Citrus Sinensis ID: 028248

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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-
Protein Sequence
MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPEGSEA
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHcccccEEEEEcHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccEEEEcccEEEccccEEcccccHHHHHHHHHHHHHHHHHHHHHHHccccccEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEccccccccccEEcccccccccccccccEEccccccEEEEEcccEEEEccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHccccccEEEccHHHHHHHHHHHHHHcccccEcHHHHHHHHHHHHHccccEEEEcccccccccEEEEcHHHHHHHHHHHcccHHHHHHHHHHHcccccccccEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcEEEEccccccccccEEEEEccccccccccccccEEEccccEEEEEcccEEEEEccccccc
Coil and Loop (DISEMBL)
msneefdnLKEELMWEGSSVVMLSSAEQKFLEASMAYvagkpimsdeEYDKLKQKLKMEgseivvegprcslrsrkvysDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYllelpepfsfifTWFAAVPLIVYLSQSLTKLIVREslilkgpcpncgtenvsFFGTILSissggttntincsncgttmvydsntrlitlpegsea
Flexible Loop (DISEMBL)
msneefdnLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKmegseivvegprcslrsrkVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTincsncgttmvydsntrlitlpegsea
Low Complexity Region (SEG)
MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPEGSEA
Disordered region (IsUnstruct)
*******************VVML*****KFLEASMAYVAG*********************EIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLIT*******
Disordered Region (DISOPRED)
***EEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILS********TINCSNCGTTMVYDSN************
Disordered Region (DISEMBL)
********LKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPEGSEA
Disordered Region (DISPRO)
*SNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLELPEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPEGSEA
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	211	2.2.26 [Sep-21-2011]
Q8H112	324	PGR5-like protein 1A, chl	yes	no	1.0	0.651	0.838	1e-104
Q8GYC7	313	PGR5-like protein 1B, chl	no	no	1.0	0.674	0.838	1e-102

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

 Score =  377 bits (968), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 177/211 (83%), Positives = 199/211 (94%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI++DEEYDKLK KLK++G
Sbjct: 114 MSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILNDEEYDKLKLKLKIDG 173

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           S+IV EGPRCSLRS+KVYSDL+VDY KMLLLNVPATVVALGLFFFLDDITGFEITY++EL
Sbjct: 174 SDIVSEGPRCSLRSKKVYSDLAVDYFKMLLLNVPATVVALGLFFFLDDITGFEITYIMEL 233

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
           PEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILKGPCPNCGTEN SFFGTILSISSGG
Sbjct: 234 PEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILKGPCPNCGTENTSFFGTILSISSGG 293

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
            TNT+ C+NCGT MVYDS +RLITLPEGS+A
Sbjct: 294 KTNTVKCTNCGTAMVYDSGSRLITLPEGSQA 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 =  369 bits (947), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 177/211 (83%), Positives = 192/211 (90%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI+SDEEYDKLK KLKM+G
Sbjct: 103 MSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILSDEEYDKLKMKLKMDG 162

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           SEIV EGPRCSLRS+KVYSDL++DY KM LLNVPATVVALGLFFFLDDITGFEITYLLEL
Sbjct: 163 SEIVCEGPRCSLRSKKVYSDLAIDYFKMFLLNVPATVVALGLFFFLDDITGFEITYLLEL 222

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
           PEPFSFIFTWFAAVP IVYL+ SLTKLI+++ LILKGPCPNCGTENVSFFGTILSI +  
Sbjct: 223 PEPFSFIFTWFAAVPAIVYLALSLTKLILKDFLILKGPCPNCGTENVSFFGTILSIPNDS 282

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
            TN + CS CGT MVYDS +RLITLPEG +A
Sbjct: 283 NTNNVKCSGCGTEMVYDSGSRLITLPEGGKA 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	211
356514103	321	PREDICTED: PGR5-like protein 1A, chlorop	1.0	0.657	0.857	1e-103
255537217	320	conserved hypothetical protein [Ricinus	1.0	0.659	0.867	1e-103
297742627	326	unnamed protein product [Vitis vinifera]	1.0	0.647	0.862	1e-102
145333783	321	PGR5-like protein 1A [Arabidopsis thalia	1.0	0.657	0.838	1e-102
145333797	322	PGR5-like protein 1A [Arabidopsis thalia	1.0	0.655	0.838	1e-102
225426724	331	PREDICTED: PGR5-like protein 1A, chlorop	1.0	0.637	0.862	1e-102
18416029	324	PGR5-like protein 1A [Arabidopsis thalia	1.0	0.651	0.838	1e-102
118487360	323	unknown [Populus trichocarpa]	1.0	0.653	0.862	1e-102
255645443	321	unknown [Glycine max]	1.0	0.657	0.853	1e-102
297803832	320	hypothetical protein ARALYDRAFT_492575 [	1.0	0.659	0.838	1e-102

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

 Score =  378 bits (971), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 181/211 (85%), Positives = 198/211 (93%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLSS EQKFLEASMAYV+GKPIMSD+E+D+LK +LK+EG
Sbjct: 111 MSNEEFDNLKEELMWEGSSVVMLSSDEQKFLEASMAYVSGKPIMSDKEFDELKLRLKIEG 170

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           SEIV EGPRCSLRSRKVYSDLSVDYLKMLLLNVPATV+ALGLFFFLDD+TGFEITYLLEL
Sbjct: 171 SEIVAEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVIALGLFFFLDDLTGFEITYLLEL 230

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
           PEPFSFIFTWFAAVPLIV+++ SLT  IV++ +ILKGPCPNCGTEN SFFGTILSIS+GG
Sbjct: 231 PEPFSFIFTWFAAVPLIVWIALSLTNAIVKDFVILKGPCPNCGTENTSFFGTILSISNGG 290

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
           +TNT+ CSNCGT M YDS TRLITLPEGS A
Sbjct: 291 STNTVKCSNCGTAMEYDSTTRLITLPEGSNA 321

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  378 bits (970), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 183/211 (86%), Positives = 194/211 (91%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLS  EQKFLEASMAYV+G PIMSDEE+D+LK +LK EG
Sbjct: 110 MSNEEFDNLKEELMWEGSSVVMLSCDEQKFLEASMAYVSGNPIMSDEEFDQLKLRLKQEG 169

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           SEIVVEGPRCSLRSRKVYSDLSVDYLKM LLNVPA VVALGLFFFLDD+TGFEITYLLEL
Sbjct: 170 SEIVVEGPRCSLRSRKVYSDLSVDYLKMFLLNVPAAVVALGLFFFLDDLTGFEITYLLEL 229

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
           PEPFSFIFTWFAAVP+IV+LS S T  IV++ LILKGPCPNCGTEN SFFGTILSISSGG
Sbjct: 230 PEPFSFIFTWFAAVPVIVWLSLSFTNAIVKDFLILKGPCPNCGTENQSFFGTILSISSGG 289

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
           TTN++ CSNCGT MVYDS TRLITLPEGS A
Sbjct: 290 TTNSVKCSNCGTDMVYDSKTRLITLPEGSNA 320

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  377 bits (969), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 182/211 (86%), Positives = 195/211 (92%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLSS EQKFLEASMAYVAG PIMSDEE+D LK KLK+EG
Sbjct: 116 MSNEEFDNLKEELMWEGSSVVMLSSDEQKFLEASMAYVAGNPIMSDEEFDDLKIKLKIEG 175

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           SEIVVEGPRCSLRS+KVYSDLSVDYLKM LLNVPA VVAL LFFFLDD+TGFEIT+LLEL
Sbjct: 176 SEIVVEGPRCSLRSKKVYSDLSVDYLKMFLLNVPAAVVALSLFFFLDDVTGFEITFLLEL 235

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
            EPFSFIFTWFAAVPLI +LSQ++TK I+++ LILKGPCPNCGTENVSFFGTILSIS+GG
Sbjct: 236 QEPFSFIFTWFAAVPLIFWLSQTITKFILKDFLILKGPCPNCGTENVSFFGTILSISNGG 295

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
           TTN + CSNC T MVYDS TRLITLPEGSEA
Sbjct: 296 TTNNLKCSNCETQMVYDSKTRLITLPEGSEA 326

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145333783|ref|NP_001078431.1| PGR5-like protein 1A [Arabidopsis thaliana] gi|332659277|gb|AEE84677.1| PGR5-like protein 1A [Arabidopsis thaliana]

 Score =  377 bits (969), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 177/211 (83%), Positives = 199/211 (94%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI++DEEYDKLK KLK++G
Sbjct: 111 MSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILNDEEYDKLKLKLKIDG 170

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           S+IV EGPRCSLRS+KVYSDL+VDY KMLLLNVPATVVALGLFFFLDDITGFEITY++EL
Sbjct: 171 SDIVSEGPRCSLRSKKVYSDLAVDYFKMLLLNVPATVVALGLFFFLDDITGFEITYIMEL 230

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
           PEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILKGPCPNCGTEN SFFGTILSISSGG
Sbjct: 231 PEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILKGPCPNCGTENTSFFGTILSISSGG 290

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
            TNT+ C+NCGT MVYDS +RLITLPEGS+A
Sbjct: 291 KTNTVKCTNCGTAMVYDSGSRLITLPEGSQA 321

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145333797|ref|NP_001078432.1| PGR5-like protein 1A [Arabidopsis thaliana] gi|332659278|gb|AEE84678.1| PGR5-like protein 1A [Arabidopsis thaliana]

 Score =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 177/211 (83%), Positives = 199/211 (94%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI++DEEYDKLK KLK++G
Sbjct: 112 MSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILNDEEYDKLKLKLKIDG 171

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           S+IV EGPRCSLRS+KVYSDL+VDY KMLLLNVPATVVALGLFFFLDDITGFEITY++EL
Sbjct: 172 SDIVSEGPRCSLRSKKVYSDLAVDYFKMLLLNVPATVVALGLFFFLDDITGFEITYIMEL 231

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
           PEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILKGPCPNCGTEN SFFGTILSISSGG
Sbjct: 232 PEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILKGPCPNCGTENTSFFGTILSISSGG 291

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
            TNT+ C+NCGT MVYDS +RLITLPEGS+A
Sbjct: 292 KTNTVKCTNCGTAMVYDSGSRLITLPEGSQA 322

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 182/211 (86%), Positives = 195/211 (92%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLSS EQKFLEASMAYVAG PIMSDEE+D LK KLK+EG
Sbjct: 121 MSNEEFDNLKEELMWEGSSVVMLSSDEQKFLEASMAYVAGNPIMSDEEFDDLKIKLKIEG 180

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           SEIVVEGPRCSLRS+KVYSDLSVDYLKM LLNVPA VVAL LFFFLDD+TGFEIT+LLEL
Sbjct: 181 SEIVVEGPRCSLRSKKVYSDLSVDYLKMFLLNVPAAVVALSLFFFLDDVTGFEITFLLEL 240

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
            EPFSFIFTWFAAVPLI +LSQ++TK I+++ LILKGPCPNCGTENVSFFGTILSIS+GG
Sbjct: 241 QEPFSFIFTWFAAVPLIFWLSQTITKFILKDFLILKGPCPNCGTENVSFFGTILSISNGG 300

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
           TTN + CSNC T MVYDS TRLITLPEGSEA
Sbjct: 301 TTNNLKCSNCETQMVYDSKTRLITLPEGSEA 331

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 177/211 (83%), Positives = 199/211 (94%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI++DEEYDKLK KLK++G
Sbjct: 114 MSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILNDEEYDKLKLKLKIDG 173

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           S+IV EGPRCSLRS+KVYSDL+VDY KMLLLNVPATVVALGLFFFLDDITGFEITY++EL
Sbjct: 174 SDIVSEGPRCSLRSKKVYSDLAVDYFKMLLLNVPATVVALGLFFFLDDITGFEITYIMEL 233

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
           PEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILKGPCPNCGTEN SFFGTILSISSGG
Sbjct: 234 PEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILKGPCPNCGTENTSFFGTILSISSGG 293

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
            TNT+ C+NCGT MVYDS +RLITLPEGS+A
Sbjct: 294 KTNTVKCTNCGTAMVYDSGSRLITLPEGSQA 324

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 182/211 (86%), Positives = 197/211 (93%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMW+GSSVVMLSS EQKFLEAS+AYV+G PIM+DEE+DKLK KLK EG
Sbjct: 113 MSNEEFDNLKEELMWQGSSVVMLSSDEQKFLEASLAYVSGNPIMNDEEFDKLKIKLKTEG 172

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           SEIVVEGPRCSLRSRKVYSDLSVDYLKM LLNVPATVVALGLFFFLDD+TGFEITYLLEL
Sbjct: 173 SEIVVEGPRCSLRSRKVYSDLSVDYLKMFLLNVPATVVALGLFFFLDDLTGFEITYLLEL 232

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
           PEPFSF+FTWFAAVPLIV+L+ +LT  IV++ LILKGPCPNCGTEN SFFGTILSISSGG
Sbjct: 233 PEPFSFLFTWFAAVPLIVWLALTLTNAIVKDFLILKGPCPNCGTENGSFFGTILSISSGG 292

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
           T+NT+ CSNC T +VYDS TRLITLPEGSEA
Sbjct: 293 TSNTLKCSNCSTELVYDSKTRLITLPEGSEA 323

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  376 bits (966), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 180/211 (85%), Positives = 197/211 (93%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLKEELMWEGSSVVMLSS EQKFLEASMAYV+GKPIMSD+E+D+LK +LK+EG
Sbjct: 111 MSNEEFDNLKEELMWEGSSVVMLSSDEQKFLEASMAYVSGKPIMSDKEFDELKLRLKIEG 170

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           SEIV EGPRCSLRSRKVYSDLSVDYLKMLLLNVPATV+ALGLFFFLDD+TGFEITYLLEL
Sbjct: 171 SEIVAEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVIALGLFFFLDDLTGFEITYLLEL 230

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
           PEPFSFIFTWF AVPLIV+++ SLT  IV++ +ILKGPCPNCGTEN SFFGTILSIS+GG
Sbjct: 231 PEPFSFIFTWFVAVPLIVWIALSLTNAIVKDFVILKGPCPNCGTENTSFFGTILSISNGG 290

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
           +TNT+ CSNCGT M YDS TRLITLPEGS A
Sbjct: 291 STNTVKCSNCGTAMEYDSTTRLITLPEGSNA 321

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297803832|ref|XP_002869800.1| hypothetical protein ARALYDRAFT_492575 [Arabidopsis lyrata subsp. lyrata] gi|297315636|gb|EFH46059.1| hypothetical protein ARALYDRAFT_492575 [Arabidopsis lyrata subsp. lyrata]

 Score =  375 bits (964), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 177/211 (83%), Positives = 198/211 (93%)

Query: 1   MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
           MSNEEFDNLK+ELMWEGSSVVMLSS EQ+FLEASMAYV+GKPI++DEEYDKLK KLK++G
Sbjct: 110 MSNEEFDNLKDELMWEGSSVVMLSSDEQRFLEASMAYVSGKPILNDEEYDKLKLKLKIDG 169

Query: 61  SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
           SEIV EGPRCSLRS+KVYSDL+VDY KMLLLNVPATVVALGLFFFLDDITGFEITY++EL
Sbjct: 170 SEIVCEGPRCSLRSKKVYSDLAVDYFKMLLLNVPATVVALGLFFFLDDITGFEITYIMEL 229

Query: 121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
            EP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILKGPCPNCGTEN SFFGTILSISSGG
Sbjct: 230 SEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILKGPCPNCGTENTSFFGTILSISSGG 289

Query: 181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
            TN + CSNCGT MVYDS +RLITLPEGS+A
Sbjct: 290 KTNAVKCSNCGTAMVYDSGSRLITLPEGSQA 320

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	211
TAIR|locus:2127233	324	PGR5-LIKE A "AT4G22890" [Arabi	1.0	0.651	0.838	4.2e-95
TAIR|locus:2118031	313	PGRL1B "AT4G11960" [Arabidopsi	1.0	0.674	0.838	2.7e-93
TAIR|locus:2148338	301	AT5G59400 "AT5G59400" [Arabido	0.355	0.249	0.392	2.8e-10

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

 Score = 946 (338.1 bits), Expect = 4.2e-95, P = 4.2e-95
 Identities = 177/211 (83%), Positives = 199/211 (94%)

Query:     1 MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
             MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI++DEEYDKLK KLK++G
Sbjct:   114 MSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILNDEEYDKLKLKLKIDG 173

Query:    61 SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
             S+IV EGPRCSLRS+KVYSDL+VDY KMLLLNVPATVVALGLFFFLDDITGFEITY++EL
Sbjct:   174 SDIVSEGPRCSLRSKKVYSDLAVDYFKMLLLNVPATVVALGLFFFLDDITGFEITYIMEL 233

Query:   121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
             PEP+SFIFTWFAAVP+IVYL+ S+TKLI+++ LILKGPCPNCGTEN SFFGTILSISSGG
Sbjct:   234 PEPYSFIFTWFAAVPVIVYLALSITKLIIKDFLILKGPCPNCGTENTSFFGTILSISSGG 293

Query:   181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
              TNT+ C+NCGT MVYDS +RLITLPEGS+A
Sbjct:   294 KTNTVKCTNCGTAMVYDSGSRLITLPEGSQA 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 = 929 (332.1 bits), Expect = 2.7e-93, P = 2.7e-93
 Identities = 177/211 (83%), Positives = 192/211 (90%)

Query:     1 MSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 60
             MSNEEFDNLKEELMWEGSSVVMLSS EQ+FLEASMAYV+G PI+SDEEYDKLK KLKM+G
Sbjct:   103 MSNEEFDNLKEELMWEGSSVVMLSSDEQRFLEASMAYVSGNPILSDEEYDKLKMKLKMDG 162

Query:    61 SEIVVEGPRCSLRSRKVYSDLSVDYLKMLLLNVPATVVALGLFFFLDDITGFEITYLLEL 120
             SEIV EGPRCSLRS+KVYSDL++DY KM LLNVPATVVALGLFFFLDDITGFEITYLLEL
Sbjct:   163 SEIVCEGPRCSLRSKKVYSDLAIDYFKMFLLNVPATVVALGLFFFLDDITGFEITYLLEL 222

Query:   121 PEPFSFIFTWFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGG 180
             PEPFSFIFTWFAAVP IVYL+ SLTKLI+++ LILKGPCPNCGTENVSFFGTILSI +  
Sbjct:   223 PEPFSFIFTWFAAVPAIVYLALSLTKLILKDFLILKGPCPNCGTENVSFFGTILSIPNDS 282

Query:   181 TTNTINCSNCGTTMVYDSNTRLITLPEGSEA 211
              TN + CS CGT MVYDS +RLITLPEG +A
Sbjct:   283 NTNNVKCSGCGTEMVYDSGSRLITLPEGGKA 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 = 2.8e-10, Sum P(2) = 2.8e-10
 Identities = 31/79 (39%), Positives = 49/79 (62%)

Query:    27 EQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEIVVEGPRCSLRSRKVYSDLSVDYL 86
             E  + +A  AY  GKP++ D+ +D+++ KL+  GS+ VV+ PRCSL  +  Y+D   D  
Sbjct:    75 EALYRQAKDAYYNGKPLIVDDMFDRVELKLRWYGSKSVVKYPRCSLLRQSTYADAEDDAS 134

Query:    87 KMLLLNVPATVVALGLFFF 105
             ++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

---

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	0.8388	1.0	0.6512	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	211
pfam08996	187	pfam08996, zf-DNA_Pol, DNA Polymerase alpha zinc f	0.004

>gnl|CDD|220087 pfam08996, zf-DNA_Pol, DNA Polymerase alpha zinc finger

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 3/41 (7%)

Query: 155 LKGPCPNCGTENVSFFGTILSISSGGTT-NTINCSNCGTTM 194
           LK  CP+CGTE    F  I + S    T + + CS C   +
Sbjct: 17  LKLKCPSCGTEFP--FEGIFASSGERVTPSGLQCSKCNALI 55

The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain. Length = 187

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	211
PRK00420	112	hypothetical protein; Validated	97.56
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	97.04
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	96.93
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	96.7
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	96.7
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	96.46
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	96.37
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	96.27
PF13248	26	zf-ribbon_3: zinc-ribbon domain	96.19
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	96.1
cd00114	307	LIGANc NAD+ dependent DNA ligase adenylation domai	95.66
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	95.66
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	95.66
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	95.47
PRK08097	562	ligB NAD-dependent DNA ligase LigB; Reviewed	95.43
smart00531	147	TFIIE Transcription initiation factor IIE.	95.34
PF01653	315	DNA_ligase_aden: NAD-dependent DNA ligase adenylat	95.2
PLN00209	86	ribosomal protein S27; Provisional	94.78
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	94.78
PRK09710	64	lar restriction alleviation and modification prote	94.76
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	94.66
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	94.61
PTZ00083	85	40S ribosomal protein S27; Provisional	94.55
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	94.55
smart00532	441	LIGANc Ligase N family.	94.54
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	94.47
PRK05978	148	hypothetical protein; Provisional	94.46
PRK02935	110	hypothetical protein; Provisional	94.45
PF14353	128	CpXC: CpXC protein	94.3
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	94.12
PRK06266	178	transcription initiation factor E subunit alpha; V	94.11
PHA00626	59	hypothetical protein	94.04
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	94.04
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	93.95
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	93.83
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	93.78
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	93.62
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	93.51
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	93.49
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	93.12
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	93.11
PRK14351	689	ligA NAD-dependent DNA ligase LigA; Provisional	92.77
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	92.63
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	92.32
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	91.57
PRK14350	669	ligA NAD-dependent DNA ligase LigA; Provisional	91.5
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	91.16
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	91.11
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	91.05
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	90.94
smart00661	52	RPOL9 RNA polymerase subunit 9.	90.88
COG5349	126	Uncharacterized protein conserved in bacteria [Fun	90.49
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	89.83
COG3877	122	Uncharacterized protein conserved in bacteria [Fun	89.67
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	89.57
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	89.42
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	89.15
smart00709	160	Zpr1 Duplicated domain in the epidermal growth fac	88.6
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	88.38
PRK00432	50	30S ribosomal protein S27ae; Validated	88.35
PF12773	50	DZR: Double zinc ribbon	88.2
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	87.62
PF10083	158	DUF2321: Uncharacterized protein conserved in bact	87.59
PRK12495	226	hypothetical protein; Provisional	87.49
PRK14892	99	putative transcription elongation factor Elf1; Pro	86.91
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	86.75
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	85.94
PRK14714	1337	DNA polymerase II large subunit; Provisional	85.92
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	85.86
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	85.77
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	85.54
COG1675	176	TFA1 Transcription initiation factor IIE, alpha su	84.48
PF09567	314	RE_MamI: MamI restriction endonuclease; InterPro:	84.35
smart00778	37	Prim_Zn_Ribbon Zinc-binding domain of primase-heli	84.12
COG1779	201	C4-type Zn-finger protein [General function predic	83.62
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	83.0
PF09851	31	SHOCT: Short C-terminal domain; InterPro: IPR01864	82.99
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	82.88
COG0675	364	Transposase and inactivated derivatives [DNA repli	82.82
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	82.57
PF01807	97	zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zin	82.23
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	82.17
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	82.14
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	81.95
TIGR00244	147	transcriptional regulator NrdR. Members of this al	81.85
PF15616	131	TerY-C: TerY-C metal binding domain	81.68
COG3677	129	Transposase and inactivated derivatives [DNA repli	80.36

>PRK00420 hypothetical protein; Validated

Probab=97.56  E-value=7.7e-05  Score=59.69  Aligned_cols=48  Identities=19%  Similarity=0.492  Sum_probs=38.9

Q ss_pred             HHHHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248          141 SQSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN  199 (211)
Q Consensus       141 a~~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~  199 (211)
                      ++.+.++.++-...|...||.||.+.|.+           ...+..||+||..+.....
T Consensus         8 ~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~l-----------k~g~~~Cp~Cg~~~~v~~~   55 (112)
T PRK00420          8 VKKAAELLLKGAKMLSKHCPVCGLPLFEL-----------KDGEVVCPVHGKVYIVKSD   55 (112)
T ss_pred             HHHHHHHHHhHHHHccCCCCCCCCcceec-----------CCCceECCCCCCeeeeccH
Confidence            34456667777766889999999999988           5779999999998887653

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

Probab=97.04  E-value=0.00069  Score=54.56  Aligned_cols=63  Identities=19%  Similarity=0.435  Sum_probs=40.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhhcc--ceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248          126 FIFTWFAAVPLIVYLSQSLTKLIVRE--SLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT  200 (211)
Q Consensus       126 ~i~~~~~~~Pvi~~~a~~lt~~~~~d--~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~  200 (211)
                      ++.+.++++.++..+++...=+|.+=  .-++-=.|||||.+....           .+. -.|..|+++|+.|++.
T Consensus        37 ~im~ifmllG~L~~l~S~~VYfwIGmlStkav~V~CP~C~K~TKmL-----------Gr~-D~CM~C~~pLTLd~~l  101 (114)
T PF11023_consen   37 IIMVIFMLLGLLAILASTAVYFWIGMLSTKAVQVECPNCGKQTKML-----------GRV-DACMHCKEPLTLDPSL  101 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcccceeeECCCCCChHhhh-----------chh-hccCcCCCcCccCchh
Confidence            44444555566655555444444322  223444599999998877           223 3899999999999864

; GO: 0005887 integral to plasma membrane

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

Probab=96.93  E-value=0.00091  Score=44.76  Aligned_cols=36  Identities=19%  Similarity=0.587  Sum_probs=26.6

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeE
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI  203 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i  203 (211)
                      .|||||.++..-       +   .....+||.||..+.+...+..+
T Consensus         5 ~C~~CG~~~~~~-------~---~~~~~~Cp~CG~~~~~~~~~~~v   40 (46)
T PRK00398          5 KCARCGREVELD-------E---YGTGVRCPYCGYRILFKERPPVV   40 (46)
T ss_pred             ECCCCCCEEEEC-------C---CCCceECCCCCCeEEEccCCCcc
Confidence            599999976542       1   12279999999999988765544

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

Probab=96.70  E-value=0.0019  Score=47.67  Aligned_cols=44  Identities=32%  Similarity=0.680  Sum_probs=37.3

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE  207 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe  207 (211)
                      |+-.||.||.|-..|       +  .++..+.|++||+.|.--+..++.+.++
T Consensus        18 l~VkCpdC~N~q~vF-------s--hast~V~C~~CG~~l~~PTGGka~i~~~   61 (67)
T COG2051          18 LRVKCPDCGNEQVVF-------S--HASTVVTCLICGTTLAEPTGGKAKISGK   61 (67)
T ss_pred             EEEECCCCCCEEEEe-------c--cCceEEEecccccEEEecCCCeEEeeee
Confidence            677899999999998       2  2688999999999999998888777654

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=96.70  E-value=0.0029  Score=44.78  Aligned_cols=44  Identities=30%  Similarity=0.544  Sum_probs=30.1

Q ss_pred             ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC--ceeEeCCC
Q 028248          156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN--TRLITLPE  207 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~--~r~i~~pe  207 (211)
                      +..||.||+++.-        .....--.+.|++||..+++-+.  .|+-..|+
T Consensus         2 ~~~CP~CG~~iev--------~~~~~GeiV~Cp~CGaeleVv~~~p~~L~~ap~   47 (54)
T TIGR01206         2 QFECPDCGAEIEL--------ENPELGELVICDECGAELEVVSLDPLRLEAAPE   47 (54)
T ss_pred             ccCCCCCCCEEec--------CCCccCCEEeCCCCCCEEEEEeCCCCEEEeCcc
Confidence            5689999998742        11112347899999999999874  44444443

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.

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=96.46  E-value=0.0025  Score=40.71  Aligned_cols=36  Identities=25%  Similarity=0.569  Sum_probs=23.7

Q ss_pred             ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248          156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY  196 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f  196 (211)
                      +-.||+||+.+..=     ...-.....+++|++||..+..
T Consensus         2 ~~~CP~C~~~~~v~-----~~~~~~~~~~v~C~~C~~~~~~   37 (38)
T TIGR02098         2 RIQCPNCKTSFRVV-----DSQLGANGGKVRCGKCGHVWYA   37 (38)
T ss_pred             EEECCCCCCEEEeC-----HHHcCCCCCEEECCCCCCEEEe
Confidence            44799999986532     1111123348999999998865

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.

>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=96.37  E-value=0.0028  Score=57.09  Aligned_cols=50  Identities=28%  Similarity=0.593  Sum_probs=25.5

Q ss_pred             HHHHHHHhhhccceeeecCCCCCccc-ceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248          140 LSQSLTKLIVRESLILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT  200 (211)
Q Consensus       140 ~a~~lt~~~~~d~liLkG~CPnCg~E-v~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~  200 (211)
                      .|..||.-|...+.    .|||||.+ ...|       +.|+......|++|++.-+..++.
T Consensus        19 ~aRVltE~Wv~~n~----yCP~Cg~~~L~~f-------~NN~PVaDF~C~~C~eeyELKSk~   69 (254)
T PF06044_consen   19 IARVLTEDWVAENM----YCPNCGSKPLSKF-------ENNRPVADFYCPNCNEEYELKSKK   69 (254)
T ss_dssp             HHHHHHHHHHHHH-------TTT--SS-EE---------------EEE-TTT--EEEEEEEE
T ss_pred             hhHHHHHHHHHHCC----cCCCCCChhHhhc-------cCCCccceeECCCCchHHhhhhhc
Confidence            45566776666554    89999999 4455       666777889999999999998864

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

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=96.27  E-value=0.0017  Score=38.41  Aligned_cols=22  Identities=50%  Similarity=1.170  Sum_probs=16.7

Q ss_pred             CCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248          159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L  194 (211)
                      ||+||.|+.              .+..-|++||++|
T Consensus         2 Cp~CG~~~~--------------~~~~fC~~CG~~l   23 (23)
T PF13240_consen    2 CPNCGAEIE--------------DDAKFCPNCGTPL   23 (23)
T ss_pred             CcccCCCCC--------------CcCcchhhhCCcC
Confidence            999999974              2233499999875

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=96.19  E-value=0.002  Score=38.81  Aligned_cols=24  Identities=42%  Similarity=0.973  Sum_probs=18.4

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L  194 (211)
                      -.|||||+++              .....-|++||++|
T Consensus         3 ~~Cp~Cg~~~--------------~~~~~fC~~CG~~L   26 (26)
T PF13248_consen    3 MFCPNCGAEI--------------DPDAKFCPNCGAKL   26 (26)
T ss_pred             CCCcccCCcC--------------CcccccChhhCCCC
Confidence            3699999975              24456799999875

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=96.10  E-value=0.0047  Score=44.62  Aligned_cols=42  Identities=31%  Similarity=0.689  Sum_probs=34.2

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeC
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL  205 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~  205 (211)
                      ++=.||.|+.|...|         ..++..++|.+||+.|.--+..+....
T Consensus        10 ~~VkCp~C~n~q~vF---------sha~t~V~C~~Cg~~L~~PtGGKa~i~   51 (59)
T PRK00415         10 LKVKCPDCGNEQVVF---------SHASTVVRCLVCGKTLAEPTGGKAKIK   51 (59)
T ss_pred             EEEECCCCCCeEEEE---------ecCCcEEECcccCCCcccCCCcceeee
Confidence            677899999999999         126889999999999987776555544

>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain

Probab=95.66  E-value=0.013  Score=53.58  Aligned_cols=27  Identities=33%  Similarity=0.641  Sum_probs=23.1

Q ss_pred             HHHHhhhc-CCCccChHHHHHHHHHHhh
Q 028248           32 EASMAYVA-GKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        32 eA~~aY~~-G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      ++-.+||. |+|+|||+|||+|.++|+.
T Consensus        12 ~~~~~YY~~~~p~IsD~eYD~L~~~L~~   39 (307)
T cd00114          12 KHDYRYYVLDEPSVSDAEYDRLYRELRA   39 (307)
T ss_pred             HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            34567887 9999999999999999974

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

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

Probab=95.66  E-value=0.0054  Score=44.55  Aligned_cols=36  Identities=31%  Similarity=0.660  Sum_probs=22.4

Q ss_pred             cceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248          151 ESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG  191 (211)
Q Consensus       151 d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~  191 (211)
                      +--+++=+|||||++.-.=  -   -..-.-.|..+|++||
T Consensus        22 ~e~~v~F~CPnCGe~~I~R--c---~~CRk~g~~Y~Cp~CG   57 (61)
T COG2888          22 GETAVKFPCPNCGEVEIYR--C---AKCRKLGNPYRCPKCG   57 (61)
T ss_pred             CCceeEeeCCCCCceeeeh--h---hhHHHcCCceECCCcC
Confidence            3345788999999554321  1   1222346788999998

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

Probab=95.66  E-value=0.02  Score=40.74  Aligned_cols=44  Identities=18%  Similarity=0.458  Sum_probs=30.4

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE  207 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe  207 (211)
                      ++=.||.|+.+...|         ..++..+.|.+|++.|.--+..+.+...+
T Consensus         6 m~VkCp~C~~~q~vF---------Sha~t~V~C~~Cg~~L~~PtGGKa~l~~~   49 (55)
T PF01667_consen    6 MDVKCPGCYNIQTVF---------SHAQTVVKCVVCGTVLAQPTGGKARLTEG   49 (55)
T ss_dssp             EEEE-TTT-SEEEEE---------TT-SS-EE-SSSTSEEEEE-SSSEEESSS
T ss_pred             EEEECCCCCCeeEEE---------ecCCeEEEcccCCCEecCCCCcCeEEeCC
Confidence            566799999999998         23688999999999998888776665543

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.

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=95.47  E-value=0.009  Score=47.43  Aligned_cols=33  Identities=30%  Similarity=0.777  Sum_probs=28.5

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      .|--||+||+.+|-+           ++.-+.||.||+...-..
T Consensus         8 tKR~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~~   40 (108)
T PF09538_consen    8 TKRTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPEP   40 (108)
T ss_pred             CcccCCCCcchhccC-----------CCCCccCCCCCCccCccc
Confidence            467899999999998           667788999999988774

The function of members of this family is unknown.

>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed

Probab=95.43  E-value=0.014  Score=57.60  Aligned_cols=50  Identities=34%  Similarity=0.529  Sum_probs=33.7

Q ss_pred             HHhhhcccCCeeEE---eChhh--H--HHHHH-----HHhhhc-CCCccChHHHHHHHHHHhh
Q 028248            9 LKEELMWEGSSVVM---LSSAE--Q--KFLEA-----SMAYVA-GKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus         9 lkeel~weGssv~~---l~~~E--q--~fLeA-----~~aY~~-G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      |---|.|..|--.+   ++..|  +  +.|.+     -.+||. |+|+|||+|||+|..+|+.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~~   70 (562)
T PRK08097          8 LISLLLWSSSAWAVCPDWSPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQ   70 (562)
T ss_pred             HHHHHHhcccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            44557888876444   44443  1  11222     246775 9999999999999999973

>smart00531 TFIIE Transcription initiation factor IIE

Probab=95.34  E-value=0.0093  Score=48.67  Aligned_cols=43  Identities=26%  Similarity=0.583  Sum_probs=28.1

Q ss_pred             ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248          156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL  202 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~  202 (211)
                      .=-||+||.... |- ......+  .+.+..||+||..|+...+...
T Consensus        99 ~Y~Cp~C~~~y~-~~-ea~~~~d--~~~~f~Cp~Cg~~l~~~dn~~~  141 (147)
T smart00531       99 YYKCPNCQSKYT-FL-EANQLLD--MDGTFTCPRCGEELEEDDNSEP  141 (147)
T ss_pred             EEECcCCCCEee-HH-HHHHhcC--CCCcEECCCCCCEEEEcCchhh
Confidence            345999996665 32 2111111  3566999999999999876543

>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=95.20  E-value=0.025  Score=51.86  Aligned_cols=26  Identities=50%  Similarity=0.833  Sum_probs=22.0

Q ss_pred             HHHhhhc-CCCccChHHHHHHHHHHhh
Q 028248           33 ASMAYVA-GKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        33 A~~aY~~-G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      +..+||. |+|+|||+|||+|.++|+.
T Consensus        17 ~~~~YY~~~~p~isD~eYD~l~~~L~~   43 (315)
T PF01653_consen   17 HNYAYYNLGEPIISDAEYDQLFRELKA   43 (315)
T ss_dssp             HHHHHHTTSSSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            3457777 8999999999999999863

It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....

>PLN00209 ribosomal protein S27; Provisional

Probab=94.78  E-value=0.036  Score=42.80  Aligned_cols=45  Identities=13%  Similarity=0.348  Sum_probs=36.8

Q ss_pred             eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248          154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE  207 (211)
Q Consensus       154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe  207 (211)
                      -++-.||.|+.+...|         ..++..+.|.+||+.|.--+..+...+++
T Consensus        34 Fm~VkCp~C~n~q~VF---------ShA~t~V~C~~Cg~~L~~PTGGKa~l~~g   78 (86)
T PLN00209         34 FMDVKCQGCFNITTVF---------SHSQTVVVCGSCQTVLCQPTGGKARLTEG   78 (86)
T ss_pred             EEEEECCCCCCeeEEE---------ecCceEEEccccCCEeeccCCCCeEecCC
Confidence            4788899999999999         12688999999999998888776665543

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=94.78  E-value=0.025  Score=36.03  Aligned_cols=30  Identities=20%  Similarity=0.462  Sum_probs=22.1

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      -.||.||.++....+       ........||.||..
T Consensus         6 y~C~~Cg~~fe~~~~-------~~~~~~~~CP~Cg~~   35 (41)
T smart00834        6 YRCEDCGHTFEVLQK-------ISDDPLATCPECGGD   35 (41)
T ss_pred             EEcCCCCCEEEEEEe-------cCCCCCCCCCCCCCc
Confidence            369999998776632       123678889999984

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=94.76  E-value=0.02  Score=42.08  Aligned_cols=35  Identities=26%  Similarity=0.640  Sum_probs=26.4

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      -|||.||++....       +..+..-.+.|+-|+..--|..
T Consensus         7 KPCPFCG~~~~~v-------~~~~g~~~v~C~~CgA~~~~~~   41 (64)
T PRK09710          7 KPCPFCGCPSVTV-------KAISGYYRAKCNGCESRTGYGG   41 (64)
T ss_pred             cCCCCCCCceeEE-------EecCceEEEEcCCCCcCccccc
Confidence            4999999998876       2223466799999999766554

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=94.66  E-value=0.029  Score=46.25  Aligned_cols=39  Identities=26%  Similarity=0.654  Sum_probs=32.0

Q ss_pred             HHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          143 SLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       143 ~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      .+.++.++-+..|--.||-||.+.|-.            +.++-||+||..
T Consensus        15 ~iA~lLl~GAkML~~hCp~Cg~PLF~K------------dG~v~CPvC~~~   53 (131)
T COG1645          15 KIAELLLQGAKMLAKHCPKCGTPLFRK------------DGEVFCPVCGYR   53 (131)
T ss_pred             HHHHHHHhhhHHHHhhCcccCCcceee------------CCeEECCCCCce
Confidence            445777888877888999999999885            567889999953

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=94.61  E-value=0.037  Score=55.40  Aligned_cols=29  Identities=31%  Similarity=0.556  Sum_probs=24.5

Q ss_pred             HHHHHHhhhc-CCCccChHHHHHHHHHHhh
Q 028248           30 FLEASMAYVA-GKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        30 fLeA~~aY~~-G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      .-++..+||. |+|+|||+|||+|.++|+.
T Consensus         5 l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~   34 (652)
T TIGR00575         5 IRHHDYRYYVLDEPSISDAEYDRLYRELQE   34 (652)
T ss_pred             HHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            3445677887 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.

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=94.55  E-value=0.045  Score=42.18  Aligned_cols=46  Identities=13%  Similarity=0.423  Sum_probs=37.3

Q ss_pred             eeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCC
Q 028248          153 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPE  207 (211)
Q Consensus       153 liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~pe  207 (211)
                      --++-.||.|+.+...|         ..++..+.|.+||+.|.--+..+.+.+++
T Consensus        32 ~Fm~VkCp~C~n~q~VF---------ShA~t~V~C~~Cg~~L~~PTGGKa~l~~g   77 (85)
T PTZ00083         32 YFMDVKCPGCSQITTVF---------SHAQTVVLCGGCSSQLCQPTGGKAKLTEG   77 (85)
T ss_pred             eEEEEECCCCCCeeEEE---------ecCceEEEccccCCEeeccCCCCeEecCC
Confidence            34788899999999999         12688999999999998888777766543

>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=94.55  E-value=0.029  Score=37.02  Aligned_cols=32  Identities=31%  Similarity=0.827  Sum_probs=23.0

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      -||+||.....+      +   ..+.+.-|++||..+.-+.
T Consensus         2 ~Cp~Cg~~~~~~------D---~~~g~~vC~~CG~Vl~e~~   33 (43)
T PF08271_consen    2 KCPNCGSKEIVF------D---PERGELVCPNCGLVLEENI   33 (43)
T ss_dssp             SBTTTSSSEEEE------E---TTTTEEEETTT-BBEE-TT
T ss_pred             CCcCCcCCceEE------c---CCCCeEECCCCCCEeeccc
Confidence            499999987433      1   2578889999999998654

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.

>smart00532 LIGANc Ligase N family

Probab=94.54  E-value=0.036  Score=53.19  Aligned_cols=26  Identities=42%  Similarity=0.714  Sum_probs=22.4

Q ss_pred             HHHhhhc-CCCccChHHHHHHHHHHhh
Q 028248           33 ASMAYVA-GKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        33 A~~aY~~-G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      +-.+||. |+|+|||+|||+|.++|+.
T Consensus        15 ~~~~YY~~~~p~IsD~eYD~L~~eL~~   41 (441)
T smart00532       15 HDYRYYVLDAPIISDAEYDRLMRELKE   41 (441)
T ss_pred             HHHHHHhcCCCCCChHHHHHHHHHHHH
Confidence            3456886 9999999999999999973

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=94.47  E-value=0.043  Score=55.09  Aligned_cols=26  Identities=38%  Similarity=0.615  Sum_probs=22.8

Q ss_pred             HHHhhh-cCCCccChHHHHHHHHHHhh
Q 028248           33 ASMAYV-AGKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        33 A~~aY~-~G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      +-.+|| .|+|+|||+|||+|.++|+.
T Consensus        19 ~~~~YY~~~~p~IsD~eYD~L~~~L~~   45 (665)
T PRK07956         19 HAYAYYVLDAPSISDAEYDRLYRELVA   45 (665)
T ss_pred             HHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence            345788 99999999999999999973

>PRK05978 hypothetical protein; Provisional

Probab=94.46  E-value=0.018  Score=48.17  Aligned_cols=35  Identities=29%  Similarity=0.829  Sum_probs=26.1

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      ++|-||+||+.=.  |++-+       +-+-.|++||..+++.+
T Consensus        32 l~grCP~CG~G~L--F~g~L-------kv~~~C~~CG~~~~~~~   66 (148)
T PRK05978         32 FRGRCPACGEGKL--FRAFL-------KPVDHCAACGEDFTHHR   66 (148)
T ss_pred             HcCcCCCCCCCcc--ccccc-------ccCCCccccCCccccCC
Confidence            7899999998632  33222       45678999999998765

>PRK02935 hypothetical protein; Provisional

Probab=94.45  E-value=0.049  Score=43.68  Aligned_cols=36  Identities=19%  Similarity=0.553  Sum_probs=27.4

Q ss_pred             eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCce
Q 028248          154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTR  201 (211)
Q Consensus       154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r  201 (211)
                      ++.-.||||+.+..-. |           -.--|..|+++|+.|+...
T Consensus        68 avqV~CP~C~K~TKmL-G-----------rvD~CM~C~~PLTLd~~le  103 (110)
T PRK02935         68 AVQVICPSCEKPTKML-G-----------RVDACMHCNQPLTLDRSLE  103 (110)
T ss_pred             ceeeECCCCCchhhhc-c-----------ceeecCcCCCcCCcCcccc
Confidence            4455899999998866 1           1236999999999988654

>PF14353 CpXC: CpXC protein

Probab=94.30  E-value=0.038  Score=43.58  Aligned_cols=40  Identities=28%  Similarity=0.563  Sum_probs=26.2

Q ss_pred             CCCCCcccceeeccc-cccccC--------CCCcCceeCCCCCceeEEe
Q 028248          158 PCPNCGTENVSFFGT-ILSISS--------GGTTNTINCSNCGTTMVYD  197 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~-i~~v~s--------~~~~~~~kC~~C~~~L~f~  197 (211)
                      .||+||++...=+=+ |.+...        +++-+.+.||+||....++
T Consensus         3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~   51 (128)
T PF14353_consen    3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE   51 (128)
T ss_pred             CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence            699999987744323 221111        3455799999999986654

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=94.12  E-value=0.031  Score=46.02  Aligned_cols=32  Identities=19%  Similarity=0.319  Sum_probs=27.3

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD  197 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~  197 (211)
                      .|-.||+||+.+|-.           ++.-+.||.||+...-.
T Consensus         8 tKr~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~   39 (129)
T TIGR02300         8 TKRICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE   39 (129)
T ss_pred             ccccCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence            467899999999988           67889999999986555

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=94.11  E-value=0.011  Score=50.15  Aligned_cols=38  Identities=24%  Similarity=0.388  Sum_probs=27.3

Q ss_pred             ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248          156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL  202 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~  202 (211)
                      -=-||||+...... -      .  -.+...||+||..|++..++..
T Consensus       117 ~Y~Cp~C~~rytf~-e------A--~~~~F~Cp~Cg~~L~~~dn~~~  154 (178)
T PRK06266        117 FFFCPNCHIRFTFD-E------A--MEYGFRCPQCGEMLEEYDNSEL  154 (178)
T ss_pred             EEECCCCCcEEeHH-H------H--hhcCCcCCCCCCCCeecccHHH
Confidence            34599999665433 1      1  2468999999999999876544

>PHA00626 hypothetical protein

Probab=94.04  E-value=0.041  Score=39.74  Aligned_cols=36  Identities=31%  Similarity=0.701  Sum_probs=24.7

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      .||+||.....==|.+.     .-+++.+|+.||-..+=++
T Consensus         2 ~CP~CGS~~Ivrcg~cr-----~~snrYkCkdCGY~ft~~~   37 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMR-----GWSDDYVCCDCGYNDSKDA   37 (59)
T ss_pred             CCCCCCCceeeeeceec-----ccCcceEcCCCCCeechhh
Confidence            59999996544433322     2378999999997766543

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=94.04  E-value=0.042  Score=35.48  Aligned_cols=29  Identities=31%  Similarity=0.773  Sum_probs=17.1

Q ss_pred             CCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      ||+||.++.-=      +..+.++.+..|+.||..
T Consensus         3 C~~CG~~l~~~------ip~gd~r~R~vC~~Cg~I   31 (34)
T PF14803_consen    3 CPQCGGPLERR------IPEGDDRERLVCPACGFI   31 (34)
T ss_dssp             -TTT--B-EEE--------TT-SS-EEEETTTTEE
T ss_pred             cccccChhhhh------cCCCCCccceECCCCCCE
Confidence            99999996433      456678999999999964

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

Probab=93.95  E-value=0.03  Score=40.54  Aligned_cols=33  Identities=30%  Similarity=0.606  Sum_probs=20.1

Q ss_pred             eeecCCCCCccc-ceeeccccccccCCCCcCceeCCCCCc
Q 028248          154 ILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       154 iLkG~CPnCg~E-v~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      +++=.|||||++ +.-=      -+--.-.|..+||+||-
T Consensus        23 ~~~F~CPnCG~~~I~RC------~~CRk~~~~Y~CP~CGF   56 (59)
T PRK14890         23 AVKFLCPNCGEVIIYRC------EKCRKQSNPYTCPKCGF   56 (59)
T ss_pred             cCEeeCCCCCCeeEeec------hhHHhcCCceECCCCCC
Confidence            356688999887 4321      11222357788888873

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=93.83  E-value=0.051  Score=38.18  Aligned_cols=37  Identities=22%  Similarity=0.518  Sum_probs=27.3

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      .||.||+.+....-.    +.+.-.---+|++|-+++.|+-
T Consensus         2 ~CPyCge~~~~~iD~----s~~~Q~yiEDC~vCC~PI~~~v   38 (52)
T PF14255_consen    2 QCPYCGEPIEILIDP----SAGDQEYIEDCQVCCRPIEVQV   38 (52)
T ss_pred             CCCCCCCeeEEEEec----CCCCeeEEeehhhcCCccEEEE
Confidence            599999999988533    2222344458999999998864

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=93.78  E-value=0.063  Score=36.32  Aligned_cols=30  Identities=30%  Similarity=0.829  Sum_probs=24.7

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      -|.+||.||..-           ....++|++||..+.|-.
T Consensus         4 ~C~~Cg~~~~~~-----------~~~~irC~~CG~rIlyK~   33 (44)
T smart00659        4 ICGECGRENEIK-----------SKDVVRCRECGYRILYKK   33 (44)
T ss_pred             ECCCCCCEeecC-----------CCCceECCCCCceEEEEe
Confidence            499999997643           356799999999999876

present in RNA polymerase I, II and III

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=93.62  E-value=0.057  Score=35.71  Aligned_cols=28  Identities=29%  Similarity=0.723  Sum_probs=22.1

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      .|+.||.++-.+.       +..+...+.||+||.
T Consensus         7 ~C~~Cg~~fe~~~-------~~~~~~~~~CP~Cg~   34 (42)
T PF09723_consen    7 RCEECGHEFEVLQ-------SISEDDPVPCPECGS   34 (42)
T ss_pred             EeCCCCCEEEEEE-------EcCCCCCCcCCCCCC
Confidence            4999999888773       223378899999998

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=93.51  E-value=0.039  Score=33.63  Aligned_cols=23  Identities=35%  Similarity=0.949  Sum_probs=17.6

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L  194 (211)
                      .||+|+++|-              .+.-.||.||-..
T Consensus         2 ~CP~C~~~V~--------------~~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVP--------------ESAKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCch--------------hhcCcCCCCCCCC
Confidence            5999999983              4456899999653

Several members are annotated as putative helicases.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=93.49  E-value=0.024  Score=47.17  Aligned_cols=38  Identities=26%  Similarity=0.479  Sum_probs=27.1

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeE
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI  203 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i  203 (211)
                      =-||+|+.... |--.        -.+...||+||..|++..++..|
T Consensus       110 Y~Cp~c~~r~t-f~eA--------~~~~F~Cp~Cg~~L~~~dn~~~i  147 (158)
T TIGR00373       110 FICPNMCVRFT-FNEA--------MELNFTCPRCGAMLDYLDNSEAI  147 (158)
T ss_pred             EECCCCCcEee-HHHH--------HHcCCcCCCCCCEeeeccCHHHH
Confidence            35999996544 4211        13689999999999998776543

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=93.12  E-value=0.074  Score=42.79  Aligned_cols=23  Identities=43%  Similarity=1.096  Sum_probs=19.2

Q ss_pred             CCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      ||+||.+..              ..+.+|++|++.++
T Consensus         1 CPvCg~~l~--------------vt~l~C~~C~t~i~   23 (113)
T PF09862_consen    1 CPVCGGELV--------------VTRLKCPSCGTEIE   23 (113)
T ss_pred             CCCCCCceE--------------EEEEEcCCCCCEEE
Confidence            999998764              35789999999885

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=93.11  E-value=0.069  Score=34.54  Aligned_cols=34  Identities=24%  Similarity=0.465  Sum_probs=21.8

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      =.||||++...-=     ..+=....-+++|++|+....
T Consensus         3 i~CP~C~~~f~v~-----~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    3 ITCPNCQTRFRVP-----DDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             EECCCCCceEEcC-----HHHcccCCcEEECCCCCcEee
Confidence            4699999864321     111123456999999998754

>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=92.77  E-value=0.13  Score=52.09  Aligned_cols=24  Identities=29%  Similarity=0.629  Sum_probs=21.1

Q ss_pred             Hhhh-cCCCccChHHHHHHHHHHhh
Q 028248           35 MAYV-AGKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        35 ~aY~-~G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      .+|| .|+|+|||++||+|.++|+.
T Consensus        48 ~~YY~~~~p~IsD~eYD~L~~eL~~   72 (689)
T PRK14351         48 HRYYVEADPVIADRAYDALFARLQA   72 (689)
T ss_pred             HHHHhCCCCCCChHHHHHHHHHHHH
Confidence            4687 57999999999999999973

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=92.63  E-value=0.095  Score=36.26  Aligned_cols=33  Identities=27%  Similarity=0.611  Sum_probs=21.6

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      |||=||......-.......+  ....+.|++||.
T Consensus         5 PCPFCG~~~~~~~~~~~~~~~--~~~~V~C~~Cga   37 (61)
T PF14354_consen    5 PCPFCGSADVLIRQDEGFDYG--MYYYVECTDCGA   37 (61)
T ss_pred             CCCCCCCcceEeecccCCCCC--CEEEEEcCCCCC
Confidence            899999988877432110000  006799999998

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=92.32  E-value=0.14  Score=34.41  Aligned_cols=28  Identities=21%  Similarity=0.572  Sum_probs=20.1

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      .|++||.++-.+...       .+.....||+||.
T Consensus         7 ~C~~Cg~~fe~~~~~-------~~~~~~~CP~Cg~   34 (52)
T TIGR02605         7 RCTACGHRFEVLQKM-------SDDPLATCPECGG   34 (52)
T ss_pred             EeCCCCCEeEEEEec-------CCCCCCCCCCCCC
Confidence            599999877766311       1246678999998

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2

Probab=91.57  E-value=0.097  Score=34.04  Aligned_cols=33  Identities=30%  Similarity=0.597  Sum_probs=24.2

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      -||+||.--...|..        ....-+|.+||..|.-|.
T Consensus         3 ~C~~Cg~~Yh~~~~p--------P~~~~~Cd~cg~~L~qR~   35 (36)
T PF05191_consen    3 ICPKCGRIYHIEFNP--------PKVEGVCDNCGGELVQRK   35 (36)
T ss_dssp             EETTTTEEEETTTB----------SSTTBCTTTTEBEBEEG
T ss_pred             CcCCCCCccccccCC--------CCCCCccCCCCCeeEeCC
Confidence            399999876665533        677889999999887554

7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....

>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional

Probab=91.50  E-value=0.21  Score=50.45  Aligned_cols=24  Identities=29%  Similarity=0.463  Sum_probs=20.8

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHh
Q 028248           34 SMAYV-AGKPIMSDEEYDKLKQKLK   57 (211)
Q Consensus        34 ~~aY~-~G~Pi~sD~efD~Lk~~Lk   57 (211)
                      -.+|| .|+|+|||++||+|.++|+
T Consensus        20 ~~~YY~~~~p~IsD~~YD~L~~eL~   44 (669)
T PRK14350         20 DKEYYVDSSPSVEDFTYDKALLRLQ   44 (669)
T ss_pred             HHHHHhCCCCCCChHHHHHHHHHHH
Confidence            35677 4799999999999999996

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=91.16  E-value=0.23  Score=33.25  Aligned_cols=38  Identities=26%  Similarity=0.674  Sum_probs=27.8

Q ss_pred             HHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248          143 SLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG  191 (211)
Q Consensus       143 ~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~  191 (211)
                      .+.++.++--..|...||.||.+.+.-           .+.+.-|++|+
T Consensus         4 ~m~~~LL~G~~ML~~~Cp~C~~PL~~~-----------k~g~~~Cv~C~   41 (41)
T PF06677_consen    4 KMGEYLLQGWTMLDEHCPDCGTPLMRD-----------KDGKIYCVSCG   41 (41)
T ss_pred             HHHHHHHHhHhHhcCccCCCCCeeEEe-----------cCCCEECCCCC
Confidence            345566666666889999999887652           35578899996

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=91.11  E-value=0.13  Score=50.48  Aligned_cols=49  Identities=22%  Similarity=0.450  Sum_probs=35.4

Q ss_pred             cceeeecCCCCCcccceeeccccccccC-CCCcCceeCCCCCceeEEecC
Q 028248          151 ESLILKGPCPNCGTENVSFFGTILSISS-GGTTNTINCSNCGTTMVYDSN  199 (211)
Q Consensus       151 d~liLkG~CPnCg~Ev~aFfg~i~~v~s-~~~~~~~kC~~C~~~L~f~~~  199 (211)
                      |----.-|||.||++..-=|..+.-.+. ...+....|+.||+.+.=.-+
T Consensus       195 dqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k  244 (557)
T PF05876_consen  195 DQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDK  244 (557)
T ss_pred             CceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHH
Confidence            3334677999999998755666654333 457788999999998875443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=91.05  E-value=0.17  Score=32.65  Aligned_cols=33  Identities=24%  Similarity=0.514  Sum_probs=21.4

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L  194 (211)
                      =.||||++...-=     .-+=+....+++|++|+...
T Consensus         3 i~Cp~C~~~y~i~-----d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    3 ITCPNCQAKYEID-----DEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EECCCCCCEEeCC-----HHHCCCCCcEEECCCCCCEe
Confidence            4699999864321     11122456689999999753

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=90.94  E-value=0.17  Score=35.75  Aligned_cols=27  Identities=33%  Similarity=0.871  Sum_probs=22.0

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      -.||+||..+..          ..+.....|++||..
T Consensus        29 q~C~~CG~~~~~----------~~~~r~~~C~~Cg~~   55 (69)
T PF07282_consen   29 QTCPRCGHRNKK----------RRSGRVFTCPNCGFE   55 (69)
T ss_pred             cCccCccccccc----------ccccceEEcCCCCCE
Confidence            459999999887          236788999999986

More information about these proteins can be found at Protein of the Month: Transposase [].

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=90.88  E-value=0.26  Score=32.86  Aligned_cols=34  Identities=24%  Similarity=0.591  Sum_probs=22.1

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecC
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSN  199 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~  199 (211)
                      -||.||.-+  +      .+....++...|+.||-..-.+.+
T Consensus         2 FCp~Cg~~l--~------~~~~~~~~~~vC~~Cg~~~~~~~~   35 (52)
T smart00661        2 FCPKCGNML--I------PKEGKEKRRFVCRKCGYEEPIEQK   35 (52)
T ss_pred             CCCCCCCcc--c------cccCCCCCEEECCcCCCeEECCCc
Confidence            399999843  2      222223468899999987655444

>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.49  E-value=0.093  Score=43.05  Aligned_cols=33  Identities=30%  Similarity=0.825  Sum_probs=25.7

Q ss_pred             eecCCCCCcccc--eeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          155 LKGPCPNCGTEN--VSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       155 LkG~CPnCg~Ev--~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      ++|-||+||+--  .+|.           +..-.|.+||..+-|.+
T Consensus        20 l~grCP~CGeGrLF~gFL-----------K~~p~C~aCG~dyg~~~   54 (126)
T COG5349          20 LRGRCPRCGEGRLFRGFL-----------KVVPACEACGLDYGFAD   54 (126)
T ss_pred             hcCCCCCCCCchhhhhhc-----------ccCchhhhccccccCCc
Confidence            789999999863  3563           34557999999998865

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=89.83  E-value=0.24  Score=41.52  Aligned_cols=37  Identities=19%  Similarity=0.533  Sum_probs=23.1

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L  194 (211)
                      .||-||.+-+.-.-+..--+++..+-..+|++||...
T Consensus         2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f   38 (154)
T PRK00464          2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF   38 (154)
T ss_pred             cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence            4999999775543222211333444449999999864

>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.67  E-value=0.29  Score=39.69  Aligned_cols=37  Identities=27%  Similarity=0.600  Sum_probs=26.4

Q ss_pred             ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE--EecCceeEeCC
Q 028248          156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV--YDSNTRLITLP  206 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~--f~~~~r~i~~p  206 (211)
                      --+||.||.+.-              ..+.+|++|++...  |+...+...+|
T Consensus         6 ~~~cPvcg~~~i--------------VTeL~c~~~etTVrg~F~~s~F~~Lt~   44 (122)
T COG3877           6 INRCPVCGRKLI--------------VTELKCSNCETTVRGNFKMSKFEYLTS   44 (122)
T ss_pred             CCCCCcccccce--------------eEEEecCCCCceEecceecccccccCH
Confidence            358999999753              35789999999874  55555554444

>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.57  E-value=0.16  Score=42.62  Aligned_cols=21  Identities=29%  Similarity=0.649  Sum_probs=13.0

Q ss_pred             hccceeeecCCCCCcccceee
Q 028248          149 VRESLILKGPCPNCGTENVSF  169 (211)
Q Consensus       149 ~~d~liLkG~CPnCg~Ev~aF  169 (211)
                      +++.+|+...||+||+.+.-.
T Consensus        23 F~evii~sf~C~~CGyk~~ev   43 (161)
T PF03367_consen   23 FKEVIIMSFECEHCGYKNNEV   43 (161)
T ss_dssp             TEEEEEEEEE-TTT--EEEEE
T ss_pred             CceEEEEEeECCCCCCEeeeE
Confidence            677777777777777777644

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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=89.42  E-value=0.22  Score=31.71  Aligned_cols=29  Identities=31%  Similarity=0.886  Sum_probs=20.4

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD  197 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~  197 (211)
                      -|..||.+|. +       +   ....++|++||..+.|.
T Consensus         2 ~C~~Cg~~~~-~-------~---~~~~irC~~CG~RIlyK   30 (32)
T PF03604_consen    2 ICGECGAEVE-L-------K---PGDPIRCPECGHRILYK   30 (32)
T ss_dssp             BESSSSSSE--B-------S---TSSTSSBSSSS-SEEBE
T ss_pred             CCCcCCCeeE-c-------C---CCCcEECCcCCCeEEEe
Confidence            3889999998 2       2   34568999999887763

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=89.15  E-value=0.36  Score=33.14  Aligned_cols=36  Identities=28%  Similarity=0.630  Sum_probs=24.1

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY  196 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f  196 (211)
                      |||-||.+-..|-..   ........-.+|+.||....+
T Consensus         3 PCPfCGg~~~~~~~~---~~~~~~~~~~~C~~Cga~~~~   38 (53)
T TIGR03655         3 PCPFCGGADVYLRRG---FDPLDLSHYFECSTCGASGPV   38 (53)
T ss_pred             CCCCCCCcceeeEec---cCCCCCEEEEECCCCCCCccc
Confidence            899999988866310   012223445589999988765

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1

Probab=88.60  E-value=0.24  Score=41.68  Aligned_cols=22  Identities=32%  Similarity=0.628  Sum_probs=17.8

Q ss_pred             hhccceeeecCCCCCcccceee
Q 028248          148 IVRESLILKGPCPNCGTENVSF  169 (211)
Q Consensus       148 ~~~d~liLkG~CPnCg~Ev~aF  169 (211)
                      .+++.+++...||+||+.+.-.
T Consensus        21 ~F~evii~sf~C~~CGyk~~ev   42 (160)
T smart00709       21 YFREVIIMSFECEHCGYRNNEV   42 (160)
T ss_pred             CcceEEEEEEECCCCCCccceE
Confidence            4788888888899998887755

Also present in archaeal proteins.

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.38  E-value=0.37  Score=31.48  Aligned_cols=34  Identities=35%  Similarity=0.805  Sum_probs=20.4

Q ss_pred             CCCCCcccceeeccccccccCC--CCcCceeCCCCCce
Q 028248          158 PCPNCGTENVSFFGTILSISSG--GTTNTINCSNCGTT  193 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~--~~~~~~kC~~C~~~  193 (211)
                      +||+||.+...|| . .-..+.  ..+--..|-+||..
T Consensus         2 ~Cp~Cg~~~a~~~-~-~Q~rsaDE~~T~fy~C~~C~~~   37 (39)
T PF01096_consen    2 KCPKCGHNEAVFF-Q-IQTRSADEPMTLFYVCCNCGHR   37 (39)
T ss_dssp             --SSS-SSEEEEE-E-ESSSSSSSSSEEEEEESSSTEE
T ss_pred             CCcCCCCCeEEEE-E-eeccCCCCCCeEEEEeCCCCCe
Confidence            6999999999887 2 112222  23556789999864

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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=88.35  E-value=0.33  Score=33.60  Aligned_cols=28  Identities=32%  Similarity=0.859  Sum_probs=20.0

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      +.--||+||.+   |...        ...+..|..||-.
T Consensus        19 ~~~fCP~Cg~~---~m~~--------~~~r~~C~~Cgyt   46 (50)
T PRK00432         19 KNKFCPRCGSG---FMAE--------HLDRWHCGKCGYT   46 (50)
T ss_pred             ccCcCcCCCcc---hhec--------cCCcEECCCcCCE
Confidence            45589999987   3211        2368899999965

>PF12773 DZR: Double zinc ribbon

Probab=88.20  E-value=0.22  Score=33.17  Aligned_cols=25  Identities=36%  Similarity=0.808  Sum_probs=14.6

Q ss_pred             CCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248          159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L  194 (211)
                      ||+||+.+.           ........|++||+.+
T Consensus        15 C~~CG~~l~-----------~~~~~~~~C~~Cg~~~   39 (50)
T PF12773_consen   15 CPHCGTPLP-----------PPDQSKKICPNCGAEN   39 (50)
T ss_pred             ChhhcCChh-----------hccCCCCCCcCCcCCC
Confidence            666666655           1134556677777754

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=87.62  E-value=0.52  Score=31.02  Aligned_cols=34  Identities=35%  Similarity=0.854  Sum_probs=22.9

Q ss_pred             CCCCCcccceeeccccccccCC--CCcCceeCCCCCce
Q 028248          158 PCPNCGTENVSFFGTILSISSG--GTTNTINCSNCGTT  193 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~--~~~~~~kC~~C~~~  193 (211)
                      +||+||...-.||-.  -..|.  ..+--.+|.+|+-.
T Consensus         2 ~Cp~C~~~~a~~~q~--Q~RsaDE~mT~fy~C~~C~~~   37 (40)
T smart00440        2 PCPKCGNREATFFQL--QTRSADEPMTVFYVCTKCGHR   37 (40)
T ss_pred             cCCCCCCCeEEEEEE--cccCCCCCCeEEEEeCCCCCE
Confidence            699999888888732  22222  23556789999853

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454

Probab=87.59  E-value=0.28  Score=41.69  Aligned_cols=38  Identities=26%  Similarity=0.617  Sum_probs=25.1

Q ss_pred             cCCCCCcccceeec--cccccccCCCCcCceeCCCCCceeE
Q 028248          157 GPCPNCGTENVSFF--GTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       157 G~CPnCg~Ev~aFf--g~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      -.||||++.+.+.+  -+++.. ++...--.-|||||.+.-
T Consensus        40 ~~Cp~C~~~IrG~y~v~gv~~~-g~~~~~PsYC~~CGkpyP   79 (158)
T PF10083_consen   40 TSCPNCSTPIRGDYHVEGVFGL-GGHYEAPSYCHNCGKPYP   79 (158)
T ss_pred             HHCcCCCCCCCCceecCCeeee-CCCCCCChhHHhCCCCCc
Confidence            36999999998543  234433 233445678999998753

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.

>PRK12495 hypothetical protein; Provisional

Probab=87.49  E-value=0.43  Score=42.61  Aligned_cols=42  Identities=14%  Similarity=0.501  Sum_probs=34.0

Q ss_pred             HHHHHhhhccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          142 QSLTKLIVRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       142 ~~lt~~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      +.+.++.+|-...+---||.||.+++.+            +....|++|++...
T Consensus        28 ~~ma~lL~~gatmsa~hC~~CG~PIpa~------------pG~~~Cp~CQ~~~~   69 (226)
T PRK12495         28 ERMSELLLQGATMTNAHCDECGDPIFRH------------DGQEFCPTCQQPVT   69 (226)
T ss_pred             HHHHHHHHhhcccchhhcccccCcccCC------------CCeeECCCCCCccc
Confidence            3456677777777888999999999955            67788999998765

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=86.91  E-value=0.51  Score=37.11  Aligned_cols=31  Identities=32%  Similarity=0.776  Sum_probs=20.7

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      .|||||+...       ++.-....-.+.|++||.--.
T Consensus        23 ~CP~Cge~~v-------~v~~~k~~~h~~C~~CG~y~~   53 (99)
T PRK14892         23 ECPRCGKVSI-------SVKIKKNIAIITCGNCGLYTE   53 (99)
T ss_pred             ECCCCCCeEe-------eeecCCCcceEECCCCCCccC
Confidence            5999995322       223333577899999997643

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

Probab=86.75  E-value=0.67  Score=47.03  Aligned_cols=25  Identities=36%  Similarity=0.573  Sum_probs=21.6

Q ss_pred             Hhhhc-CCCccChHHHHHHHHHHhhh
Q 028248           35 MAYVA-GKPIMSDEEYDKLKQKLKME   59 (211)
Q Consensus        35 ~aY~~-G~Pi~sD~efD~Lk~~Lk~~   59 (211)
                      .+||- ++|+|+|+|||+|.++|+.-
T Consensus        23 ~~Yyv~d~P~VsD~eYD~L~reL~~l   48 (667)
T COG0272          23 YRYYVLDAPSVSDAEYDQLYRELQEL   48 (667)
T ss_pred             HHHhccCCCCCChHHHHHHHHHHHHH
Confidence            46666 99999999999999999753

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=85.94  E-value=0.92  Score=40.59  Aligned_cols=65  Identities=25%  Similarity=0.494  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhhccceeeecCCCCCccc-ceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          130 WFAAVPLIVYLSQSLTKLIVRESLILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       130 ~~~~~Pvi~~~a~~lt~~~~~d~liLkG~CPnCg~E-v~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      |.++-|+....+..+..-+....---+|-||+||.. +.+.+..   ... ...-...|+.|++.=.|.+
T Consensus       146 ~aaL~~~~~~~a~~l~~~~~~~~~w~~g~CPvCGs~P~~s~l~~---~~~-~G~R~L~Cs~C~t~W~~~R  211 (290)
T PF04216_consen  146 WAALQPFLAALAAALDAALLPPEGWQRGYCPVCGSPPVLSVLRG---GER-EGKRYLHCSLCGTEWRFVR  211 (290)
T ss_dssp             HHHHHHHHHHHHHT--TTSSS---TT-SS-TTT---EEEEEEE----------EEEEEETTT--EEE--T
T ss_pred             HHHHHHHHHHHHHhccccccccCCccCCcCCCCCCcCceEEEec---CCC-CccEEEEcCCCCCeeeecC
Confidence            455557776666544333333333356999999987 5566422   111 1234456777776665554

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=85.92  E-value=0.49  Score=51.04  Aligned_cols=46  Identities=24%  Similarity=0.411  Sum_probs=27.8

Q ss_pred             ceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248          152 SLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT  200 (211)
Q Consensus       152 ~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~  200 (211)
                      .-+-.-.||+||++++..|=..=   +........|++||..+..+..+
T Consensus       663 VEV~~rkCPkCG~~t~~~fCP~C---Gs~te~vy~CPsCGaev~~des~  708 (1337)
T PRK14714        663 VEVGRRRCPSCGTETYENRCPDC---GTHTEPVYVCPDCGAEVPPDESG  708 (1337)
T ss_pred             EEEEEEECCCCCCccccccCccc---CCcCCCceeCccCCCccCCCccc
Confidence            45566789999999887653321   11122345677777766655433

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=85.86  E-value=0.33  Score=29.33  Aligned_cols=11  Identities=55%  Similarity=1.259  Sum_probs=8.7

Q ss_pred             eeecCCCCCcc
Q 028248          154 ILKGPCPNCGT  164 (211)
Q Consensus       154 iLkG~CPnCg~  164 (211)
                      ++.=+|||||+
T Consensus        14 ~v~f~CPnCG~   24 (24)
T PF07754_consen   14 AVPFPCPNCGF   24 (24)
T ss_pred             CceEeCCCCCC
Confidence            45678999996

It is likely to bind zinc via its four well-conserved cysteine residues.

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=85.77  E-value=0.62  Score=40.61  Aligned_cols=43  Identities=28%  Similarity=0.557  Sum_probs=32.3

Q ss_pred             hccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCCCC
Q 028248          149 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPEG  208 (211)
Q Consensus       149 ~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~peg  208 (211)
                      .+|.=.++.-|++|+++..-            .-++.+|||||..     .+|.|-.+=+
T Consensus       142 ~~dlGVI~A~CsrC~~~L~~------------~~~~l~Cp~Cg~t-----EkRKia~~y~  184 (188)
T COG1096         142 GNDLGVIYARCSRCRAPLVK------------KGNMLKCPNCGNT-----EKRKIAKDYG  184 (188)
T ss_pred             CCcceEEEEEccCCCcceEE------------cCcEEECCCCCCE-----Eeeeeccccc
Confidence            68887799999999998754            2568899999963     4566655433

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=85.54  E-value=0.89  Score=36.99  Aligned_cols=18  Identities=17%  Similarity=0.547  Sum_probs=12.6

Q ss_pred             cCceeCCCCCce-eEEecC
Q 028248          182 TNTINCSNCGTT-MVYDSN  199 (211)
Q Consensus       182 ~~~~kC~~C~~~-L~f~~~  199 (211)
                      .....||.||+. +.....
T Consensus       105 ~~~~~CP~Cgs~~~~i~~G  123 (135)
T PRK03824        105 HAFLKCPKCGSRDFEIVKG  123 (135)
T ss_pred             ccCcCCcCCCCCCcEEecC
Confidence            345679999975 666654

>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]

Probab=84.48  E-value=0.2  Score=42.98  Aligned_cols=37  Identities=24%  Similarity=0.551  Sum_probs=27.0

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeE
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLI  203 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i  203 (211)
                      .||||...+. |=      +.  ..+...||.||..|++..+.+.|
T Consensus       115 ~C~~~~~r~s-fd------eA--~~~~F~Cp~Cg~~L~~~d~s~~i  151 (176)
T COG1675         115 VCPNCHVKYS-FD------EA--MELGFTCPKCGEDLEEYDSSEEI  151 (176)
T ss_pred             eCCCCCCccc-HH------HH--HHhCCCCCCCCchhhhccchHHH
Confidence            5999987754 30      11  25668999999999998877654

>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV

Probab=84.35  E-value=0.43  Score=43.86  Aligned_cols=24  Identities=42%  Similarity=1.003  Sum_probs=20.7

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L  194 (211)
                      |.|-|||.+|..+              +..||||++.=
T Consensus        83 ~~C~~CGa~V~~~--------------e~~Cp~C~Stn  106 (314)
T PF09567_consen   83 GKCNNCGANVSRL--------------EESCPNCGSTN  106 (314)
T ss_pred             hhhccccceeeeh--------------hhcCCCCCccc
Confidence            7899999999888              56899999763

All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system

>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase

Probab=84.12  E-value=0.93  Score=29.81  Aligned_cols=30  Identities=43%  Similarity=0.978  Sum_probs=18.7

Q ss_pred             ecCCCCCccc-ceeeccccccccCCCCcCceeCCCCCc
Q 028248          156 KGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       156 kG~CPnCg~E-v~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      .+|||+||-. -|.| .+      ...+...-|..|+.
T Consensus         3 ~~pCP~CGG~DrFr~-~d------~~g~G~~~C~~Cg~   33 (37)
T smart00778        3 HGPCPNCGGSDRFRF-DD------KDGRGTWFCSVCGA   33 (37)
T ss_pred             ccCCCCCCCcccccc-cc------CCCCcCEEeCCCCC
Confidence            5899999763 3343 11      12346678888863

This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.

>COG1779 C4-type Zn-finger protein [General function prediction only]

Probab=83.62  E-value=0.58  Score=41.20  Aligned_cols=31  Identities=35%  Similarity=0.821  Sum_probs=22.8

Q ss_pred             eecCCCCCccccee--------eccccccccCCCCcCceeCCCCCc
Q 028248          155 LKGPCPNCGTENVS--------FFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       155 LkG~CPnCg~Ev~a--------Ffg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      -...||+||....+        |||.++       -....|.+||-
T Consensus        13 ~~~~CPvCg~~l~~~~~~~~IPyFG~V~-------i~t~~C~~CgY   51 (201)
T COG1779          13 TRIDCPVCGGTLKAHMYLYDIPYFGEVL-------ISTGVCERCGY   51 (201)
T ss_pred             eeecCCcccceeeEEEeeecCCccceEE-------EEEEEccccCC
Confidence            56789999986543        677765       45678999984

>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated

Probab=83.00  E-value=1.1  Score=40.01  Aligned_cols=35  Identities=31%  Similarity=0.637  Sum_probs=24.9

Q ss_pred             ccceeeec----CCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248          150 RESLILKG----PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       150 ~d~liLkG----~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      ++.+-+.|    |||+||+.+....     +.   .+...=||+|..
T Consensus       235 ~~~l~Vy~R~g~pC~~Cg~~I~~~~-----~~---gR~t~~CP~CQ~  273 (274)
T PRK01103        235 QQSLQVYGREGEPCRRCGTPIEKIK-----QG---GRSTFFCPRCQK  273 (274)
T ss_pred             cceeEEcCCCCCCCCCCCCeeEEEE-----EC---CCCcEECcCCCC
Confidence            44455665    7999999987541     11   478889999974

>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function

Probab=82.99  E-value=1.9  Score=26.88  Aligned_cols=25  Identities=40%  Similarity=0.590  Sum_probs=19.8

Q ss_pred             HHHHHh-hhcCCCccChHHHHHHHHHHh
Q 028248           31 LEASMA-YVAGKPIMSDEEYDKLKQKLK   57 (211)
Q Consensus        31 LeA~~a-Y~~G~Pi~sD~efD~Lk~~Lk   57 (211)
                      |+.+.. |.+|  +||++||++.|.+|.
T Consensus         5 L~~L~~l~~~G--~IseeEy~~~k~~ll   30 (31)
T PF09851_consen    5 LEKLKELYDKG--EISEEEYEQKKARLL   30 (31)
T ss_pred             HHHHHHHHHcC--CCCHHHHHHHHHHHh
Confidence            455555 7777  799999999999884

>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines

Probab=82.88  E-value=1.1  Score=33.84  Aligned_cols=37  Identities=22%  Similarity=0.470  Sum_probs=20.2

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD  197 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~  197 (211)
                      =.||.|+.+...=..    +........+.|.+||..-+++
T Consensus        23 F~CPfC~~~~sV~v~----idkk~~~~~~~C~~Cg~~~~~~   59 (81)
T PF05129_consen   23 FDCPFCNHEKSVSVK----IDKKEGIGILSCRVCGESFQTK   59 (81)
T ss_dssp             ---TTT--SS-EEEE----EETTTTEEEEEESSS--EEEEE
T ss_pred             EcCCcCCCCCeEEEE----EEccCCEEEEEecCCCCeEEEc
Confidence            379999966554432    2444678899999998776654

; PDB: 1WII_A.

>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=82.82  E-value=0.74  Score=39.49  Aligned_cols=23  Identities=30%  Similarity=0.928  Sum_probs=18.1

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L  194 (211)
                      -.||+||.    +           +.....|++||...
T Consensus       310 ~~C~~cg~----~-----------~~r~~~C~~cg~~~  332 (364)
T COG0675         310 KTCPCCGH----L-----------SGRLFKCPRCGFVH  332 (364)
T ss_pred             ccccccCC----c-----------cceeEECCCCCCee
Confidence            45999999    2           45678999999764

>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation

Probab=82.57  E-value=0.69  Score=36.38  Aligned_cols=35  Identities=23%  Similarity=0.451  Sum_probs=21.0

Q ss_pred             eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCcee-EEecCc
Q 028248          154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM-VYDSNT  200 (211)
Q Consensus       154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L-~f~~~~  200 (211)
                      -+++-|++||.+...=            .+...||.||+.- ...+..
T Consensus        68 p~~~~C~~Cg~~~~~~------------~~~~~CP~Cgs~~~~i~~G~  103 (113)
T PF01155_consen   68 PARARCRDCGHEFEPD------------EFDFSCPRCGSPDVEIISGR  103 (113)
T ss_dssp             --EEEETTTS-EEECH------------HCCHH-SSSSSS-EEEEESS
T ss_pred             CCcEECCCCCCEEecC------------CCCCCCcCCcCCCcEEccCC
Confidence            3678899999986422            3346799999973 555543

The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.

>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=82.23  E-value=0.69  Score=35.31  Aligned_cols=31  Identities=29%  Similarity=0.598  Sum_probs=17.6

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      ..+.||-|++...+|.     |.  .+.+..+|+.||.
T Consensus        32 ~~~~CPfH~d~~pS~~-----i~--~~k~~~~Cf~Cg~   62 (97)
T PF01807_consen   32 YRCLCPFHDDKTPSFS-----IN--PDKNRFKCFGCGK   62 (97)
T ss_dssp             EEE--SSS--SS--EE-----EE--TTTTEEEETTT--
T ss_pred             EEEECcCCCCCCCceE-----EE--CCCCeEEECCCCC
Confidence            5789999999888773     32  2567899999996

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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.

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

Probab=82.17  E-value=1.3  Score=29.34  Aligned_cols=25  Identities=20%  Similarity=0.457  Sum_probs=20.7

Q ss_pred             CceeCCCCCceeEEecCceeEeCCC
Q 028248          183 NTINCSNCGTTMVYDSNTRLITLPE  207 (211)
Q Consensus       183 ~~~kC~~C~~~L~f~~~~r~i~~pe  207 (211)
                      ...+|++||..++++.....++-|.
T Consensus         2 ~~y~C~~CG~~~~~~~~~~~~~Cp~   26 (46)
T PRK00398          2 AEYKCARCGREVELDEYGTGVRCPY   26 (46)
T ss_pred             CEEECCCCCCEEEECCCCCceECCC
Confidence            3579999999999998766777775

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=82.14  E-value=1.2  Score=35.21  Aligned_cols=34  Identities=15%  Similarity=0.323  Sum_probs=21.1

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce-eEEecC
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT-MVYDSN  199 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~-L~f~~~  199 (211)
                      ..+-|++||+++..-           ..+...||.||.. +...+.
T Consensus        69 ~~~~C~~Cg~~~~~~-----------~~~~~~CP~Cgs~~~~i~~G  103 (114)
T PRK03681         69 AECWCETCQQYVTLL-----------TQRVRRCPQCHGDMLRIVAD  103 (114)
T ss_pred             cEEEcccCCCeeecC-----------CccCCcCcCcCCCCcEEccC
Confidence            567899999632211           1233679999975 444443

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=81.95  E-value=0.81  Score=36.21  Aligned_cols=33  Identities=15%  Similarity=0.450  Sum_probs=21.7

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce-eEEecC
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT-MVYDSN  199 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~-L~f~~~  199 (211)
                      +.+-|++||++.. .           ..+...||.||.. ....+.
T Consensus        69 ~~~~C~~Cg~~~~-~-----------~~~~~~CP~Cgs~~~~i~~G  102 (115)
T TIGR00100        69 VECECEDCSEEVS-P-----------EIDLYRCPKCHGIMLQVRAG  102 (115)
T ss_pred             cEEEcccCCCEEe-c-----------CCcCccCcCCcCCCcEEecC
Confidence            6789999994332 2           2335679999985 355544

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

>TIGR00244 transcriptional regulator NrdR

Probab=81.85  E-value=0.95  Score=38.09  Aligned_cols=37  Identities=19%  Similarity=0.456  Sum_probs=28.8

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCcee
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L  194 (211)
                      .||-||.+...-.-+=.+..++.-+-+-+|.+||...
T Consensus         2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF   38 (147)
T TIGR00244         2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF   38 (147)
T ss_pred             CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence            4999999988876555555666667788999999864

Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.

>PF15616 TerY-C: TerY-C metal binding domain

Probab=81.68  E-value=1.6  Score=36.07  Aligned_cols=44  Identities=23%  Similarity=0.641  Sum_probs=29.9

Q ss_pred             eeecCCCCCccc-ceee--ccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248          154 ILKGPCPNCGTE-NVSF--FGTILSISSGGTTNTINCSNCGTTMVYDSNT  200 (211)
Q Consensus       154 iLkG~CPnCg~E-v~aF--fg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~  200 (211)
                      +=..-||.||.+ .++-  =|-++=+.   ....+-||.||....|....
T Consensus        75 ~g~PgCP~CGn~~~fa~C~CGkl~Ci~---g~~~~~CPwCg~~g~~~~~~  121 (131)
T PF15616_consen   75 IGAPGCPHCGNQYAFAVCGCGKLFCID---GEGEVTCPWCGNEGSFGAGD  121 (131)
T ss_pred             cCCCCCCCCcChhcEEEecCCCEEEeC---CCCCEECCCCCCeeeecccC
Confidence            344889999998 2221  12233333   36699999999999998853

>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=80.36  E-value=1.6  Score=35.41  Aligned_cols=49  Identities=22%  Similarity=0.477  Sum_probs=33.9

Q ss_pred             hccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCcee
Q 028248          149 VRESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRL  202 (211)
Q Consensus       149 ~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~  202 (211)
                      -....+.+=.||-|+.++ .. ..  + .......+.+||.|+...+.+.++.+
T Consensus        23 ~~~~~~~~~~cP~C~s~~-~~-k~--g-~~~~~~qRyrC~~C~~tf~~~~~~~~   71 (129)
T COG3677          23 AIRMQITKVNCPRCKSSN-VV-KI--G-GIRRGHQRYKCKSCGSTFTVETGSPL   71 (129)
T ss_pred             HHhhhcccCcCCCCCccc-ee-eE--C-CccccccccccCCcCcceeeeccCcc
Confidence            344555677899999999 33 11  1 11223778999999999999887544

---

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	211
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	1e-04

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 13/52 (25%)

Query: 159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLPEGSE 210
           CP C          +   S G   + + C+ CG  +    + +L+     SE
Sbjct: 24  CPECKVYPPKI---VERFSEG---DVV-CALCGLVL----SDKLVD--TRSE 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	211
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	96.75
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	95.78
1b04_A	318	Protein (DNA ligase); DNA replication; 2.80A {Geob	95.77
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	95.49
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	94.55
3jsl_A	318	DNA ligase; NAD+-dependent, DNA damage, DNA repair	94.52
3uq8_A	322	DNA ligase; adenylated protein, ATP-grAsp, rossman	94.46
4glw_A	305	DNA ligase; inhibitor, ligase-ligase inhibitor com	94.41
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	94.27
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	94.01
1ta8_A	332	DNA ligase, NAD-dependent; nucleotidyl transferase	93.94
1zau_A	328	DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu	93.94
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	93.21
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	93.12
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	92.96
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	92.26
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	91.72
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	90.8
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	90.51
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	89.62
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	89.58
3flo_B	206	DNA polymerase alpha catalytic subunit A; protein-	88.74
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	87.94
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	86.94
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	85.9
1x3z_A	335	Peptide: N-glycanase; hydrolase-hydrolase inhibito	85.75
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	84.01
3v2d_5	60	50S ribosomal protein L32; ribosome associated inh	83.44
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	83.3
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	83.24
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	82.87
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	82.77
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	81.36
2qkd_A	404	Zinc finger protein ZPR1; helical hairpins, beta h	80.55
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	80.31

>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=96.75  E-value=0.0011  Score=58.42  Aligned_cols=50  Identities=24%  Similarity=0.468  Sum_probs=37.1

Q ss_pred             HHHHHHHhhhccceeeecCCCCCccc-ceeeccccccccCCCCcCceeCCCCCceeEEecCc
Q 028248          140 LSQSLTKLIVRESLILKGPCPNCGTE-NVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNT  200 (211)
Q Consensus       140 ~a~~lt~~~~~d~liLkG~CPnCg~E-v~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~  200 (211)
                      .|..||.-|+..+.    -|||||.. ...|       ++|+.....-|++|.+..+..++.
T Consensus        22 ~aRVLTE~Wv~~n~----yCPnCG~~~l~~f-------~nN~PVaDF~C~~C~EeyELKSk~   72 (257)
T 4esj_A           22 KARILTEDWVYRQS----YCPNCGNNPLNHF-------ENNRPVADFYCNHCSEEFELKSKK   72 (257)
T ss_dssp             HHHHHHHHHHHHHC----CCTTTCCSSCEEC-----------CCCEEECTTTCCEEEEEEEE
T ss_pred             eehhhhHHHHHHCC----cCCCCCChhhhhc-------cCCCcccccccCCcchhheecccc
Confidence            46677887777665    89999996 4466       667777889999999999998863

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

Probab=95.78  E-value=0.0088  Score=43.08  Aligned_cols=43  Identities=26%  Similarity=0.538  Sum_probs=35.5

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCC
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLP  206 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~p  206 (211)
                      ++=.||.|+.+...|         ..++..+.|.+|++.|.--+..+.+.+.
T Consensus         6 m~VKCp~C~niq~VF---------ShA~tvV~C~~Cg~~L~~PTGGKA~l~~   48 (66)
T 1qxf_A            6 VKVKCPDCEHEQVIF---------DHPSTIVKCIICGRTVAEPTGGKGNIKA   48 (66)
T ss_dssp             EEEECTTTCCEEEEE---------SSCSSCEECSSSCCEEEECCSSSCEECS
T ss_pred             EEEECCCCCCceEEE---------ecCceEEEcccCCCEEeecCCcceeeeh
Confidence            677899999999999         2368899999999999888876665553

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

Probab=95.77  E-value=0.0084  Score=54.02  Aligned_cols=25  Identities=36%  Similarity=0.634  Sum_probs=21.6

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 028248           34 SMAYV-AGKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        34 ~~aY~-~G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      -.+|| .|+|+|||+|||+|.++|+.
T Consensus        21 ~~~YY~~d~p~IsD~eYD~L~~eL~~   46 (318)
T 1b04_A           21 GYEYYVLDRPSVPDAEYDRLMQELIA   46 (318)
T ss_dssp             HHHHHTTCSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            34676 69999999999999999874

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

Probab=95.49  E-value=0.016  Score=41.37  Aligned_cols=43  Identities=28%  Similarity=0.632  Sum_probs=35.0

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCC
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLP  206 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~p  206 (211)
                      ++=.||.|+.+...|         ..++..+.|.+|++.|.--+..+.+...
T Consensus        14 m~VkCp~C~~~q~VF---------Sha~t~V~C~~Cgt~L~~PTGGKa~l~~   56 (63)
T 3j20_W           14 LRVKCIDCGNEQIVF---------SHPATKVRCLICGATLVEPTGGKGIVKA   56 (63)
T ss_dssp             EEEECSSSCCEEEEE---------SSCSSCEECSSSCCEEEECCSSSCEECS
T ss_pred             EEEECCCCCCeeEEE---------ecCCeEEEccCcCCEEecCCCCcEEEEE
Confidence            677899999999998         2268899999999999888766655543

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

Probab=94.55  E-value=0.051  Score=40.50  Aligned_cols=42  Identities=19%  Similarity=0.486  Sum_probs=36.3

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeC
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITL  205 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~  205 (211)
                      ++-.||.|+.+...|       +  .++..+.|.+|++.|.--+..+.+.+
T Consensus        31 m~VkCp~C~n~q~VF-------S--hA~t~V~C~~Cg~~L~~PTGGKA~l~   72 (81)
T 2xzm_6           31 MDVKCAQCQNIQMIF-------S--NAQSTIICEKCSAILCKPTGGKVQIQ   72 (81)
T ss_dssp             EEEECSSSCCEEEEE-------T--TCSSCEECSSSCCEEEEECSSCEEEC
T ss_pred             EEeECCCCCCeeEEE-------e--cCccEEEccCCCCEEeecCCCCeEec
Confidence            777899999999999       1  36889999999999999888777766

>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=94.52  E-value=0.03  Score=50.50  Aligned_cols=25  Identities=40%  Similarity=0.620  Sum_probs=21.2

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 028248           34 SMAYVA-GKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        34 ~~aY~~-G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      -.+||. |+|+|||+|||+|.++|+.
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

>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=94.46  E-value=0.031  Score=50.47  Aligned_cols=26  Identities=35%  Similarity=0.590  Sum_probs=22.1

Q ss_pred             HHHhhhc-CCCccChHHHHHHHHHHhh
Q 028248           33 ASMAYVA-GKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        33 A~~aY~~-G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      +-.+||. ++|+|||+|||+|.++|+.
T Consensus        16 ~~~~YY~~d~p~IsD~eYD~L~~eL~~   42 (322)
T 3uq8_A           16 YEYEYHVLDNPSVPDSEYDRLFHQLKA   42 (322)
T ss_dssp             HHHHHHTSSCCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            3457886 9999999999999999865

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

Probab=94.41  E-value=0.0069  Score=53.98  Aligned_cols=25  Identities=36%  Similarity=0.632  Sum_probs=3.8

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 028248           34 SMAYV-AGKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        34 ~~aY~-~G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      -.+|| .|+|+|||+|||+|.++|+.
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            45777 59999999999999988874

>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b

Probab=94.27  E-value=0.041  Score=41.12  Aligned_cols=44  Identities=20%  Similarity=0.467  Sum_probs=36.1

Q ss_pred             eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCC
Q 028248          154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLP  206 (211)
Q Consensus       154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~p  206 (211)
                      -++-.||.|+.+...|       +  .++..+.|.+|++.|.--+....+.+.
T Consensus        32 Fm~VkCp~C~~~q~VF-------S--ha~t~V~C~~Cg~~L~~PTGGKa~l~e   75 (82)
T 3u5c_b           32 FLDVKCPGCLNITTVF-------S--HAQTAVTCESCSTILCTPTGGKAKLSE   75 (82)
T ss_dssp             EEEEECTTSCSCEEEE-------S--BCSSCCCCSSSCCCCEECCSSBCEECS
T ss_pred             EEEEECCCCCCeeEEE-------e--cCCeEEEccccCCEEeccCCCCeEecC
Confidence            3677899999999999       1  268899999999999988877666554

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

Probab=94.01  E-value=0.043  Score=53.87  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=21.5

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 028248           34 SMAYV-AGKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        34 ~~aY~-~G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      -.+|| .++|+|||+|||+|.++|+.
T Consensus        19 ~~~YY~~d~p~isD~eYD~L~~eL~~   44 (671)
T 2owo_A           19 EYLYHVMDAPEIPDAEYDRLMRELRE   44 (671)
T ss_dssp             HHHHHHTTCSSBCCTHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            45666 68999999999999999875

>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=93.94  E-value=0.036  Score=50.23  Aligned_cols=25  Identities=28%  Similarity=0.410  Sum_probs=21.6

Q ss_pred             Hhhh-cCCCccChHHHHHHHHHHhhh
Q 028248           35 MAYV-AGKPIMSDEEYDKLKQKLKME   59 (211)
Q Consensus        35 ~aY~-~G~Pi~sD~efD~Lk~~Lk~~   59 (211)
                      .+|| .|+|+|||+|||+|.++|+.-
T Consensus        27 ~~YY~~d~p~IsD~eYD~L~~eL~~l   52 (332)
T 1ta8_A           27 HEYYVKDQPSVEDYVYDRLYKELVDI   52 (332)
T ss_dssp             HHHHTSSCCSSCHHHHHHHHHHHHHH
T ss_pred             HHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence            4676 699999999999999998753

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

Probab=93.94  E-value=0.045  Score=49.43  Aligned_cols=25  Identities=36%  Similarity=0.670  Sum_probs=21.6

Q ss_pred             Hhhh-cCCCccChHHHHHHHHHHhhh
Q 028248           35 MAYV-AGKPIMSDEEYDKLKQKLKME   59 (211)
Q Consensus        35 ~aY~-~G~Pi~sD~efD~Lk~~Lk~~   59 (211)
                      .+|| .|+|+|||+|||+|.++|+.-
T Consensus        29 ~~YY~~d~p~IsD~eYD~L~~eL~~l   54 (328)
T 1zau_A           29 FRYYVRDAPIISDAEFDELLRRLEAL   54 (328)
T ss_dssp             HHHTTTCCCSSCTHHHHHHHHHHHHH
T ss_pred             HHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence            4677 599999999999999999753

>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2

Probab=93.21  E-value=0.04  Score=46.37  Aligned_cols=33  Identities=27%  Similarity=0.610  Sum_probs=22.1

Q ss_pred             eeecCCCCCcc-cceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248          154 ILKGPCPNCGT-ENVSFFGTILSISSGGTTNTINCSNCGTTMVY  196 (211)
Q Consensus       154 iLkG~CPnCg~-Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f  196 (211)
                      .-+++||+||- .-+.||.     .+     ...||+||..-.+
T Consensus        12 ~~~~~CP~Cg~~d~~~~~~-----dg-----~~~C~~Cg~~~~~   45 (255)
T 1nui_A           12 LYHIPCDNCGSSDGNSLFS-----DG-----HTFCYVCEKWTAG   45 (255)
T ss_dssp             EEEECCSSSCCSSCEEEET-----TS-----CEEETTTCCEEC-
T ss_pred             ecCCcCCCCCCCCCceEeC-----CC-----CeecccCCCcCCC
Confidence            36899999987 3344441     11     3999999977544

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

Probab=93.12  E-value=0.055  Score=52.29  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=21.5

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhh
Q 028248           34 SMAYV-AGKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        34 ~~aY~-~G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      -.+|| .|+|+|||+|||+|.++|+.
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 59999999999999999875

>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=92.96  E-value=0.053  Score=53.15  Aligned_cols=27  Identities=37%  Similarity=0.567  Sum_probs=22.7

Q ss_pred             HHhhh-cCCCccChHHHHHHHHHHhhhC
Q 028248           34 SMAYV-AGKPIMSDEEYDKLKQKLKMEG   60 (211)
Q Consensus        34 ~~aY~-~G~Pi~sD~efD~Lk~~Lk~~G   60 (211)
                      -.+|| .++|+|||+|||+|.++|+.-=
T Consensus        21 ~~~YY~~d~p~isD~eYD~l~~eL~~lE   48 (667)
T 1dgs_A           21 NYRYYVLADPEISDAEYDRLLRELKELE   48 (667)
T ss_dssp             HHHHHTTCCCCSCSSSSHHHHHHHHHHT
T ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHHHH
Confidence            34677 6999999999999999998543

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=92.26  E-value=0.057  Score=40.65  Aligned_cols=44  Identities=14%  Similarity=0.358  Sum_probs=34.8

Q ss_pred             eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEeCC
Q 028248          154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLITLP  206 (211)
Q Consensus       154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~~p  206 (211)
                      -++-.||.|+.+...|         ..++..+.|.+|++.|.--+..+.+.+.
T Consensus        34 Fm~VkCp~C~~~~~VF---------ShA~t~V~C~~CgtvL~~PTGGKa~l~e   77 (86)
T 3iz6_X           34 FMDVKCQGCFNITTVF---------SHSQTVVVCPGCQTVLCQPTGGKARLTE   77 (86)
T ss_dssp             EEEEECTTTCCEEEEE---------TTCSSCCCCSSSCCCCSCCCSSSCCCSC
T ss_pred             EeEEECCCCCCeeEEE---------ecCCcEEEccCCCCEeecCCCCCEEecC
Confidence            3777899999999999         2268899999999999777666555443

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=91.72  E-value=0.086  Score=34.54  Aligned_cols=29  Identities=24%  Similarity=0.710  Sum_probs=21.5

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      .||+||.+...|      +   ..+.+..|+.||..+.
T Consensus         7 ~CP~C~~~~l~~------d---~~~gelvC~~CG~v~~   35 (50)
T 1pft_A            7 VCPACESAELIY------D---PERGEIVCAKCGYVIE   35 (50)
T ss_dssp             SCTTTSCCCEEE------E---TTTTEEEESSSCCBCC
T ss_pred             eCcCCCCcceEE------c---CCCCeEECcccCCccc
Confidence            699999865555      1   1467899999998653

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=90.80  E-value=0.14  Score=34.45  Aligned_cols=38  Identities=26%  Similarity=0.652  Sum_probs=24.4

Q ss_pred             ecCCCCCcccceeecccccc-ccCCCCcCceeCCCCCcee
Q 028248          156 KGPCPNCGTENVSFFGTILS-ISSGGTTNTINCSNCGTTM  194 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~-v~s~~~~~~~kC~~C~~~L  194 (211)
                      .-+||.||.....|+-. -. .+....+.-.+|.+||..-
T Consensus        15 ~~~Cp~Cg~~~~~~~q~-Q~rsadep~T~fy~C~~Cg~~w   53 (57)
T 1qyp_A           15 KITCPKCGNDTAYWWEM-QTRAGDEPSTIFYKCTKCGHTW   53 (57)
T ss_dssp             ECCCTTTCCSEEEEEEE-CCSSSSCSSEEEEEESSSCCEE
T ss_pred             EeECCCCCCCEEEEEEe-ecccCCCCCcEEEEcCCCCCEe
Confidence            56899999977676622 21 1112234567999999753

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=90.51  E-value=0.15  Score=34.27  Aligned_cols=29  Identities=28%  Similarity=0.629  Sum_probs=21.6

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      +.--||.||..++-.  .        ...+..|+.||-+
T Consensus        18 ~~k~CP~CG~~~fm~--~--------~~~R~~C~kCG~t   46 (50)
T 3j20_Y           18 KNKFCPRCGPGVFMA--D--------HGDRWACGKCGYT   46 (50)
T ss_dssp             SSEECSSSCSSCEEE--E--------CSSEEECSSSCCE
T ss_pred             ecccCCCCCCceEEe--c--------CCCeEECCCCCCE
Confidence            556799999987644  1        2468899999854

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=89.62  E-value=0.13  Score=36.89  Aligned_cols=40  Identities=25%  Similarity=0.639  Sum_probs=27.3

Q ss_pred             eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec-CceeEe
Q 028248          154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS-NTRLIT  204 (211)
Q Consensus       154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~-~~r~i~  204 (211)
                      -+.=.|++||.+|---           ....+.|+.||..+.|.. +.|.+.
T Consensus        26 ~v~Y~C~~CG~~~e~~-----------~~d~irCp~CG~RILyK~R~~r~v~   66 (70)
T 1twf_L           26 TLKYICAECSSKLSLS-----------RTDAVRCKDCGHRILLKARTKRLVQ   66 (70)
T ss_dssp             CCCEECSSSCCEECCC-----------TTSTTCCSSSCCCCCBCCCCSSCEE
T ss_pred             eEEEECCCCCCcceeC-----------CCCCccCCCCCceEeEecCCCccEE
Confidence            3566799999997533           234568999999666655 444443

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=89.58  E-value=0.2  Score=34.40  Aligned_cols=29  Identities=21%  Similarity=0.401  Sum_probs=22.2

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      .||+||.+...|      +   ....+..|.+||..+.
T Consensus        13 ~Cp~C~~~~lv~------D---~~~ge~vC~~CGlVl~   41 (58)
T 1dl6_A           13 TCPNHPDAILVE------D---YRAGDMICPECGLVVG   41 (58)
T ss_dssp             SBTTBSSSCCEE------C---SSSCCEECTTTCCEEC
T ss_pred             cCcCCCCCceeE------e---CCCCeEEeCCCCCEEe
Confidence            699999866555      1   2577899999998774

>3flo_B DNA polymerase alpha catalytic subunit A; protein-protein complex, phosphoesterase fold, OB fold, zinc motif, DNA replication, nucleus; HET: DNA; 2.50A {Saccharomyces cerevisiae}

Probab=88.74  E-value=0.14  Score=43.47  Aligned_cols=52  Identities=23%  Similarity=0.507  Sum_probs=33.6

Q ss_pred             HHHHHH-hhhccceeeecCCCCCcccceeeccccccccCC-CCcCceeCCCCCcee
Q 028248          141 SQSLTK-LIVRESLILKGPCPNCGTENVSFFGTILSISSG-GTTNTINCSNCGTTM  194 (211)
Q Consensus       141 a~~lt~-~~~~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~-~~~~~~kC~~C~~~L  194 (211)
                      .+.++. .-++|-.=|+=.||.|++++.  |+++...... -..+...|++|+..+
T Consensus         6 esqi~DeeRfr~c~~l~l~Cp~C~~~~~--F~gv~~~~~~~~~~sg~~C~~C~~~~   59 (206)
T 3flo_B            6 ETTITDVERFKDTVTLELSCPSCDKRFP--FGGIVSSNYYRVSYNGLQCKHCEQLF   59 (206)
T ss_dssp             -----CTTTTTTCCCEEEECTTTCCEEE--ECSSSCCSSEEEETTEEEETTTCCBC
T ss_pred             cccCCHHHHhCcCceeEEECCCCCCccC--CCCcccCCCcccccccccCCCCCCcC
Confidence            334444 357888888999999999864  5665532111 256788999999864

>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubre like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A

Probab=87.94  E-value=0.16  Score=41.92  Aligned_cols=26  Identities=35%  Similarity=0.655  Sum_probs=18.5

Q ss_pred             ecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      +--|++||.-..   |+..       +.  +||+||.+
T Consensus       155 ~~~C~~CG~~~~---g~~~-------p~--~CP~C~~~  180 (191)
T 1lko_A          155 KWRCRNCGYVHE---GTGA-------PE--LCPACAHP  180 (191)
T ss_dssp             EEEETTTCCEEE---EEEC-------CS--BCTTTCCB
T ss_pred             eEEECCCCCEee---CCCC-------CC--CCCCCcCC
Confidence            677999997643   4422       22  99999985

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

Probab=86.94  E-value=0.085  Score=51.35  Aligned_cols=24  Identities=38%  Similarity=0.736  Sum_probs=21.1

Q ss_pred             Hhhh-cCCCccChHHHHHHHHHHhh
Q 028248           35 MAYV-AGKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        35 ~aY~-~G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      .+|| .++|+|||+|||+|.++|+.
T Consensus        29 ~~YY~~d~p~IsD~eYD~L~~eL~~   53 (615)
T 3sgi_A           29 FRYYVRDAPIISDAEFDELLRRLEA   53 (615)
T ss_dssp             HHHHHHSCCCSSCCSSCSSSSHHHH
T ss_pred             HHHHcCCCCCCCHHHHHHHHHHHHH
Confidence            5777 79999999999999888864

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=85.90  E-value=0.34  Score=35.78  Aligned_cols=30  Identities=30%  Similarity=0.680  Sum_probs=21.8

Q ss_pred             ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      +=+||+||.+  ..|..        .+..-+|+.|+....
T Consensus        27 ~y~Cp~CG~~--~v~r~--------atGiW~C~~Cg~~~a   56 (83)
T 1vq8_Z           27 DHACPNCGED--RVDRQ--------GTGIWQCSYCDYKFT   56 (83)
T ss_dssp             CEECSSSCCE--EEEEE--------ETTEEEETTTCCEEE
T ss_pred             cCcCCCCCCc--ceecc--------CCCeEECCCCCCEec
Confidence            5689999984  33333        356899999998754

>1x3z_A Peptide: N-glycanase; hydrolase-hydrolase inhibitor complex; HET: SUC; 2.80A {Saccharomyces cerevisiae} SCOP: d.3.1.4 PDB: 1x3w_A* 3esw_A*

Probab=85.75  E-value=0.53  Score=42.86  Aligned_cols=59  Identities=20%  Similarity=0.424  Sum_probs=36.7

Q ss_pred             HHHHHHHhhhccc--eeeecCCCCCcccc--eee-cccccccc-----CCCCcCceeCCCCCceeEEec
Q 028248          140 LSQSLTKLIVRES--LILKGPCPNCGTEN--VSF-FGTILSIS-----SGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       140 ~a~~lt~~~~~d~--liLkG~CPnCg~Ev--~aF-fg~i~~v~-----s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      +...|.+|..+|+  -+.+-||+.||.+-  ..+ .|...+..     +.......+|+.||....|-+
T Consensus       101 ll~~LL~WFk~~fF~wvn~p~C~~Cg~~~~~~~~~~g~~~p~~~E~~~ga~~vE~y~C~~C~~~~rFPR  169 (335)
T 1x3z_A          101 LVKELLRYFKQDFFKWCNKPDCNHCGQNTSENMTPLGSQGPNGEESKFNCGTVEIYKCNRCGNITRFPR  169 (335)
T ss_dssp             HHHHHHHHHHHTTCEECSSCCCSSSCSSCCSSEEEEEEECCCSGGGSSSEEEEEEEEETTTCCEEEEEE
T ss_pred             HHHHHHHHHHhcCCEeeCCCCccccCCCccccccccCCCCCChhhhccCCceEEEeecCCCCcccccCC
Confidence            3445566666664  24689999999773  344 46643221     111233467999999998855

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=84.01  E-value=0.48  Score=34.14  Aligned_cols=29  Identities=31%  Similarity=0.613  Sum_probs=21.4

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      -|| ||.-.++=          ..+-..+|+ ||+.+.++.
T Consensus         6 ~C~-C~~~~~~~----------~~~kT~~C~-CG~~~~~~k   34 (71)
T 1gh9_A            6 RCD-CGRALYSR----------EGAKTRKCV-CGRTVNVKD   34 (71)
T ss_dssp             EET-TSCCEEEE----------TTCSEEEET-TTEEEECCS
T ss_pred             ECC-CCCEEEEc----------CCCcEEECC-CCCeeeece
Confidence            389 99864332          156778898 999998876

>3v2d_5 50S ribosomal protein L32; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_4 2hgj_4 2hgu_4 2j03_5 2jl6_5 2jl8_5 2v47_5 2v49_5 2wdi_5 2wdj_5 2wdl_5 2wdn_5 2wh2_5 2wh4_5 2wrj_5 2wrl_5 2wro_5 2wrr_5 2x9s_5 2x9u_5 ...

Probab=83.44  E-value=0.52  Score=32.87  Aligned_cols=20  Identities=40%  Similarity=1.198  Sum_probs=14.6

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG  191 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~  191 (211)
                      -.||+||+-.              -+|.+ |++||
T Consensus        31 ~~c~~cGe~~--------------~~H~v-c~~CG   50 (60)
T 3v2d_5           31 VPCPECKAMK--------------PPHTV-CPECG   50 (60)
T ss_dssp             EECTTTCCEE--------------CTTSC-CTTTC
T ss_pred             eECCCCCCee--------------cceEE-cCCCC
Confidence            4699999832              25554 99999

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=83.30  E-value=0.62  Score=35.44  Aligned_cols=35  Identities=11%  Similarity=0.341  Sum_probs=24.0

Q ss_pred             ceeeecCCCCCcccceeeccccccccCCCCcCce-eCCCCCce-eEEec
Q 028248          152 SLILKGPCPNCGTENVSFFGTILSISSGGTTNTI-NCSNCGTT-MVYDS  198 (211)
Q Consensus       152 ~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~-kC~~C~~~-L~f~~  198 (211)
                      ..-+..-|++||+++..            ..... .||.||.. +.+.+
T Consensus        69 ~~p~~~~C~~CG~~~e~------------~~~~~~~CP~Cgs~~~~i~~  105 (119)
T 2kdx_A           69 DEKVELECKDCSHVFKP------------NALDYGVCEKCHSKNVIITQ  105 (119)
T ss_dssp             EECCEEECSSSSCEECS------------CCSTTCCCSSSSSCCCEEEE
T ss_pred             eccceEEcCCCCCEEeC------------CCCCCCcCccccCCCcEEec
Confidence            33467889999987543            13456 89999988 44444

>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A

Probab=83.24  E-value=0.52  Score=38.44  Aligned_cols=25  Identities=32%  Similarity=0.745  Sum_probs=16.7

Q ss_pred             ecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      +--|||||.-..   +.        .+.  +||+||.+
T Consensus       138 ~~~C~~CG~i~~---~~--------~p~--~CP~Cg~~  162 (170)
T 3pwf_A          138 VYICPICGYTAV---DE--------APE--YCPVCGAP  162 (170)
T ss_dssp             EEECTTTCCEEE---SC--------CCS--BCTTTCCB
T ss_pred             eeEeCCCCCeeC---CC--------CCC--CCCCCCCC
Confidence            345999997543   21        232  99999964

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=82.87  E-value=0.48  Score=33.54  Aligned_cols=33  Identities=27%  Similarity=0.734  Sum_probs=26.5

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      ++=-|..||.||.-=           .....+|+.||..+.|-.
T Consensus        20 v~Y~C~~Cg~~~~l~-----------~~~~iRC~~CG~RILyK~   52 (63)
T 3h0g_L           20 MIYLCADCGARNTIQ-----------AKEVIRCRECGHRVMYKM   52 (63)
T ss_dssp             CCCBCSSSCCBCCCC-----------SSSCCCCSSSCCCCCBCC
T ss_pred             eEEECCCCCCeeecC-----------CCCceECCCCCcEEEEEe
Confidence            667899999998621           246799999999988865

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=82.77  E-value=0.53  Score=37.27  Aligned_cols=31  Identities=19%  Similarity=0.536  Sum_probs=21.9

Q ss_pred             eeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          153 LILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       153 liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      ..=.-.|+.||.+.-.+            .....||.||..+.
T Consensus       129 ~~~~y~C~~Cg~~~~~~------------~~~~~Cp~CG~~~~  159 (165)
T 2lcq_A          129 IKWRYVCIGCGRKFSTL------------PPGGVCPDCGSKVK  159 (165)
T ss_dssp             CCCCEEESSSCCEESSC------------CGGGBCTTTCCBEE
T ss_pred             ccEEEECCCCCCcccCC------------CCCCcCCCCCCcce
Confidence            33456799999876544            23458999999853

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=81.36  E-value=0.93  Score=36.87  Aligned_cols=32  Identities=34%  Similarity=0.732  Sum_probs=24.6

Q ss_pred             ccceeeecCCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          150 RESLILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       150 ~d~liLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      +++=.+..-||.||....--           + ++.+|++||..
T Consensus       134 ~~lGvv~a~~~~~g~~m~~~-----------~-~~~~cp~~g~~  165 (179)
T 3m7n_A          134 EEMGVLRALCSNCKTEMVRE-----------G-DILKCPECGRV  165 (179)
T ss_dssp             TTCEEEECBCTTTCCBCEEC-----------S-SSEECSSSCCE
T ss_pred             CCCCEEEecccccCCceEEC-----------C-CEEECCCCCCE
Confidence            45555889999999887432           4 78999999974

>2qkd_A Zinc finger protein ZPR1; helical hairpins, beta helix, anti-parrallel beta sheet, double straded anti-parallel beta helix, metal binding protein; 2.00A {Mus musculus}

Probab=80.55  E-value=0.45  Score=44.18  Aligned_cols=31  Identities=29%  Similarity=0.845  Sum_probs=17.9

Q ss_pred             eecCCCCCcccc--------eeeccccccccCCCCcCceeCCCCCc
Q 028248          155 LKGPCPNCGTEN--------VSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       155 LkG~CPnCg~Ev--------~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      +...|||||+.-        --|||.|.       -....|+.||-
T Consensus        11 ~~s~Cp~C~~~g~t~~~~~~IP~F~eVi-------i~Sf~C~~CGy   49 (404)
T 2qkd_A           11 IESLCMNCYRNGTTRLLLTKIPFFREII-------VSSFSCEHCGW   49 (404)
T ss_dssp             CEEECTTTSSEEEEEEEEEEETTTEEEE-------EEEEECTTTCC
T ss_pred             ccccCCCCCCCceEEEEEEcCCCCceEE-------EEEEECCCCCC
Confidence            456677777432        23555555       34567777773

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4

Probab=80.31  E-value=1.1  Score=33.17  Aligned_cols=36  Identities=22%  Similarity=0.408  Sum_probs=25.7

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEE
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVY  196 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f  196 (211)
                      =.||.|+.|...=..-    ........+.|.+||..-++
T Consensus        24 F~CPfCnh~~sV~vki----dk~~~~g~l~C~~Cg~~~~~   59 (85)
T 1wii_A           24 FTCPFCNHEKSCDVKM----DRARNTGVISCTVCLEEFQT   59 (85)
T ss_dssp             CCCTTTCCSSCEEEEE----ETTTTEEEEEESSSCCEEEE
T ss_pred             EcCCCCCCCCeEEEEE----EccCCEEEEEcccCCCeEEe
Confidence            3799999996443322    23346889999999986655

---

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	211
d1b04a_	312	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	3e-05
d1ta8a_	313	d.142.2.2 (A:) Adenylation domain of NAD+-dependen	4e-05
d1dgsa3	314	d.142.2.2 (A:1-314) Adenylation domain of NAD+-dep	6e-05

>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 = 3e-05
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 37 YVAGKPIMSDEEYDKLKQKLK 57
          YV  +P + D EYD+L Q+L 
Sbjct: 24 YVLDRPSVPDAEYDRLMQELI 44

>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 = 4e-05
 Identities = 8/21 (38%), Positives = 13/21 (61%)

Query: 37 YVAGKPIMSDEEYDKLKQKLK 57
          YV  +P + D  YD+L ++L 
Sbjct: 26 YVKDQPSVEDYVYDRLYKELV 46

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

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

 Score = 40.7 bits (94), Expect = 6e-05
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 37 YVAGKPIMSDEEYDKLKQKLK 57
          YV   P +SD EYD+L ++LK
Sbjct: 25 YVLADPEISDAEYDRLLRELK 45

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	211
d1ta8a_	313	Adenylation domain of NAD+-dependent DNA ligase {E	96.95
d1b04a_	312	Adenylation domain of NAD+-dependent DNA ligase {B	96.84
d1dgsa3	314	Adenylation domain of NAD+-dependent DNA ligase {T	96.59
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	96.07
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	94.13
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	94.07
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	90.77
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	90.16
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	90.1
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	89.98
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	89.07
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	87.75
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	86.64
d2j0151	59	Ribosomal protein L32p {Thermus thermophilus [TaxI	85.54
d2f4ma1	287	Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus)	83.97
d1d0qa_	102	Zinc-binding domain of DNA primase {Bacillus stear	83.88
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	83.52
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	81.7
d2qam01	56	Ribosomal protein L32p {Escherichia coli [TaxId: 5	81.06
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	80.79

>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=96.95  E-value=0.00029  Score=59.33  Aligned_cols=27  Identities=30%  Similarity=0.434  Sum_probs=22.9

Q ss_pred             HHHHhhh-cCCCccChHHHHHHHHHHhh
Q 028248           32 EASMAYV-AGKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        32 eA~~aY~-~G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      ++-.+|| .|+|+|||+|||.|+.+|+.
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            3446788 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=96.84  E-value=0.00037  Score=59.13  Aligned_cols=25  Identities=36%  Similarity=0.651  Sum_probs=22.0

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 028248           34 SMAYVA-GKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        34 ~~aY~~-G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      -.+||. |+|+|||++||.|+++|+.
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            357886 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=96.59  E-value=0.00078  Score=57.30  Aligned_cols=25  Identities=40%  Similarity=0.678  Sum_probs=22.2

Q ss_pred             HHhhhc-CCCccChHHHHHHHHHHhh
Q 028248           34 SMAYVA-GKPIMSDEEYDKLKQKLKM   58 (211)
Q Consensus        34 ~~aY~~-G~Pi~sD~efD~Lk~~Lk~   58 (211)
                      -.+||. |+|+|||++||+|+.+|+.
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            457985 9999999999999999975

>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=96.07  E-value=0.0027  Score=43.04  Aligned_cols=41  Identities=27%  Similarity=0.579  Sum_probs=33.8

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEecCceeEe
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDSNTRLIT  204 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~~~r~i~  204 (211)
                      ++=.||.|+.|...|         +.++..+.|.+||+.|.--+......
T Consensus         6 ~~VkC~~C~n~~ivF---------sha~t~V~C~~Cg~~L~~PtGGKa~i   46 (58)
T d1qxfa_           6 VKVKCPDCEHEQVIF---------DHPSTIVKCIICGRTVAEPTGGKGNI   46 (58)
T ss_dssp             EEEECTTTCCEEEEE---------SSCSSCEECSSSCCEEEECCSSSCEE
T ss_pred             EEeECCCCCCeEEEE---------ecCceEEEccccCCEEeccCCCeEEE
Confidence            677899999999999         23688999999999998887655443

>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Escherichia coli [TaxId: 562]

Probab=94.13  E-value=0.0083  Score=36.79  Aligned_cols=26  Identities=38%  Similarity=1.011  Sum_probs=19.6

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      ++|.||.|+.|. ++              --+|.+||..+.
T Consensus         1 V~G~CP~C~~~~-a~--------------GDqCe~CG~~~~   26 (35)
T d1pfva3           1 VKGTCPKCKSPD-QY--------------GDNCEVCGATYS   26 (35)
T ss_dssp             EEEECTTTCCSS-EE--------------TTBCTTTCCBCC
T ss_pred             CeeECCCCCCcc-cc--------------cccHHHcCCcCC
Confidence            589999999874 22              237999998763

>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Pyrococcus abyssi [TaxId: 29292]

Probab=94.07  E-value=0.0096  Score=36.49  Aligned_cols=26  Identities=35%  Similarity=0.967  Sum_probs=19.1

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      ++|.||.||.|.               ..--+|.+||+.+.
T Consensus         1 V~G~CP~C~~~~---------------a~GDqCe~CG~~~~   26 (35)
T d1rqga3           1 VIGTCPYCGAED---------------QKGDQCEVCGRPLT   26 (35)
T ss_dssp             CCSBCSSSCCSC---------------CCTTTCSSSCCCCC
T ss_pred             CeEECCCCCCCc---------------ccCcchhhcCCccC
Confidence            589999999763               22237999998763

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=90.77  E-value=0.048  Score=32.99  Aligned_cols=30  Identities=23%  Similarity=0.464  Sum_probs=23.6

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      -||+||+--.-+|..        ....-+|.+||..|.
T Consensus         4 ~C~~CG~~Yh~~~~p--------Pk~~g~CD~cg~~L~   33 (35)
T d1s3ga2           4 ICKVCGTSYHLLFNP--------PQVEGKCDKDGGELY   33 (35)
T ss_dssp             EETTTCCEEETTTBC--------CSBTTBCTTTCCBEE
T ss_pred             CCcCcCchhccccCC--------CCCCCccCCCCCCce
Confidence            399999876666533        677889999999885

>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.16  E-value=0.054  Score=33.35  Aligned_cols=33  Identities=18%  Similarity=0.282  Sum_probs=24.7

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeEEec
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYDS  198 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~~  198 (211)
                      -||+||+--...|..        ....-+|.+||..|.-|.
T Consensus         4 ~C~~cG~~Yh~~~~p--------pk~~g~CD~cg~~L~qR~   36 (38)
T d1akya2           4 IHPASGRSYHKIFNP--------PKEDMKDDVTGEALVQRS   36 (38)
T ss_dssp             ECTTTCCEEETTTBC--------CSSTTBCTTTCCBCBCCT
T ss_pred             CCcCccchhhhhccC--------cCcCCccCCCCCEeeecC
Confidence            399999876666533        567779999999887543

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.10  E-value=0.086  Score=34.96  Aligned_cols=33  Identities=18%  Similarity=0.352  Sum_probs=25.5

Q ss_pred             eeecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          154 ILKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       154 iLkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      +.+-.||+||..+..+      .   ..+.+.-|.+||..++
T Consensus         9 ~~~~~Cp~Cgs~~ii~------D---~~~Ge~vC~~CG~Vle   41 (58)
T d1dl6a_           9 LPRVTCPNHPDAILVE------D---YRAGDMICPECGLVVG   41 (58)
T ss_dssp             CSCCSBTTBSSSCCEE------C---SSSCCEECTTTCCEEC
T ss_pred             ccccCCCCCCCCCEEE------E---CCCCcEecccCCCEec
Confidence            3788999999887655      1   2467899999998764

>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=89.98  E-value=0.063  Score=32.46  Aligned_cols=30  Identities=27%  Similarity=0.625  Sum_probs=22.4

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      -||+||+---..|.        -....-+|.+||..|.
T Consensus         4 ~C~~CG~~Yh~~~~--------pPk~~g~CD~cG~~L~   33 (35)
T d1zina2           4 ICRNCGATYHLIFH--------PPAKPGVCDKCGGELY   33 (35)
T ss_dssp             EETTTCCEEETTTB--------CCSSTTBCTTTCCBEE
T ss_pred             CCcCcCchhccccC--------CCCCCCcCCCCCCCcc
Confidence            39999985544442        2677789999999875

>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=89.07  E-value=0.049  Score=33.40  Aligned_cols=31  Identities=16%  Similarity=0.058  Sum_probs=23.8

Q ss_pred             CCCCcccceeeccccccccCCCCcCceeCCCCCceeEEe
Q 028248          159 CPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMVYD  197 (211)
Q Consensus       159 CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~f~  197 (211)
                      ||+||.----.|        +.....-.|.+||..|.=|
T Consensus         5 c~~cG~~Yh~~~--------~pPk~~g~CD~cg~~L~qR   35 (37)
T d2ak3a2           5 HPGSGRVYNIEF--------NPPKTMGIDDLTGEPLVQR   35 (37)
T ss_dssp             ETTTTEEEETTT--------BCCSSTTBCTTTCCBCBCC
T ss_pred             eCCcCChhhhcc--------CCccccCCccCCCCcCEec
Confidence            999998655554        3377888999999988644

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=87.75  E-value=0.11  Score=33.30  Aligned_cols=31  Identities=23%  Similarity=0.669  Sum_probs=22.9

Q ss_pred             ecCCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          156 KGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       156 kG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      +..||+||.....+      +   ..+.+.-|.+||..++
T Consensus         5 ~~~Cp~Cgs~~iv~------D---~~~Ge~vC~~CG~Vie   35 (50)
T d1pfta_           5 QKVCPACESAELIY------D---PERGEIVCAKCGYVIE   35 (50)
T ss_dssp             CCSCTTTSCCCEEE------E---TTTTEEEESSSCCBCC
T ss_pred             cccCcCCCCCcEEE------E---CCCCeEecccCCcEec
Confidence            35799999876544      1   2467899999998763

>d1e4va2 g.41.2.1 (A:122-156) Microbial and mitochondrial ADK, insert "zinc finger" domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Escherichia coli [TaxId: 562]

Probab=86.64  E-value=0.091  Score=31.69  Aligned_cols=30  Identities=10%  Similarity=-0.012  Sum_probs=22.6

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCceeE
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTTMV  195 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~L~  195 (211)
                      -||+||.---..|..        ...+-.|.+||..|.
T Consensus         4 ~c~~cG~~Yh~~~~P--------Pk~~g~CD~cg~~L~   33 (35)
T d1e4va2           4 VHAPSGRVYHVKFNP--------PKVEGKDDVTGEELT   33 (35)
T ss_dssp             EETTTTEEEETTTBC--------CSSTTBCTTTCCBCB
T ss_pred             CCcCcCChhhhccCc--------cccCCcccCCCCEee
Confidence            399999866555532        667779999999875

>d2j0151 g.41.8.5 (5:2-60) Ribosomal protein L32p {Thermus thermophilus [TaxId: 274]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Thermus thermophilus [TaxId: 274]

Probab=85.54  E-value=0.17  Score=33.63  Aligned_cols=21  Identities=38%  Similarity=1.111  Sum_probs=15.3

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      -.|||||+..              -+|.+ |++||.
T Consensus        30 ~~C~~CG~~~--------------~pHrv-C~~CG~   50 (59)
T d2j0151          30 VPCPECKAMK--------------PPHTV-CPECGY   50 (59)
T ss_dssp             BCCSSSSSCB--------------CTTCB-CTTTCC
T ss_pred             eECCCCCCcc--------------cceeE-CCCCCe
Confidence            4699999832              25664 999994

>d2f4ma1 d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Cysteine proteinases
superfamily: Cysteine proteinases
family: Transglutaminase core
domain: Peptide:N-glycanase 1, PNG1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.97  E-value=0.65  Score=39.09  Aligned_cols=57  Identities=18%  Similarity=0.256  Sum_probs=35.9

Q ss_pred             HHHHhhhccc--eeeecCCCCCcccceeeccccccc-----cCCCCcCceeCCCCCceeEEecC
Q 028248          143 SLTKLIVRES--LILKGPCPNCGTENVSFFGTILSI-----SSGGTTNTINCSNCGTTMVYDSN  199 (211)
Q Consensus       143 ~lt~~~~~d~--liLkG~CPnCg~Ev~aFfg~i~~v-----~s~~~~~~~kC~~C~~~L~f~~~  199 (211)
                      .|.+|.-+++  -+.+-||+.||.+.....+...+.     -+.......+|+.|+....|-+.
T Consensus        66 eLL~wFk~~fF~wv~~ppC~~C~~~~~~~~~~~~p~~~e~~~ga~rVE~~~C~~C~~~~rfpRy  129 (287)
T d2f4ma1          66 ELLHWFKEEFFRWVNNIVCSKCGGETRSRDEALLPNDDELKWGAKNVENHYCDACQLSNRFPRY  129 (287)
T ss_dssp             HHHHHHHHTTCEECSSCCCTTTCCCCEECSSCBCCCSHHHHTTCCCEEEEEETTTTEEEEEECC
T ss_pred             HHHHHHhhcCceecCCCCCcccCCccccccCCCCCChhhhccCCceEEEEEcCCCCCceeCCCC
Confidence            3444444444  345679999999988775543221     11223445679999999999664

>d1d0qa_ g.41.3.2 (A:) Zinc-binding domain of DNA primase {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: DNA primase zinc finger
domain: Zinc-binding domain of DNA primase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=83.88  E-value=0.26  Score=35.08  Aligned_cols=31  Identities=35%  Similarity=0.724  Sum_probs=24.9

Q ss_pred             eecCCCCCcccceeeccccccccCCCCcCceeCCCCCc
Q 028248          155 LKGPCPNCGTENVSFFGTILSISSGGTTNTINCSNCGT  192 (211)
Q Consensus       155 LkG~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~  192 (211)
                      -++.||.|+....+|     +|.  ..++...|+.|+.
T Consensus        35 ~~~~CPfh~d~~~S~-----~v~--~~~~~~~Cf~Cg~   65 (102)
T d1d0qa_          35 YFGLCPFHGEKTPSF-----SVS--PEKQIFHCFGCGA   65 (102)
T ss_dssp             EEECCSSSCCSSCCE-----EEE--TTTTEEEETTTCC
T ss_pred             eEEeccccCCCCcce-----eEc--CCchheeeehhcc
Confidence            468899999999888     343  3578999999986

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=83.52  E-value=0.27  Score=29.95  Aligned_cols=23  Identities=35%  Similarity=0.840  Sum_probs=15.5

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      -||+||.-..   |+        .+  -+||+||..
T Consensus         7 ~C~vCG~i~~---g~--------~P--~~CPvCg~~   29 (37)
T d1nnqa2           7 ICPICGYTAV---DE--------AP--EYCPVCGAP   29 (37)
T ss_dssp             ECTTTCCEEE---SC--------CC--SBCTTTCCB
T ss_pred             ECCCCCCEec---CC--------CC--CcCCCCCCc
Confidence            4999997554   22        12  379999964

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=81.70  E-value=0.33  Score=29.39  Aligned_cols=23  Identities=30%  Similarity=0.648  Sum_probs=15.3

Q ss_pred             CCCCCcccceeeccccccccCCCCcCceeCCCCCce
Q 028248          158 PCPNCGTENVSFFGTILSISSGGTTNTINCSNCGTT  193 (211)
Q Consensus       158 ~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~~~  193 (211)
                      -||+||.-..   |.        .+  -+||+||.+
T Consensus         7 vC~vCGyi~~---g~--------~P--e~CPvCg~~   29 (36)
T d1yuza2           7 LCPICGYIHK---GE--------DF--EKCPICFRP   29 (36)
T ss_dssp             ECSSSCCEEE---SS--------CC--SBCTTTCCB
T ss_pred             ECCCCCCEee---CC--------CC--CcCCCCCCc
Confidence            4999997543   21        22  379999965

>d2qam01 g.41.8.5 (0:1-56) Ribosomal protein L32p {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Escherichia coli [TaxId: 562]

Probab=81.06  E-value=0.28  Score=32.20  Aligned_cols=11  Identities=9%  Similarity=0.187  Sum_probs=8.1

Q ss_pred             cCCCCCcccce
Q 028248          157 GPCPNCGTENV  167 (211)
Q Consensus       157 G~CPnCg~Ev~  167 (211)
                      -.|||||+...
T Consensus        28 ~~c~~CG~~~l   38 (56)
T d2qam01          28 SVDKTSGEKHL   38 (56)
T ss_dssp             EECSSSCCEEC
T ss_pred             eECCCCCCCcc
Confidence            35999998653

>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: Endonuclease VIII
species: Escherichia coli [TaxId: 562]

Probab=80.79  E-value=0.38  Score=29.45  Aligned_cols=27  Identities=26%  Similarity=0.589  Sum_probs=19.9

Q ss_pred             cCCCCCcccceeeccccccccCCCCcCceeCCCCC
Q 028248          157 GPCPNCGTENVSFFGTILSISSGGTTNTINCSNCG  191 (211)
Q Consensus       157 G~CPnCg~Ev~aFfg~i~~v~s~~~~~~~kC~~C~  191 (211)
                      -|||+||..+....     + +  .+...=||+|-
T Consensus        13 ~pC~~C~~~I~~~~-----~-~--gR~t~~Cp~CQ   39 (40)
T d1k3xa3          13 EPCERCGSIIEKTT-----L-S--SRPFYWCPGCQ   39 (40)
T ss_dssp             SBCTTTCCBCEEEE-----E-T--TEEEEECTTTC
T ss_pred             CccCcCCCEEEEEE-----E-C--CCCCEEChhhC
Confidence            37999999988762     1 1  47778898884