Citrus Sinensis ID: 021649

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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-------31
Protein Sequence
MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKRMFLSLGPYYQFLVVEPPTLLTAQIVEPPWFMTQTQG
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccEEEEEcHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccEEEEcccEEEcccEEEccccHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEEcccccccHHHcccccccccEEEEEEcccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHcccccccccEEEcccccccEEcccccccccccccccccccccEEEEccccccccccHcHHcccccccccccccccccEEEEcccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccEEEccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccEEEEccEEEEcccEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHccccEEEEEEEccccEEEEEEEcccccEccccc
Coil and Loop (DISEMBL)
magkvasgftpqaqrvfavpvqkpaaalapfpsssrahsnsntqfngrqftvrrrsfvlpskattdqqgqvegdevvDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYegkavmsneEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYvagkpimsdeEYDKLKQKLKMEgseivvegprcslrsrkvysDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYllelpepfsfifTWFAAVPLIVYLSQSLTKLIVRESLILKRMFLslgpyyqflvvepptlltaqiveppwfmtqtqg
Flexible Loop (DISEMBL)
magkvasgftpqaqrVFAVPVQKPAAALAPfpsssrahsnsntqfngrqftvRRRSFVLpskattdqqgqvegdevvdSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKmegseivvegprcslrsrkVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKRMFLSLGPYYQFLVVEPPTLLTAQIVEPPWFMTQTQG
Low Complexity Region (SEG)
MAGKVASGFTPQAQRVFAVPVQKpaaalapfpsssraHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKRMFLSLGPYYQFLVVEPPTLLTAQIVEPPWFMTQTQG
Disordered region (IsUnstruct)
********************************************************************************ILQY*****************FLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGK********************EIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKRMFLSLGPYYQFLVVEPPTLLTAQIVEPPWFM*****
Disordered Region (DISOPRED)
********FTPQAQRVFA*************************************************************KILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKRMFLSLGPYYQFLVVEPPTLLTAQIVEPPWFMTQ***
Disordered Region (DISEMBL)
********FTPQAQRVFAVPVQKPAAALAP*************QFNGRQFTVRRRSFVLPS*************EVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKRMFLSLGPYYQFLVVEPPTLLTAQIVEPPWFMTQTQG
Disordered Region (DISPRO)
******S*FTPQAQRVFAVPVQKPAAALAPFPS***************QFTVRRRSFVLPSK*********EGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKRMFLSLGPYYQFLVVEPPTLLTAQIVEPPWFMT****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKRMFLSLGPYYQFLVVEPPTLLTAQIVEPPWFMTQTQG
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	309	2.2.26 [Sep-21-2011]
Q8H112	324	PGR5-like protein 1A, chl	yes	no	0.728	0.694	0.778	1e-103
Q8GYC7	313	PGR5-like protein 1B, chl	no	no	0.754	0.744	0.782	1e-101

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

 Score =  374 bits (961), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 176/226 (77%), Positives = 208/226 (92%), Gaps = 1/226 (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 GFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
           GFEITY++ELPEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILK
Sbjct: 224 GFEITYIMELPEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILK 269

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 =  369 bits (946), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 187/239 (78%), Positives = 213/239 (89%), Gaps = 6/239 (2%)

Query: 39  SNSNTQF-----NGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKK 93
           S+S TQ      +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 VALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
           VALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVP IVYL+ SLTKLI+++ LILK
Sbjct: 200 VALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPAIVYLALSLTKLILKDFLILK 258

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	309
224071670	327	predicted protein [Populus trichocarpa]	0.873	0.825	0.737	1e-107
255537217	320	conserved hypothetical protein [Ricinus	0.854	0.825	0.736	1e-107
118487360	323	unknown [Populus trichocarpa]	0.864	0.826	0.739	1e-106
356514103	321	PREDICTED: PGR5-like protein 1A, chlorop	0.844	0.813	0.738	1e-106
225426724	331	PREDICTED: PGR5-like protein 1A, chlorop	0.877	0.818	0.731	1e-106
297742627	326	unnamed protein product [Vitis vinifera]	0.877	0.831	0.731	1e-106
255645443	321	unknown [Glycine max]	0.844	0.813	0.735	1e-106
449460457	321	PREDICTED: PGR5-like protein 1A, chlorop	0.802	0.772	0.776	1e-105
224058627	327	predicted protein [Populus trichocarpa]	0.864	0.816	0.707	1e-104
18416029	324	PGR5-like protein 1A [Arabidopsis thalia	0.728	0.694	0.778	1e-101

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

 Score =  394 bits (1012), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 202/274 (73%), Positives = 232/274 (84%), Gaps = 4/274 (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 IVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPE 238
           IVVEGPRCSLRSRKVYSDLSVDYLKM LLNVPATVVALGLFFFLDD+TGFEITYLLELPE
Sbjct: 179 IVVEGPRCSLRSRKVYSDLSVDYLKMFLLNVPATVVALGLFFFLDDLTGFEITYLLELPE 238

Query: 239 PFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
           PFSF+FTWFAAVPLIV+L+ +LT  IV++ LILK
Sbjct: 239 PFSFLFTWFAAVPLIVWLALTLTNAIVKDFLILK 272

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 =  393 bits (1009), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 201/273 (73%), Positives = 228/273 (83%), Gaps = 9/273 (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 VVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEP 239
           VVEGPRCSLRSRKVYSDLSVDYLKM LLNVPA VVALGLFFFLDD+TGFEITYLLELPEP
Sbjct: 173 VVEGPRCSLRSRKVYSDLSVDYLKMFLLNVPAAVVALGLFFFLDDLTGFEITYLLELPEP 232

Query: 240 FSFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
           FSFIFTWFAAVP+IV+LS S T  IV++ LILK
Sbjct: 233 FSFIFTWFAAVPVIVWLSLSFTNAIVKDFLILK 265

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  392 bits (1007), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 202/273 (73%), Positives = 232/273 (84%), Gaps = 6/273 (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 VVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEP 239
           VVEGPRCSLRSRKVYSDLSVDYLKM LLNVPATVVALGLFFFLDD+TGFEITYLLELPEP
Sbjct: 176 VVEGPRCSLRSRKVYSDLSVDYLKMFLLNVPATVVALGLFFFLDDLTGFEITYLLELPEP 235

Query: 240 FSFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
           FSF+FTWFAAVPLIV+L+ +LT  IV++ LILK
Sbjct: 236 FSFLFTWFAAVPLIVWLALTLTNAIVKDFLILK 268

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  392 bits (1006), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 198/268 (73%), Positives = 220/268 (82%), Gaps = 7/268 (2%)

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  GQVE----GDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDN 124
           G+VE        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 RCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIF 244
           RCSLRSRKVYSDLSVDYLKMLLLNVPATV+ALGLFFFLDD+TGFEITYLLELPEPFSFIF
Sbjct: 179 RCSLRSRKVYSDLSVDYLKMLLLNVPATVIALGLFFFLDDLTGFEITYLLELPEPFSFIF 238

Query: 245 TWFAAVPLIVYLSQSLTKLIVRESLILK 272
           TWFAAVPLIV+++ SLT  IV++ +ILK
Sbjct: 239 TWFAAVPLIVWIALSLTNAIVKDFVILK 266

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 =  392 bits (1006), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 199/272 (73%), Positives = 227/272 (83%), Gaps = 1/272 (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 VEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPF 240
           VEGPRCSLRS+KVYSDLSVDYLKM LLNVPA VVAL LFFFLDD+TGFEIT+LLEL EPF
Sbjct: 185 VEGPRCSLRSKKVYSDLSVDYLKMFLLNVPAAVVALSLFFFLDDVTGFEITFLLELQEPF 244

Query: 241 SFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
           SFIFTWFAAVPLI +LSQ++TK I+++ LILK
Sbjct: 245 SFIFTWFAAVPLIFWLSQTITKFILKDFLILK 276

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 199/272 (73%), Positives = 227/272 (83%), Gaps = 1/272 (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 VEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPF 240
           VEGPRCSLRS+KVYSDLSVDYLKM LLNVPA VVAL LFFFLDD+TGFEIT+LLEL EPF
Sbjct: 180 VEGPRCSLRSKKVYSDLSVDYLKMFLLNVPAAVVALSLFFFLDDVTGFEITFLLELQEPF 239

Query: 241 SFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
           SFIFTWFAAVPLI +LSQ++TK I+++ LILK
Sbjct: 240 SFIFTWFAAVPLIFWLSQTITKFILKDFLILK 271

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  390 bits (1001), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 197/268 (73%), Positives = 219/268 (81%), Gaps = 7/268 (2%)

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  GQVE----GDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDN 124
           G+VE        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 RCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIF 244
           RCSLRSRKVYSDLSVDYLKMLLLNVPATV+ALGLFFFLDD+TGFEITYLLELPEPFSFIF
Sbjct: 179 RCSLRSRKVYSDLSVDYLKMLLLNVPATVIALGLFFFLDDLTGFEITYLLELPEPFSFIF 238

Query: 245 TWFAAVPLIVYLSQSLTKLIVRESLILK 272
           TWF AVPLIV+++ SLT  IV++ +ILK
Sbjct: 239 TWFVAVPLIVWIALSLTNAIVKDFVILK 266

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 195/251 (77%), Positives = 219/251 (87%), Gaps = 3/251 (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 LKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLT 261
            KM LLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVP +V+L+ +LT
Sbjct: 199 FKMFLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPFLVWLALTLT 258

Query: 262 KLIVRESLILK 272
             +VR+SLILK
Sbjct: 259 NAVVRDSLILK 269

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 =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 196/277 (70%), Positives = 225/277 (81%), Gaps = 10/277 (3%)

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 LPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
           LPEPFSF+FTWFAAVPLIV+L+ +LT  IV++ LILK
Sbjct: 236 LPEPFSFLFTWFAAVPLIVWLALTLTNAIVKDFLILK 272

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18416029|ref|NP_567672.1| PGR5-like protein 1A [Arabidopsis thaliana] gi|30685973|ref|NP_849422.1| PGR5-like protein 1A [Arabidopsis thaliana] gi|30685977|ref|NP_849423.1| PGR5-like protein 1A [Arabidopsis thaliana] gi|75151862|sp|Q8H112.1|PGL1A_ARATH RecName: Full=PGR5-like protein 1A, chloroplastic; Flags: Precursor gi|24030260|gb|AAN41305.1| unknown protein [Arabidopsis thaliana] gi|332659274|gb|AEE84674.1| PGR5-like protein 1A [Arabidopsis thaliana] gi|332659275|gb|AEE84675.1| PGR5-like protein 1A [Arabidopsis thaliana] gi|332659276|gb|AEE84676.1| PGR5-like protein 1A [Arabidopsis thaliana]

 Score =  374 bits (961), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 176/226 (77%), Positives = 208/226 (92%), Gaps = 1/226 (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 GFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
           GFEITY++ELPEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILK
Sbjct: 224 GFEITYIMELPEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILK 269

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	309
TAIR|locus:2118031	313	PGRL1B "AT4G11960" [Arabidopsi	0.754	0.744	0.786	3.3e-95
TAIR|locus:2127233	324	PGR5-LIKE A "AT4G22890" [Arabi	0.741	0.706	0.770	2.1e-93
TAIR|locus:2148338	301	AT5G59400 "AT5G59400" [Arabido	0.242	0.249	0.392	7.2e-06

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

 Score = 947 (338.4 bits), Expect = 3.3e-95, P = 3.3e-95
 Identities = 188/239 (78%), Positives = 214/239 (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 VALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
             VALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVP IVYL+ SLTKLI+++ LILK
Sbjct:   200 VALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPAIVYLALSLTKLILKDFLILK 258

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 = 930 (332.4 bits), Expect = 2.1e-93, P = 2.1e-93
 Identities = 178/231 (77%), Positives = 211/231 (91%)

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 LDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILK 272
             LDDITGFEITY++ELPEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILK
Sbjct:   219 LDDITGFEITYIMELPEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILK 269

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 = 7.2e-06, P = 7.2e-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        0.320   0.135   0.382    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      309       295   0.00092  115 3  11 22  0.37    34
                                                     33  0.44    37


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:  595 (63 KB)
  Total size of DFA:  184 KB (2106 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  23.92u 0.19s 24.11t   Elapsed:  00:00:02
  Total cpu time:  23.92u 0.19s 24.11t   Elapsed:  00:00:02
  Start:  Fri May 10 05:12:46 2013   End:  Fri May 10 05:12:48 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	0.7787	0.7281	0.6944	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

Your Input: grail3.0018022902 SubName- Full=Putative uncharacterized protein; (327 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	309
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	95.01
cd00114	307	LIGANc NAD+ dependent DNA ligase adenylation domai	94.82
PF01653	315	DNA_ligase_aden: NAD-dependent DNA ligase adenylat	94.15
smart00532	441	LIGANc Ligase N family.	93.4
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	93.16
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	93.11
cd00114	307	LIGANc NAD+ dependent DNA ligase adenylation domai	90.6
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	90.52
PF01653	315	DNA_ligase_aden: NAD-dependent DNA ligase adenylat	88.68
smart00532	441	LIGANc Ligase N family.	88.58
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	88.06
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	86.9
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	86.24
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	85.86
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	85.71
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	82.33
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	80.89
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	80.51

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=95.01  E-value=0.026  Score=58.42  Aligned_cols=49  Identities=35%  Similarity=0.497  Sum_probs=33.9

Q ss_pred             hHhhhhhcCCe---eEEeChhh--H--HHH-----HHHHhhhc-CCCccChHHHHHHHHHHh
Q 021649          125 LKEELMWEGSS---VVMLSSAE--Q--KFL-----EASMAYVA-GKPIMSDEEYDKLKQKLK  173 (309)
Q Consensus       125 LkEeL~WeGSs---vv~L~~~E--Q--~FL-----EA~~AY~~-GkPimsDeEFD~LK~kLk  173 (309)
                      |-.-|.|..|-   |.+++..|  +  +.|     ++-.+||. |+|+|||+|||+|..+|+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~   69 (562)
T PRK08097          8 LISLLLWSSSAWAVCPDWSPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLT   69 (562)
T ss_pred             HHHHHHhcccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            33457788876   55566554  1  112     22346775 999999999999999997

>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain

Probab=94.82  E-value=0.029  Score=53.69  Aligned_cols=28  Identities=32%  Similarity=0.583  Sum_probs=23.5

Q ss_pred             HHHHHhhhc-CCCccChHHHHHHHHHHhh
Q 021649          147 LEASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       147 LEA~~AY~~-GkPimsDeEFD~LK~kLk~  174 (309)
                      -++-.+||. |+|+|||+|||.|.++|+.
T Consensus        11 ~~~~~~YY~~~~p~IsD~eYD~L~~~L~~   39 (307)
T cd00114          11 NKHDYRYYVLDEPSVSDAEYDRLYRELRA   39 (307)
T ss_pred             HHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            344567887 9999999999999999974

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=94.15  E-value=0.055  Score=51.96  Aligned_cols=26  Identities=50%  Similarity=0.847  Sum_probs=22.1

Q ss_pred             HHHHhhhc-CCCccChHHHHHHHHHHh
Q 021649          148 EASMAYVA-GKPIMSDEEYDKLKQKLK  173 (309)
Q Consensus       148 EA~~AY~~-GkPimsDeEFD~LK~kLk  173 (309)
                      ++..+||. |+|+|||+|||.|..+|+
T Consensus        16 ~~~~~YY~~~~p~isD~eYD~l~~~L~   42 (315)
T PF01653_consen   16 RHNYAYYNLGEPIISDAEYDQLFRELK   42 (315)
T ss_dssp             HHHHHHHTTSSSSSSHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            34557777 899999999999999986

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=93.40  E-value=0.08  Score=53.25  Aligned_cols=26  Identities=42%  Similarity=0.755  Sum_probs=22.5

Q ss_pred             HHHHhhhc-CCCccChHHHHHHHHHHh
Q 021649          148 EASMAYVA-GKPIMSDEEYDKLKQKLK  173 (309)
Q Consensus       148 EA~~AY~~-GkPimsDeEFD~LK~kLk  173 (309)
                      ++..+||. |+|+|||+|||+|..+|+
T Consensus        14 ~~~~~YY~~~~p~IsD~eYD~L~~eL~   40 (441)
T smart00532       14 KHDYRYYVLDAPIISDAEYDRLMRELK   40 (441)
T ss_pred             HHHHHHHhcCCCCCChHHHHHHHHHHH
Confidence            34556876 999999999999999997

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=93.16  E-value=0.09  Score=55.26  Aligned_cols=27  Identities=37%  Similarity=0.597  Sum_probs=23.5

Q ss_pred             HHHHhhh-cCCCccChHHHHHHHHHHhh
Q 021649          148 EASMAYV-AGKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       148 EA~~AY~-~GkPimsDeEFD~LK~kLk~  174 (309)
                      ++-.+|| .|+|+|||+|||.|.++|+.
T Consensus        18 ~~~~~YY~~~~p~IsD~eYD~L~~~L~~   45 (665)
T PRK07956         18 HHAYAYYVLDAPSISDAEYDRLYRELVA   45 (665)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            4456788 99999999999999999973

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=93.11  E-value=0.1  Score=54.78  Aligned_cols=29  Identities=31%  Similarity=0.556  Sum_probs=24.5

Q ss_pred             HHHHHHhhhc-CCCccChHHHHHHHHHHhh
Q 021649          146 FLEASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       146 FLEA~~AY~~-GkPimsDeEFD~LK~kLk~  174 (309)
                      .-++..+||. |+|+|||+|||.|.++|+.
T Consensus         5 l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~   34 (652)
T TIGR00575         5 IRHHDYRYYVLDEPSISDAEYDRLYRELQE   34 (652)
T ss_pred             HHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            3455667886 9999999999999999974

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=90.60  E-value=0.31  Score=46.77  Aligned_cols=35  Identities=26%  Similarity=0.366  Sum_probs=27.7

Q ss_pred             hHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           96 GELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        96 ge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      -++...--.+=..||..+.+++||+|||.|.++|.
T Consensus         4 ~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~   38 (307)
T cd00114           4 AELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELR   38 (307)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            34555555556678888999999999999999984

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.

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=90.52  E-value=0.27  Score=52.11  Aligned_cols=27  Identities=30%  Similarity=0.600  Sum_probs=22.7

Q ss_pred             HHHHhhh-cCCCccChHHHHHHHHHHhh
Q 021649          148 EASMAYV-AGKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       148 EA~~AY~-~GkPimsDeEFD~LK~kLk~  174 (309)
                      ++-.+|| .|+|+|||+|||.|.++|+.
T Consensus        45 ~~~~~YY~~~~p~IsD~eYD~L~~eL~~   72 (689)
T PRK14351         45 EHDHRYYVEADPVIADRAYDALFARLQA   72 (689)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            4455777 57999999999999999973

>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=88.68  E-value=0.57  Score=45.10  Aligned_cols=35  Identities=34%  Similarity=0.582  Sum_probs=27.7

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL  129 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL  129 (309)
                      +-++...--.+=..||..+.++|||+|||.|.++|
T Consensus         7 i~~L~~~i~~~~~~YY~~~~p~isD~eYD~l~~~L   41 (315)
T PF01653_consen    7 IEELRKEINRHNYAYYNLGEPIISDAEYDQLFREL   41 (315)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence            34455555566678999999999999999999885

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=88.58  E-value=0.47  Score=47.87  Aligned_cols=36  Identities=25%  Similarity=0.420  Sum_probs=28.6

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      +-++...-..+-..||..+.+++||+|||.|.+||.
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            444555555566678889999999999999999985

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=88.06  E-value=0.53  Score=49.89  Aligned_cols=25  Identities=28%  Similarity=0.397  Sum_probs=21.3

Q ss_pred             HHHhhh-cCCCccChHHHHHHHHHHh
Q 021649          149 ASMAYV-AGKPIMSDEEYDKLKQKLK  173 (309)
Q Consensus       149 A~~AY~-~GkPimsDeEFD~LK~kLk  173 (309)
                      .-.+|| .|+|+|||++||.|..+|+
T Consensus        19 ~~~~YY~~~~p~IsD~~YD~L~~eL~   44 (669)
T PRK14350         19 WDKEYYVDSSPSVEDFTYDKALLRLQ   44 (669)
T ss_pred             HHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            345677 5799999999999999996

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=86.90  E-value=0.62  Score=48.58  Aligned_cols=36  Identities=28%  Similarity=0.535  Sum_probs=28.4

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      +-++...--.+=..||..+.|++||+|||.|.+||.
T Consensus        34 i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~   69 (562)
T PRK08097         34 IAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLT   69 (562)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            444444555556679999999999999999999984

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=86.24  E-value=0.53  Score=35.34  Aligned_cols=29  Identities=17%  Similarity=0.291  Sum_probs=26.0

Q ss_pred             cCCCCccceeecccCCCceeeeeeeCCCc
Q 021649          274 MFLSLGPYYQFLVVEPPTLLTAQIVEPPW  302 (309)
Q Consensus       274 pCPNCGee~aFv~~~~p~~~~~~~~~~~~  302 (309)
                      .||+||.++.-+..++++|-.|.-++--|
T Consensus        24 ~Cp~CGaeleVv~~~p~~L~~ap~~~eDw   52 (54)
T TIGR01206        24 ICDECGAELEVVSLDPLRLEAAPEEAEDW   52 (54)
T ss_pred             eCCCCCCEEEEEeCCCCEEEeCccccccc
Confidence            79999999888999999999888887777

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=85.86  E-value=0.89  Score=48.02  Aligned_cols=36  Identities=31%  Similarity=0.504  Sum_probs=28.1

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      +-++...--.+=..||..+.+++||+|||.|.++|.
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            344444455555678889999999999999999986

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=85.71  E-value=0.76  Score=48.83  Aligned_cols=36  Identities=19%  Similarity=0.390  Sum_probs=30.1

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      +-++...--.+=..||..+.+++||+|||.|.+||.
T Consensus        36 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~   71 (689)
T PRK14351         36 AEQLREAIREHDHRYYVEADPVIADRAYDALFARLQ   71 (689)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            556666666666789999999999999999999996

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=82.33  E-value=1.2  Score=46.81  Aligned_cols=27  Identities=26%  Similarity=0.411  Sum_probs=23.0

Q ss_pred             HHHHHhhhcCccccChHHHhhhHhhhh
Q 021649          104 QALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus       104 ~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      .+-..||..+.|++||+|||.|.+||.
T Consensus         7 ~~~~~YY~~~~p~IsD~eYD~L~~~L~   33 (652)
T TIGR00575         7 HHDYRYYVLDEPSISDAEYDRLYRELQ   33 (652)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            344568888999999999999999985

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.

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=80.89  E-value=1.4  Score=46.79  Aligned_cols=36  Identities=11%  Similarity=0.200  Sum_probs=27.0

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      +-++...--..=..||..+.|++||+|||.|.+||.
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            444444444445568889999999999999999984

>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

Probab=80.51  E-value=1.8  Score=46.39  Aligned_cols=25  Identities=36%  Similarity=0.616  Sum_probs=21.5

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 021649          150 SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       150 ~~AY~~-GkPimsDeEFD~LK~kLk~  174 (309)
                      ..+||- ++|+|+|+|||+|.++|..
T Consensus        22 ~~~Yyv~d~P~VsD~eYD~L~reL~~   47 (667)
T COG0272          22 DYRYYVLDAPSVSDAEYDQLYRELQE   47 (667)
T ss_pred             HHHHhccCCCCCChHHHHHHHHHHHH
Confidence            456666 9999999999999999975

---

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	309
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-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 = 48.7 bits (115), Expect = 2e-06
 Identities = 44/254 (17%), Positives = 77/254 (30%), Gaps = 79/254 (31%)

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

Query: 129 --LMW----EGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVE 182
             L W    +   +V      QKF+E  +             Y  L   +K E  +  + 
Sbjct: 65  LRLFWTLLSKQEEMV------QKFVEEVL----------RINYKFLMSPIKTEQRQPSMM 108

Query: 183 GPRCSLRSRKVYSDLSVDYLKMLLLNVP--ATVVALGLFFFLDDITGFEITYLLEL-PEP 239
                 +  ++Y+D  V + K    NV      + L                LLEL P  
Sbjct: 109 TRMYIEQRDRLYNDNQV-FAKY---NVSRLQPYLKL-------------RQALLELRPAK 151

Query: 240 FSFIFTWFAAVPLIVY-LS----QSLTKLIVRESLILKRMF-----LSLGPYYQF-LVVE 288
                       +++  +       +   +     +  +M      L+L        V+E
Sbjct: 152 N-----------VLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE 200

Query: 289 PPTLLTAQIVEPPW 302
               L  QI +P W
Sbjct: 201 MLQKLLYQI-DPNW 213

>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 = 42.5 bits (99), Expect = 1e-04
 Identities = 52/364 (14%), Positives = 85/364 (23%), Gaps = 143/364 (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  ------------DKKEKKSLGELEQEFL--QALQAFYYEGKAVMSNEEFDNLKEELMWEG 133
                             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------RKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITY-LLELPEPF 240
           L        RK++  LSV                     F        I   LL L    
Sbjct: 363 LNVLEPAEYRKMFDRLSV---------------------FPPSA---HIPTILLSL---- 394

Query: 241 SFIFTWFAAVPLIVYLSQSLTKLIVRESLILKR---MFLSLGPYYQFLVVEPPTL--LTA 295
                WF    +I      +   + + SL+ K+     +S+   Y  L V+      L  
Sbjct: 395 ----IWFD---VIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR 447

Query: 296 QIVE 299
            IV+
Sbjct: 448 SIVD 451

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	309
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	93.84
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	92.97
4glw_A	305	DNA ligase; inhibitor, ligase-ligase inhibitor com	92.72
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	92.11
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	92.0
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	91.9
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	91.17
4glw_A	305	DNA ligase; inhibitor, ligase-ligase inhibitor com	88.31
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	86.82
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	86.55
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	86.54
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	86.38
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	86.29
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	86.03
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	85.97
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	85.09
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	80.54

>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=93.84  E-value=0.049  Score=51.52  Aligned_cols=27  Identities=33%  Similarity=0.589  Sum_probs=22.5

Q ss_pred             HHHHhhhc-CCCccChHHHHHHHHHHhh
Q 021649          148 EASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       148 EA~~AY~~-GkPimsDeEFD~LK~kLk~  174 (309)
                      ++-.+||. |+|+|||+|||+|.++|+.
T Consensus        15 ~~~~~YY~~d~p~IsD~eYD~L~~eL~~   42 (322)
T 3uq8_A           15 QYEYEYHVLDNPSVPDSEYDRLFHQLKA   42 (322)
T ss_dssp             HHHHHHHTSSCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            33557775 9999999999999999865

>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=92.97  E-value=0.074  Score=50.29  Aligned_cols=25  Identities=40%  Similarity=0.620  Sum_probs=21.2

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 021649          150 SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       150 ~~AY~~-GkPimsDeEFD~LK~kLk~  174 (309)
                      -.+||. |+|+|||+|||+|..+|+.
T Consensus        19 ~~~YY~~d~p~IsD~eYD~L~~eL~~   44 (318)
T 3jsl_A           19 SYEYYVEDNPSVPDSEYDKLLHELIK   44 (318)
T ss_dssp             HHHHHTSCCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCCCCHHHHHHHHHHHHH
Confidence            446775 9999999999999998864

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

Probab=92.72  E-value=0.02  Score=53.32  Aligned_cols=26  Identities=35%  Similarity=0.580  Sum_probs=3.8

Q ss_pred             HHHhhh-cCCCccChHHHHHHHHHHhh
Q 021649          149 ASMAYV-AGKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       149 A~~AY~-~GkPimsDeEFD~LK~kLk~  174 (309)
                      +-.+|| .|+|+|||+|||.|..+|+.
T Consensus        15 ~~~~YY~~~~p~IsD~eYD~L~~eL~~   41 (305)
T 4glw_A           15 YATEYYTSDNPSVSDSEYDRLYRELVE   41 (305)
T ss_dssp             ----------------------CHHHH
T ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            345777 59999999999999998874

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

Probab=92.11  E-value=0.1  Score=49.36  Aligned_cols=26  Identities=35%  Similarity=0.646  Sum_probs=22.0

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhhh
Q 021649          150 SMAYV-AGKPIMSDEEYDKLKQKLKME  175 (309)
Q Consensus       150 ~~AY~-~GkPimsDeEFD~LK~kLk~e  175 (309)
                      -.+|| .|+|+|||+|||+|..+|+.-
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            44676 699999999999999999753

>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=92.00  E-value=0.11  Score=49.23  Aligned_cols=25  Identities=32%  Similarity=0.476  Sum_probs=21.7

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 021649          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       150 ~~AY~-~GkPimsDeEFD~LK~kLk~  174 (309)
                      -.+|| .|+|+|||+|||+|..+|+.
T Consensus        26 ~~~YY~~d~p~IsD~eYD~L~~eL~~   51 (332)
T 1ta8_A           26 SHEYYVKDQPSVEDYVYDRLYKELVD   51 (332)
T ss_dssp             HHHHHTSSCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            44676 69999999999999999875

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

Probab=91.90  E-value=0.11  Score=49.03  Aligned_cols=25  Identities=36%  Similarity=0.634  Sum_probs=21.6

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 021649          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       150 ~~AY~-~GkPimsDeEFD~LK~kLk~  174 (309)
                      -.+|| .|+|+|||+|||+|..+|+.
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            44676 69999999999999999874

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

Probab=91.17  E-value=0.11  Score=52.44  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=21.6

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 021649          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       150 ~~AY~-~GkPimsDeEFD~LK~kLk~  174 (309)
                      -.+|| .|+|+|||+|||.|.++|+.
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            45677 59999999999999999875

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

Probab=88.31  E-value=0.076  Score=49.47  Aligned_cols=34  Identities=26%  Similarity=0.419  Sum_probs=3.2

Q ss_pred             HHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           97 ELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        97 e~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      ++...--.+=.+||..|.|++||+|||.|.+||.
T Consensus         7 ~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~   40 (305)
T 4glw_A            7 ELVALLNRYATEYYTSDNPSVSDSEYDRLYRELV   40 (305)
T ss_dssp             C-----------------------------CHHH
T ss_pred             HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            3444444455789999999999999999998864

>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=86.82  E-value=0.54  Score=44.47  Aligned_cols=35  Identities=20%  Similarity=0.294  Sum_probs=27.5

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL  129 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL  129 (309)
                      +.++...--.+=.+||..+.|++||+|||.|..||
T Consensus         6 i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL   40 (322)
T 3uq8_A            6 LDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQL   40 (322)
T ss_dssp             HHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence            34455555556678999999999999999998875

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

Probab=86.55  E-value=0.55  Score=44.27  Aligned_cols=36  Identities=22%  Similarity=0.388  Sum_probs=28.2

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      +.++...--.+=.+||..+.|++||+|||.|..||.
T Consensus        10 ~~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~   45 (318)
T 1b04_A           10 AAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELI   45 (318)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            445555555556688999999999999999999964

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

Probab=86.54  E-value=0.55  Score=44.45  Aligned_cols=37  Identities=24%  Similarity=0.406  Sum_probs=29.8

Q ss_pred             chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        94 slge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      -+.++...--.+=.+||..+.|++||+|||.|..||.
T Consensus        16 ~i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~   52 (328)
T 1zau_A           16 QWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLE   52 (328)
T ss_dssp             THHHHHHHHHHHHHHHTTTCCCSSCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            4556666666666789999999999999999999863

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

Probab=86.38  E-value=0.42  Score=49.16  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=21.5

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 021649          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       150 ~~AY~-~GkPimsDeEFD~LK~kLk~  174 (309)
                      -.+|| .++|+|||+|||+|.++|+.
T Consensus        19 ~~~YY~~d~p~isD~eYD~L~~eL~~   44 (671)
T 2owo_A           19 EYLYHVMDAPEIPDAEYDRLMRELRE   44 (671)
T ss_dssp             HHHHHHTTCSSBCCTHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            45666 68999999999999999875

>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=86.29  E-value=0.61  Score=44.08  Aligned_cols=35  Identities=29%  Similarity=0.459  Sum_probs=27.4

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL  129 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL  129 (309)
                      +.++...--.+=.+||..+.|++||+|||.|..||
T Consensus         8 i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL   42 (318)
T 3jsl_A            8 VNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHEL   42 (318)
T ss_dssp             HHHHHHHHHHHHHHHHTSCCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            44555555556667888999999999999998885

>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=86.03  E-value=0.62  Score=44.20  Aligned_cols=36  Identities=22%  Similarity=0.402  Sum_probs=28.3

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      +.++...--.+=.+||..+.|++||+|||.|..||.
T Consensus        15 i~~L~~~l~~~~~~YY~~d~p~IsD~eYD~L~~eL~   50 (332)
T 1ta8_A           15 AQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELV   50 (332)
T ss_dssp             HHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            455555555556678999999999999999999864

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

Probab=85.97  E-value=0.53  Score=47.67  Aligned_cols=36  Identities=22%  Similarity=0.288  Sum_probs=28.4

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      +.++...--.+=.+||..+.|++||+|||.|.+||.
T Consensus         8 i~~L~~~i~~~~~~Yy~~~~p~IsD~eYD~L~~eL~   43 (586)
T 4glx_A            8 LTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELR   43 (586)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCSSBCCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            445555555666789999999999999999998864

>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=85.09  E-value=0.38  Score=49.42  Aligned_cols=26  Identities=38%  Similarity=0.599  Sum_probs=22.2

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhhh
Q 021649          150 SMAYV-AGKPIMSDEEYDKLKQKLKME  175 (309)
Q Consensus       150 ~~AY~-~GkPimsDeEFD~LK~kLk~e  175 (309)
                      -.+|| .++|+|||.|||+|.++|+.-
T Consensus        21 ~~~YY~~d~p~isD~eYD~l~~eL~~l   47 (667)
T 1dgs_A           21 NYRYYVLADPEISDAEYDRLLRELKEL   47 (667)
T ss_dssp             HHHHHTTCCCCSCSSSSHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence            44666 699999999999999999853

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}

Probab=80.54  E-value=0.21  Score=50.97  Aligned_cols=25  Identities=36%  Similarity=0.709  Sum_probs=21.6

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 021649          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       150 ~~AY~-~GkPimsDeEFD~LK~kLk~  174 (309)
                      -.+|| .++|+|||+|||+|.++|+.
T Consensus        28 ~~~YY~~d~p~IsD~eYD~L~~eL~~   53 (615)
T 3sgi_A           28 QFRYYVRDAPIISDAEFDELLRRLEA   53 (615)
T ss_dssp             HHHHHHHSCCCSSCCSSCSSSSHHHH
T ss_pred             HHHHHcCCCCCCCHHHHHHHHHHHHH
Confidence            45777 79999999999999888864

---

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	309
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	2e-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	0.002

>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 = 40.7 bits (94), 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 = 39.5 bits (91), 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 = 2e-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 = 39.9 bits (92), 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 = 37.2 bits (85), Expect = 0.002
 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	309
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	96.61
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	96.52
d1dgsa3	314	Adenylation domain of NAD+-dependent DNA ligase {T	95.79
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	95.52
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	95.35
d1dgsa3	314	Adenylation domain of NAD+-dependent DNA ligase {T	93.41

>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=96.61  E-value=0.00064  Score=59.44  Aligned_cols=27  Identities=30%  Similarity=0.434  Sum_probs=23.1

Q ss_pred             HHHHhhh-cCCCccChHHHHHHHHHHhh
Q 021649          148 EASMAYV-AGKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       148 EA~~AY~-~GkPimsDeEFD~LK~kLk~  174 (309)
                      ++-.+|| .|+|+|||+|||.|+.+|+.
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            4456788 59999999999999999975

>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=96.52  E-value=0.00072  Score=59.68  Aligned_cols=25  Identities=36%  Similarity=0.651  Sum_probs=22.1

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 021649          150 SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       150 ~~AY~~-GkPimsDeEFD~LK~kLk~  174 (309)
                      -.+||. |+|+|||+|||.|+++|+.
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            457886 9999999999999999965

>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=95.79  E-value=0.0017  Score=57.40  Aligned_cols=26  Identities=38%  Similarity=0.641  Sum_probs=22.6

Q ss_pred             HHHhhhc-CCCccChHHHHHHHHHHhh
Q 021649          149 ASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (309)
Q Consensus       149 A~~AY~~-GkPimsDeEFD~LK~kLk~  174 (309)
                      +-.+||. |+|+|||++||.|+.+|+.
T Consensus        20 ~~~~YY~~~~p~IsD~~YD~L~~eL~~   46 (314)
T d1dgsa3          20 HNYRYYVLADPEISDAEYDRLLRELKE   46 (314)
T ss_dssp             HHHHHHTTCCCCSCSSSSHHHHHHHHH
T ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            3557985 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=95.52  E-value=0.0048  Score=53.69  Aligned_cols=36  Identities=22%  Similarity=0.385  Sum_probs=31.7

Q ss_pred             chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 021649           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL  129 (309)
Q Consensus        94 slge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL  129 (309)
                      -+.+++..--++=.+||+.|.++|||+|||.|+++|
T Consensus        10 ~~~~L~~~i~~~~~~Yy~~~~p~iSD~eYD~L~~~L   45 (313)
T d1ta8a_          10 RAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKEL   45 (313)
T ss_dssp             HHHHHHHHHHHHHHHHHTSSCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence            356777777888889999999999999999999987

>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=95.35  E-value=0.0057  Score=53.74  Aligned_cols=38  Identities=21%  Similarity=0.378  Sum_probs=33.0

Q ss_pred             ccchhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 021649           92 KKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL  129 (309)
Q Consensus        92 k~slge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL  129 (309)
                      ++-+.|++..--.+=.+||+.|.|+|||+|||.|+++|
T Consensus         6 ~~~i~~L~~~i~~~~~~Yy~~~~p~isD~eYD~L~~~L   43 (312)
T d1b04a_           6 ERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQEL   43 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCSCCSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence            44567788777788889999999999999999999997

>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=93.41  E-value=0.019  Score=50.55  Aligned_cols=37  Identities=24%  Similarity=0.340  Sum_probs=29.5

Q ss_pred             chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (309)
Q Consensus        94 slge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~  130 (309)
                      -+-+++..--.+=.+||..|.|+|||+|||.|++||.
T Consensus         9 ~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~   45 (314)
T d1dgsa3           9 RINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELK   45 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCCSCSSSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            3455555555666888889999999999999999874