Citrus Sinensis ID: 019981

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330---
Protein Sequence
MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccEEEEEcHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccEEEEcccEEEcccEEEEccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEccccccccccEEcccccccccccccccccccccccccccccEEEEEcccEEEEccccccc
Secondary Structure Prediction (SSPRO)
cccHHHccccccccccccccccccccccccccccccccccccccccccEEEEccEEEEccccccHHcccccccccccccccccccEccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccEEEEcHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccEEEEccEEEccccEEEccHHHHHHHHHHHcccHHHHHHHHHHHHccccccccEHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEccccccccccEEEEEcEEEEccccccccccccccccccEEccEEEEEcccEEEEEccccccc
Coil and Loop (DISEMBL)
magkvasgftpqaqrvfavpvqkpaaalapfpsssrahsnsntqfngrqftvrrrsfvlpskattdqqgqvegdevvDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYegkavmsneEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYvagkpimsdeEYDKLKQKLKMEgseivvegprcslrsrkvysDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYllelpepfsfifTWFAAVPLIVYLSQSLTKLIVREslilkgpcpncgtenvsFFGTILSissggttntincsnltfcfscgttmvydsntrlitlpegsea
Flexible Loop (DISEMBL)
magkvasgftpqaqrVFAVPVQKPAAALAPfpsssrahsnsntqfngrqftvRRRSFVLpskattdqqgqvegdevvdSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKmegseivvegprcslrsrkVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTrlitlpegsea
Low Complexity Region (SEG)
MAGKVASGFTPQAQRVFAVPVQKpaaalapfpsssraHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA
Disordered region (IsUnstruct)
********************************************************************************ILQY*****************FLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGK********************EIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLIT*******
Disordered Region (DISOPRED)
*********TPQAQRV**************************************************************SKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSIS*******INCSNLTFCFSCGTTMVYDSNT****L******
Disordered Region (DISEMBL)
********FTPQAQRVFAVPVQKPAAALAP*************QFNGRQFTVRRRSFVLPS*************EVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA
Disordered Region (DISPRO)
**********************************************GRQFTVRRRSFVLPSK*********EGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPE****
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGKVASGFTPQAQRVFAVPVQKPAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA
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	333	2.2.26 [Sep-21-2011]
Q8H112	324	PGR5-like protein 1A, chl	yes	no	0.840	0.864	0.773	1e-132
Q8GYC7	313	PGR5-like protein 1B, chl	no	no	0.843	0.897	0.777	1e-126

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

 Score =  470 bits (1209), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 222/287 (77%), Positives = 258/287 (89%), Gaps = 7/287 (2%)

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 GFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFF 286
           GFEITY++ELPEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILKGPCPNCGTEN SFF
Sbjct: 224 GFEITYIMELPEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILKGPCPNCGTENTSFF 283

Query: 287 GTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           GTILSISSGG TNT+ C+N      CGT MVYDS +RLITLPEGS+A
Sbjct: 284 GTILSISSGGKTNTVKCTN------CGTAMVYDSGSRLITLPEGSQA 324

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 =  450 bits (1158), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 224/288 (77%), Positives = 253/288 (87%), Gaps = 7/288 (2%)

Query: 46  NGRQFTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQA 105
           +GR  ++RRR  +LP KA+TDQ GQV G+EV DSKIL YCSI+K EK+++GE+EQEFLQA
Sbjct: 33  HGRSISLRRRLTLLPLKASTDQSGQVGGEEV-DSKILPYCSINKNEKRTIGEMEQEFLQA 91

Query: 106 LQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEY 165
           +Q+FYYEGKA+MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI+SDEEY
Sbjct: 92  MQSFYYEGKAIMSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILSDEEY 151

Query: 166 DKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDI 225
           DKLK KLKM+GSEIV EGPRCSLRS+KVYSDL++DY KM LLNVPATVVALGLFFFLDDI
Sbjct: 152 DKLKMKLKMDGSEIVCEGPRCSLRSKKVYSDLAIDYFKMFLLNVPATVVALGLFFFLDDI 211

Query: 226 TGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSF 285
           TGFEITYLLELPEPFSFIFTWFAAVP IVYL+ SLTKLI+++ LILKGPCPNCGTENVSF
Sbjct: 212 TGFEITYLLELPEPFSFIFTWFAAVPAIVYLALSLTKLILKDFLILKGPCPNCGTENVSF 271

Query: 286 FGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           FGTILSI +   TN + CS       CGT MVYDS +RLITLPEG +A
Sbjct: 272 FGTILSIPNDSNTNNVKCSG------CGTEMVYDSGSRLITLPEGGKA 313

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	333
255537217	320	conserved hypothetical protein [Ricinus	0.957	0.996	0.745	1e-137
225426724	331	PREDICTED: PGR5-like protein 1A, chlorop	0.978	0.984	0.741	1e-136
297742627	326	unnamed protein product [Vitis vinifera]	0.978	1.0	0.741	1e-136
224071670	327	predicted protein [Populus trichocarpa]	0.975	0.993	0.740	1e-135
118487360	323	unknown [Populus trichocarpa]	0.966	0.996	0.745	1e-135
356514103	321	PREDICTED: PGR5-like protein 1A, chlorop	0.948	0.984	0.744	1e-135
255645443	321	unknown [Glycine max]	0.948	0.984	0.741	1e-134
224058627	327	predicted protein [Populus trichocarpa]	0.966	0.984	0.718	1e-133
449460457	321	PREDICTED: PGR5-like protein 1A, chlorop	0.900	0.934	0.760	1e-131
18416029	324	PGR5-like protein 1A [Arabidopsis thalia	0.840	0.864	0.773	1e-130

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

 Score =  492 bits (1267), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 249/334 (74%), Positives = 278/334 (83%), Gaps = 15/334 (4%)

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 FSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTN 299
           FSFIFTWFAAVP+IV+LS S T  IV++ LILKGPCPNCGTEN SFFGTILSISSGGTTN
Sbjct: 233 FSFIFTWFAAVPVIVWLSLSFTNAIVKDFLILKGPCPNCGTENQSFFGTILSISSGGTTN 292

Query: 300 TINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           ++ CSN      CGT MVYDS TRLITLPEGS A
Sbjct: 293 SVKCSN------CGTDMVYDSKTRLITLPEGSNA 320

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  491 bits (1265), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 247/333 (74%), Positives = 277/333 (83%), Gaps = 7/333 (2%)

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 SFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNT 300
           SFIFTWFAAVPLI +LSQ++TK I+++ LILKGPCPNCGTENVSFFGTILSIS+GGTTN 
Sbjct: 245 SFIFTWFAAVPLIFWLSQTITKFILKDFLILKGPCPNCGTENVSFFGTILSISNGGTTNN 304

Query: 301 INCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           + CSN      C T MVYDS TRLITLPEGSEA
Sbjct: 305 LKCSN------CETQMVYDSKTRLITLPEGSEA 331

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 =  491 bits (1264), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 247/333 (74%), Positives = 277/333 (83%), Gaps = 7/333 (2%)

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 SFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNT 300
           SFIFTWFAAVPLI +LSQ++TK I+++ LILKGPCPNCGTENVSFFGTILSIS+GGTTN 
Sbjct: 240 SFIFTWFAAVPLIFWLSQTITKFILKDFLILKGPCPNCGTENVSFFGTILSISNGGTTNN 299

Query: 301 INCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           + CSN      C T MVYDS TRLITLPEGSEA
Sbjct: 300 LKCSN------CETQMVYDSKTRLITLPEGSEA 326

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  488 bits (1257), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 248/335 (74%), Positives = 281/335 (83%), Gaps = 10/335 (2%)

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 PFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTT 298
           PFSF+FTWFAAVPLIV+L+ +LT  IV++ LILKGPCPNCGTEN SFFGTILSISSGG +
Sbjct: 239 PFSFLFTWFAAVPLIVWLALTLTNAIVKDFLILKGPCPNCGTENGSFFGTILSISSGGAS 298

Query: 299 NTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           NT+ CSN      C T +VYDS TRLITLPEGSEA
Sbjct: 299 NTLKCSN------CSTELVYDSKTRLITLPEGSEA 327

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  488 bits (1256), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 249/334 (74%), Positives = 282/334 (84%), Gaps = 12/334 (3%)

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 FSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTN 299
           FSF+FTWFAAVPLIV+L+ +LT  IV++ LILKGPCPNCGTEN SFFGTILSISSGGT+N
Sbjct: 236 FSFLFTWFAAVPLIVWLALTLTNAIVKDFLILKGPCPNCGTENGSFFGTILSISSGGTSN 295

Query: 300 TINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           T+ CSN      C T +VYDS TRLITLPEGSEA
Sbjct: 296 TLKCSN------CSTELVYDSKTRLITLPEGSEA 323

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 =  486 bits (1252), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 245/329 (74%), Positives = 270/329 (82%), Gaps = 13/329 (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 RCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIF 244
           RCSLRSRKVYSDLSVDYLKMLLLNVPATV+ALGLFFFLDD+TGFEITYLLELPEPFSFIF
Sbjct: 179 RCSLRSRKVYSDLSVDYLKMLLLNVPATVIALGLFFFLDDLTGFEITYLLELPEPFSFIF 238

Query: 245 TWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCS 304
           TWFAAVPLIV+++ SLT  IV++ +ILKGPCPNCGTEN SFFGTILSIS+GG+TNT+ CS
Sbjct: 239 TWFAAVPLIVWIALSLTNAIVKDFVILKGPCPNCGTENTSFFGTILSISNGGSTNTVKCS 298

Query: 305 NLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           N      CGT M YDS TRLITLPEGS A
Sbjct: 299 N------CGTAMEYDSTTRLITLPEGSNA 321

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 =  484 bits (1247), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 244/329 (74%), Positives = 269/329 (81%), Gaps = 13/329 (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 RCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIF 244
           RCSLRSRKVYSDLSVDYLKMLLLNVPATV+ALGLFFFLDD+TGFEITYLLELPEPFSFIF
Sbjct: 179 RCSLRSRKVYSDLSVDYLKMLLLNVPATVIALGLFFFLDDLTGFEITYLLELPEPFSFIF 238

Query: 245 TWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCS 304
           TWF AVPLIV+++ SLT  IV++ +ILKGPCPNCGTEN SFFGTILSIS+GG+TNT+ CS
Sbjct: 239 TWFVAVPLIVWIALSLTNAIVKDFVILKGPCPNCGTENTSFFGTILSISNGGSTNTVKCS 298

Query: 305 NLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           N      CGT M YDS TRLITLPEGS A
Sbjct: 299 N------CGTAMEYDSTTRLITLPEGSNA 321

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  481 bits (1237), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 243/338 (71%), Positives = 275/338 (81%), Gaps = 16/338 (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 LPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSG 295
           LPEPFSF+FTWFAAVPLIV+L+ +LT  IV++ LILKGPCPNCGTEN SFFGTILSISSG
Sbjct: 236 LPEPFSFLFTWFAAVPLIVWLALTLTNAIVKDFLILKGPCPNCGTENGSFFGTILSISSG 295

Query: 296 GTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           GTTNT+ CSN      C T +VY+S TRLITLPEGSEA
Sbjct: 296 GTTNTLKCSN------CSTELVYNSKTRLITLPEGSEA 327

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  472 bits (1215), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 235/309 (76%), Positives = 263/309 (85%), Gaps = 9/309 (2%)

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 KLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSN 321
             +VR+SLILKGPCPNCGTENVSFFGTILS+SSGG  N I C+N      C T +VY+S 
Sbjct: 259 NAVVRDSLILKGPCPNCGTENVSFFGTILSVSSGGNKNNIKCTN------CATELVYNSK 312

Query: 322 TRLITLPEG 330
           TRLITLPE 
Sbjct: 313 TRLITLPEA 321

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  470 bits (1209), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 222/287 (77%), Positives = 258/287 (89%), Gaps = 7/287 (2%)

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 GFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFF 286
           GFEITY++ELPEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILKGPCPNCGTEN SFF
Sbjct: 224 GFEITYIMELPEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILKGPCPNCGTENTSFF 283

Query: 287 GTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
           GTILSISSGG TNT+ C+N      CGT MVYDS +RLITLPEGS+A
Sbjct: 284 GTILSISSGGKTNTVKCTN------CGTAMVYDSGSRLITLPEGSQA 324

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	333
TAIR|locus:2127233	324	PGR5-LIKE A "AT4G22890" [Arabi	0.852	0.876	0.767	6e-119
TAIR|locus:2118031	313	PGRL1B "AT4G11960" [Arabidopsi	0.864	0.920	0.763	1.4e-117
TAIR|locus:2148338	301	AT5G59400 "AT5G59400" [Arabido	0.225	0.249	0.392	4.4e-08

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

 Score = 1171 (417.3 bits), Expect = 6.0e-119, P = 6.0e-119
 Identities = 224/292 (76%), Positives = 261/292 (89%)

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 LDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTE 281
             LDDITGFEITY++ELPEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILKGPCPNCGTE
Sbjct:   219 LDDITGFEITYIMELPEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILKGPCPNCGTE 278

Query:   282 NVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
             N SFFGTILSISSGG TNT+ C+N      CGT MVYDS +RLITLPEGS+A
Sbjct:   279 NTSFFGTILSISSGGKTNTVKCTN------CGTAMVYDSGSRLITLPEGSQA 324

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

 Score = 1158 (412.7 bits), Expect = 1.4e-117, P = 1.4e-117
 Identities = 229/300 (76%), Positives = 259/300 (86%)

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 VALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKG 273
             VALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVP IVYL+ SLTKLI+++ LILKG
Sbjct:   200 VALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPAIVYLALSLTKLILKDFLILKG 259

Query:   274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPEGSEA 333
             PCPNCGTENVSFFGTILSI +   TN + CS       CGT MVYDS +RLITLPEG +A
Sbjct:   260 PCPNCGTENVSFFGTILSIPNDSNTNNVKCSG------CGTEMVYDSGSRLITLPEGGKA 313

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

 Score = 129 (50.5 bits), Expect = 4.4e-08, Sum P(2) = 4.4e-08
 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

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

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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	0.7735	0.8408	0.8641	yes	no
Q8GYC7	PGL1B_ARATH	No assigned EC number	0.7777	0.8438	0.8977	no	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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00001064001 SubName- Full=Chromosome chr2 scaffold_112, whole genome shotgun sequence; (326 aa) (Vitis vinifera)

Predicted Functional Partners:

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

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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	333
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	94.99
cd00114	307	LIGANc NAD+ dependent DNA ligase adenylation domai	94.46
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	94.44
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	93.88
PF01653	315	DNA_ligase_aden: NAD-dependent DNA ligase adenylat	93.74
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	93.7
smart00532	441	LIGANc Ligase N family.	92.81
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	92.69
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	92.59
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	92.54
PRK00420	112	hypothetical protein; Validated	91.6
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	91.46
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	89.97
cd00114	307	LIGANc NAD+ dependent DNA ligase adenylation domai	89.77
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	89.77
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	89.62
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	89.56
PF13248	26	zf-ribbon_3: zinc-ribbon domain	89.56
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	89.27
PF01653	315	DNA_ligase_aden: NAD-dependent DNA ligase adenylat	87.71
smart00532	441	LIGANc Ligase N family.	87.56
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	87.17
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	86.98
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	86.34
smart00531	147	TFIIE Transcription initiation factor IIE.	86.08
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	85.76
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	85.03
PRK05978	148	hypothetical protein; Provisional	84.97
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	84.53
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	84.5
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	83.63
PHA00626	59	hypothetical protein	81.82
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	81.55
PRK02935	110	hypothetical protein; Provisional	81.24
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	80.61
PLN00209	86	ribosomal protein S27; Provisional	80.25

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=94.99  E-value=0.026  Score=59.16  Aligned_cols=49  Identities=35%  Similarity=0.531  Sum_probs=34.5

Q ss_pred             hHhhhhhcCCe---eEEeChhh--HH--HHHH-----HHhhhc-CCCccChHHHHHHHHHHh
Q 019981          125 LKEELMWEGSS---VVMLSSAE--QK--FLEA-----SMAYVA-GKPIMSDEEYDKLKQKLK  173 (333)
Q Consensus       125 LkEeL~weGSs---vv~L~~~E--q~--fLEA-----~~AY~s-GkPimsDeeFD~LK~kLk  173 (333)
                      |---|.|..|-   |.+++..|  ++  .|.+     -.+||. |+|+|||+|||+|..+|+
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            34457898887   55666644  11  2222     246775 999999999999999997

>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain

Probab=94.46  E-value=0.038  Score=53.62  Aligned_cols=27  Identities=33%  Similarity=0.641  Sum_probs=22.9

Q ss_pred             HHHHhhhc-CCCccChHHHHHHHHHHhh
Q 019981          148 EASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       148 EA~~AY~s-GkPimsDeeFD~LK~kLk~  174 (333)
                      ++-.+||. |+|+|||+|||.|.++|+.
T Consensus        12 ~~~~~YY~~~~p~IsD~eYD~L~~~L~~   39 (307)
T cd00114          12 KHDYRYYVLDEPSVSDAEYDRLYRELRA   39 (307)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            34456887 9999999999999999973

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.

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=94.44  E-value=0.039  Score=39.28  Aligned_cols=37  Identities=22%  Similarity=0.613  Sum_probs=26.1

Q ss_pred             CCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEeccceeee
Q 019981          274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLIT  326 (333)
Q Consensus       274 ~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R~it  326 (333)
                      -|||||.++-. -.       ..  ..++|+.      ||..+.|....++|.
T Consensus         5 ~C~~CG~~~~~-~~-------~~--~~~~Cp~------CG~~~~~~~~~~~v~   41 (46)
T PRK00398          5 KCARCGREVEL-DE-------YG--TGVRCPY------CGYRILFKERPPVVK   41 (46)
T ss_pred             ECCCCCCEEEE-CC-------CC--CceECCC------CCCeEEEccCCCcce
Confidence            59999997543 11       11  1689999      999999986666553

>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins

Probab=93.88  E-value=0.058  Score=46.59  Aligned_cols=64  Identities=19%  Similarity=0.447  Sum_probs=37.1

Q ss_pred             hHHHHHhhhhHHHHHHHHHHhhhhc--ceeeeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEe
Q 019981          242 FIFTWFAAVPLIVYLSQSLTKLIVR--ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYD  319 (333)
Q Consensus       242 fi~t~~~~~P~i~~~a~~Lt~l~~~--D~~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~  319 (333)
                      ++.+.++.+.++..+++...=.|.+  -.-+.--.|||||.+....=         +..   -|.+      |+++|+.|
T Consensus        37 ~im~ifmllG~L~~l~S~~VYfwIGmlStkav~V~CP~C~K~TKmLG---------r~D---~CM~------C~~pLTLd   98 (114)
T PF11023_consen   37 IIMVIFMLLGLLAILASTAVYFWIGMLSTKAVQVECPNCGKQTKMLG---------RVD---ACMH------CKEPLTLD   98 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcccceeeECCCCCChHhhhc---------hhh---ccCc------CCCcCccC
Confidence            4444455555555444443333321  11223334999999987652         222   6877      99999999


Q ss_pred             ccce
Q 019981          320 SNTR  323 (333)
Q Consensus       320 tk~R  323 (333)
                      +..+
T Consensus        99 ~~le  102 (114)
T PF11023_consen   99 PSLE  102 (114)
T ss_pred             chhh
Confidence            7654

; GO: 0005887 integral to plasma membrane

>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=93.74  E-value=0.072  Score=51.86  Aligned_cols=25  Identities=52%  Similarity=0.875  Sum_probs=21.6

Q ss_pred             HHHhhhc-CCCccChHHHHHHHHHHh
Q 019981          149 ASMAYVA-GKPIMSDEEYDKLKQKLK  173 (333)
Q Consensus       149 A~~AY~s-GkPimsDeeFD~LK~kLk  173 (333)
                      +-.+||. |+|+|||+|||.|..+|+
T Consensus        17 ~~~~YY~~~~p~isD~eYD~l~~~L~   42 (315)
T PF01653_consen   17 HNYAYYNLGEPIISDAEYDQLFRELK   42 (315)
T ss_dssp             HHHHHHTTSSSSSSHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            3457777 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 ....

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

Probab=93.70  E-value=0.071  Score=42.33  Aligned_cols=45  Identities=29%  Similarity=0.659  Sum_probs=36.4

Q ss_pred             eeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEeccceeeecCC
Q 019981          270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITLPE  329 (333)
Q Consensus       270 iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R~itl~~  329 (333)
                      -|+--||.||.|--.|         .+++..|+|..      ||+.|..-+.-++...++
T Consensus        17 Fl~VkCpdC~N~q~vF---------shast~V~C~~------CG~~l~~PTGGka~i~~~   61 (67)
T COG2051          17 FLRVKCPDCGNEQVVF---------SHASTVVTCLI------CGTTLAEPTGGKAKISGK   61 (67)
T ss_pred             EEEEECCCCCCEEEEe---------ccCceEEEecc------cccEEEecCCCeEEeeee
Confidence            4667799999998888         45777889987      999999888877766654

>smart00532 LIGANc Ligase N family

Probab=92.81  E-value=0.11  Score=52.99  Aligned_cols=25  Identities=44%  Similarity=0.769  Sum_probs=22.0

Q ss_pred             HHHhhhc-CCCccChHHHHHHHHHHh
Q 019981          149 ASMAYVA-GKPIMSDEEYDKLKQKLK  173 (333)
Q Consensus       149 A~~AY~s-GkPimsDeeFD~LK~kLk  173 (333)
                      +-.+||. |+|+|||+|||+|..+|+
T Consensus        15 ~~~~YY~~~~p~IsD~eYD~L~~eL~   40 (441)
T smart00532       15 HDYRYYVLDAPIISDAEYDRLMRELK   40 (441)
T ss_pred             HHHHHHhcCCCCCChHHHHHHHHHHH
Confidence            3456886 999999999999999997

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=92.69  E-value=0.12  Score=54.87  Aligned_cols=29  Identities=31%  Similarity=0.556  Sum_probs=24.4

Q ss_pred             HHHHHHhhhc-CCCccChHHHHHHHHHHhh
Q 019981          146 FLEASMAYVA-GKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       146 fLEA~~AY~s-GkPimsDeeFD~LK~kLk~  174 (333)
                      .-++-.+||. |+|+|||+|||.|.++|+.
T Consensus         5 l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~   34 (652)
T TIGR00575         5 IRHHDYRYYVLDEPSISDAEYDRLYRELQE   34 (652)
T ss_pred             HHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            3445667886 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.

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=92.59  E-value=0.12  Score=55.20  Aligned_cols=26  Identities=38%  Similarity=0.629  Sum_probs=22.9

Q ss_pred             HHHHhhh-cCCCccChHHHHHHHHHHh
Q 019981          148 EASMAYV-AGKPIMSDEEYDKLKQKLK  173 (333)
Q Consensus       148 EA~~AY~-sGkPimsDeeFD~LK~kLk  173 (333)
                      ++-.+|| .|+|+|||+|||.|.++|+
T Consensus        18 ~~~~~YY~~~~p~IsD~eYD~L~~~L~   44 (665)
T PRK07956         18 HHAYAYYVLDAPSISDAEYDRLYRELV   44 (665)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            3445788 9999999999999999997

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=92.54  E-value=0.21  Score=37.88  Aligned_cols=44  Identities=27%  Similarity=0.538  Sum_probs=28.4

Q ss_pred             eecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEecc--ceeeecC
Q 019981          271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSN--TRLITLP  328 (333)
Q Consensus       271 LKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk--~R~itl~  328 (333)
                      |+..||.||+++--        +..-.--.+.|+.      ||..|+.-++  .||-..|
T Consensus         1 ~~~~CP~CG~~iev--------~~~~~GeiV~Cp~------CGaeleVv~~~p~~L~~ap   46 (54)
T TIGR01206         1 MQFECPDCGAEIEL--------ENPELGELVICDE------CGAELEVVSLDPLRLEAAP   46 (54)
T ss_pred             CccCCCCCCCEEec--------CCCccCCEEeCCC------CCCEEEEEeCCCCEEEeCc
Confidence            36789999998732        2222233678887      9999998755  4443333

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.

>PRK00420 hypothetical protein; Validated

Probab=91.60  E-value=0.17  Score=43.44  Aligned_cols=46  Identities=17%  Similarity=0.457  Sum_probs=32.9

Q ss_pred             HHHHHhhhhcceeeeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEe
Q 019981          257 SQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYD  319 (333)
Q Consensus       257 a~~Lt~l~~~D~~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~  319 (333)
                      ++.+..++++=...|-..||.||.+.|.+-.           ..+-|++      ||..+...
T Consensus         8 ~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~lk~-----------g~~~Cp~------Cg~~~~v~   53 (112)
T PRK00420          8 VKKAAELLLKGAKMLSKHCPVCGLPLFELKD-----------GEVVCPV------HGKVYIVK   53 (112)
T ss_pred             HHHHHHHHHhHHHHccCCCCCCCCcceecCC-----------CceECCC------CCCeeeec
Confidence            3445556666566688999999999887632           2567877      99977764

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=91.46  E-value=0.16  Score=34.41  Aligned_cols=36  Identities=25%  Similarity=0.587  Sum_probs=22.9

Q ss_pred             ecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEE
Q 019981          272 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVY  318 (333)
Q Consensus       272 KG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f  318 (333)
                      +-.||+||+.+..=-..   +  .....+++|++      ||..+..
T Consensus         2 ~~~CP~C~~~~~v~~~~---~--~~~~~~v~C~~------C~~~~~~   37 (38)
T TIGR02098         2 RIQCPNCKTSFRVVDSQ---L--GANGGKVRCGK------CGHVWYA   37 (38)
T ss_pred             EEECCCCCCEEEeCHHH---c--CCCCCEEECCC------CCCEEEe
Confidence            45799999985422111   1  12223799999      9998764

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=89.97  E-value=0.14  Score=32.51  Aligned_cols=9  Identities=67%  Similarity=1.497  Sum_probs=8.0

Q ss_pred             CCCCccccc
Q 019981          275 CPNCGTENV  283 (333)
Q Consensus       275 CPNCGeEv~  283 (333)
                      ||+||.+|-
T Consensus         2 Cp~CG~~~~   10 (23)
T PF13240_consen    2 CPNCGAEIE   10 (23)
T ss_pred             CcccCCCCC
Confidence            999999874

>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain

Probab=89.77  E-value=0.39  Score=46.73  Aligned_cols=35  Identities=26%  Similarity=0.366  Sum_probs=27.8

Q ss_pred             hHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           96 GELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        96 ge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      -++...--.+=..||..+.+++||+|||.|.++|.
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.

>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements

Probab=89.77  E-value=0.14  Score=49.40  Aligned_cols=51  Identities=25%  Similarity=0.511  Sum_probs=24.7

Q ss_pred             HHHHHHhhhhcceeeeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEeccc
Q 019981          256 LSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNT  322 (333)
Q Consensus       256 ~a~~Lt~l~~~D~~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~  322 (333)
                      .|..||..|    |+=.+.|||||.+..+=|      +.|+....+.|++      |+...+..++.
T Consensus        19 ~aRVltE~W----v~~n~yCP~Cg~~~L~~f------~NN~PVaDF~C~~------C~eeyELKSk~   69 (254)
T PF06044_consen   19 IARVLTEDW----VAENMYCPNCGSKPLSKF------ENNRPVADFYCPN------CNEEYELKSKK   69 (254)
T ss_dssp             HHHHHHHHH----HHHH---TTT--SS-EE--------------EEE-TT------T--EEEEEEEE
T ss_pred             hhHHHHHHH----HHHCCcCCCCCChhHhhc------cCCCccceeECCC------CchHHhhhhhc
Confidence            344455544    455678999999977666      5699999999999      99998888775

The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=89.62  E-value=0.35  Score=51.96  Aligned_cols=25  Identities=28%  Similarity=0.610  Sum_probs=21.7

Q ss_pred             HHHhhh-cCCCccChHHHHHHHHHHh
Q 019981          149 ASMAYV-AGKPIMSDEEYDKLKQKLK  173 (333)
Q Consensus       149 A~~AY~-sGkPimsDeeFD~LK~kLk  173 (333)
                      +-.+|| .|+|+|||+|||.|.++|+
T Consensus        46 ~~~~YY~~~~p~IsD~eYD~L~~eL~   71 (689)
T PRK14351         46 HDHRYYVEADPVIADRAYDALFARLQ   71 (689)
T ss_pred             HHHHHHhCCCCCCChHHHHHHHHHHH
Confidence            345687 5799999999999999997

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=89.56  E-value=0.27  Score=38.18  Aligned_cols=41  Identities=32%  Similarity=0.735  Sum_probs=31.8

Q ss_pred             eeeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEecccee
Q 019981          269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRL  324 (333)
Q Consensus       269 ~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R~  324 (333)
                      --|+--||.|+.|...|         ..++..|+|.+      ||+.|.--+..++
T Consensus         8 ~F~~VkCp~C~n~q~vF---------sha~t~V~C~~------Cg~~L~~PtGGKa   48 (59)
T PRK00415          8 RFLKVKCPDCGNEQVVF---------SHASTVVRCLV------CGKTLAEPTGGKA   48 (59)
T ss_pred             eEEEEECCCCCCeEEEE---------ecCCcEEECcc------cCCCcccCCCcce
Confidence            34677899999999888         45777899988      9999876554443

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=89.56  E-value=0.16  Score=32.73  Aligned_cols=10  Identities=60%  Similarity=1.168  Sum_probs=8.2

Q ss_pred             cCCCCCcccc
Q 019981          273 GPCPNCGTEN  282 (333)
Q Consensus       273 G~CPNCGeEv  282 (333)
                      -.|||||.+|
T Consensus         3 ~~Cp~Cg~~~   12 (26)
T PF13248_consen    3 MFCPNCGAEI   12 (26)
T ss_pred             CCCcccCCcC
Confidence            3699999976

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=89.27  E-value=0.17  Score=39.58  Aligned_cols=34  Identities=26%  Similarity=0.550  Sum_probs=21.6

Q ss_pred             ceeeeecCCCCCccccceeccccccccCCCCccceeCCC
Q 019981          267 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSN  305 (333)
Q Consensus       267 D~~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~  305 (333)
                      +--+.+=+||||||++--  +   .-....-.|..+|++
T Consensus        22 ~e~~v~F~CPnCGe~~I~--R---c~~CRk~g~~Y~Cp~   55 (61)
T COG2888          22 GETAVKFPCPNCGEVEIY--R---CAKCRKLGNPYRCPK   55 (61)
T ss_pred             CCceeEeeCCCCCceeee--h---hhhHHHcCCceECCC
Confidence            334677899999965431  1   113445567889988

>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=87.71  E-value=0.7  Score=45.12  Aligned_cols=36  Identities=33%  Similarity=0.553  Sum_probs=28.3

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      +-++...-..+=..||..+.++|||+|||.|.++|.
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            344555555666789999999999999999998863

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=87.56  E-value=0.59  Score=47.82  Aligned_cols=36  Identities=25%  Similarity=0.420  Sum_probs=28.7

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      +-++...-..+-..||..+.+++||+|||.|.++|.
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            445555555566678889999999999999999995

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=87.17  E-value=0.67  Score=49.76  Aligned_cols=24  Identities=29%  Similarity=0.463  Sum_probs=20.8

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHh
Q 019981          150 SMAYV-AGKPIMSDEEYDKLKQKLK  173 (333)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~kLk  173 (333)
                      -.+|| .|+|+|||++||.|..+|+
T Consensus        20 ~~~YY~~~~p~IsD~~YD~L~~eL~   44 (669)
T PRK14350         20 DKEYYVDSSPSVEDFTYDKALLRLQ   44 (669)
T ss_pred             HHHHHhCCCCCCChHHHHHHHHHHH
Confidence            35677 5799999999999999996

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=86.98  E-value=0.32  Score=37.81  Aligned_cols=30  Identities=27%  Similarity=0.477  Sum_probs=19.2

Q ss_pred             eeecCCCCCccc-cceeccccccccCCCCccceeCCC
Q 019981          270 ILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSN  305 (333)
Q Consensus       270 iLKG~CPNCGeE-v~aFfgtilsv~s~~~~n~vkC~~  305 (333)
                      +.+=.|||||++ +.-=-      .-..-.|.++|++
T Consensus        23 ~~~F~CPnCG~~~I~RC~------~CRk~~~~Y~CP~   53 (59)
T PRK14890         23 AVKFLCPNCGEVIIYRCE------KCRKQSNPYTCPK   53 (59)
T ss_pred             cCEeeCCCCCCeeEeech------hHHhcCCceECCC
Confidence            455689999998 44321      2344557888888

>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=86.34  E-value=1.1  Score=34.32  Aligned_cols=42  Identities=19%  Similarity=0.508  Sum_probs=27.4

Q ss_pred             eeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEeccceeee
Q 019981          270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLIT  326 (333)
Q Consensus       270 iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R~it  326 (333)
                      -|+--||.|+++...|         ..++..|+|.+      |++.|.--+..++..
T Consensus         5 Fm~VkCp~C~~~q~vF---------Sha~t~V~C~~------Cg~~L~~PtGGKa~l   46 (55)
T PF01667_consen    5 FMDVKCPGCYNIQTVF---------SHAQTVVKCVV------CGTVLAQPTGGKARL   46 (55)
T ss_dssp             EEEEE-TTT-SEEEEE---------TT-SS-EE-SS------STSEEEEE-SSSEEE
T ss_pred             EEEEECCCCCCeeEEE---------ecCCeEEEccc------CCCEecCCCCcCeEE
Confidence            3566799999999887         55777899988      999998776654443

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

>smart00531 TFIIE Transcription initiation factor IIE

Probab=86.08  E-value=0.43  Score=41.41  Aligned_cols=55  Identities=24%  Similarity=0.453  Sum_probs=32.0

Q ss_pred             HHhhhhcceeeeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEecccee
Q 019981          260 LTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRL  324 (333)
Q Consensus       260 Lt~l~~~D~~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R~  324 (333)
                      |..-+..+.--..=-|||||.. |+|-- ....  +..+.++.|++      ||..|++.-....
T Consensus        87 L~~~l~~e~~~~~Y~Cp~C~~~-y~~~e-a~~~--~d~~~~f~Cp~------Cg~~l~~~dn~~~  141 (147)
T smart00531       87 LEDKLEDETNNAYYKCPNCQSK-YTFLE-ANQL--LDMDGTFTCPR------CGEELEEDDNSEP  141 (147)
T ss_pred             HHHHHhcccCCcEEECcCCCCE-eeHHH-HHHh--cCCCCcEECCC------CCCEEEEcCchhh
Confidence            4444433333334459999954 44532 2211  12355699999      9999999865444

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=85.76  E-value=0.76  Score=48.55  Aligned_cols=36  Identities=28%  Similarity=0.535  Sum_probs=28.6

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      +-++...-..+=..||..+.|++||+|||.|.+||.
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            445555555556679999999999999999999985

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=85.03  E-value=0.58  Score=32.90  Aligned_cols=32  Identities=31%  Similarity=0.828  Sum_probs=22.1

Q ss_pred             CCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEec
Q 019981          274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDS  320 (333)
Q Consensus       274 ~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~t  320 (333)
                      -||+||... ..+        .....++-|.+      ||..++.+.
T Consensus         2 ~Cp~Cg~~~-~~~--------D~~~g~~vC~~------CG~Vl~e~~   33 (43)
T PF08271_consen    2 KCPNCGSKE-IVF--------DPERGELVCPN------CGLVLEENI   33 (43)
T ss_dssp             SBTTTSSSE-EEE--------ETTTTEEEETT------T-BBEE-TT
T ss_pred             CCcCCcCCc-eEE--------cCCCCeEECCC------CCCEeeccc
Confidence            499999977 233        34566778998      999988663

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>PRK05978 hypothetical protein; Provisional

Probab=84.97  E-value=0.44  Score=42.58  Aligned_cols=34  Identities=29%  Similarity=0.839  Sum_probs=23.3

Q ss_pred             eecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEe
Q 019981          271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYD  319 (333)
Q Consensus       271 LKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~  319 (333)
                      |+|-||+||+.-.  |++-+.+       +-+|++      ||..+++.
T Consensus        32 l~grCP~CG~G~L--F~g~Lkv-------~~~C~~------CG~~~~~~   65 (148)
T PRK05978         32 FRGRCPACGEGKL--FRAFLKP-------VDHCAA------CGEDFTHH   65 (148)
T ss_pred             HcCcCCCCCCCcc--ccccccc-------CCCccc------cCCccccC
Confidence            6899999998643  3333322       446776      99988775

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=84.53  E-value=1.1  Score=48.35  Aligned_cols=36  Identities=19%  Similarity=0.390  Sum_probs=30.3

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      +-++...--.+=..||..+.+++||+|||.|.++|.
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

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=84.50  E-value=1.1  Score=48.01  Aligned_cols=36  Identities=31%  Similarity=0.504  Sum_probs=28.2

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      +-++...--.+=..||..+.+++||+|||.|.++|.
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            344444555555678889999999999999999986

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=83.63  E-value=0.85  Score=34.38  Aligned_cols=37  Identities=24%  Similarity=0.506  Sum_probs=25.9

Q ss_pred             CCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEec
Q 019981          274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDS  320 (333)
Q Consensus       274 ~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~t  320 (333)
                      .||.||+.+-...-.     |.+++.-+     -||.||-+++.|.-
T Consensus         2 ~CPyCge~~~~~iD~-----s~~~Q~yi-----EDC~vCC~PI~~~v   38 (52)
T PF14255_consen    2 QCPYCGEPIEILIDP-----SAGDQEYI-----EDCQVCCRPIEVQV   38 (52)
T ss_pred             CCCCCCCeeEEEEec-----CCCCeeEE-----eehhhcCCccEEEE
Confidence            599999999988743     33333222     35667999999873

>PHA00626 hypothetical protein

Probab=81.82  E-value=1.1  Score=34.92  Aligned_cols=35  Identities=31%  Similarity=0.722  Sum_probs=22.9

Q ss_pred             CCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEe
Q 019981          274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYD  319 (333)
Q Consensus       274 ~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~  319 (333)
                      .||+||..+..==|.+     +.-.++.+|+.      ||-..+-|
T Consensus         2 ~CP~CGS~~Ivrcg~c-----r~~snrYkCkd------CGY~ft~~   36 (59)
T PHA00626          2 SCPKCGSGNIAKEKTM-----RGWSDDYVCCD------CGYNDSKD   36 (59)
T ss_pred             CCCCCCCceeeeecee-----cccCcceEcCC------CCCeechh
Confidence            5999999655433332     34467888877      98765544

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=81.55  E-value=1.9  Score=31.26  Aligned_cols=34  Identities=32%  Similarity=0.819  Sum_probs=25.1

Q ss_pred             CCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEe-cccee
Q 019981          274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYD-SNTRL  324 (333)
Q Consensus       274 ~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~-tk~R~  324 (333)
                      -|.+||.||..-           ....++|++      ||..+.|- ++.|.
T Consensus         4 ~C~~Cg~~~~~~-----------~~~~irC~~------CG~rIlyK~R~~~~   38 (44)
T smart00659        4 ICGECGRENEIK-----------SKDVVRCRE------CGYRILYKKRTKRL   38 (44)
T ss_pred             ECCCCCCEeecC-----------CCCceECCC------CCceEEEEeCCCce
Confidence            499999997632           235689999      99999987 34443

present in RNA polymerase I, II and III

>PRK02935 hypothetical protein; Provisional

Probab=81.24  E-value=1.6  Score=37.77  Aligned_cols=36  Identities=17%  Similarity=0.468  Sum_probs=25.7

Q ss_pred             eeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEeccce
Q 019981          270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTR  323 (333)
Q Consensus       270 iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R  323 (333)
                      +..-.||||+.+..--=+.         .   -|-+      |+++|+.|...+
T Consensus        68 avqV~CP~C~K~TKmLGrv---------D---~CM~------C~~PLTLd~~le  103 (110)
T PRK02935         68 AVQVICPSCEKPTKMLGRV---------D---ACMH------CNQPLTLDRSLE  103 (110)
T ss_pred             ceeeECCCCCchhhhccce---------e---ecCc------CCCcCCcCcccc
Confidence            3444899999988754222         1   5777      999999987654

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=80.61  E-value=1.5  Score=46.79  Aligned_cols=27  Identities=26%  Similarity=0.411  Sum_probs=23.0

Q ss_pred             HHHHHhhhcCccccChHHHhhhHhhhh
Q 019981          104 QALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus       104 ~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      .+-..||..+.|++||+|||.|.++|.
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.

>PLN00209 ribosomal protein S27; Provisional

Probab=80.25  E-value=2  Score=35.77  Aligned_cols=45  Identities=16%  Similarity=0.408  Sum_probs=34.5

Q ss_pred             cceeeeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEeccceee
Q 019981          266 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLI  325 (333)
Q Consensus       266 ~D~~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R~i  325 (333)
                      .|---|+--||.|+.+...|         ..++..|.|.+      ||+.|.--+..+..
T Consensus        30 PnS~Fm~VkCp~C~n~q~VF---------ShA~t~V~C~~------Cg~~L~~PTGGKa~   74 (86)
T PLN00209         30 PNSFFMDVKCQGCFNITTVF---------SHSQTVVVCGS------CQTVLCQPTGGKAR   74 (86)
T ss_pred             CCCEEEEEECCCCCCeeEEE---------ecCceEEEccc------cCCEeeccCCCCeE
Confidence            34456788899999999888         45777889988      99999766654443

---

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	333
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05

>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 = 49.9 bits (118), Expect = 7e-07
 Identities = 34/199 (17%), Positives = 66/199 (33%), Gaps = 52/199 (26%)

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-GLFFFLDDITGFEITYL-- 233
           ++  +      R +          L+  LL + PA  V + G+        G   T++  
Sbjct: 124 QVFAKYNVS--RLQPYLK------LRQALLELRPAKNVLIDGVL-------GSGKTWVAL 168

Query: 234 -----LELPEPFSF-IFTW 246
                 ++     F IF W
Sbjct: 169 DVCLSYKVQCKMDFKIF-W 186

>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 = 44.5 bits (104), Expect = 4e-05
 Identities = 58/359 (16%), Positives = 101/359 (28%), Gaps = 116/359 (32%)

Query: 4   KVASGFTP-QAQRVFA----VPVQK-PAAALAPFPSSSRAHSNSNTQFNGRQFTVRRRSF 57
             +   TP + + +         Q  P   L   P   R  S               R  
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNP---RRLS---------IIAESIRDG 340

Query: 58  VLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVM 117
                AT D    V  D++  + I+         + SL  LE    +      ++  +V 
Sbjct: 341 ----LATWDNWKHVNCDKL--TTII---------ESSLNVLEPAEYRK----MFDRLSVF 381

Query: 118 SNEEFDNLKEELM---WEGSSVVMLSSAEQKFLEASMAYVAGKP----IMSDEEYDKLKQ 170
                 ++   L+   W       +     K  + S+     K     I S   Y +LK 
Sbjct: 382 PPSA--HIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS--IYLELKV 437

Query: 171 KLKMEGS--EIVVEGPRCSLRSRKVY--SDLSVDYLKMLLLNVPATVVALGLFFFL---- 222
           KL+ E +    +V+         K +   DL   YL                +  +    
Sbjct: 438 KLENEYALHRSIVD----HYNIPKTFDSDDLIPPYLDQYF------------YSHIGHHL 481

Query: 223 ------DDITGFEITYLLELPEPFSFI--------FTWFAAVPLIVYLSQSLTKLIVRES 268
                 + +T F + +L      F F+          W A+  ++  L Q    L   + 
Sbjct: 482 KNIEHPERMTLFRMVFL-----DFRFLEQKIRHDSTAWNASGSILNTLQQ----LKFYKP 532

Query: 269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITL 327
            I    C N        +  ++        N I    L F       ++    T L+ +
Sbjct: 533 YI----CDNDPK-----YERLV--------NAI----LDFLPKIEENLICSKYTDLLRI 570

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	333
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	93.35
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	92.48
4glw_A	305	DNA ligase; inhibitor, ligase-ligase inhibitor com	92.21
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	91.5
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	91.4
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	91.29
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	91.14
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	90.32
4glw_A	305	DNA ligase; inhibitor, ligase-ligase inhibitor com	87.48
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	86.44
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	85.97
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	85.72
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	85.28
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	85.26
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	85.17
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	85.16
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	84.89
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	84.74
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	83.77
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	80.18

>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=93.35  E-value=0.066  Score=51.32  Aligned_cols=25  Identities=36%  Similarity=0.643  Sum_probs=21.6

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 019981          150 SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       150 ~~AY~s-GkPimsDeeFD~LK~kLk~  174 (333)
                      -.+||. |+|+|||+|||+|.++|+.
T Consensus        17 ~~~YY~~d~p~IsD~eYD~L~~eL~~   42 (322)
T 3uq8_A           17 EYEYHVLDNPSVPDSEYDRLFHQLKA   42 (322)
T ss_dssp             HHHHHTSSCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            457875 9999999999999998865

>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=92.48  E-value=0.093  Score=50.25  Aligned_cols=25  Identities=40%  Similarity=0.620  Sum_probs=21.0

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 019981          150 SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       150 ~~AY~s-GkPimsDeeFD~LK~kLk~  174 (333)
                      -.+||. |+|+|||+|||+|..+|+.
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            346775 9999999999999998864

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

Probab=92.21  E-value=0.026  Score=53.33  Aligned_cols=25  Identities=36%  Similarity=0.632  Sum_probs=3.8

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 019981          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~kLk~  174 (333)
                      -.+|| .|+|+|||+|||.|..+|+.
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            35777 59999999999999998864

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

Probab=91.50  E-value=0.13  Score=49.29  Aligned_cols=24  Identities=38%  Similarity=0.736  Sum_probs=21.2

Q ss_pred             Hhhh-cCCCccChHHHHHHHHHHhh
Q 019981          151 MAYV-AGKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       151 ~AY~-sGkPimsDeeFD~LK~kLk~  174 (333)
                      .+|| .|+|+|||+|||+|..+|+.
T Consensus        29 ~~YY~~d~p~IsD~eYD~L~~eL~~   53 (328)
T 1zau_A           29 FRYYVRDAPIISDAEFDELLRRLEA   53 (328)
T ss_dssp             HHHTTTCCCSSCTHHHHHHHHHHHH
T ss_pred             HHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            4677 69999999999999999975

>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=91.40  E-value=0.14  Score=49.17  Aligned_cols=24  Identities=29%  Similarity=0.465  Sum_probs=21.2

Q ss_pred             Hhhh-cCCCccChHHHHHHHHHHhh
Q 019981          151 MAYV-AGKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       151 ~AY~-sGkPimsDeeFD~LK~kLk~  174 (333)
                      .+|| .|+|+|||+|||+|..+|+.
T Consensus        27 ~~YY~~d~p~IsD~eYD~L~~eL~~   51 (332)
T 1ta8_A           27 HEYYVKDQPSVEDYVYDRLYKELVD   51 (332)
T ss_dssp             HHHHTSSCCSSCHHHHHHHHHHHHH
T ss_pred             HHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            4676 69999999999999999874

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

Probab=91.29  E-value=0.14  Score=48.99  Aligned_cols=24  Identities=38%  Similarity=0.654  Sum_probs=21.1

Q ss_pred             Hhhh-cCCCccChHHHHHHHHHHhh
Q 019981          151 MAYV-AGKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       151 ~AY~-sGkPimsDeeFD~LK~kLk~  174 (333)
                      .+|| .|+|+|||+|||+|..+|+.
T Consensus        22 ~~YY~~d~p~IsD~eYD~L~~eL~~   46 (318)
T 1b04_A           22 YEYYVLDRPSVPDAEYDRLMQELIA   46 (318)
T ss_dssp             HHHHTTCSCCSSCHHHHHHHHHHHH
T ss_pred             HHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            4676 69999999999999999874

>4esj_A Type-2 restriction enzyme DPNI; restriction endonuclease-DNA complex, type IIM, type IIE, RE enzyme, DPNI; HET: DNA 6MA; 2.05A {Streptococcus pneumoniae}

Probab=91.14  E-value=0.091  Score=49.34  Aligned_cols=51  Identities=24%  Similarity=0.520  Sum_probs=37.4

Q ss_pred             HHHHHHhhhhcceeeeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEeccc
Q 019981          256 LSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNT  322 (333)
Q Consensus       256 ~a~~Lt~l~~~D~~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~  322 (333)
                      .|..||..|+    +=.+.|||||....+=|      +.|+......|++      |....|.-++.
T Consensus        22 ~aRVLTE~Wv----~~n~yCPnCG~~~l~~f------~nN~PVaDF~C~~------C~EeyELKSk~   72 (257)
T 4esj_A           22 KARILTEDWV----YRQSYCPNCGNNPLNHF------ENNRPVADFYCNH------CSEEFELKSKK   72 (257)
T ss_dssp             HHHHHHHHHH----HHHCCCTTTCCSSCEEC----------CCCEEECTT------TCCEEEEEEEE
T ss_pred             eehhhhHHHH----HHCCcCCCCCChhhhhc------cCCCcccccccCC------cchhheecccc
Confidence            4566676664    44678999999877666      5699999999999      99999988774

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

Probab=90.32  E-value=0.15  Score=52.26  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=21.5

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 019981          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~kLk~  174 (333)
                      -.+|| .|+|+|||+|||+|..+|+.
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            35677 59999999999999999874

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

Probab=87.48  E-value=0.096  Score=49.46  Aligned_cols=36  Identities=25%  Similarity=0.425  Sum_probs=4.0

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      +.++...--.+=.+||..+.|++||+|||.|.+||.
T Consensus         5 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~   40 (305)
T 4glw_A            5 MNELVALLNRYATEYYTSDNPSVSDSEYDRLYRELV   40 (305)
T ss_dssp             HHC-----------------------------CHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            334444444556789999999999999999998864

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=86.44  E-value=0.58  Score=36.07  Aligned_cols=39  Identities=28%  Similarity=0.637  Sum_probs=31.4

Q ss_pred             eecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEecccee
Q 019981          271 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRL  324 (333)
Q Consensus       271 LKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R~  324 (333)
                      |+--||.|+++...|         ..++..|+|.+      |++.|.--+..++
T Consensus         6 m~VKCp~C~niq~VF---------ShA~tvV~C~~------Cg~~L~~PTGGKA   44 (66)
T 1qxf_A            6 VKVKCPDCEHEQVIF---------DHPSTIVKCII------CGRTVAEPTGGKG   44 (66)
T ss_dssp             EEEECTTTCCEEEEE---------SSCSSCEECSS------SCCEEEECCSSSC
T ss_pred             EEEECCCCCCceEEE---------ecCceEEEccc------CCCEEeecCCcce
Confidence            677799999999888         55777899988      9999987665443

>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=85.97  E-value=0.76  Score=35.08  Aligned_cols=42  Identities=29%  Similarity=0.638  Sum_probs=32.6

Q ss_pred             eeeeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEecccee
Q 019981          268 SLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRL  324 (333)
Q Consensus       268 ~~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R~  324 (333)
                      ---++--||.|+++...|         ..++..|+|.+      |++.|.--+..+.
T Consensus        11 S~Fm~VkCp~C~~~q~VF---------Sha~t~V~C~~------Cgt~L~~PTGGKa   52 (63)
T 3j20_W           11 SRFLRVKCIDCGNEQIVF---------SHPATKVRCLI------CGATLVEPTGGKG   52 (63)
T ss_dssp             CCEEEEECSSSCCEEEEE---------SSCSSCEECSS------SCCEEEECCSSSC
T ss_pred             CcEEEEECCCCCCeeEEE---------ecCCeEEEccC------cCCEEecCCCCcE
Confidence            345677899999999887         45777899988      9999987665443

>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=85.72  E-value=0.65  Score=44.48  Aligned_cols=35  Identities=20%  Similarity=0.294  Sum_probs=27.5

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL  129 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL  129 (333)
                      +.++...--.+=.+||..+.|++||+|||.|..||
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            34455555566678999999999999999998875

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

Probab=85.28  E-value=0.67  Score=44.44  Aligned_cols=37  Identities=24%  Similarity=0.406  Sum_probs=29.9

Q ss_pred             chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        94 slge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      -+.++...--.+=.+||..+.|++||+|||.|..+|.
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            4566666666666789999999999999999999864

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

Probab=85.26  E-value=0.67  Score=44.26  Aligned_cols=36  Identities=22%  Similarity=0.388  Sum_probs=28.4

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      +.++...--.+=.+||..+.|++||+|||.|..+|.
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            445555555556678999999999999999999864

>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=85.17  E-value=0.73  Score=44.11  Aligned_cols=35  Identities=29%  Similarity=0.459  Sum_probs=27.5

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL  129 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL  129 (333)
                      +.++...--++=.+||..+.|++||+|||.|..||
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            44555555556667888999999999999998875

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

Probab=85.16  E-value=0.52  Score=49.12  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=21.4

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 019981          150 SMAYV-AGKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~kLk~  174 (333)
                      -.+|| .++|+|||+|||+|.++|+.
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            34666 68999999999999999875

>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=84.89  E-value=0.75  Score=44.23  Aligned_cols=37  Identities=22%  Similarity=0.389  Sum_probs=28.8

Q ss_pred             chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        94 slge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      -+.++...--.+=.+||..+.|++||+|||.|..+|.
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            3455555555556678999999999999999999864

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

Probab=84.74  E-value=0.63  Score=47.74  Aligned_cols=36  Identities=22%  Similarity=0.288  Sum_probs=28.6

Q ss_pred             hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        95 lge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      +.++...--.+=.+||..+.|++||+|||.|.+||.
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            445555555666789999999999999999998874

>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=83.77  E-value=0.47  Score=49.41  Aligned_cols=26  Identities=38%  Similarity=0.599  Sum_probs=22.1

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhhc
Q 019981          150 SMAYV-AGKPIMSDEEYDKLKQKLKME  175 (333)
Q Consensus       150 ~~AY~-sGkPimsDeeFD~LK~kLk~~  175 (333)
                      -.+|| .++|+|||+|||+|.++|+.-
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            34677 699999999999999999853

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=80.18  E-value=2  Score=34.16  Aligned_cols=44  Identities=16%  Similarity=0.458  Sum_probs=34.7

Q ss_pred             eeeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEeccceeeec
Q 019981          269 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTRLITL  327 (333)
Q Consensus       269 ~iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R~itl  327 (333)
                      --|+--||.|+++...|         ..++..|.|.+      |++.|.--+..++...
T Consensus        29 ~Fm~VkCp~C~n~q~VF---------ShA~t~V~C~~------Cg~~L~~PTGGKA~l~   72 (81)
T 2xzm_6           29 YFMDVKCAQCQNIQMIF---------SNAQSTIICEK------CSAILCKPTGGKVQIQ   72 (81)
T ss_dssp             CEEEEECSSSCCEEEEE---------TTCSSCEECSS------SCCEEEEECSSCEEEC
T ss_pred             cEEEeECCCCCCeeEEE---------ecCccEEEccC------CCCEEeecCCCCeEec
Confidence            44777899999998888         46777899988      9999988776555443

---

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	333
d1b04a_	312	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	8e-05
d1b04a_	312	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	2e-04
d1ta8a_	313	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	1e-04
d1ta8a_	313	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	0.004
d1dgsa3	314	d.142.2.2 (A:1-314) Adenylation domain of NAD+-dep	1e-04
d1dgsa3	314	d.142.2.2 (A:1-314) Adenylation domain of NAD+-dep	0.001
d1nuia2	54	g.41.3.2 (A:10-63) Zinc-binding domain of primase-	0.004

>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 = 41.5 bits (96), Expect = 8e-05
 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 = 40.7 bits (94), Expect = 2e-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 = 41.1 bits (95), 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

>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 = 36.1 bits (82), Expect = 0.004
 Identities = 8/44 (18%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 87  IDKKEKKS-LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL 129
           +      +   EL ++  Q    +Y + +  + +  +D L +EL
Sbjct: 2   LTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKEL 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 = 40.7 bits (94), Expect = 1e-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 = 38.0 bits (87), 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

>d1nuia2 g.41.3.2 (A:10-63) Zinc-binding domain of primase-helicase {Bacteriophage T7 [TaxId: 10760]} Length = 54

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: DNA primase zinc finger
domain: Zinc-binding domain of primase-helicase
species: Bacteriophage T7 [TaxId: 10760]

 Score = 32.9 bits (75), Expect = 0.004
 Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 15/49 (30%)

Query: 274 PCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNT 322
           PC NCG             SS G  N++     TFC+ C      + +T
Sbjct: 7   PCDNCG-------------SSDG--NSLFSDGHTFCYVCEKWTAGNEDT 40

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	333
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	96.44
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	96.32
d1dgsa3	314	Adenylation domain of NAD+-dependent DNA ligase {T	95.5
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	95.32
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	95.08
d1dgsa3	314	Adenylation domain of NAD+-dependent DNA ligase {T	92.9
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	89.7

>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=96.44  E-value=0.0011  Score=58.94  Aligned_cols=27  Identities=30%  Similarity=0.434  Sum_probs=22.8

Q ss_pred             HHHHhhh-cCCCccChHHHHHHHHHHhh
Q 019981          148 EASMAYV-AGKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       148 EA~~AY~-sGkPimsDeeFD~LK~kLk~  174 (333)
                      ++-.+|| .|+|+|||+|||.|+.+|+.
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            3445788 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=96.32  E-value=0.0011  Score=59.40  Aligned_cols=25  Identities=36%  Similarity=0.651  Sum_probs=22.0

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 019981          150 SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       150 ~~AY~s-GkPimsDeeFD~LK~kLk~  174 (333)
                      -.+||. |+|+|||++||.|+++|+.
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            347886 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=95.50  E-value=0.0026  Score=57.11  Aligned_cols=25  Identities=40%  Similarity=0.678  Sum_probs=22.1

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 019981          150 SMAYVA-GKPIMSDEEYDKLKQKLKM  174 (333)
Q Consensus       150 ~~AY~s-GkPimsDeeFD~LK~kLk~  174 (333)
                      -.+||. |+|+|||++||.|+.+|+.
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            357985 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=95.32  E-value=0.006  Score=53.91  Aligned_cols=36  Identities=22%  Similarity=0.385  Sum_probs=31.9

Q ss_pred             chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 019981           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL  129 (333)
Q Consensus        94 slge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL  129 (333)
                      -+.+++..--++=.+||+.|.++|||+|||.|+++|
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            456777788888889999999999999999999987

>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=95.08  E-value=0.0074  Score=53.80  Aligned_cols=38  Identities=21%  Similarity=0.378  Sum_probs=33.2

Q ss_pred             ccchhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 019981           92 KKSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL  129 (333)
Q Consensus        92 k~slge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL  129 (333)
                      ++-+.|++..--.+=.+||+.|.|+|||+|||.|+++|
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            44677888888888889999999999999999999997

>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=92.90  E-value=0.024  Score=50.60  Aligned_cols=37  Identities=24%  Similarity=0.340  Sum_probs=29.8

Q ss_pred             chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 019981           94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM  130 (333)
Q Consensus        94 slge~E~~fl~Al~~fY~~gk~~~sdeefd~LkEeL~  130 (333)
                      -+-+++..--.+=.+||..|.|+|||+|||.|++||.
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            4555666666667888889999999999999999874

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27e
domain: Ribosomal protein S27e
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.70  E-value=0.13  Score=36.92  Aligned_cols=39  Identities=28%  Similarity=0.683  Sum_probs=31.4

Q ss_pred             eeecCCCCCccccceeccccccccCCCCccceeCCCCccccccCceeEEeccce
Q 019981          270 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNLTFCFSCGTTMVYDSNTR  323 (333)
Q Consensus       270 iLKG~CPNCGeEv~aFfgtilsv~s~~~~n~vkC~~~aeCHVC~t~L~f~tk~R  323 (333)
                      -|+--||.|++|.-.|         .+++..|.|..      |++.|.--+..+
T Consensus         5 F~~VkC~~C~n~~ivF---------sha~t~V~C~~------Cg~~L~~PtGGK   43 (58)
T d1qxfa_           5 FVKVKCPDCEHEQVIF---------DHPSTIVKCII------CGRTVAEPTGGK   43 (58)
T ss_dssp             EEEEECTTTCCEEEEE---------SSCSSCEECSS------SCCEEEECCSSS
T ss_pred             eEEeECCCCCCeEEEE---------ecCceEEEccc------cCCEEeccCCCe
Confidence            3567799999999988         56777889988      999998765543