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	89.04
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	89.03
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	88.64
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	88.52
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	85.98
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	85.32

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=94.89  E-value=0.034  Score=55.58  Aligned_cols=49  Identities=35%  Similarity=0.479  Sum_probs=33.9

Q ss_pred             HHHhhhcCC---eeEEeChhh-H---HHHHH-----HHhhhc-CCCCCChHHHHHHHHHHHh
Q 026445          126 KEELMWEGS---SVVMLSSAE-Q---KFLEA-----SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       126 KEeL~WEGS---svv~L~~~E-q---~fLEA-----~~AY~s-GkPimsDeeFD~LK~eLk~  174 (238)
                      ---|.|..|   .|.++++.+ +   +.|.+     -.+||. |+|+|+|+|||+|..+|+.
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~~   70 (562)
T PRK08097          9 ISLLLWSSSAWAVCPDWSPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQ   70 (562)
T ss_pred             HHHHHhcccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            345678777   566666664 1   12222     336664 9999999999999999974

>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain

Probab=94.31  E-value=0.05  Score=50.17  Aligned_cols=27  Identities=33%  Similarity=0.641  Sum_probs=22.8

Q ss_pred             HHHHhhhc-CCCCCChHHHHHHHHHHHh
Q 026445          148 EASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       148 EA~~AY~s-GkPimsDeeFD~LK~eLk~  174 (238)
                      .+-.+||. |+|+|||+|||+|..+|+.
T Consensus        12 ~~~~~YY~~~~p~IsD~eYD~L~~~L~~   39 (307)
T cd00114          12 KHDYRYYVLDEPSVSDAEYDRLYRELRA   39 (307)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            34556776 9999999999999999975

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=93.93  E-value=0.09  Score=53.22  Aligned_cols=27  Identities=37%  Similarity=0.597  Sum_probs=23.3

Q ss_pred             HHHHhhh-cCCCCCChHHHHHHHHHHHh
Q 026445          148 EASMAYV-AGKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       148 EA~~AY~-sGkPimsDeeFD~LK~eLk~  174 (238)
                      ++-.+|| .|+|+|||+|||+|..+|+.
T Consensus        18 ~~~~~YY~~~~p~IsD~eYD~L~~~L~~   45 (665)
T PRK07956         18 HHAYAYYVLDAPSISDAEYDRLYRELVA   45 (665)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            3455777 99999999999999999974

>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose

Probab=93.55  E-value=0.089  Score=48.65  Aligned_cols=27  Identities=48%  Similarity=0.807  Sum_probs=22.1

Q ss_pred             HHHHhhhc-CCCCCChHHHHHHHHHHHh
Q 026445          148 EASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       148 EA~~AY~s-GkPimsDeeFD~LK~eLk~  174 (238)
                      .+-.+||. |+|+|||++||+|..+|+.
T Consensus        16 ~~~~~YY~~~~p~isD~eYD~l~~~L~~   43 (315)
T PF01653_consen   16 RHNYAYYNLGEPIISDAEYDQLFRELKA   43 (315)
T ss_dssp             HHHHHHHTTSSSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            34457766 8999999999999999863

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). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....

>smart00532 LIGANc Ligase N family

Probab=92.67  E-value=0.13  Score=49.91  Aligned_cols=26  Identities=42%  Similarity=0.714  Sum_probs=22.2

Q ss_pred             HHHhhhc-CCCCCChHHHHHHHHHHHh
Q 026445          149 ASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       149 A~~AY~s-GkPimsDeeFD~LK~eLk~  174 (238)
                      +-.+||. |+|+|+|+|||+|..+|+.
T Consensus        15 ~~~~YY~~~~p~IsD~eYD~L~~eL~~   41 (441)
T smart00532       15 HDYRYYVLDAPIISDAEYDRLMRELKE   41 (441)
T ss_pred             HHHHHHhcCCCCCChHHHHHHHHHHHH
Confidence            3556765 9999999999999999974

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=92.40  E-value=0.15  Score=51.54  Aligned_cols=28  Identities=32%  Similarity=0.564  Sum_probs=23.8

Q ss_pred             HHHHHhhhc-CCCCCChHHHHHHHHHHHh
Q 026445          147 LEASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       147 LEA~~AY~s-GkPimsDeeFD~LK~eLk~  174 (238)
                      -.+-.+||. |+|+|||+|||+|..+|+.
T Consensus         6 ~~~~~~YY~~~~p~IsD~eYD~L~~~L~~   34 (652)
T TIGR00575         6 RHHDYRYYVLDEPSISDAEYDRLYRELQE   34 (652)
T ss_pred             HHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            345667876 9999999999999999985

The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.

>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain

Probab=91.85  E-value=0.24  Score=45.77  Aligned_cols=36  Identities=25%  Similarity=0.382  Sum_probs=28.4

Q ss_pred             hhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        95 lge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      +.++...--.+-..||..|.|++||+|||.|.++|.
T Consensus         3 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~   38 (307)
T cd00114           3 IAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELR   38 (307)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            344555555666778888999999999999999985

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.

>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose

Probab=90.95  E-value=0.3  Score=45.19  Aligned_cols=36  Identities=33%  Similarity=0.553  Sum_probs=29.1

Q ss_pred             hhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        95 lge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      +.++...--++-..||..|.|+|||+|||.|.++|.
T Consensus         7 i~~L~~~i~~~~~~YY~~~~p~isD~eYD~l~~~L~   42 (315)
T PF01653_consen    7 IEELRKEINRHNYAYYNLGEPIISDAEYDQLFRELK   42 (315)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            445555566667788999999999999999999874

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). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....

>smart00532 LIGANc Ligase N family

Probab=90.67  E-value=0.32  Score=47.23  Aligned_cols=36  Identities=25%  Similarity=0.420  Sum_probs=29.3

Q ss_pred             hhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        95 lge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      +-++...--.+-..||..+.|++||+|||.|.++|.
T Consensus         5 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~   40 (441)
T smart00532        5 ISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELK   40 (441)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHH
Confidence            445555556666778888999999999999999986

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=89.07  E-value=0.47  Score=47.67  Aligned_cols=37  Identities=27%  Similarity=0.522  Sum_probs=30.2

Q ss_pred             chhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        94 slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      .+.++..+--.+-..||..+.|++||+|||.|.++|.
T Consensus        33 ~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~   69 (562)
T PRK08097         33 EIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLT   69 (562)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            3555555666667789999999999999999999985

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=89.04  E-value=0.46  Score=48.57  Aligned_cols=37  Identities=19%  Similarity=0.381  Sum_probs=31.2

Q ss_pred             chhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        94 slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      .+.++..+--.+-..||..+.|++||+|||.|.++|.
T Consensus        35 ~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~   71 (689)
T PRK14351         35 QAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQ   71 (689)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            3566666666777789999999999999999999996

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=89.03  E-value=0.5  Score=48.30  Aligned_cols=27  Identities=30%  Similarity=0.600  Sum_probs=22.6

Q ss_pred             HHHHhhh-cCCCCCChHHHHHHHHHHHh
Q 026445          148 EASMAYV-AGKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       148 EA~~AY~-sGkPimsDeeFD~LK~eLk~  174 (238)
                      ++-.+|| .|+|+|||++||+|.++|+.
T Consensus        45 ~~~~~YY~~~~p~IsD~eYD~L~~eL~~   72 (689)
T PRK14351         45 EHDHRYYVEADPVIADRAYDALFARLQA   72 (689)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            3455677 68999999999999999984

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=88.64  E-value=0.6  Score=47.68  Aligned_cols=24  Identities=29%  Similarity=0.463  Sum_probs=20.7

Q ss_pred             HHhhh-cCCCCCChHHHHHHHHHHH
Q 026445          150 SMAYV-AGKPIMSDEEYDKLKQKLK  173 (238)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~eLk  173 (238)
                      -.+|| .|+|+|||++||+|..+|+
T Consensus        20 ~~~YY~~~~p~IsD~~YD~L~~eL~   44 (669)
T PRK14350         20 DKEYYVDSSPSVEDFTYDKALLRLQ   44 (669)
T ss_pred             HHHHHhCCCCCCChHHHHHHHHHHH
Confidence            44666 5899999999999999996

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=88.52  E-value=0.52  Score=47.85  Aligned_cols=36  Identities=31%  Similarity=0.504  Sum_probs=29.1

Q ss_pred             hhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        95 lge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      +-++..+--.+-..||..+.|++||+|||.|.++|.
T Consensus         9 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~   44 (665)
T PRK07956          9 IEELREELNHHAYAYYVLDAPSISDAEYDRLYRELV   44 (665)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            445555555666778889999999999999999986

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=85.98  E-value=0.8  Score=46.78  Aligned_cols=36  Identities=11%  Similarity=0.200  Sum_probs=28.2

Q ss_pred             hhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        95 lge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      +.++-.+--..=..||..+.|++||+|||.|.++|.
T Consensus         9 i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~   44 (669)
T PRK14350          9 ILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQ   44 (669)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            445555555556678889999999999999999985

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=85.32  E-value=0.89  Score=46.08  Aligned_cols=27  Identities=26%  Similarity=0.411  Sum_probs=23.2

Q ss_pred             HHHHHHhhcCccccChHHHHhHHHHhh
Q 026445          104 QALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus       104 ~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      .+-..||..+.|++||+|||.|.++|.
T Consensus         7 ~~~~~YY~~~~p~IsD~eYD~L~~~L~   33 (652)
T TIGR00575         7 HHDYRYYVLDEPSISDAEYDRLYRELQ   33 (652)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            345667888999999999999999985

The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	238
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>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 = 47.9 bits (113), Expect = 1e-06
 Identities = 27/160 (16%), Positives = 54/160 (33%), Gaps = 35/160 (21%)

Query: 78  DSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEG--KAVMSNEEFDNLKEE------- 128
           ++   QY       K  L   E  F+        +   K+++S EE D++          
Sbjct: 10  ETGEHQYQY-----KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64

Query: 129 --LMW----EGSSVV--MLSSAEQK---FLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS 177
             L W    +   +V   +    +    FL + +     +P M    Y + + +L    +
Sbjct: 65  LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL-YNDN 123

Query: 178 EIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNV-PATVVAL 216
           ++  +      R +          L+  LL + PA  V +
Sbjct: 124 QVFAKYNVS--RLQPYLK------LRQALLELRPAKNVLI 155

>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 = 40.6 bits (94), Expect = 3e-04
 Identities = 37/278 (13%), Positives = 65/278 (23%), Gaps = 111/278 (39%)

Query: 1   MAGKVASGFTPQAQRVFAV------PVQKPAAALAPF---------PSSSRAHSNSNTQF 45
           +A  V   +  Q +  F +          P   L              +SR+  +SN + 
Sbjct: 166 VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225

Query: 46  NGRQFTVRRRSF-----------VLPSKATTDQQGQVEGDEVVDSKILQY----CSI--- 87
                    R             VL                V ++K        C I   
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVL--------------LNVQNAKAWNAFNLSCKILLT 271

Query: 88  --DK----------KEKKSLGELEQEFL--QALQAFYYEGKAVMSNEEFDNLKEELMWEG 133
              K              SL          +         K +  +    +L  E +   
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL---LKYL--DCRPQDLPRE-VLTT 325

Query: 134 SSVVMLSSAEQKFLEASM--AYVAGKPIMSDE----EYDKLKQKLKMEGSEIVVEGPRCS 187
           +   +           S+    +       D       DKL   ++             S
Sbjct: 326 NPRRL-----------SIIAESIRDGLATWDNWKHVNCDKLTTIIES------------S 362

Query: 188 LRS------RKVYSDLSV---DYLKMLLLNVPATVVAL 216
           L        RK++  LSV           ++P  +++L
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPS------AHIPTILLSL 394

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	238
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	92.11
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	91.96
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	91.34
4glw_A	305	DNA ligase; inhibitor, ligase-ligase inhibitor com	90.36
4glw_A	305	DNA ligase; inhibitor, ligase-ligase inhibitor com	90.27
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	89.91
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	89.7
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	89.5
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	89.49
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	89.32
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	89.2
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	89.09
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	88.87
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	88.55
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	83.64
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	82.45
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	82.06
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	80.65

>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA replication, magnesium, manganese, metal-binding, NAD, zinc; HET: DNA; 1.80A {Staphylococcus aureus} SCOP: d.142.2.2 PDB: 3jsn_A*

Probab=92.11  E-value=0.13  Score=46.94  Aligned_cols=26  Identities=38%  Similarity=0.561  Sum_probs=21.6

Q ss_pred             HHhhh-cCCCCCChHHHHHHHHHHHhc
Q 026445          150 SMAYV-AGKPIMSDEEYDKLKQKLKME  175 (238)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~eLk~~  175 (238)
                      -.+|| .|+|+|||+|||+|..+|+..
T Consensus        19 ~~~YY~~d~p~IsD~eYD~L~~eL~~l   45 (318)
T 3jsl_A           19 SYEYYVEDNPSVPDSEYDKLLHELIKI   45 (318)
T ss_dssp             HHHHHTSCCCSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCCCCHHHHHHHHHHHHHH
Confidence            44666 599999999999999998754

>3uq8_A DNA ligase; adenylated protein, ATP-grAsp, rossman fold, adenylation; HET: DNA NAD AMP; 1.70A {Haemophilus influenzae} PDB: 3pn1_A* 3bac_A*

Probab=91.96  E-value=0.14  Score=46.58  Aligned_cols=27  Identities=33%  Similarity=0.534  Sum_probs=22.4

Q ss_pred             HHHhhhc-CCCCCChHHHHHHHHHHHhc
Q 026445          149 ASMAYVA-GKPIMSDEEYDKLKQKLKME  175 (238)
Q Consensus       149 A~~AY~s-GkPimsDeeFD~LK~eLk~~  175 (238)
                      +-.+||. |+|+|||+|||+|..+|+..
T Consensus        16 ~~~~YY~~d~p~IsD~eYD~L~~eL~~l   43 (322)
T 3uq8_A           16 YEYEYHVLDNPSVPDSEYDRLFHQLKAL   43 (322)
T ss_dssp             HHHHHHTSSCCSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence            3456775 99999999999999998764

>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis} SCOP: d.142.2.2 PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*

Probab=91.34  E-value=0.14  Score=46.76  Aligned_cols=26  Identities=31%  Similarity=0.423  Sum_probs=22.1

Q ss_pred             HHhhh-cCCCCCChHHHHHHHHHHHhc
Q 026445          150 SMAYV-AGKPIMSDEEYDKLKQKLKME  175 (238)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~eLk~~  175 (238)
                      -.+|| .|+|+|+|+|||+|..+|+..
T Consensus        26 ~~~YY~~d~p~IsD~eYD~L~~eL~~l   52 (332)
T 1ta8_A           26 SHEYYVKDQPSVEDYVYDRLYKELVDI   52 (332)
T ss_dssp             HHHHHTSSCCSSCHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence            44665 799999999999999999864

>4glw_A DNA ligase; inhibitor, ligase-ligase inhibitor complex; HET: DNA 0XT NMN; 2.00A {Streptococcus pneumoniae}

Probab=90.36  E-value=0.052  Score=48.69  Aligned_cols=25  Identities=36%  Similarity=0.632  Sum_probs=3.9

Q ss_pred             HHhhh-cCCCCCChHHHHHHHHHHHh
Q 026445          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~eLk~  174 (238)
                      -.+|| .|+|+|||+|||+|..+|+.
T Consensus        16 ~~~YY~~~~p~IsD~eYD~L~~eL~~   41 (305)
T 4glw_A           16 ATEYYTSDNPSVSDSEYDRLYRELVE   41 (305)
T ss_dssp             ---------------------CHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            44676 69999999999999998875

>4glw_A DNA ligase; inhibitor, ligase-ligase inhibitor complex; HET: DNA 0XT NMN; 2.00A {Streptococcus pneumoniae}

Probab=90.27  E-value=0.046  Score=49.03  Aligned_cols=35  Identities=26%  Similarity=0.411  Sum_probs=3.8

Q ss_pred             hHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           96 GELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        96 ge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      .++..+--.+-.+||..|.|++||+|||.|.++|.
T Consensus         6 ~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~   40 (305)
T 4glw_A            6 NELVALLNRYATEYYTSDNPSVSDSEYDRLYRELV   40 (305)
T ss_dssp             HC-----------------------------CHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            33444444556788999999999999999998875

>3uq8_A DNA ligase; adenylated protein, ATP-grAsp, rossman fold, adenylation; HET: DNA NAD AMP; 1.70A {Haemophilus influenzae} PDB: 3pn1_A* 3bac_A*

Probab=89.91  E-value=0.27  Score=44.79  Aligned_cols=36  Identities=19%  Similarity=0.273  Sum_probs=28.5

Q ss_pred             hhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        95 lge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      +.++..+--.+-.+||..+.|++||+|||.|.++|.
T Consensus         6 i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~   41 (322)
T 3uq8_A            6 LDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLK   41 (322)
T ss_dssp             HHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            445555556667788889999999999999988763

>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}

Probab=89.70  E-value=0.17  Score=46.13  Aligned_cols=26  Identities=35%  Similarity=0.646  Sum_probs=22.1

Q ss_pred             HHhhh-cCCCCCChHHHHHHHHHHHhc
Q 026445          150 SMAYV-AGKPIMSDEEYDKLKQKLKME  175 (238)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~eLk~~  175 (238)
                      -.+|| .|+|+|+|+|||+|..+|+..
T Consensus        28 ~~~YY~~d~p~IsD~eYD~L~~eL~~l   54 (328)
T 1zau_A           28 QFRYYVRDAPIISDAEFDELLRRLEAL   54 (328)
T ss_dssp             HHHHTTTCCCSSCTHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence            34665 699999999999999999864

>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2

Probab=89.50  E-value=0.17  Score=46.02  Aligned_cols=25  Identities=36%  Similarity=0.634  Sum_probs=21.5

Q ss_pred             HHhhh-cCCCCCChHHHHHHHHHHHh
Q 026445          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~eLk~  174 (238)
                      -.+|| .|+|+|+|+|||+|..+|+.
T Consensus        21 ~~~YY~~d~p~IsD~eYD~L~~eL~~   46 (318)
T 1b04_A           21 GYEYYVLDRPSVPDAEYDRLMQELIA   46 (318)
T ss_dssp             HHHHHTTCSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            34665 79999999999999999875

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=89.49  E-value=0.2  Score=48.76  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=21.6

Q ss_pred             HHhhh-cCCCCCChHHHHHHHHHHHh
Q 026445          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~eLk~  174 (238)
                      -.+|| .|+|+|||+|||+|..+|+.
T Consensus        19 ~~~Yy~~~~p~IsD~eYD~L~~eL~~   44 (586)
T 4glx_A           19 EYLYHVMDAPEIPDAEYDRLMRELRE   44 (586)
T ss_dssp             HHHHHHTTCSSBCCTHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            44676 69999999999999999975

>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA replication, magnesium, manganese, metal-binding, NAD, zinc; HET: DNA; 1.80A {Staphylococcus aureus} SCOP: d.142.2.2 PDB: 3jsn_A*

Probab=89.32  E-value=0.32  Score=44.26  Aligned_cols=37  Identities=27%  Similarity=0.455  Sum_probs=29.0

Q ss_pred             chhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        94 slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      .+.++...--++-.+||..+.|++||+|||.|.++|.
T Consensus         7 ~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~   43 (318)
T 3jsl_A            7 RVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELI   43 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCCCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence            3455555556666788889999999999999988764

>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}

Probab=89.20  E-value=0.34  Score=44.14  Aligned_cols=38  Identities=24%  Similarity=0.419  Sum_probs=30.9

Q ss_pred             cchhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           93 KSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        93 ~slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      .-+.++..+--.+-.+||..+.|++||.|||.|.++|.
T Consensus        15 ~~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~   52 (328)
T 1zau_A           15 RQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLE   52 (328)
T ss_dssp             TTHHHHHHHHHHHHHHHTTTCCCSSCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            34566666666667788999999999999999999975

>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2

Probab=89.09  E-value=0.37  Score=43.80  Aligned_cols=37  Identities=22%  Similarity=0.376  Sum_probs=29.6

Q ss_pred             chhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        94 slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      -+.++..+--.+-.+||..+.|++||.|||.|.++|.
T Consensus         9 ~~~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~   45 (318)
T 1b04_A            9 RAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELI   45 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            3455555555666788889999999999999999975

>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis} SCOP: d.142.2.2 PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*

Probab=88.87  E-value=0.41  Score=43.74  Aligned_cols=37  Identities=22%  Similarity=0.389  Sum_probs=29.7

Q ss_pred             chhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        94 slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      -+.++...--.+-..||..+.|++||.|||.|.++|.
T Consensus        14 ~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~   50 (332)
T 1ta8_A           14 RAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELV   50 (332)
T ss_dssp             HHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            4555555555666788889999999999999999875

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=88.55  E-value=0.31  Score=47.46  Aligned_cols=37  Identities=22%  Similarity=0.282  Sum_probs=29.7

Q ss_pred             chhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        94 slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      -+.++..+--.+-.+||..+.|++||+|||.|.++|.
T Consensus         7 ~i~~L~~~i~~~~~~Yy~~~~p~IsD~eYD~L~~eL~   43 (586)
T 4glx_A            7 QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELR   43 (586)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCSSBCCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            3455555666667788999999999999999998874

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=83.64  E-value=0.9  Score=44.99  Aligned_cols=37  Identities=22%  Similarity=0.282  Sum_probs=29.6

Q ss_pred             chhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        94 slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      -+.++..+--++-.+||..+.|++||.|||.|.++|.
T Consensus         7 ~~~~L~~~l~~~~~~YY~~d~p~isD~eYD~L~~eL~   43 (671)
T 2owo_A            7 QLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELR   43 (671)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCSSBCCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            3455555556667788999999999999999999875

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=82.45  E-value=0.49  Score=46.84  Aligned_cols=27  Identities=37%  Similarity=0.567  Sum_probs=22.8

Q ss_pred             HHhhh-cCCCCCChHHHHHHHHHHHhcC
Q 026445          150 SMAYV-AGKPIMSDEEYDKLKQKLKMEG  176 (238)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~eLk~~G  176 (238)
                      -.+|| .++|+|+|+|||+|..+|+..-
T Consensus        21 ~~~YY~~d~p~isD~eYD~l~~eL~~lE   48 (667)
T 1dgs_A           21 NYRYYVLADPEISDAEYDRLLRELKELE   48 (667)
T ss_dssp             HHHHHTTCCCCSCSSSSHHHHHHHHHHT
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHHHH
Confidence            44666 7999999999999999998654

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=82.06  E-value=0.6  Score=46.24  Aligned_cols=26  Identities=31%  Similarity=0.540  Sum_probs=21.8

Q ss_pred             HHhhh-cCCCCCChHHHHHHHHHHHhc
Q 026445          150 SMAYV-AGKPIMSDEEYDKLKQKLKME  175 (238)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~eLk~~  175 (238)
                      -.+|| .|+|+|+|+|||+|..+|+..
T Consensus        19 ~~~YY~~d~p~isD~eYD~L~~eL~~l   45 (671)
T 2owo_A           19 EYLYHVMDAPEIPDAEYDRLMRELREL   45 (671)
T ss_dssp             HHHHHHTTCSSBCCTHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence            44655 699999999999999998763

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=80.65  E-value=0.96  Score=44.78  Aligned_cols=36  Identities=25%  Similarity=0.351  Sum_probs=28.9

Q ss_pred             hhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        95 lge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      +.++..+--++-..||..+.|++||.|||.|.++|.
T Consensus        10 ~~~L~~~l~~~~~~YY~~d~p~isD~eYD~l~~eL~   45 (667)
T 1dgs_A           10 INELRDLIRYHNYRYYVLADPEISDAEYDRLLRELK   45 (667)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            445555555666788999999999999999999875

---

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	238
d1b04a_	312	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	1e-04
d1b04a_	312	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	3e-04
d1ta8a_	313	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	1e-04
d1dgsa3	314	d.142.2.2 (A:1-314) Adenylation domain of NAD+-dep	2e-04
d1dgsa3	314	d.142.2.2 (A:1-314) Adenylation domain of NAD+-dep	0.001

>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]} Length = 312

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 40.3 bits (93), Expect = 1e-04
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 153 YVAGKPIMSDEEYDKLKQKLK 173
           YV  +P + D EYD+L Q+L 
Sbjct: 24  YVLDRPSVPDAEYDRLMQELI 44

>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]} Length = 312

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 39.2 bits (90), Expect = 3e-04
 Identities = 9/43 (20%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 88  DKKE-KKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL 129
           D+++ ++   EL +   +    +Y   +  + + E+D L +EL
Sbjct: 1   DRQQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQEL 43

>d1ta8a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]} Length = 313

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Enterococcus faecalis [TaxId: 1351]

 Score = 40.0 bits (92), Expect = 1e-04
 Identities = 8/21 (38%), Positives = 13/21 (61%)

Query: 153 YVAGKPIMSDEEYDKLKQKLK 173
           YV  +P + D  YD+L ++L 
Sbjct: 26  YVKDQPSVEDYVYDRLYKELV 46

>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]} Length = 314

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]

 Score = 39.5 bits (91), Expect = 2e-04
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 153 YVAGKPIMSDEEYDKLKQKLK 173
           YV   P +SD EYD+L ++LK
Sbjct: 25  YVLADPEISDAEYDRLLRELK 45

>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]} Length = 314

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]

 Score = 36.8 bits (84), Expect = 0.001
 Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 88  DKKE-KKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL 129
            ++E ++ + EL          +Y      +S+ E+D L  EL
Sbjct: 2   TREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLREL 44

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	238
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	96.57
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	96.47
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	95.88
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	95.84
d1dgsa3	314	Adenylation domain of NAD+-dependent DNA ligase {T	95.49
d1dgsa3	314	Adenylation domain of NAD+-dependent DNA ligase {T	94.32

>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.57  E-value=0.00084  Score=56.89  Aligned_cols=25  Identities=36%  Similarity=0.651  Sum_probs=21.9

Q ss_pred             HHhhhc-CCCCCChHHHHHHHHHHHh
Q 026445          150 SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       150 ~~AY~s-GkPimsDeeFD~LK~eLk~  174 (238)
                      -.+||. |+|+|||++||.|+++|+.
T Consensus        20 ~~~Yy~~~~p~isD~eYD~L~~~L~~   45 (312)
T d1b04a_          20 GYEYYVLDRPSVPDAEYDRLMQELIA   45 (312)
T ss_dssp             HHHHHTTCSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            447875 9999999999999999975

>d1ta8a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Enterococcus faecalis [TaxId: 1351]

Probab=96.47  E-value=0.0012  Score=55.40  Aligned_cols=27  Identities=30%  Similarity=0.434  Sum_probs=22.9

Q ss_pred             HHHHhhh-cCCCCCChHHHHHHHHHHHh
Q 026445          148 EASMAYV-AGKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       148 EA~~AY~-sGkPimsDeeFD~LK~eLk~  174 (238)
                      ++-.+|| .|+|+|||+|||.|+.+|+.
T Consensus        20 ~~~~~Yy~~~~p~iSD~eYD~L~~~L~~   47 (313)
T d1ta8a_          20 QYSHEYYVKDQPSVEDYVYDRLYKELVD   47 (313)
T ss_dssp             HHHHHHHTSSCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            3455787 59999999999999999975

>d1ta8a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Enterococcus faecalis [TaxId: 1351]

Probab=95.88  E-value=0.0036  Score=52.33  Aligned_cols=37  Identities=22%  Similarity=0.389  Sum_probs=32.0

Q ss_pred             chhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        94 slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      -+.+++..--++-.+||..|.|+|||+|||.|+++|.
T Consensus        10 ~~~~L~~~i~~~~~~Yy~~~~p~iSD~eYD~L~~~L~   46 (313)
T d1ta8a_          10 RAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELV   46 (313)
T ss_dssp             HHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            4566777778888899999999999999999999884

>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.84  E-value=0.0029  Score=53.45  Aligned_cols=39  Identities=21%  Similarity=0.390  Sum_probs=33.8

Q ss_pred             ccchhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           92 KKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        92 k~slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      ++-+.+++..--.+-.+||..|.|+|||+|||.|+++|.
T Consensus         6 ~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L~   44 (312)
T d1b04a_           6 ERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELI   44 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            456778888888888898889999999999999999984

>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]

Probab=95.49  E-value=0.0026  Score=54.02  Aligned_cols=25  Identities=40%  Similarity=0.678  Sum_probs=22.1

Q ss_pred             HHhhhc-CCCCCChHHHHHHHHHHHh
Q 026445          150 SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (238)
Q Consensus       150 ~~AY~s-GkPimsDeeFD~LK~eLk~  174 (238)
                      -.+||. |+|+|||++||+|+.+|+.
T Consensus        21 ~~~YY~~~~p~IsD~~YD~L~~eL~~   46 (314)
T d1dgsa3          21 NYRYYVLADPEISDAEYDRLLRELKE   46 (314)
T ss_dssp             HHHHHTTCCCCSCSSSSHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            457875 9999999999999999986

>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]}

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: Adenylation domain of NAD+-dependent DNA ligase
domain: Adenylation domain of NAD+-dependent DNA ligase
species: Thermus filiformis [TaxId: 276]

Probab=94.32  E-value=0.0099  Score=50.32  Aligned_cols=38  Identities=24%  Similarity=0.355  Sum_probs=30.8

Q ss_pred             cchhHHHHHHHHHHHHHhhcCccccChHHHHhHHHHhh
Q 026445           93 KSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (238)
Q Consensus        93 ~slge~E~~Fl~Al~sfY~~gk~~msdeEfd~LKEeL~  130 (238)
                      +-+.+++..--.+-.+||..|.|+|||+|||.|.++|.
T Consensus         8 ~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~   45 (314)
T d1dgsa3           8 RRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELK   45 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            34556666666677888889999999999999999986