Citrus Sinensis ID: 025946

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-----
Protein Sequence
MTTLIQFSINLSALYTIQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCFFERGKDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSNNARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSRKGRESSTSVVDVEAEIKDAD
Secondary Structure (PSIPRED)
ccccEEEEEEcccccccccccccccccEEccccccccccccccccccccccccccHHccccccccEEEEEccccccccEEEEEEEccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccEEEEccEEEEEccccccccccccccccccccccccccccccEEEEEEEEEEccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEcccccccccccccccEEcccccccccEEccccEEEEccccccEEEEEcccccccEEEEEccccccccEEEEEEEccccccccccccccccccccEHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEEcccccccccccccccEEEEEccEEEEcccccccccccccccHcccccccccccccccEEEEEEEEEEccc
Coil and Loop (DISEMBL)
MTTLIQFSINLSALYTIQsnfgknrtscysltrpkigsfqgnscklrafgdqrqklcffergkdgilvkeeglknkkKRVVLVRFNedfgfngggggggnnsnnaRILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASrdivqdscpncgndFQIFKSTLndelqlcpycsqpfsvvddkfvresvrfsnesttfgqafsdffpgsrkgresstsvVDVEAEIKDAD
Flexible Loop (DISEMBL)
MTTLIQFSINLSALYTIQSNFGKNRTSCYSLTrpkigsfqgnsCKLRAFGDQRQKlcffergkdgilvkeeglknkkkrvVLVRFNEDFgfngggggggnnsNNARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRfsnesttfgqafsdffpgsrkgresstsvvdveaeikdad
Low Complexity Region (SEG)
MTTLIQFSINLSALYTIQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCFFERGKDGILVKEEGlknkkkrvvlvrFNEDfgfngggggggnnsnnARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSRKGRESSTSVVDVEAEIKDAD
Disordered region (IsUnstruct)
***LIQFSINLSALYTIQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCFFERGKDGILVKEEGLKNKKKRVVLVRFNEDF****************RILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSN**TTFGQAF****************************
Disordered Region (DISOPRED)
**TLIQFSINLSALYTIQSNFGKNRTSCYSLT***********************LCFFERGKDGILVKEEGLKNKKKRVVLVRFNEDF**************NARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTF**********************DVEAEIK***
Disordered Region (DISEMBL)
MTTLIQFSINLSALYTIQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCFFERGKDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSNNARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPG************DVEAEIKDAD
Disordered Region (DISPRO)
*TTLIQFSINLSALYTIQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCFFERGKDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSNNARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFP*******SSTSVVDVEAEIKDA*
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTTLIQFSINLSALYTIQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCFFERGKDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSNNARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSRKGRESSTSVVDVEAEIKDAD
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

No hits with e-value below 0.001 by BLAST

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	245
255586088	255	conserved hypothetical protein [Ricinus	0.975	0.937	0.635	1e-73
356549773	244	PREDICTED: uncharacterized protein LOC10	0.975	0.979	0.616	1e-65
225461332	254	PREDICTED: uncharacterized protein LOC10	0.995	0.960	0.564	3e-65
356543998	240	PREDICTED: uncharacterized protein LOC10	0.963	0.983	0.606	2e-64
302143070	148	unnamed protein product [Vitis vinifera]	0.595	0.986	0.773	8e-64
388502666	239	unknown [Medicago truncatula]	0.975	1.0	0.579	3e-62
449463138	246	PREDICTED: uncharacterized protein LOC10	0.967	0.963	0.566	7e-62
18416979	235	uncharacterized protein [Arabidopsis tha	0.571	0.595	0.721	1e-57
297799244	237	hypothetical protein ARALYDRAFT_913802 [	0.571	0.590	0.725	2e-52
224123044	131	predicted protein [Populus trichocarpa]	0.506	0.946	0.717	3e-48

>gi|255586088|ref|XP_002533708.1| conserved hypothetical protein [Ricinus communis] gi|223526382|gb|EEF28671.1| conserved hypothetical protein [Ricinus communis]

 Score =  282 bits (721), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 164/258 (63%), Positives = 193/258 (74%), Gaps = 19/258 (7%)

Query: 2   TTLIQFSINLSALY--TIQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCFF 59
           TTL+Q SI  S L   T+  +  K   S +S +  KI SF     KL AF   R+K   F
Sbjct: 3   TTLLQISILFSPLNLNTLHDDVCKKPISFHSPSHSKIASFNRKRFKLSAF---REKWSLF 59

Query: 60  E--RGKDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSNNARILGNLALAIGL 117
           E  RG+ GILV++EG K ++KR+VLVRFN+ FG  GGGGGG +NS   R+LGN+ALAIGL
Sbjct: 60  EVGRGRGGILVQDEGWK-RRKRIVLVRFNQGFG-FGGGGGGRDNSETVRLLGNVALAIGL 117

Query: 118 TYFSMTGQLGWVLDAI-------VSIWL---LAVIVPIVGFGAFLWWASRDIVQDSCPNC 167
           TY SMTGQLGWV DAI       +SIWL   LAV++PIVG GAFLWWA RDI+Q +CPNC
Sbjct: 118 TYLSMTGQLGWVFDAIGWVLDIVISIWLYEVLAVLIPIVGLGAFLWWAGRDILQGTCPNC 177

Query: 168 GNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSRKG 227
           GNDFQIFKSTLNDELQLCPYCSQPFSVV D+FV +SV+FSN ST FG+AF DF  GS+KG
Sbjct: 178 GNDFQIFKSTLNDELQLCPYCSQPFSVVGDEFVSDSVKFSNRSTAFGEAFRDFSSGSKKG 237

Query: 228 RESSTSVVDVEAEIKDAD 245
           +ESS++VVDVEAEIKDAD
Sbjct: 238 KESSSAVVDVEAEIKDAD 255

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356549773|ref|XP_003543265.1| PREDICTED: uncharacterized protein LOC100789383 [Glycine max]

 Score =  255 bits (651), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 154/250 (61%), Positives = 188/250 (75%), Gaps = 11/250 (4%)

Query: 1   MTTLIQFSINLSALYT--IQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCF 58
           MTTL+QFSI  S L          K  T  +S    K GSF GN+ KL A    R  L F
Sbjct: 1   MTTLVQFSIKCSNLKPNFFHHGIYKRPTRSFSRIETKFGSFNGNNLKLTA---GRVSLFF 57

Query: 59  F--ERGKDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSN-NARILGNLALAI 115
              E  K+G+L +E+G K +KKRVVLV+ N+ FGFNGGGGGGG +    ARILGNLALAI
Sbjct: 58  LGGEVFKNGVLWEEKGCK-RKKRVVLVKNNQGFGFNGGGGGGGRDDGATARILGNLALAI 116

Query: 116 GLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFK 175
           GLTY SMTGQLGW+LDAIVSIWL+AV++PIVG GAFLWWA RDI+Q +CPNCGNDFQ+FK
Sbjct: 117 GLTYLSMTGQLGWILDAIVSIWLVAVLIPIVGLGAFLWWAGRDIMQGTCPNCGNDFQVFK 176

Query: 176 STLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSRKGRESSTSVV 235
           S+LND+LQLCP+C QPFSVV ++FV++SV+FSN++TTFGQAF++ F  SRK ++S  + +
Sbjct: 177 SSLNDDLQLCPFCGQPFSVVGNEFVKDSVKFSNQTTTFGQAFNN-FTRSRKEKDSGKA-I 234

Query: 236 DVEAEIKDAD 245
           DVEAEI D D
Sbjct: 235 DVEAEINDVD 244

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461332|ref|XP_002284589.1| PREDICTED: uncharacterized protein LOC100257260 isoform 1 [Vitis vinifera] gi|359493886|ref|XP_003634686.1| PREDICTED: uncharacterized protein LOC100257260 isoform 2 [Vitis vinifera] gi|359493888|ref|XP_003634687.1| PREDICTED: uncharacterized protein LOC100257260 isoform 3 [Vitis vinifera]

 Score =  253 bits (647), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 144/255 (56%), Positives = 186/255 (72%), Gaps = 11/255 (4%)

Query: 1   MTTLIQFSINLSALYTIQSNFGKNRTSC----------YSLTRPKIGSFQGNSCKLRAFG 50
           M+T +Q  IN SA  ++ ++  K ++            Y L+R   G+F  N  KLR+ G
Sbjct: 1   MSTGLQICINFSAFSSLCNDSCKKQSYSGLKLPQPIKFYCLSRTNNGAFHQNEFKLRS-G 59

Query: 51  DQRQKLCFFERGKDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSNNARILGN 110
            +R        G  G+ +++E  + K++ VV+          GGGGGG ++   ARILGN
Sbjct: 60  GKRWSFLRGSGGGAGVFLRDERWRRKRRVVVVGFNQGFGFNGGGGGGGKDDGGTARILGN 119

Query: 111 LALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGND 170
           LALAIGLTY S+TGQLGWVLDAIVSIWL+AV++PIVG GAFLWWA RDIVQ +CPNCGN+
Sbjct: 120 LALAIGLTYLSVTGQLGWVLDAIVSIWLIAVLLPIVGLGAFLWWAGRDIVQSTCPNCGNE 179

Query: 171 FQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSRKGRES 230
           FQIFKS +N++LQLCPYCSQPFSV D+KF++E V+FSN++TTF QAFSDFFPGS+KG+ES
Sbjct: 180 FQIFKSLMNNDLQLCPYCSQPFSVEDNKFIKEPVKFSNQATTFEQAFSDFFPGSKKGKES 239

Query: 231 STSVVDVEAEIKDAD 245
           ST+VVDVEAEI+DA+
Sbjct: 240 STAVVDVEAEIRDAE 254

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543998|ref|XP_003540443.1| PREDICTED: uncharacterized protein LOC100780992 [Glycine max]

 Score =  251 bits (641), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 151/249 (60%), Positives = 185/249 (74%), Gaps = 13/249 (5%)

Query: 1   MTTLIQFSINLSALYT--IQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCF 58
           MTTL+QFSI  S L          K  T  +S    K GSF GNS KLR     R+ LCF
Sbjct: 1   MTTLVQFSIKCSNLKHNFFHHGIYKRPTCSFSRIETKFGSFNGNSLKLRV---GRESLCF 57

Query: 59  FERG--KDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSNNARILGNLALAIG 116
                 K+G   +E+G K ++KR VLV+ N+ FGFNGGGGGG ++   ARILGNLALAIG
Sbjct: 58  LGGAVFKNG---EEKGCK-REKRAVLVKNNQGFGFNGGGGGGRDDGATARILGNLALAIG 113

Query: 117 LTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKS 176
           LTY SMTGQLGW+LDAIVSIWL+AV++PIVG GAFL WA RDI+Q +CPNCGNDFQ+FKS
Sbjct: 114 LTYLSMTGQLGWILDAIVSIWLIAVLIPIVGLGAFLLWAGRDIMQGTCPNCGNDFQVFKS 173

Query: 177 TLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSRKGRESSTSVVD 236
           +LND+LQLCP+C QPFSVV ++FV++SV+FSN+STTFGQAF++ F  SR  ++S  + +D
Sbjct: 174 SLNDDLQLCPFCGQPFSVVGNEFVKDSVKFSNQSTTFGQAFNN-FTRSRNEKDSGKA-ID 231

Query: 237 VEAEIKDAD 245
           VEAEIKD D
Sbjct: 232 VEAEIKDVD 240

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143070|emb|CBI20365.3| unnamed protein product [Vitis vinifera]

 Score =  249 bits (635), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 113/146 (77%), Positives = 135/146 (92%)

Query: 100 NNSNNARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDI 159
           ++   ARILGNLALAIGLTY S+TGQLGWVLDAIVSIWL+AV++PIVG GAFLWWA RDI
Sbjct: 3   DDGGTARILGNLALAIGLTYLSVTGQLGWVLDAIVSIWLIAVLLPIVGLGAFLWWAGRDI 62

Query: 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSD 219
           VQ +CPNCGN+FQIFKS +N++LQLCPYCSQPFSV D+KF++E V+FSN++TTF QAFSD
Sbjct: 63  VQSTCPNCGNEFQIFKSLMNNDLQLCPYCSQPFSVEDNKFIKEPVKFSNQATTFEQAFSD 122

Query: 220 FFPGSRKGRESSTSVVDVEAEIKDAD 245
           FFPGS+KG+ESST+VVDVEAEI+DA+
Sbjct: 123 FFPGSKKGKESSTAVVDVEAEIRDAE 148

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388502666|gb|AFK39399.1| unknown [Medicago truncatula]

 Score =  244 bits (622), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 142/245 (57%), Positives = 173/245 (70%), Gaps = 6/245 (2%)

Query: 1   MTTLIQFSINLSALYTIQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCFFE 60
           M+TL+QFSI  S L    S +    T  +S   PK  SF   S KLRA  D R       
Sbjct: 1   MSTLVQFSIKFSHLKPNDSIYKTQPTFSFSNLDPKFNSFHLGSFKLRACRD-RWSFLGGA 59

Query: 61  RGKDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSNNARILGNLALAIGLTYF 120
             K+G + +E+G K K+KRVVLV+ N+  GF    GGG ++ + ARILGNLALA GLTY 
Sbjct: 60  VFKNGGMCEEKGCK-KEKRVVLVKNNQ--GFGFNNGGGRDDGSTARILGNLALAAGLTYL 116

Query: 121 SMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKSTLND 180
           SMTGQLGW++DAIVSIW+ AV+VPIVG GAFLWWA RDI++ +CPNCGNDFQ+FKSTLN+
Sbjct: 117 SMTGQLGWIIDAIVSIWIFAVLVPIVGIGAFLWWAGRDIMKGTCPNCGNDFQVFKSTLNE 176

Query: 181 ELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSRKGRESSTSVVDVEAE 240
           ELQLCP+C QPFSV  ++FV+E V FSN+ TTFGQAF +F   S K  + S   +DVEAE
Sbjct: 177 ELQLCPFCGQPFSVDGNEFVKEPVNFSNQFTTFGQAFDNF--SSSKNDKDSGKAIDVEAE 234

Query: 241 IKDAD 245
           IKDAD
Sbjct: 235 IKDAD 239

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463138|ref|XP_004149291.1| PREDICTED: uncharacterized protein LOC101205846 [Cucumis sativus] gi|449507737|ref|XP_004163117.1| PREDICTED: uncharacterized LOC101205846 [Cucumis sativus]

 Score =  243 bits (619), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 144/254 (56%), Positives = 182/254 (71%), Gaps = 17/254 (6%)

Query: 1   MTTLIQFSINLSALYTIQSNFGKNRTSCYSLTRPKIGSFQGNSCKLRAFGDQRQKLCFFE 60
           MT+ I+FS        + +NF    T    L  PK+   + +  +LR +G    +L F  
Sbjct: 1   MTSFIRFS----TFNILHNNFCNKPTKFNPLPPPKVVFCKPSGLRLRFYG---WRLLFPG 53

Query: 61  RG--KDGILVKEEGLKNKKKRVVLVRFNEDFGFNGGGGGGGNNSN------NARILGNLA 112
            G     +  K  G K K+ R+++ RFN+ FGFNGGGG GG+  +       AR++GN+A
Sbjct: 54  GGWVDQRVFGKHGGFKGKRGRLIVARFNQGFGFNGGGGDGGDGGDGGDDGATARLVGNIA 113

Query: 113 LAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQ 172
           LA GLTY S+TGQLGWVLDAIVSIWL+AV+VPIVG  AF+WWA RDIVQ +CPNCGN+FQ
Sbjct: 114 LAAGLTYLSVTGQLGWVLDAIVSIWLVAVLVPIVGVAAFIWWAGRDIVQSNCPNCGNEFQ 173

Query: 173 IFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE-STTFGQAFSDFFPGSRKGRESS 231
           IFKSTLN+ELQLCP+CSQPFSVVDDKFVR+SV+FSN+ S+TFGQAFSD F   RKG+E+S
Sbjct: 174 IFKSTLNEELQLCPFCSQPFSVVDDKFVRDSVKFSNKTSSTFGQAFSD-FTSPRKGKETS 232

Query: 232 TSVVDVEAEIKDAD 245
            +VVD+EAE+KD D
Sbjct: 233 GAVVDIEAEVKDVD 246

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18416979|ref|NP_567772.1| uncharacterized protein [Arabidopsis thaliana] gi|14423404|gb|AAK62384.1|AF386939_1 putative protein [Arabidopsis thaliana] gi|14335172|gb|AAK59866.1| AT4g27390/M4I22_200 [Arabidopsis thaliana] gi|15529163|gb|AAK97676.1| AT4g27390/M4I22_200 [Arabidopsis thaliana] gi|16974363|gb|AAL31107.1| AT4g27390/M4I22_200 [Arabidopsis thaliana] gi|332659931|gb|AEE85331.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  228 bits (582), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 101/140 (72%), Positives = 122/140 (87%)

Query: 106 RILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCP 165
           RILGNLALAIGLTY SMTGQLGW+LDAIVS+WL+ VIVPI+G GAF WWA RDIVQ +CP
Sbjct: 96  RILGNLALAIGLTYLSMTGQLGWILDAIVSVWLIVVIVPILGLGAFFWWAQRDIVQSNCP 155

Query: 166 NCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSR 225
           NCGN+FQIFKS ++DE+QLCP+C+QPFSVVDDKFV+E V+FSN++T FGQ  + F    +
Sbjct: 156 NCGNEFQIFKSAMDDEVQLCPFCTQPFSVVDDKFVKEPVKFSNQTTAFGQDLNGFSSKPK 215

Query: 226 KGRESSTSVVDVEAEIKDAD 245
           KG+ SST+VVD+EAE+ DAD
Sbjct: 216 KGKGSSTAVVDIEAEVTDAD 235

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799244|ref|XP_002867506.1| hypothetical protein ARALYDRAFT_913802 [Arabidopsis lyrata subsp. lyrata] gi|297313342|gb|EFH43765.1| hypothetical protein ARALYDRAFT_913802 [Arabidopsis lyrata subsp. lyrata]

 Score =  211 bits (538), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/142 (72%), Positives = 122/142 (85%), Gaps = 2/142 (1%)

Query: 106 RILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCP 165
           RILGNLALAIGLTY SMTGQLGW+LDAIVS+WL+ VIVPI+G GAFLWWA RDIVQ +CP
Sbjct: 96  RILGNLALAIGLTYLSMTGQLGWILDAIVSVWLIVVIVPILGLGAFLWWAQRDIVQSNCP 155

Query: 166 NCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDF--FPG 223
           NCG +FQIFKS  NDE+QLCP+C+QPFSVVDDKFV+E V+FSN++T FGQ  + F   P 
Sbjct: 156 NCGYEFQIFKSATNDEVQLCPFCTQPFSVVDDKFVKEPVKFSNQTTAFGQDLNGFSSKPK 215

Query: 224 SRKGRESSTSVVDVEAEIKDAD 245
            +KG+ SST+VVD+EAE+ DAD
Sbjct: 216 PKKGKGSSTAVVDIEAEVTDAD 237

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123044|ref|XP_002330427.1| predicted protein [Populus trichocarpa] gi|222871812|gb|EEF08943.1| predicted protein [Populus trichocarpa]

 Score =  197 bits (501), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 94/131 (71%), Positives = 109/131 (83%), Gaps = 7/131 (5%)

Query: 122 MTGQLGWV-------LDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIF 174
           MTGQLGWV       LD ++SIWLLAV +PIVG G FLWWA RDI+Q +CPNCGN+FQIF
Sbjct: 1   MTGQLGWVFDTVGWILDTLISIWLLAVFIPIVGLGVFLWWAGRDILQGTCPNCGNEFQIF 60

Query: 175 KSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSRKGRESSTSV 234
           KSTLNDELQLCP+CSQPFSVV D+FV +SVRFS +ST FGQAFSD   G +KG+ESS++V
Sbjct: 61  KSTLNDELQLCPFCSQPFSVVGDEFVSDSVRFSKKSTPFGQAFSDLSSGFKKGKESSSAV 120

Query: 235 VDVEAEIKDAD 245
           VDVEAE+KD D
Sbjct: 121 VDVEAEVKDVD 131

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	245
TAIR|locus:2131699	235	AT4G27390 "AT4G27390" [Arabido	0.571	0.595	0.721	2.3e-55

TAIR|locus:2131699 AT4G27390 "AT4G27390" [Arabidopsis thaliana (taxid:3702)]

 Score = 571 (206.1 bits), Expect = 2.3e-55, P = 2.3e-55
 Identities = 101/140 (72%), Positives = 122/140 (87%)

Query:   106 RILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCP 165
             RILGNLALAIGLTY SMTGQLGW+LDAIVS+WL+ VIVPI+G GAF WWA RDIVQ +CP
Sbjct:    96 RILGNLALAIGLTYLSMTGQLGWILDAIVSVWLIVVIVPILGLGAFFWWAQRDIVQSNCP 155

Query:   166 NCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNESTTFGQAFSDFFPGSR 225
             NCGN+FQIFKS ++DE+QLCP+C+QPFSVVDDKFV+E V+FSN++T FGQ  + F    +
Sbjct:   156 NCGNEFQIFKSAMDDEVQLCPFCTQPFSVVDDKFVKEPVKFSNQTTAFGQDLNGFSSKPK 215

Query:   226 KGRESSTSVVDVEAEIKDAD 245
             KG+ SST+VVD+EAE+ DAD
Sbjct:   216 KGKGSSTAVVDIEAEVTDAD 235


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.323   0.138   0.423    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      245       217   0.00090  112 3  11 22  0.48    32
                                                     32  0.39    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  596 (63 KB)
  Total size of DFA:  175 KB (2102 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  17.51u 0.10s 17.61t   Elapsed:  00:00:01
  Total cpu time:  17.51u 0.10s 17.61t   Elapsed:  00:00:01
  Start:  Sat May 11 09:50:01 2013   End:  Sat May 11 09:50:02 2013

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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	245
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	98.87
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	98.63
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	98.44
PRK00420	112	hypothetical protein; Validated	98.28
COG4530	129	Uncharacterized protein conserved in bacteria [Fun	98.18
PRK02935	110	hypothetical protein; Provisional	98.14
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	98.11
PF13248	26	zf-ribbon_3: zinc-ribbon domain	97.95
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	97.76
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	97.62
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	97.59
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	97.58
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	97.51
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	97.48
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	97.3
smart00531	147	TFIIE Transcription initiation factor IIE.	97.26
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	96.97
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	96.9
PF14353	128	CpXC: CpXC protein	96.9
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	96.59
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	96.56
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	96.51
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	96.47
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	96.46
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	96.44
PRK06266	178	transcription initiation factor E subunit alpha; V	96.43
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	96.11
COG1592	166	Rubrerythrin [Energy production and conversion]	95.96
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	95.86
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	95.84
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	95.48
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	95.46
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	95.33
PF03966	68	Trm112p: Trm112p-like protein; InterPro: IPR005651	95.16
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	95.14
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	95.07
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	95.02
PF12773	50	DZR: Double zinc ribbon	94.95
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	94.8
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	94.6
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	94.49
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	94.38
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	94.27
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.22
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	94.2
PF12773	50	DZR: Double zinc ribbon	93.99
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	93.89
PRK12496	164	hypothetical protein; Provisional	93.65
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	93.6
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	93.55
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	93.18
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	93.12
COG0675	364	Transposase and inactivated derivatives [DNA repli	92.84
COG3877	122	Uncharacterized protein conserved in bacteria [Fun	92.77
PRK00432	50	30S ribosomal protein S27ae; Validated	92.73
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	92.64
COG4888	104	Uncharacterized Zn ribbon-containing protein [Gene	92.57
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	92.48
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	92.47
PHA00626	59	hypothetical protein	92.1
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	92.02
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	91.88
COG1675	176	TFA1 Transcription initiation factor IIE, alpha su	91.7
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	91.59
PRK11827	60	hypothetical protein; Provisional	91.53
COG1545	140	Predicted nucleic-acid-binding protein containing	91.41
PRK05978	148	hypothetical protein; Provisional	91.32
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	91.28
PRK14892	99	putative transcription elongation factor Elf1; Pro	91.14
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	91.12
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	91.08
PF09845	131	DUF2072: Zn-ribbon containing protein (DUF2072); I	91.02
COG5216	67	Uncharacterized conserved protein [Function unknow	91.01
TIGR00515	285	accD acetyl-CoA carboxylase, carboxyl transferase,	91.0
PRK06260	397	threonine synthase; Validated	90.76
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	90.26
PHA02942	383	putative transposase; Provisional	90.17
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	90.15
PRK14559	645	putative protein serine/threonine phosphatase; Pro	90.13
PRK05654	292	acetyl-CoA carboxylase subunit beta; Validated	90.12
PF01783	56	Ribosomal_L32p: Ribosomal L32p protein family; Int	89.93
PRK12495	226	hypothetical protein; Provisional	89.61
PF09889	59	DUF2116: Uncharacterized protein containing a Zn-r	89.39
PRK10220	111	hypothetical protein; Provisional	89.25
COG2835	60	Uncharacterized conserved protein [Function unknow	89.19
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	89.15
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	88.83
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	88.82
PRK14559	645	putative protein serine/threonine phosphatase; Pro	88.29
COG3357	97	Predicted transcriptional regulator containing an	88.18
PRK15103	419	paraquat-inducible membrane protein A; Provisional	88.04
TIGR01031	55	rpmF_bact ribosomal protein L32. This protein desc	87.97
KOG2923	67	consensus Uncharacterized conserved protein [Funct	87.87
PRK08270	656	anaerobic ribonucleoside triphosphate reductase; P	87.87
PF09334	391	tRNA-synt_1g: tRNA synthetases class I (M); InterP	87.82
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	87.77
TIGR00155	403	pqiA_fam integral membrane protein, PqiA family. T	87.6
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	87.55
PRK00481	242	NAD-dependent deacetylase; Provisional	87.48
PLN00209	86	ribosomal protein S27; Provisional	87.3
CHL00174	296	accD acetyl-CoA carboxylase beta subunit; Reviewed	87.25
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	87.22
COG4260	345	Membrane protease subunit, stomatin/prohibitin fam	87.09
cd01412	224	SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaea	87.01
PTZ00083	85	40S ribosomal protein S27; Provisional	86.99
PF08996	188	zf-DNA_Pol: DNA Polymerase alpha zinc finger; Inte	86.98
PF12172	37	DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35	86.9
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	86.88
PRK07591	421	threonine synthase; Validated	86.87
COG3364	112	Zn-ribbon containing protein [General function pre	86.85
COG2331	82	Uncharacterized protein conserved in bacteria [Fun	86.82
PF11781	36	RRN7: RNA polymerase I-specific transcription init	86.81
PF13395	54	HNH_4: HNH endonuclease	86.77
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	86.66
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	86.39
PRK14714	1337	DNA polymerase II large subunit; Provisional	86.25
PRK08579	625	anaerobic ribonucleoside triphosphate reductase; P	86.15
PF10005	343	DUF2248: Uncharacterized protein conserved in bact	86.05
COG1655	267	Uncharacterized protein conserved in bacteria [Fun	85.96
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	85.88
KOG2593	436	consensus Transcription initiation factor IIE, alp	85.74
PF02146	178	SIR2: Sir2 family; InterPro: IPR003000 These seque	85.4
PF07295	146	DUF1451: Protein of unknown function (DUF1451); In	85.28
PF12677	49	DUF3797: Domain of unknown function (DUF3797); Int	85.25
COG0777	294	AccD Acetyl-CoA carboxylase beta subunit [Lipid me	84.76
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	84.45
PRK07111	735	anaerobic ribonucleoside triphosphate reductase; P	84.45
COG4031	227	Predicted metal-binding protein [General function	84.26
COG4640	465	Predicted membrane protein [Function unknown]	84.24
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	84.18
PRK06450	338	threonine synthase; Validated	84.14
PF10083	158	DUF2321: Uncharacterized protein conserved in bact	83.83
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	83.82
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	83.77
cd01407	218	SIR2-fam SIR2 family of proteins includes silent i	83.75
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	83.63
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	83.48
PRK10445	263	endonuclease VIII; Provisional	83.47
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	83.4
COG4391	62	Uncharacterized protein conserved in bacteria [Fun	82.85
PRK11032	160	hypothetical protein; Provisional	82.83
PRK14714	1337	DNA polymerase II large subunit; Provisional	82.79
PF13597	546	NRDD: Anaerobic ribonucleoside-triphosphate reduct	82.71
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	82.47
PF10263	157	SprT-like: SprT-like family; InterPro: IPR006640 T	82.44
PRK08271	623	anaerobic ribonucleoside triphosphate reductase; P	82.18
TIGR03844	398	cysteate_syn cysteate synthase. Members of this fa	82.15
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	82.13
COG1656	165	Uncharacterized conserved protein [Function unknow	81.91
PF14311	55	DUF4379: Domain of unknown function (DUF4379)	81.9
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	81.67
cd01410	206	SIRT7 SIRT7: Eukaryotic and prokaryotic group (cla	81.62
PF13005	47	zf-IS66: zinc-finger binding domain of transposase	81.59
KOG1088	124	consensus Uncharacterized conserved protein [Funct	81.23
PRK09263	711	anaerobic ribonucleoside triphosphate reductase; P	81.19
PF14353	128	CpXC: CpXC protein	81.11
COG2260	59	Predicted Zn-ribbon RNA-binding protein [Translati	81.11
TIGR02827	586	RNR_anaer_Bdell anaerobic ribonucleoside-triphosph	80.82
TIGR00577	272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	80.64
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	80.38
PF05180	66	zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc	80.04

>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=98.87  E-value=7.7e-10  Score=88.82  Aligned_cols=31  Identities=35%  Similarity=0.894  Sum_probs=29.4

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      .++||+||++||+    ||++|++||+||+.++++
T Consensus         9 KR~Cp~CG~kFYD----Lnk~PivCP~CG~~~~~~   39 (108)
T PF09538_consen    9 KRTCPSCGAKFYD----LNKDPIVCPKCGTEFPPE   39 (108)
T ss_pred             cccCCCCcchhcc----CCCCCccCCCCCCccCcc
Confidence            4699999999999    999999999999999888

The function of members of this family is unknown.

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=98.63  E-value=1.2e-08  Score=85.04  Aligned_cols=31  Identities=32%  Similarity=0.636  Sum_probs=28.8

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      .++||+||++||+    ||++|++||+||+.++.+
T Consensus         9 Kr~Cp~cg~kFYD----Lnk~p~vcP~cg~~~~~~   39 (129)
T TIGR02300         9 KRICPNTGSKFYD----LNRRPAVSPYTGEQFPPE   39 (129)
T ss_pred             cccCCCcCccccc----cCCCCccCCCcCCccCcc
Confidence            4699999999999    999999999999998766

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.

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

Probab=98.44  E-value=5.9e-07  Score=73.83  Aligned_cols=60  Identities=27%  Similarity=0.630  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcC---cceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          134 VSIWLLAVIVPIVGFGAFLWWASR---DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       134 ~~L~LlllllPIl~~~Gf~WWl~r---nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      .+++.++=++-+++..+.-.|++=   +-+|.+||+|++..-.    |.+. ..|++|++|+..|.+.
T Consensus        39 m~ifmllG~L~~l~S~~VYfwIGmlStkav~V~CP~C~K~TKm----LGr~-D~CM~C~~pLTLd~~l  101 (114)
T PF11023_consen   39 MVIFMLLGLLAILASTAVYFWIGMLSTKAVQVECPNCGKQTKM----LGRV-DACMHCKEPLTLDPSL  101 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhcccceeeECCCCCChHhh----hchh-hccCcCCCcCccCchh
Confidence            333333334444455666667764   6788899999988765    4444 4999999999987653

; GO: 0005887 integral to plasma membrane

>PRK00420 hypothetical protein; Validated

Probab=98.28  E-value=2.8e-07  Score=74.97  Aligned_cols=39  Identities=26%  Similarity=0.577  Sum_probs=35.0

Q ss_pred             cCcceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          156 SRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       156 ~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      ++..+..+||+||.+++-    +++++.+||+||+++.+++++
T Consensus        18 Ga~ml~~~CP~Cg~pLf~----lk~g~~~Cp~Cg~~~~v~~~e   56 (112)
T PRK00420         18 GAKMLSKHCPVCGLPLFE----LKDGEVVCPVHGKVYIVKSDE   56 (112)
T ss_pred             HHHHccCCCCCCCCccee----cCCCceECCCCCCeeeeccHH
Confidence            556678899999999999    799999999999999998866

>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=98.18  E-value=4.4e-07  Score=75.36  Aligned_cols=30  Identities=23%  Similarity=0.470  Sum_probs=27.3

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      .++||+||++||+    ||++|++|||||+.++.
T Consensus         9 KridPetg~KFYD----LNrdPiVsPytG~s~P~   38 (129)
T COG4530           9 KRIDPETGKKFYD----LNRDPIVSPYTGKSYPR   38 (129)
T ss_pred             cccCccccchhhc----cCCCccccCcccccchH
Confidence            3589999999999    99999999999998853

>PRK02935 hypothetical protein; Provisional

Probab=98.14  E-value=7.7e-06  Score=66.96  Aligned_cols=60  Identities=22%  Similarity=0.592  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhc---CcceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          134 VSIWLLAVIVPIVGFGAFLWWAS---RDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       134 ~~L~LlllllPIl~~~Gf~WWl~---rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      ..+++++=++-+++..+.-+|++   -+-+|.+||+|++.--.    |. ..-.|++|+|||..|.++
T Consensus        40 m~ifm~~G~l~~l~S~vvYFwiGmlStkavqV~CP~C~K~TKm----LG-rvD~CM~C~~PLTLd~~l  102 (110)
T PRK02935         40 MTIFMLLGFLAVIASTVVYFWIGMLSTKAVQVICPSCEKPTKM----LG-RVDACMHCNQPLTLDRSL  102 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhcccceeeECCCCCchhhh----cc-ceeecCcCCCcCCcCccc
Confidence            33444444445555566677876   58899999999987665    33 345899999999988765

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=98.11  E-value=2e-06  Score=56.06  Aligned_cols=35  Identities=26%  Similarity=0.651  Sum_probs=29.3

Q ss_pred             eeccCCCCCceeeecccccCCC--cccCCCCCCceee
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDE--LQLCPYCSQPFSV  194 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d--~iqCPnCGE~L~V  194 (245)
                      +..+||+|++.|+..++.+.+.  .++||+||+++.+
T Consensus         1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~   37 (38)
T TIGR02098         1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA   37 (38)
T ss_pred             CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence            3568999999999988877654  6999999999864

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.

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=97.95  E-value=2.7e-06  Score=52.71  Aligned_cols=26  Identities=31%  Similarity=0.974  Sum_probs=21.7

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      ++..||+||++...       +...||+||++|
T Consensus         1 m~~~Cp~Cg~~~~~-------~~~fC~~CG~~L   26 (26)
T PF13248_consen    1 MEMFCPNCGAEIDP-------DAKFCPNCGAKL   26 (26)
T ss_pred             CcCCCcccCCcCCc-------ccccChhhCCCC
Confidence            57799999986444       899999999975

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

Probab=97.76  E-value=2.4e-05  Score=53.27  Aligned_cols=35  Identities=20%  Similarity=0.556  Sum_probs=27.6

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      ++..||+||.++..++..   +...||+||.++..+++
T Consensus         2 ~~y~C~~CG~~~~~~~~~---~~~~Cp~CG~~~~~~~~   36 (46)
T PRK00398          2 AEYKCARCGREVELDEYG---TGVRCPYCGYRILFKER   36 (46)
T ss_pred             CEEECCCCCCEEEECCCC---CceECCCCCCeEEEccC
Confidence            466899999999884333   38999999999886654

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=97.62  E-value=6e-05  Score=48.93  Aligned_cols=34  Identities=29%  Similarity=0.808  Sum_probs=27.1

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      +|+-.||.||++|......-......||.||..+
T Consensus         3 ~Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~   36 (41)
T smart00834        3 IYEYRCEDCGHTFEVLQKISDDPLATCPECGGDV   36 (41)
T ss_pred             CEEEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence            5778999999999875544346789999999854

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.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=97.59  E-value=3.5e-05  Score=51.14  Aligned_cols=35  Identities=31%  Similarity=0.722  Sum_probs=28.8

Q ss_pred             eeccCCCCCceeeecccccCC--CcccCCCCCCceee
Q 025946          160 VQDSCPNCGNDFQIFKSTLND--ELQLCPYCSQPFSV  194 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~V  194 (245)
                      +..+||+|+..|.+.++-|..  ..+.||+|++.+.+
T Consensus         1 M~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~v   37 (37)
T PF13719_consen    1 MIITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFRV   37 (37)
T ss_pred             CEEECCCCCceEEcCHHHcccCCcEEECCCCCcEeeC
Confidence            356899999999998776544  58999999998754

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=97.58  E-value=2.1e-05  Score=48.06  Aligned_cols=23  Identities=39%  Similarity=1.224  Sum_probs=19.8

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      -||+||++..+       +...||+||.+|
T Consensus         1 ~Cp~CG~~~~~-------~~~fC~~CG~~l   23 (23)
T PF13240_consen    1 YCPNCGAEIED-------DAKFCPNCGTPL   23 (23)
T ss_pred             CCcccCCCCCC-------cCcchhhhCCcC
Confidence            39999999665       899999999875

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=97.51  E-value=5.2e-05  Score=50.30  Aligned_cols=33  Identities=24%  Similarity=0.635  Sum_probs=27.7

Q ss_pred             eeccCCCCCceeeecccccCCC--cccCCCCCCce
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDE--LQLCPYCSQPF  192 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d--~iqCPnCGE~L  192 (245)
                      +..+||+|+++|.+.|+.+-..  .++||+||+.+
T Consensus         1 M~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    1 MIITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             CEEECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            4578999999999987776653  79999999876

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=97.48  E-value=8.6e-05  Score=53.81  Aligned_cols=34  Identities=35%  Similarity=0.825  Sum_probs=29.2

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      +.+||.||.++...++.+ ...+.||.||..|++.
T Consensus         2 ~~~CP~CG~~iev~~~~~-GeiV~Cp~CGaeleVv   35 (54)
T TIGR01206         2 QFECPDCGAEIELENPEL-GELVICDECGAELEVV   35 (54)
T ss_pred             ccCCCCCCCEEecCCCcc-CCEEeCCCCCCEEEEE
Confidence            458999999999866666 6789999999999975

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.

>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=97.30  E-value=0.00027  Score=47.90  Aligned_cols=34  Identities=29%  Similarity=0.790  Sum_probs=28.1

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCC-ce
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ-PF  192 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE-~L  192 (245)
                      +|+-.|+.||.+|-..-..-.+++..||.||+ .+
T Consensus         3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~   37 (42)
T PF09723_consen    3 IYEYRCEECGHEFEVLQSISEDDPVPCPECGSTEV   37 (42)
T ss_pred             CEEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCce
Confidence            68889999999999865554568999999998 44

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.

>smart00531 TFIIE Transcription initiation factor IIE

Probab=97.26  E-value=0.00013  Score=59.97  Aligned_cols=38  Identities=24%  Similarity=0.616  Sum_probs=29.5

Q ss_pred             eccCCCCCceeeecccccC-C--CcccCCCCCCceeeeCCe
Q 025946          161 QDSCPNCGNDFQIFKSTLN-D--ELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln-~--d~iqCPnCGE~L~Vd~~~  198 (245)
                      .-.||+||.+|..+|.... +  +...||+||+++..+++.
T Consensus        99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~  139 (147)
T smart00531       99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNS  139 (147)
T ss_pred             EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCch
Confidence            3489999999998665532 2  248999999999988774

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=96.97  E-value=0.00072  Score=46.34  Aligned_cols=32  Identities=31%  Similarity=0.841  Sum_probs=24.4

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      +|+-.|+.||.+|-.....=.++.+.||.||.
T Consensus         3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~   34 (52)
T TIGR02605         3 IYEYRCTACGHRFEVLQKMSDDPLATCPECGG   34 (52)
T ss_pred             CEEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence            57889999999888843221236788999998

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.

>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=96.90  E-value=0.00057  Score=46.03  Aligned_cols=30  Identities=30%  Similarity=0.763  Sum_probs=22.0

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      .||+||.+...+ | -.+++.+||+||.+++-
T Consensus         2 ~Cp~Cg~~~~~~-D-~~~g~~vC~~CG~Vl~e   31 (43)
T PF08271_consen    2 KCPNCGSKEIVF-D-PERGELVCPNCGLVLEE   31 (43)
T ss_dssp             SBTTTSSSEEEE-E-TTTTEEEETTT-BBEE-
T ss_pred             CCcCCcCCceEE-c-CCCCeEECCCCCCEeec
Confidence            699999987432 2 45689999999999863

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.

>PF14353 CpXC: CpXC protein

Probab=96.90  E-value=0.001  Score=52.83  Aligned_cols=44  Identities=23%  Similarity=0.663  Sum_probs=30.6

Q ss_pred             eccCCCCCceeee-cccccCC--C-------------cccCCCCCCceeeeCCeeEEecc
Q 025946          161 QDSCPNCGNDFQI-FKSTLND--E-------------LQLCPYCSQPFSVVDDKFVRESV  204 (245)
Q Consensus       161 E~tCPnCG~eF~~-~ed~Ln~--d-------------~iqCPnCGE~L~Vd~~~F~R~~~  204 (245)
                      |.+||+||++|.. ..+.+|-  +             ..+||+||+.+.++-.=-..|+.
T Consensus         1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~   60 (128)
T PF14353_consen    1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPE   60 (128)
T ss_pred             CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCC
Confidence            5699999999876 2222332  1             57899999998887665555544

>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=96.59  E-value=0.001  Score=41.97  Aligned_cols=24  Identities=33%  Similarity=1.045  Sum_probs=20.7

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      +||.|+.+...       +...||+||-.|.
T Consensus         2 ~CP~C~~~V~~-------~~~~Cp~CG~~F~   25 (26)
T PF10571_consen    2 TCPECGAEVPE-------SAKFCPHCGYDFE   25 (26)
T ss_pred             cCCCCcCCchh-------hcCcCCCCCCCCc
Confidence            79999999766       8999999998763

Several members are annotated as putative helicases.

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

Probab=96.56  E-value=0.0011  Score=54.36  Aligned_cols=28  Identities=29%  Similarity=0.859  Sum_probs=25.5

Q ss_pred             CCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEE
Q 025946          164 CPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVR  201 (245)
Q Consensus       164 CPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R  201 (245)
                      ||+||.++.+       +...||+|++.+   +|+|.-
T Consensus         1 CPvCg~~l~v-------t~l~C~~C~t~i---~G~F~l   28 (113)
T PF09862_consen    1 CPVCGGELVV-------TRLKCPSCGTEI---EGEFEL   28 (113)
T ss_pred             CCCCCCceEE-------EEEEcCCCCCEE---Eeeecc
Confidence            9999999999       899999999998   677864

>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=96.51  E-value=0.0015  Score=45.07  Aligned_cols=31  Identities=23%  Similarity=0.651  Sum_probs=27.5

Q ss_pred             hcCcceeccCCCCCceeeecccccCCCcccCCCCC
Q 025946          155 ASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCS  189 (245)
Q Consensus       155 l~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCG  189 (245)
                      .+|.++..+||.||.+..-    ..++.+.||.|+
T Consensus        11 ~G~~ML~~~Cp~C~~PL~~----~k~g~~~Cv~C~   41 (41)
T PF06677_consen   11 QGWTMLDEHCPDCGTPLMR----DKDGKIYCVSCG   41 (41)
T ss_pred             HhHhHhcCccCCCCCeeEE----ecCCCEECCCCC
Confidence            5788999999999999887    577899999996

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

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=96.47  E-value=0.0013  Score=48.08  Aligned_cols=32  Identities=31%  Similarity=0.895  Sum_probs=26.6

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      |+....||.||.+|..     .+|-++||.||+|+..
T Consensus         2 ~~~~~~C~~Cg~~~~~-----~dDiVvCp~CgapyHR   33 (54)
T PF14446_consen    2 NYEGCKCPVCGKKFKD-----GDDIVVCPECGAPYHR   33 (54)
T ss_pred             CccCccChhhCCcccC-----CCCEEECCCCCCcccH
Confidence            4567799999999975     5588999999999853

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=96.46  E-value=0.0014  Score=55.10  Aligned_cols=35  Identities=23%  Similarity=0.467  Sum_probs=27.4

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      .-.||+|+.+++. +++++ ..-.||.||++|.-.|+
T Consensus       109 ~Y~Cp~c~~r~tf-~eA~~-~~F~Cp~Cg~~L~~~dn  143 (158)
T TIGR00373       109 FFICPNMCVRFTF-NEAME-LNFTCPRCGAMLDYLDN  143 (158)
T ss_pred             eEECCCCCcEeeH-HHHHH-cCCcCCCCCCEeeeccC
Confidence            3489999988776 55555 46999999999986664

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.

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=96.44  E-value=0.003  Score=43.85  Aligned_cols=32  Identities=19%  Similarity=0.438  Sum_probs=25.9

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      .-.|..||.++..    -..+++.||+||..+-...
T Consensus         2 ~Y~C~~Cg~~~~~----~~~~~irC~~CG~rIlyK~   33 (44)
T smart00659        2 IYICGECGRENEI----KSKDVVRCRECGYRILYKK   33 (44)
T ss_pred             EEECCCCCCEeec----CCCCceECCCCCceEEEEe
Confidence            4579999999987    2468999999999876554

present in RNA polymerase I, II and III

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=96.43  E-value=0.0015  Score=56.05  Aligned_cols=36  Identities=25%  Similarity=0.486  Sum_probs=27.5

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      ..-.||+|+.+++.+ ++++ ..-.||.||++|.-.|+
T Consensus       116 ~~Y~Cp~C~~rytf~-eA~~-~~F~Cp~Cg~~L~~~dn  151 (178)
T PRK06266        116 MFFFCPNCHIRFTFD-EAME-YGFRCPQCGEMLEEYDN  151 (178)
T ss_pred             CEEECCCCCcEEeHH-HHhh-cCCcCCCCCCCCeeccc
Confidence            334899999888874 4554 47999999999986543

>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=96.11  E-value=0.0037  Score=41.18  Aligned_cols=27  Identities=22%  Similarity=0.679  Sum_probs=20.7

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .|..||.++..    -..++++||+||-.+-
T Consensus         2 ~C~~Cg~~~~~----~~~~~irC~~CG~RIl   28 (32)
T PF03604_consen    2 ICGECGAEVEL----KPGDPIRCPECGHRIL   28 (32)
T ss_dssp             BESSSSSSE-B----STSSTSSBSSSS-SEE
T ss_pred             CCCcCCCeeEc----CCCCcEECCcCCCeEE
Confidence            59999999986    4568999999997653

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 ....

>COG1592 Rubrerythrin [Energy production and conversion]

Probab=95.96  E-value=0.0036  Score=54.18  Aligned_cols=23  Identities=35%  Similarity=1.032  Sum_probs=20.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .||+||+...+      ..|-+||.||.+
T Consensus       136 vC~vCGy~~~g------e~P~~CPiCga~  158 (166)
T COG1592         136 VCPVCGYTHEG------EAPEVCPICGAP  158 (166)
T ss_pred             EcCCCCCcccC------CCCCcCCCCCCh
Confidence            79999998876      369999999976

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

Probab=95.86  E-value=0.004  Score=52.42  Aligned_cols=29  Identities=28%  Similarity=0.801  Sum_probs=24.4

Q ss_pred             CcceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946          157 RDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       157 rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      -.++.-+||.||.+++-     +++.+.||.||.
T Consensus        24 AkML~~hCp~Cg~PLF~-----KdG~v~CPvC~~   52 (131)
T COG1645          24 AKMLAKHCPKCGTPLFR-----KDGEVFCPVCGY   52 (131)
T ss_pred             hHHHHhhCcccCCccee-----eCCeEECCCCCc
Confidence            34566799999999886     779999999994

>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase

Probab=95.84  E-value=0.0069  Score=39.80  Aligned_cols=24  Identities=33%  Similarity=0.895  Sum_probs=19.6

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .|++||+....     ++.|..||.||.+
T Consensus         4 ~C~~CG~i~~g-----~~~p~~CP~Cg~~   27 (34)
T cd00729           4 VCPVCGYIHEG-----EEAPEKCPICGAP   27 (34)
T ss_pred             ECCCCCCEeEC-----CcCCCcCcCCCCc
Confidence            79999988766     3357899999985

In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed

Probab=95.48  E-value=0.0075  Score=44.22  Aligned_cols=33  Identities=36%  Similarity=0.792  Sum_probs=24.2

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccccccc
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE  209 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~~  209 (245)
                      ..||+||.  |.    |   ..+||.||++..      ...+++||-.
T Consensus         6 r~C~~Cgv--YT----L---k~~CP~CG~~t~------~~~P~rfSp~   38 (56)
T PRK13130          6 RKCPKCGV--YT----L---KEICPVCGGKTK------NPHPPRFSPE   38 (56)
T ss_pred             eECCCCCC--EE----c---cccCcCCCCCCC------CCCCCCCCCC
Confidence            38999993  33    2   678999999864      3467888763

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=95.46  E-value=0.011  Score=38.29  Aligned_cols=24  Identities=33%  Similarity=0.944  Sum_probs=19.5

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .|++||+....     ...+-.||.||.+
T Consensus         3 ~C~~CGy~y~~-----~~~~~~CP~Cg~~   26 (33)
T cd00350           3 VCPVCGYIYDG-----EEAPWVCPVCGAP   26 (33)
T ss_pred             ECCCCCCEECC-----CcCCCcCcCCCCc
Confidence            69999988765     3378899999984

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=95.33  E-value=0.016  Score=47.85  Aligned_cols=40  Identities=28%  Similarity=0.644  Sum_probs=24.5

Q ss_pred             ccCCCCCceeeecc---c-------------ccCCCcccCCCCCCc-eeee-CCeeEE
Q 025946          162 DSCPNCGNDFQIFK---S-------------TLNDELQLCPYCSQP-FSVV-DDKFVR  201 (245)
Q Consensus       162 ~tCPnCG~eF~~~e---d-------------~Ln~d~iqCPnCGE~-L~Vd-~~~F~R  201 (245)
                      ..|++||+.+...+   +             .+.+....||+||.. +.+. ++.+.=
T Consensus        71 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~el~i  128 (135)
T PRK03824         71 LKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGRGVYI  128 (135)
T ss_pred             EECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCceEEE
Confidence            38999998887631   0             001234679999985 6644 444443

>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function

Probab=95.16  E-value=0.015  Score=42.39  Aligned_cols=20  Identities=20%  Similarity=0.694  Sum_probs=18.2

Q ss_pred             cCCCcccCCCCCCceeeeCC
Q 025946          178 LNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       178 Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      .-++..+||+||..|+++||
T Consensus        49 i~eg~L~Cp~c~r~YPI~dG   68 (68)
T PF03966_consen   49 IVEGELICPECGREYPIRDG   68 (68)
T ss_dssp             TTTTEEEETTTTEEEEEETT
T ss_pred             ccCCEEEcCCCCCEEeCCCC
Confidence            67789999999999999986

The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.

>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function

Probab=95.14  E-value=0.011  Score=51.63  Aligned_cols=34  Identities=29%  Similarity=0.689  Sum_probs=22.9

Q ss_pred             eccCCCCCceeeecccc--------------------cCC---CcccCCCCCCceeee
Q 025946          161 QDSCPNCGNDFQIFKST--------------------LND---ELQLCPYCSQPFSVV  195 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~--------------------Ln~---d~iqCPnCGE~L~Vd  195 (245)
                      +.+||+|+++|... .+                    +|.   +..+||+||-....+
T Consensus         5 ~~~CPvC~~~F~~~-~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~   61 (214)
T PF09986_consen    5 KITCPVCGKEFKTK-KVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE   61 (214)
T ss_pred             ceECCCCCCeeeee-EEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence            45899999999862 11                    111   257899999776433

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=95.07  E-value=0.019  Score=46.07  Aligned_cols=34  Identities=24%  Similarity=0.553  Sum_probs=22.8

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCc-eeee-CCeeE
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQP-FSVV-DDKFV  200 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~-L~Vd-~~~F~  200 (245)
                      ..|+.||++|..     .+....||.||.. +.+. +.++.
T Consensus        71 ~~C~~Cg~~~~~-----~~~~~~CP~Cgs~~~~i~~G~El~  106 (113)
T PRK12380         71 AWCWDCSQVVEI-----HQHDAQCPHCHGERLRVDTGDSLI  106 (113)
T ss_pred             EEcccCCCEEec-----CCcCccCcCCCCCCcEEccCCeEE
Confidence            389999988887     2234459999974 4544 44443

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=95.02  E-value=0.019  Score=46.08  Aligned_cols=34  Identities=24%  Similarity=0.659  Sum_probs=22.5

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCc-eee-eCCeeE
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP-FSV-VDDKFV  200 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~-L~V-d~~~F~  200 (245)
                      .|+.||+.|..    .......||.||.. +.+ .+++|.
T Consensus        72 ~C~~Cg~~~~~----~~~~~~~CP~Cgs~~~~i~~G~El~  107 (114)
T PRK03681         72 WCETCQQYVTL----LTQRVRRCPQCHGDMLRIVADDGLQ  107 (114)
T ss_pred             EcccCCCeeec----CCccCCcCcCcCCCCcEEccCCeEE
Confidence            89999988776    22223679999975 444 444443

>PF12773 DZR: Double zinc ribbon

Probab=94.95  E-value=0.01  Score=40.28  Aligned_cols=26  Identities=27%  Similarity=0.815  Sum_probs=13.0

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .||.||..+..    -.....+||+||+++
T Consensus        14 fC~~CG~~l~~----~~~~~~~C~~Cg~~~   39 (50)
T PF12773_consen   14 FCPHCGTPLPP----PDQSKKICPNCGAEN   39 (50)
T ss_pred             CChhhcCChhh----ccCCCCCCcCCcCCC
Confidence            55566655541    122345566666554

>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=94.80  E-value=0.011  Score=47.23  Aligned_cols=34  Identities=24%  Similarity=0.586  Sum_probs=21.5

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce-e-eeCCeeEE
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF-S-VVDDKFVR  201 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L-~-Vd~~~F~R  201 (245)
                      .|+.||++|...     +....||+||..- . ++++.+.=
T Consensus        72 ~C~~Cg~~~~~~-----~~~~~CP~Cgs~~~~i~~G~el~i  107 (113)
T PF01155_consen   72 RCRDCGHEFEPD-----EFDFSCPRCGSPDVEIISGRELRI  107 (113)
T ss_dssp             EETTTS-EEECH-----HCCHH-SSSSSS-EEEEESS-EEE
T ss_pred             ECCCCCCEEecC-----CCCCCCcCCcCCCcEEccCCeEEE
Confidence            899999999872     2336799999973 4 45555543

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.

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=94.60  E-value=0.027  Score=40.58  Aligned_cols=35  Identities=23%  Similarity=0.674  Sum_probs=26.8

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      ++-.|-.||+++..   .-+.+.+.||+||..+-+...
T Consensus         5 ~~Y~C~~Cg~~~~~---~~~~~~irCp~Cg~rIl~K~R   39 (49)
T COG1996           5 MEYKCARCGREVEL---DQETRGIRCPYCGSRILVKER   39 (49)
T ss_pred             EEEEhhhcCCeeeh---hhccCceeCCCCCcEEEEecc
Confidence            45589999999943   245589999999998766543

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=94.49  E-value=0.033  Score=44.69  Aligned_cols=36  Identities=17%  Similarity=0.450  Sum_probs=24.5

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCce-e-eeCCeeEEe
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF-S-VVDDKFVRE  202 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L-~-Vd~~~F~R~  202 (245)
                      ..|++||++|..     .+....||.||..- . +.++++.=+
T Consensus        71 ~~C~~Cg~~~~~-----~~~~~~CP~Cgs~~~~i~~G~El~I~  108 (115)
T TIGR00100        71 CECEDCSEEVSP-----EIDLYRCPKCHGIMLQVRAGKELNLK  108 (115)
T ss_pred             EEcccCCCEEec-----CCcCccCcCCcCCCcEEecCCeEEEE
Confidence            399999988876     22357799999853 4 445555443

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.

>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=94.38  E-value=0.025  Score=40.44  Aligned_cols=30  Identities=23%  Similarity=0.632  Sum_probs=23.4

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      +||.||...-.   .+++....||+||....-|
T Consensus        30 ~C~~CG~~~~~---~~~~r~~~C~~Cg~~~~rD   59 (69)
T PF07282_consen   30 TCPRCGHRNKK---RRSGRVFTCPNCGFEMDRD   59 (69)
T ss_pred             CccCccccccc---ccccceEEcCCCCCEECcH
Confidence            89999987665   4666799999999876433

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

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=94.27  E-value=0.031  Score=45.09  Aligned_cols=37  Identities=16%  Similarity=0.383  Sum_probs=24.7

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCc-ee-eeCCeeEEec
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP-FS-VVDDKFVRES  203 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~-L~-Vd~~~F~R~~  203 (245)
                      .|+.||+.|...    ......||.||.+ +. +.+++|.=++
T Consensus        73 ~C~~Cg~~~~~~----~~~~~~CP~Cgs~~~~i~~G~El~I~~  111 (117)
T PRK00564         73 ECKDCSHVFKPN----ALDYGVCEKCHSKNVIITQGNEMRLLS  111 (117)
T ss_pred             EhhhCCCccccC----CccCCcCcCCCCCceEEecCCEEEEEE
Confidence            899999888761    1233459999985 45 4555665443

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.22  E-value=0.055  Score=36.61  Aligned_cols=34  Identities=21%  Similarity=0.472  Sum_probs=23.7

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      -||.||...+..++. ++...+||.||-...++..
T Consensus         2 FCp~Cg~~l~~~~~~-~~~~~vC~~Cg~~~~~~~~   35 (52)
T smart00661        2 FCPKCGNMLIPKEGK-EKRRFVCRKCGYEEPIEQK   35 (52)
T ss_pred             CCCCCCCccccccCC-CCCEEECCcCCCeEECCCc
Confidence            599999988773211 1237899999987666554

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=94.20  E-value=0.041  Score=40.67  Aligned_cols=38  Identities=29%  Similarity=0.568  Sum_probs=27.8

Q ss_pred             cCCCCCceee--ecc-cccCCCcccCCCCCCceeeeCCeeE
Q 025946          163 SCPNCGNDFQ--IFK-STLNDELQLCPYCSQPFSVVDDKFV  200 (245)
Q Consensus       163 tCPnCG~eF~--~~e-d~Ln~d~iqCPnCGE~L~Vd~~~F~  200 (245)
                      -||.||.+-.  .-+ .+|.+=|..||.|-+.--++=.+|+
T Consensus         6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v~~~~   46 (55)
T PF14205_consen    6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDVKQLK   46 (55)
T ss_pred             ECCCCCCccceeeecCceeccccccCCCCCceEEEEeeccE
Confidence            7999996543  333 4488889999999987766655554

>PF12773 DZR: Double zinc ribbon

Probab=93.99  E-value=0.027  Score=38.16  Aligned_cols=23  Identities=35%  Similarity=1.084  Sum_probs=19.3

Q ss_pred             CCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          164 CPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       164 CPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ||.||+....       +...||+||+++.
T Consensus         1 Cp~Cg~~~~~-------~~~fC~~CG~~l~   23 (50)
T PF12773_consen    1 CPHCGTPNPD-------DAKFCPHCGTPLP   23 (50)
T ss_pred             CCCcCCcCCc-------cccCChhhcCChh
Confidence            8999988444       7889999999998

>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=93.89  E-value=0.02  Score=52.85  Aligned_cols=39  Identities=31%  Similarity=0.905  Sum_probs=19.1

Q ss_pred             HhcCcceeccCCCCCce-eeecccccCCC---cccCCCCCCceeeeCCe
Q 025946          154 WASRDIVQDSCPNCGND-FQIFKSTLNDE---LQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       154 Wl~rnLIE~tCPnCG~e-F~~~ed~Ln~d---~iqCPnCGE~L~Vd~~~  198 (245)
                      |+.+|.   -||+||.+ ..-+   -|+.   .-.||+|+|.+++...+
T Consensus        27 Wv~~n~---yCP~Cg~~~L~~f---~NN~PVaDF~C~~C~eeyELKSk~   69 (254)
T PF06044_consen   27 WVAENM---YCPNCGSKPLSKF---ENNRPVADFYCPNCNEEYELKSKK   69 (254)
T ss_dssp             HHHHH------TTT--SS-EE-----------EEE-TTT--EEEEEEEE
T ss_pred             HHHHCC---cCCCCCChhHhhc---cCCCccceeECCCCchHHhhhhhc
Confidence            555544   69999988 5542   2333   56899999999988766

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

>PRK12496 hypothetical protein; Provisional

Probab=93.65  E-value=0.035  Score=47.11  Aligned_cols=58  Identities=12%  Similarity=0.213  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCcc-eeccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          131 DAIVSIWLLAVIVPIVGFGAFLWWASRDI-VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       131 d~~~~L~LlllllPIl~~~Gf~WWl~rnL-IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      |..+--++-.+=++++.+-.-+  ++..+ -.-.||.||++|-.     +.....||.||.++...
T Consensus        98 D~~~~~vA~~lgi~v~~~~~~~--i~~~~~w~~~C~gC~~~~~~-----~~~~~~C~~CG~~~~r~  156 (164)
T PRK12496         98 DYGIQNVAKKLNIKFENIKTKG--IKKVIKWRKVCKGCKKKYPE-----DYPDDVCEICGSPVKRK  156 (164)
T ss_pred             HHHHHHHHHHcCCeEecccccc--chhheeeeEECCCCCccccC-----CCCCCcCCCCCChhhhc
Confidence            5555555555555665532111  11111 12379999987753     23456899999998543

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=93.60  E-value=0.047  Score=40.68  Aligned_cols=40  Identities=23%  Similarity=0.630  Sum_probs=30.0

Q ss_pred             CcceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCe
Q 025946          157 RDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDK  198 (245)
Q Consensus       157 rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~  198 (245)
                      -.++...||.|+++-.++.  =.++.+.|+.||..|. ..+|+
T Consensus         7 S~F~~VkCp~C~n~q~vFs--ha~t~V~C~~Cg~~L~~PtGGK   47 (59)
T PRK00415          7 SRFLKVKCPDCGNEQVVFS--HASTVVRCLVCGKTLAEPTGGK   47 (59)
T ss_pred             CeEEEEECCCCCCeEEEEe--cCCcEEECcccCCCcccCCCcc
Confidence            3578889999999987731  2346999999999985 44444

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

Probab=93.55  E-value=0.047  Score=41.76  Aligned_cols=34  Identities=24%  Similarity=0.726  Sum_probs=26.5

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .++.+.||.||++-..+.  =....+.|+.||..|-
T Consensus        16 ~Fl~VkCpdC~N~q~vFs--hast~V~C~~CG~~l~   49 (67)
T COG2051          16 RFLRVKCPDCGNEQVVFS--HASTVVTCLICGTTLA   49 (67)
T ss_pred             eEEEEECCCCCCEEEEec--cCceEEEecccccEEE
Confidence            467789999999988731  1236899999999885

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=93.18  E-value=0.038  Score=42.36  Aligned_cols=27  Identities=33%  Similarity=0.854  Sum_probs=14.6

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      -+..|+.|...|..        ...||.|+++|++
T Consensus        16 ~~~~C~~C~~~~~~--------~a~CPdC~~~Le~   42 (70)
T PF07191_consen   16 GHYHCEACQKDYKK--------EAFCPDCGQPLEV   42 (70)
T ss_dssp             TEEEETTT--EEEE--------EEE-TTT-SB-EE
T ss_pred             CEEECcccccccee--------cccCCCcccHHHH
Confidence            34456666665555        7788888888875

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

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

Probab=93.12  E-value=0.05  Score=40.97  Aligned_cols=31  Identities=29%  Similarity=0.533  Sum_probs=14.2

Q ss_pred             ceeccCCCCCceeee-cccc-cCCCcccCCCCC
Q 025946          159 IVQDSCPNCGNDFQI-FKST-LNDELQLCPYCS  189 (245)
Q Consensus       159 LIE~tCPnCG~eF~~-~ed~-Ln~d~iqCPnCG  189 (245)
                      .+.-.|||||++... -+.- -...+.+||+||
T Consensus        25 ~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG   57 (61)
T COG2888          25 AVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCG   57 (61)
T ss_pred             eeEeeCCCCCceeeehhhhHHHcCCceECCCcC
Confidence            344467777733222 1111 112366677776

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

Probab=92.84  E-value=0.042  Score=46.74  Aligned_cols=25  Identities=36%  Similarity=0.841  Sum_probs=19.2

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      +||.||.        +......||+||....-|
T Consensus       311 ~C~~cg~--------~~~r~~~C~~cg~~~~rD  335 (364)
T COG0675         311 TCPCCGH--------LSGRLFKCPRCGFVHDRD  335 (364)
T ss_pred             cccccCC--------ccceeEECCCCCCeehhh
Confidence            8999998        344788999998765443

>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.77  E-value=0.062  Score=44.90  Aligned_cols=29  Identities=24%  Similarity=0.676  Sum_probs=24.6

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEE
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVR  201 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R  201 (245)
                      .||+||.+..+       ++..||+|+..+   .|.|.-
T Consensus         8 ~cPvcg~~~iV-------TeL~c~~~etTV---rg~F~~   36 (122)
T COG3877           8 RCPVCGRKLIV-------TELKCSNCETTV---RGNFKM   36 (122)
T ss_pred             CCCccccccee-------EEEecCCCCceE---ecceec
Confidence            79999999998       899999999987   455543

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=92.73  E-value=0.061  Score=38.20  Aligned_cols=26  Identities=27%  Similarity=0.582  Sum_probs=20.2

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .||.||.+|..    ..++...|+.||-..
T Consensus        22 fCP~Cg~~~m~----~~~~r~~C~~Cgyt~   47 (50)
T PRK00432         22 FCPRCGSGFMA----EHLDRWHCGKCGYTE   47 (50)
T ss_pred             cCcCCCcchhe----ccCCcEECCCcCCEE
Confidence            89999987555    455788999998654

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

Probab=92.64  E-value=0.099  Score=35.00  Aligned_cols=31  Identities=23%  Similarity=0.546  Sum_probs=21.5

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ++||+||..+-.. ..--+.+-.|.+||++|.
T Consensus         2 r~C~~Cg~~Yh~~-~~pP~~~~~Cd~cg~~L~   32 (36)
T PF05191_consen    2 RICPKCGRIYHIE-FNPPKVEGVCDNCGGELV   32 (36)
T ss_dssp             EEETTTTEEEETT-TB--SSTTBCTTTTEBEB
T ss_pred             cCcCCCCCccccc-cCCCCCCCccCCCCCeeE
Confidence            4899999776651 111224789999999874

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 ....

>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]

Probab=92.57  E-value=0.083  Score=43.33  Aligned_cols=45  Identities=27%  Similarity=0.540  Sum_probs=35.3

Q ss_pred             cCCCCCceeee---cccccCCCcccCCCCCCceeeeCCeeEEecccccc
Q 025946          163 SCPNCGNDFQI---FKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSN  208 (245)
Q Consensus       163 tCPnCG~eF~~---~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~  208 (245)
                      +||.||.+...   .|-..+...+.|-+||..++.+-.+-. +++..||
T Consensus        24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~-~~vDvYs   71 (104)
T COG4888          24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELS-EPVDVYS   71 (104)
T ss_pred             ecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccc-cchhHHH
Confidence            99999998877   666778889999999999998877654 3344443

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

Probab=92.48  E-value=0.077  Score=33.35  Aligned_cols=23  Identities=26%  Similarity=0.648  Sum_probs=16.0

Q ss_pred             CCCCCceeeecccccC-CCcccCCCCCC
Q 025946          164 CPNCGNDFQIFKSTLN-DELQLCPYCSQ  190 (245)
Q Consensus       164 CPnCG~eF~~~ed~Ln-~d~iqCPnCGE  190 (245)
                      |..||..+..    .+ -.+-.|||||+
T Consensus         1 C~sC~~~i~~----r~~~v~f~CPnCG~   24 (24)
T PF07754_consen    1 CTSCGRPIAP----REQAVPFPCPNCGF   24 (24)
T ss_pred             CccCCCcccC----cccCceEeCCCCCC
Confidence            6678777666    33 24788999985

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

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=92.47  E-value=0.1  Score=43.09  Aligned_cols=30  Identities=20%  Similarity=0.751  Sum_probs=24.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      .||.|+.+++-    -..+...||.|+-.+..++
T Consensus         4 ~CP~C~seytY----~dg~~~iCpeC~~EW~~~~   33 (109)
T TIGR00686         4 PCPKCNSEYTY----HDGTQLICPSCLYEWNENE   33 (109)
T ss_pred             cCCcCCCcceE----ecCCeeECccccccccccc
Confidence            79999988876    3446899999999987554

The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).

>PHA00626 hypothetical protein

Probab=92.10  E-value=0.14  Score=38.39  Aligned_cols=33  Identities=27%  Similarity=0.464  Sum_probs=21.7

Q ss_pred             cCCCCCceeeecccccCC--CcccCCCCCCceeee
Q 025946          163 SCPNCGNDFQIFKSTLND--ELQLCPYCSQPFSVV  195 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~Vd  195 (245)
                      .||+||..-..--...++  ....||.||-.+.-|
T Consensus         2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~   36 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD   36 (59)
T ss_pred             CCCCCCCceeeeeceecccCcceEcCCCCCeechh
Confidence            599999853332222333  688999998766543

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

Probab=92.02  E-value=0.1  Score=39.06  Aligned_cols=8  Identities=63%  Similarity=1.535  Sum_probs=3.8

Q ss_pred             cCCCCCce
Q 025946          163 SCPNCGND  170 (245)
Q Consensus       163 tCPnCG~e  170 (245)
                      .||+||++
T Consensus        27 ~CPnCG~~   34 (59)
T PRK14890         27 LCPNCGEV   34 (59)
T ss_pred             eCCCCCCe
Confidence            45555544

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=91.88  E-value=0.11  Score=42.24  Aligned_cols=42  Identities=14%  Similarity=0.374  Sum_probs=24.5

Q ss_pred             eccCCCCCceeeecccccCCC--cccCCCCCC-cee-eeCCeeEEec
Q 025946          161 QDSCPNCGNDFQIFKSTLNDE--LQLCPYCSQ-PFS-VVDDKFVRES  203 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d--~iqCPnCGE-~L~-Vd~~~F~R~~  203 (245)
                      +..| .||++|...++.+..-  ...||.||. .+. +.++++.=++
T Consensus        70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~  115 (124)
T PRK00762         70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGRECNVKN  115 (124)
T ss_pred             eEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCCeEEEEE
Confidence            3389 9998877632111111  257999994 444 5555665544

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

Probab=91.70  E-value=0.056  Score=47.29  Aligned_cols=32  Identities=25%  Similarity=0.558  Sum_probs=25.4

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      .||+|..++.-+|....  +..||.||+.|.-.+
T Consensus       115 ~C~~~~~r~sfdeA~~~--~F~Cp~Cg~~L~~~d  146 (176)
T COG1675         115 VCPNCHVKYSFDEAMEL--GFTCPKCGEDLEEYD  146 (176)
T ss_pred             eCCCCCCcccHHHHHHh--CCCCCCCCchhhhcc
Confidence            89999999887655543  489999999997544

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=91.59  E-value=0.093  Score=48.01  Aligned_cols=30  Identities=27%  Similarity=0.576  Sum_probs=22.5

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ..||.||.+-.+ +| ...++++|.+||.+++
T Consensus        12 ~~Cp~Cg~~~iv-~d-~~~Ge~vC~~CG~Vl~   41 (310)
T PRK00423         12 LVCPECGSDKLI-YD-YERGEIVCADCGLVIE   41 (310)
T ss_pred             CcCcCCCCCCee-EE-CCCCeEeecccCCccc
Confidence            379999974332 22 3679999999999885

>PRK11827 hypothetical protein; Provisional

Probab=91.53  E-value=0.12  Score=38.46  Aligned_cols=33  Identities=18%  Similarity=0.471  Sum_probs=27.2

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      .||.|..++.-++   ...+..|+.|+-.|++.||-
T Consensus        10 aCP~ckg~L~~~~---~~~~Lic~~~~laYPI~dgI   42 (60)
T PRK11827         10 ACPVCNGKLWYNQ---EKQELICKLDNLAFPLRDGI   42 (60)
T ss_pred             ECCCCCCcCeEcC---CCCeEECCccCeeccccCCc
Confidence            8999999988632   23689999999999999873

>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]

Probab=91.41  E-value=0.11  Score=43.12  Aligned_cols=29  Identities=21%  Similarity=0.632  Sum_probs=25.1

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      +++-..|++||+.++=       ....||+||.+-.
T Consensus        26 kl~g~kC~~CG~v~~P-------Pr~~Cp~C~~~~~   54 (140)
T COG1545          26 KLLGTKCKKCGRVYFP-------PRAYCPKCGSETE   54 (140)
T ss_pred             cEEEEEcCCCCeEEcC-------CcccCCCCCCCCc
Confidence            6777799999999887       7899999998853

>PRK05978 hypothetical protein; Provisional

Probab=91.32  E-value=0.12  Score=44.12  Aligned_cols=35  Identities=23%  Similarity=0.666  Sum_probs=24.4

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      ..||+||+-=. ++ .+.+-...||+||+.++.++.-
T Consensus        34 grCP~CG~G~L-F~-g~Lkv~~~C~~CG~~~~~~~a~   68 (148)
T PRK05978         34 GRCPACGEGKL-FR-AFLKPVDHCAACGEDFTHHRAD   68 (148)
T ss_pred             CcCCCCCCCcc-cc-cccccCCCccccCCccccCCcc
Confidence            48999996422 11 1445678999999999877543

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

Probab=91.28  E-value=0.16  Score=37.31  Aligned_cols=39  Identities=21%  Similarity=0.463  Sum_probs=24.3

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCe
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDK  198 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~  198 (245)
                      .++.+.||.|+++-.++  .=.+..+.|..||+.|. ..+|+
T Consensus         4 ~Fm~VkCp~C~~~q~vF--Sha~t~V~C~~Cg~~L~~PtGGK   43 (55)
T PF01667_consen    4 YFMDVKCPGCYNIQTVF--SHAQTVVKCVVCGTVLAQPTGGK   43 (55)
T ss_dssp             -EEEEE-TTT-SEEEEE--TT-SS-EE-SSSTSEEEEE-SSS
T ss_pred             cEEEEECCCCCCeeEEE--ecCCeEEEcccCCCEecCCCCcC
Confidence            46788999999998883  12346999999999985 44444

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.

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=91.14  E-value=0.14  Score=41.10  Aligned_cols=32  Identities=22%  Similarity=0.398  Sum_probs=20.4

Q ss_pred             cCCCCCceee-ecccccCCCcccCCCCCCceeee
Q 025946          163 SCPNCGNDFQ-IFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       163 tCPnCG~eF~-~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      +||+||.... ..-+ =+...+.||+||.-...+
T Consensus        23 ~CP~Cge~~v~v~~~-k~~~h~~C~~CG~y~~~~   55 (99)
T PRK14892         23 ECPRCGKVSISVKIK-KNIAIITCGNCGLYTEFE   55 (99)
T ss_pred             ECCCCCCeEeeeecC-CCcceEECCCCCCccCEE
Confidence            8999994322 1101 144699999999876443

>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues

Probab=91.12  E-value=0.085  Score=34.45  Aligned_cols=27  Identities=33%  Similarity=1.005  Sum_probs=14.6

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      ..||.|+.++.-    ..+...+||.|+..+
T Consensus         3 p~Cp~C~se~~y----~D~~~~vCp~C~~ew   29 (30)
T PF08274_consen    3 PKCPLCGSEYTY----EDGELLVCPECGHEW   29 (30)
T ss_dssp             ---TTT-----E----E-SSSEEETTTTEEE
T ss_pred             CCCCCCCCccee----ccCCEEeCCcccccC
Confidence            479999988776    445789999998654

The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=91.08  E-value=0.14  Score=33.94  Aligned_cols=32  Identities=22%  Similarity=0.457  Sum_probs=22.0

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      -||.||+-.+..++....-  .|+.||-..++++
T Consensus         3 FCp~C~nlL~p~~~~~~~~--~C~~C~Y~~~~~~   34 (35)
T PF02150_consen    3 FCPECGNLLYPKEDKEKRV--ACRTCGYEEPISQ   34 (35)
T ss_dssp             BETTTTSBEEEEEETTTTE--EESSSS-EEE-SS
T ss_pred             eCCCCCccceEcCCCccCc--CCCCCCCccCCCC
Confidence            5999999999854443322  7999998877653

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function

Probab=91.02  E-value=0.12  Score=43.74  Aligned_cols=33  Identities=27%  Similarity=0.582  Sum_probs=22.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEecc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESV  204 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~  204 (245)
                      .|-+||+.|-+-...+.   .=||+||      +++|+-.+.
T Consensus         3 ~Ct~Cg~~f~dgs~eil---~GCP~CG------g~kF~yv~~   35 (131)
T PF09845_consen    3 QCTKCGRVFEDGSKEIL---SGCPECG------GNKFQYVPE   35 (131)
T ss_pred             ccCcCCCCcCCCcHHHH---ccCcccC------CcceEEcCC
Confidence            69999999988332222   3499999      456665543

>COG5216 Uncharacterized conserved protein [Function unknown]

Probab=91.01  E-value=0.14  Score=39.00  Aligned_cols=37  Identities=30%  Similarity=0.707  Sum_probs=26.7

Q ss_pred             cCcceeccCCCCCceeee-cccccCC-CcccCCCCCCcee
Q 025946          156 SRDIVQDSCPNCGNDFQI-FKSTLND-ELQLCPYCSQPFS  193 (245)
Q Consensus       156 ~rnLIE~tCPnCG~eF~~-~ed~Ln~-d~iqCPnCGE~L~  193 (245)
                      ..+.+.-.|| ||.+|.+ +||+.|. ...+||.|.-.+-
T Consensus        17 e~~~ftyPCP-CGDRFeIsLeDl~~GE~VArCPSCSLiv~   55 (67)
T COG5216          17 EEKTFTYPCP-CGDRFEISLEDLRNGEVVARCPSCSLIVC   55 (67)
T ss_pred             CCceEEecCC-CCCEeEEEHHHhhCCceEEEcCCceEEEE
Confidence            3467778999 9999998 4555433 4789999975443

>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit

Probab=91.00  E-value=0.086  Score=48.67  Aligned_cols=39  Identities=26%  Similarity=0.711  Sum_probs=29.8

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceee----------eCCeeEEec
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV----------VDDKFVRES  203 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V----------d~~~F~R~~  203 (245)
                      .||.|++.+|.  ..|.+...+||+||--+..          |++.|+.-+
T Consensus        28 ~c~~c~~~~~~--~~l~~~~~vc~~c~~h~rl~areRi~~L~D~gsF~E~~   76 (285)
T TIGR00515        28 KCPKCGQVLYT--KELERNLEVCPKCDHHMRMDARERIESLLDEGSFEEFN   76 (285)
T ss_pred             ECCCCcchhhH--HHHHhhCCCCCCCCCcCcCCHHHHHHHceeCCeeEEeC
Confidence            79999999887  2356667899999986654          677776553

The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.

>PRK06260 threonine synthase; Validated

Probab=90.76  E-value=0.15  Score=47.64  Aligned_cols=32  Identities=22%  Similarity=0.625  Sum_probs=24.6

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      +.-.|+.||+++-.     +.-...||.||.+|.++=
T Consensus         2 ~~~~C~~cg~~~~~-----~~~~~~Cp~cg~~l~~~y   33 (397)
T PRK06260          2 YWLKCIECGKEYDP-----DEIIYTCPECGGLLEVIY   33 (397)
T ss_pred             CEEEECCCCCCCCC-----CCccccCCCCCCeEEEEe
Confidence            45689999998654     233578999999988773

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=90.26  E-value=0.14  Score=37.46  Aligned_cols=20  Identities=40%  Similarity=1.079  Sum_probs=16.1

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      .||+||..-.        ....||+||.
T Consensus        29 ~C~~CG~~~~--------~H~vC~~CG~   48 (57)
T PRK12286         29 ECPNCGEPKL--------PHRVCPSCGY   48 (57)
T ss_pred             ECCCCCCccC--------CeEECCCCCc
Confidence            7999996433        5899999993

>PHA02942 putative transposase; Provisional

Probab=90.17  E-value=0.17  Score=47.92  Aligned_cols=27  Identities=30%  Similarity=0.770  Sum_probs=19.9

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      +||.||..-..    +.+-.-.||+||....
T Consensus       327 ~Cs~CG~~~~~----l~~r~f~C~~CG~~~d  353 (383)
T PHA02942        327 SCPKCGHKMVE----IAHRYFHCPSCGYEND  353 (383)
T ss_pred             cCCCCCCccCc----CCCCEEECCCCCCEeC
Confidence            79999976432    4455789999988653

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=90.15  E-value=0.18  Score=32.15  Aligned_cols=28  Identities=21%  Similarity=0.481  Sum_probs=15.0

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .-||.||.+....   -..-..+||.||...
T Consensus         4 rfC~~CG~~t~~~---~~g~~r~C~~Cg~~~   31 (32)
T PF09297_consen    4 RFCGRCGAPTKPA---PGGWARRCPSCGHEH   31 (32)
T ss_dssp             SB-TTT--BEEE----SSSS-EEESSSS-EE
T ss_pred             cccCcCCccccCC---CCcCEeECCCCcCEe
Confidence            3589999887772   222478899998653

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=90.13  E-value=0.13  Score=52.31  Aligned_cols=22  Identities=32%  Similarity=1.078  Sum_probs=11.4

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .||.||++...       +.-.||+||++
T Consensus        29 ~Cp~CG~~~~~-------~~~fC~~CG~~   50 (645)
T PRK14559         29 PCPQCGTEVPV-------DEAHCPNCGAE   50 (645)
T ss_pred             cCCCCCCCCCc-------ccccccccCCc
Confidence            45555554333       55566666654

>PRK05654 acetyl-CoA carboxylase subunit beta; Validated

Probab=90.12  E-value=0.11  Score=47.99  Aligned_cols=40  Identities=30%  Similarity=0.759  Sum_probs=30.2

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceee----------eCCeeEEecc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV----------VDDKFVRESV  204 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V----------d~~~F~R~~~  204 (245)
                      .||.|+..+|. + .|.+...+||.||--+.+          |++.|+--..
T Consensus        29 ~c~~c~~~~~~-~-~l~~~~~vc~~c~~h~rl~areRi~~L~D~gsF~E~~~   78 (292)
T PRK05654         29 KCPSCGQVLYR-K-ELEANLNVCPKCGHHMRISARERLDLLLDEGSFVELDA   78 (292)
T ss_pred             ECCCccchhhH-H-HHHhcCCCCCCCCCCeeCCHHHHHHHHccCCccEEecC
Confidence            89999999887 2 355567899999987765          5777765543

>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=89.93  E-value=0.17  Score=36.26  Aligned_cols=20  Identities=40%  Similarity=1.158  Sum_probs=16.2

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCC
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCS  189 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCG  189 (245)
                      ..||+||. +..       ..-.||+||
T Consensus        27 ~~c~~cg~-~~~-------~H~vc~~cG   46 (56)
T PF01783_consen   27 VKCPNCGE-PKL-------PHRVCPSCG   46 (56)
T ss_dssp             EESSSSSS-EES-------TTSBCTTTB
T ss_pred             eeeccCCC-Eec-------ccEeeCCCC
Confidence            58999994 333       689999998

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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....

>PRK12495 hypothetical protein; Provisional

Probab=89.61  E-value=0.17  Score=46.22  Aligned_cols=33  Identities=27%  Similarity=0.708  Sum_probs=26.8

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      ......||+||..+.-    + .+.+.||.|++.+.-+
T Consensus        39 tmsa~hC~~CG~PIpa----~-pG~~~Cp~CQ~~~~~~   71 (226)
T PRK12495         39 TMTNAHCDECGDPIFR----H-DGQEFCPTCQQPVTED   71 (226)
T ss_pred             ccchhhcccccCcccC----C-CCeeECCCCCCccccc
Confidence            4455699999999985    4 7899999999887643

>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown

Probab=89.39  E-value=0.045  Score=40.53  Aligned_cols=25  Identities=28%  Similarity=0.934  Sum_probs=18.5

Q ss_pred             ccCCCCCceeeecccccCCCcccC-CCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLC-PYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqC-PnCGE~L~  193 (245)
                      ..||+||++.-.       ++..| |.|++.+.
T Consensus         4 kHC~~CG~~Ip~-------~~~fCS~~C~~~~~   29 (59)
T PF09889_consen    4 KHCPVCGKPIPP-------DESFCSPKCREEYR   29 (59)
T ss_pred             CcCCcCCCcCCc-------chhhhCHHHHHHHH
Confidence            368888877554       78888 68877664

They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.

>PRK10220 hypothetical protein; Provisional

Probab=89.25  E-value=0.24  Score=41.12  Aligned_cols=30  Identities=20%  Similarity=0.871  Sum_probs=24.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      .||.|+.+++-    -..+...||.|+-.++.++
T Consensus         5 ~CP~C~seytY----~d~~~~vCpeC~hEW~~~~   34 (111)
T PRK10220          5 HCPKCNSEYTY----EDNGMYICPECAHEWNDAE   34 (111)
T ss_pred             cCCCCCCcceE----cCCCeEECCcccCcCCccc
Confidence            79999988876    2336899999999887665

>COG2835 Uncharacterized conserved protein [Function unknown]

Probab=89.19  E-value=0.25  Score=37.10  Aligned_cols=38  Identities=18%  Similarity=0.566  Sum_probs=29.9

Q ss_pred             cceec-cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          158 DIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       158 nLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      ++++. .||.|.-.++.+++   +....||.|+..++++||-
T Consensus         4 ~LLeiLaCP~~kg~L~~~~~---~~~L~c~~~~~aYpI~dGI   42 (60)
T COG2835           4 RLLEILACPVCKGPLVYDEE---KQELICPRCKLAYPIRDGI   42 (60)
T ss_pred             hhheeeeccCcCCcceEecc---CCEEEecccCceeecccCc
Confidence            44554 89999999887422   2699999999999999873

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=89.15  E-value=0.23  Score=35.92  Aligned_cols=13  Identities=38%  Similarity=1.298  Sum_probs=10.6

Q ss_pred             ccCCCCCCceeee
Q 025946          183 QLCPYCSQPFSVV  195 (245)
Q Consensus       183 iqCPnCGE~L~Vd  195 (245)
                      ++|||||+++.+.
T Consensus         1 i~CPyCge~~~~~   13 (52)
T PF14255_consen    1 IQCPYCGEPIEIL   13 (52)
T ss_pred             CCCCCCCCeeEEE
Confidence            5799999988764

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=88.83  E-value=0.23  Score=38.28  Aligned_cols=28  Identities=25%  Similarity=0.662  Sum_probs=22.6

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      .||.||..++.     ..+...||+||...+.+
T Consensus         2 fC~~Cg~~l~~-----~~~~~~C~~C~~~~~~~   29 (104)
T TIGR01384         2 FCPKCGSLMTP-----KNGVYVCPSCGYEKEKK   29 (104)
T ss_pred             CCcccCccccc-----CCCeEECcCCCCccccc
Confidence            69999998875     34689999999887653

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=88.82  E-value=0.12  Score=34.18  Aligned_cols=21  Identities=38%  Similarity=0.722  Sum_probs=17.5

Q ss_pred             ccCCCCCCceeeeCCeeEEec
Q 025946          183 QLCPYCSQPFSVVDDKFVRES  203 (245)
Q Consensus       183 iqCPnCGE~L~Vd~~~F~R~~  203 (245)
                      ++||+|++.+.+++.+....+
T Consensus         3 i~CP~C~~~f~v~~~~l~~~~   23 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDKLPAGG   23 (37)
T ss_pred             EECCCCCceEEcCHHHcccCC
Confidence            689999999999998865443

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=88.29  E-value=0.21  Score=50.82  Aligned_cols=16  Identities=25%  Similarity=0.667  Sum_probs=9.6

Q ss_pred             ccCCCCCCceeeeCCe
Q 025946          183 QLCPYCSQPFSVVDDK  198 (245)
Q Consensus       183 iqCPnCGE~L~Vd~~~  198 (245)
                      ..||+||+.++.+...
T Consensus        28 ~~Cp~CG~~~~~~~~f   43 (645)
T PRK14559         28 KPCPQCGTEVPVDEAH   43 (645)
T ss_pred             CcCCCCCCCCCccccc
Confidence            3577777776655443

>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]

Probab=88.18  E-value=0.31  Score=39.61  Aligned_cols=36  Identities=28%  Similarity=0.732  Sum_probs=26.1

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEe
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRE  202 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~  202 (245)
                      .|-+||++|.++  -+ +-|..||.|-... +++-+|.-+
T Consensus        60 ~CkkCGfef~~~--~i-k~pSRCP~CKSE~-Ie~prF~ie   95 (97)
T COG3357          60 RCKKCGFEFRDD--KI-KKPSRCPKCKSEW-IEEPRFVIE   95 (97)
T ss_pred             hhcccCcccccc--cc-CCcccCCcchhhc-ccCCceeec
Confidence            899999999882  11 2489999998776 555555544

>PRK15103 paraquat-inducible membrane protein A; Provisional

Probab=88.04  E-value=0.52  Score=45.49  Aligned_cols=24  Identities=25%  Similarity=0.607  Sum_probs=18.5

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .||.|+.-..       .+...||.||..+.
T Consensus       223 ~C~~Cd~l~~-------~~~a~CpRC~~~L~  246 (419)
T PRK15103        223 SCSCCTAILP-------ADQPVCPRCHTKGY  246 (419)
T ss_pred             cCCCCCCCCC-------CCCCCCCCCCCcCc
Confidence            4999997532       25668999999984

>TIGR01031 rpmF_bact ribosomal protein L32

Probab=87.97  E-value=0.24  Score=35.81  Aligned_cols=19  Identities=42%  Similarity=1.078  Sum_probs=15.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCS  189 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCG  189 (245)
                      .||+||+.-.        ..-+||+||
T Consensus        28 ~C~~cG~~~~--------~H~vc~~cG   46 (55)
T TIGR01031        28 VCPNCGEFKL--------PHRVCPSCG   46 (55)
T ss_pred             ECCCCCCccc--------CeeECCccC
Confidence            7999995332        689999998

This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.

>KOG2923 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.87  E-value=0.34  Score=37.17  Aligned_cols=38  Identities=34%  Similarity=0.740  Sum_probs=29.0

Q ss_pred             cCcceeccCCCCCceeeecccccCC--CcccCCCCCCceee
Q 025946          156 SRDIVQDSCPNCGNDFQIFKSTLND--ELQLCPYCSQPFSV  194 (245)
Q Consensus       156 ~rnLIE~tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~V  194 (245)
                      ..+.+.-.|| ||..|.+.++.|.+  +-.+||.|.=.+.|
T Consensus        17 e~~~y~yPCp-CGDrf~It~edL~~ge~Va~CpsCSL~I~V   56 (67)
T KOG2923|consen   17 ENQTYYYPCP-CGDRFQITLEDLENGEDVARCPSCSLIIRV   56 (67)
T ss_pred             CCCeEEcCCC-CCCeeeecHHHHhCCCeeecCCCceEEEEE
Confidence            3456667898 99999997777655  57899999766554

>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=87.87  E-value=0.28  Score=49.90  Aligned_cols=28  Identities=25%  Similarity=0.507  Sum_probs=19.9

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      |.--+.|++||+. ..       ..-.||+||.+++
T Consensus       623 n~~~~~C~~CG~~-~g-------~~~~CP~CG~~~~  650 (656)
T PRK08270        623 TPTFSICPKHGYL-SG-------EHEFCPKCGEETE  650 (656)
T ss_pred             CCCCcccCCCCCc-CC-------CCCCCcCCcCccc
Confidence            3444599999973 33       3688999998754

>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6

Probab=87.82  E-value=0.17  Score=47.83  Aligned_cols=12  Identities=25%  Similarity=0.769  Sum_probs=8.9

Q ss_pred             cccCCCCCCcee
Q 025946          182 LQLCPYCSQPFS  193 (245)
Q Consensus       182 ~iqCPnCGE~L~  193 (245)
                      .-+|+.||.+++
T Consensus       149 g~~Ce~cG~~~~  160 (391)
T PF09334_consen  149 GDQCENCGRPLE  160 (391)
T ss_dssp             TTEETTTSSBEE
T ss_pred             CCcccCCCCCcc
Confidence            456778888877

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....

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

Probab=87.77  E-value=0.3  Score=48.36  Aligned_cols=47  Identities=17%  Similarity=0.408  Sum_probs=33.3

Q ss_pred             cceeccCCCCCceeeec-cccc-------CCCcccCCCCCCceee-------eCCeeEEecc
Q 025946          158 DIVQDSCPNCGNDFQIF-KSTL-------NDELQLCPYCSQPFSV-------VDDKFVRESV  204 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~-ed~L-------n~d~iqCPnCGE~L~V-------d~~~F~R~~~  204 (245)
                      ..+...||.||..+... +++.       ..--.+||.||..++-       ..|+++.+.+
T Consensus       197 r~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~~~~  258 (557)
T PF05876_consen  197 RRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVATNP  258 (557)
T ss_pred             eEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEeccc
Confidence            35667999999888763 2221       1126799999998874       4688888777

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 [].

>TIGR00155 pqiA_fam integral membrane protein, PqiA family

Probab=87.60  E-value=0.63  Score=44.62  Aligned_cols=25  Identities=32%  Similarity=0.801  Sum_probs=19.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .||.|+.....      ..+..||.||.++.
T Consensus       217 ~C~~Cd~~~~~------~~~a~CpRC~~~L~  241 (403)
T TIGR00155       217 SCSACHTTILP------AQEPVCPRCSTPLY  241 (403)
T ss_pred             cCCCCCCccCC------CCCcCCcCCCCccc
Confidence            49999985432      35788999999993

This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.

>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family

Probab=87.55  E-value=0.26  Score=38.04  Aligned_cols=18  Identities=17%  Similarity=0.333  Sum_probs=12.5

Q ss_pred             cCCCcccCCCCCCceeee
Q 025946          178 LNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       178 Ln~d~iqCPnCGE~L~Vd  195 (245)
                      ++-.-..||.||+.+...
T Consensus        27 v~~~~~~C~~CGe~~~~~   44 (127)
T TIGR03830        27 IGVPGWYCPACGEELLDP   44 (127)
T ss_pred             EeeeeeECCCCCCEEEcH
Confidence            333567899999977543

This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.

>PRK00481 NAD-dependent deacetylase; Provisional

Probab=87.48  E-value=0.31  Score=42.70  Aligned_cols=31  Identities=26%  Similarity=0.677  Sum_probs=21.3

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ..|..|++.+ ..++.+..+...||.||.++.
T Consensus       123 ~~C~~C~~~~-~~~~~~~~~~p~C~~Cgg~lr  153 (242)
T PRK00481        123 ARCTKCGQTY-DLDEYLKPEPPRCPKCGGILR  153 (242)
T ss_pred             eeeCCCCCCc-ChhhhccCCCCCCCCCCCccC
Confidence            3999998764 445555555556999987653

>PLN00209 ribosomal protein S27; Provisional

Probab=87.30  E-value=0.4  Score=38.26  Aligned_cols=40  Identities=18%  Similarity=0.363  Sum_probs=29.5

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCee
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDKF  199 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~F  199 (245)
                      .++.+.||.|+++-.++.  =....+.|..||+.|. ..+|+.
T Consensus        33 ~Fm~VkCp~C~n~q~VFS--hA~t~V~C~~Cg~~L~~PTGGKa   73 (86)
T PLN00209         33 FFMDVKCQGCFNITTVFS--HSQTVVVCGSCQTVLCQPTGGKA   73 (86)
T ss_pred             EEEEEECCCCCCeeEEEe--cCceEEEccccCCEeeccCCCCe
Confidence            456779999999888731  2346999999999984 445543

>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed

Probab=87.25  E-value=0.17  Score=47.43  Aligned_cols=39  Identities=15%  Similarity=0.359  Sum_probs=30.0

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee----------eeCCeeEEec
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS----------VVDDKFVRES  203 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~----------Vd~~~F~R~~  203 (245)
                      .||+|++.+|.  ..|.+...+||+||--+.          +|++.|+.-.
T Consensus        40 kc~~C~~~~~~--~~l~~~~~vcp~c~~h~rltAreRI~~L~D~gSF~E~~   88 (296)
T CHL00174         40 QCENCYGLNYK--KFLKSKMNICEQCGYHLKMSSSDRIELLIDPGTWNPMD   88 (296)
T ss_pred             ECCCccchhhH--HHHHHcCCCCCCCCCCcCCCHHHHHHHHccCCccEEcC
Confidence            89999999987  336777899999998554          5667776554

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=87.22  E-value=0.4  Score=40.96  Aligned_cols=31  Identities=29%  Similarity=0.711  Sum_probs=19.1

Q ss_pred             cCCCCCcee-eecccc-cCCC-----cccCCCCCCcee
Q 025946          163 SCPNCGNDF-QIFKST-LNDE-----LQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF-~~~ed~-Ln~d-----~iqCPnCGE~L~  193 (245)
                      .||-||.+. ..-++. +.++     --+||+||-.+.
T Consensus         2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~   39 (154)
T PRK00464          2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT   39 (154)
T ss_pred             cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence            599999866 332222 2221     268999988765

>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]

Probab=87.09  E-value=0.25  Score=47.26  Aligned_cols=28  Identities=36%  Similarity=0.675  Sum_probs=19.7

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .||+||..++.+  .-|...-.||+||+++
T Consensus       317 fc~ncG~~~t~~--~~ng~a~fcp~cgq~~  344 (345)
T COG4260         317 FCLNCGCGTTAD--FDNGKAKFCPECGQGF  344 (345)
T ss_pred             cccccCcccccC--CccchhhhChhhcCCC
Confidence            788888666652  1233588999999875

>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E

Probab=87.01  E-value=0.38  Score=41.46  Aligned_cols=31  Identities=26%  Similarity=0.557  Sum_probs=21.9

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .|+.|+++.+..+.......-.||.||.++.
T Consensus       111 ~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~lr  141 (224)
T cd01412         111 RCSSCGYVGENNEEIPEEELPRCPKCGGLLR  141 (224)
T ss_pred             ccCCCCCCCCcchhhhccCCCCCCCCCCccC
Confidence            9999999877632222334578999998653

coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=86.99  E-value=0.43  Score=38.02  Aligned_cols=47  Identities=23%  Similarity=0.476  Sum_probs=32.1

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCeeE-Eecccc
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDKFV-RESVRF  206 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~F~-R~~~~f  206 (245)
                      .++.+.||.|+++-.++.  =.++.+.|..||+.|. ..+|+.. .|+..|
T Consensus        32 ~Fm~VkCp~C~n~q~VFS--hA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~f   80 (85)
T PTZ00083         32 YFMDVKCPGCSQITTVFS--HAQTVVLCGGCSSQLCQPTGGKAKLTEGCSF   80 (85)
T ss_pred             eEEEEECCCCCCeeEEEe--cCceEEEccccCCEeeccCCCCeEecCCceE
Confidence            456779999999888731  2346999999999994 4444432 334444

>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.98  E-value=0.38  Score=41.28  Aligned_cols=33  Identities=33%  Similarity=0.904  Sum_probs=17.5

Q ss_pred             eeccCCCCCceeeecccccC-------CCcccCCCCCCcee
Q 025946          160 VQDSCPNCGNDFQIFKSTLN-------DELQLCPYCSQPFS  193 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln-------~d~iqCPnCGE~L~  193 (245)
                      ++.+||.|++++.. +.+..       ..-..||+|+..++
T Consensus        17 l~~~C~~C~~~~~f-~g~~~~~~~~~~~~~~~C~~C~~~~~   56 (188)
T PF08996_consen   17 LKLTCPSCGTEFEF-PGVFEEDGDDVSPSGLQCPNCSTPLS   56 (188)
T ss_dssp             EEEE-TTT--EEEE--SSS--SSEEEETTEEEETTT--B--
T ss_pred             eEeECCCCCCCccc-cccccCCccccccCcCcCCCCCCcCC
Confidence            45699999999876 33333       34789999998543

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. 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. The 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 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.

>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins

Probab=86.90  E-value=0.37  Score=31.34  Aligned_cols=26  Identities=23%  Similarity=0.672  Sum_probs=15.9

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      .++-..|+.||...+-       ....||+||.
T Consensus         8 ~l~~~rC~~Cg~~~~p-------Pr~~Cp~C~s   33 (37)
T PF12172_consen    8 RLLGQRCRDCGRVQFP-------PRPVCPHCGS   33 (37)
T ss_dssp             -EEEEE-TTT--EEES---------SEETTTT-
T ss_pred             EEEEEEcCCCCCEecC-------CCcCCCCcCc
Confidence            4556689999988776       6789999985

The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.

>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

Probab=86.88  E-value=0.31  Score=45.10  Aligned_cols=31  Identities=23%  Similarity=0.499  Sum_probs=23.2

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      ..||+||.+-.  .....+++.+|-.||..++-
T Consensus         2 ~~CpeCg~~~~--~~d~~~ge~VC~~CG~Vi~~   32 (285)
T COG1405           2 MSCPECGSTNI--ITDYERGEIVCADCGLVLED   32 (285)
T ss_pred             CCCCCCCCccc--eeeccCCeEEeccCCEEecc
Confidence            47999998822  22245799999999998853

>PRK07591 threonine synthase; Validated

Probab=86.87  E-value=0.43  Score=45.32  Aligned_cols=31  Identities=26%  Similarity=0.765  Sum_probs=24.3

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      ..-.|+.||+++-.     . ....||.||.+|.++=
T Consensus        17 ~~l~C~~Cg~~~~~-----~-~~~~C~~cg~~l~~~y   47 (421)
T PRK07591         17 VALKCRECGAEYPL-----G-PIHVCEECFGPLEVAY   47 (421)
T ss_pred             eEEEeCCCCCcCCC-----C-CCccCCCCCCeEEEEe
Confidence            34589999998754     2 2378999999999884

>COG3364 Zn-ribbon containing protein [General function prediction only]

Probab=86.85  E-value=0.25  Score=40.95  Aligned_cols=35  Identities=29%  Similarity=0.631  Sum_probs=23.2

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccc
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVR  205 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~  205 (245)
                      -.|..||+.|-+-+..+   -.=||+||-      ++|...+..
T Consensus         3 H~CtrCG~vf~~g~~~i---l~GCp~CG~------nkF~yv~~e   37 (112)
T COG3364           3 HQCTRCGEVFDDGSEEI---LSGCPKCGC------NKFLYVPEE   37 (112)
T ss_pred             ceecccccccccccHHH---HccCccccc------hheEecccc
Confidence            47999998887722222   335999994      567666543

>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=86.82  E-value=0.15  Score=40.26  Aligned_cols=44  Identities=23%  Similarity=0.615  Sum_probs=30.6

Q ss_pred             ceeccCCCCCceeeecccccCCC-cccCCCCCCceeeeCCeeEEecccc
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDE-LQLCPYCSQPFSVVDDKFVRESVRF  206 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d-~iqCPnCGE~L~Vd~~~F~R~~~~f  206 (245)
                      +|-..|-+||+.+... +.++++ ...||.||.++   ...|.|.+.-|
T Consensus        10 tY~Y~c~~cg~~~dvv-q~~~ddplt~ce~c~a~~---kk~l~~vgi~f   54 (82)
T COG2331          10 TYSYECTECGNRFDVV-QAMTDDPLTTCEECGARL---KKLLNAVGIVF   54 (82)
T ss_pred             ceEEeecccchHHHHH-HhcccCccccChhhChHH---HHhhccceEEE
Confidence            3455899999988763 335554 67899999977   45555555544

>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[]

Probab=86.81  E-value=0.37  Score=32.28  Aligned_cols=26  Identities=27%  Similarity=0.765  Sum_probs=22.2

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .||+||..++.    .+++...|-.||...
T Consensus        10 ~C~~C~~~~~~----~~dG~~yC~~cG~~~   35 (36)
T PF11781_consen   10 PCPVCGSRWFY----SDDGFYYCDRCGHQS   35 (36)
T ss_pred             cCCCCCCeEeE----ccCCEEEhhhCceEc
Confidence            59999999877    788899999998764

>PF13395 HNH_4: HNH endonuclease

Probab=86.77  E-value=0.37  Score=33.82  Aligned_cols=25  Identities=32%  Similarity=0.804  Sum_probs=18.3

Q ss_pred             CCCCCCceeeeC--------CeeEEeccccccc
Q 025946          185 CPYCSQPFSVVD--------DKFVRESVRFSNE  209 (245)
Q Consensus       185 CPnCGE~L~Vd~--------~~F~R~~~~f~~~  209 (245)
                      |||||+++..++        +||.--+..+.+.
T Consensus         1 C~Y~g~~i~~~~l~~~~~~iDHiiP~s~~~~~s   33 (54)
T PF13395_consen    1 CPYCGKPISIENLFKNKYEIDHIIPRSRGGDDS   33 (54)
T ss_pred             CCCCCCCCChhhcccCCceeEEEecccccCCCC
Confidence            999999999888        6666555554443

>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors []

Probab=86.66  E-value=0.54  Score=31.05  Aligned_cols=29  Identities=24%  Similarity=0.810  Sum_probs=22.4

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ..|+.|+......   -+++..+||.||..++
T Consensus         4 ~~C~~C~~~~i~~---~~~~~~~C~~Cg~~~~   32 (33)
T PF08792_consen    4 KKCSKCGGNGIVN---KEDDYEVCIFCGSSFP   32 (33)
T ss_pred             eEcCCCCCCeEEE---ecCCeEEcccCCcEee
Confidence            4799999876541   3557999999998765

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=86.39  E-value=0.2  Score=32.39  Aligned_cols=21  Identities=33%  Similarity=0.729  Sum_probs=16.9

Q ss_pred             ccCCCCCCceeeeCCeeEEec
Q 025946          183 QLCPYCSQPFSVVDDKFVRES  203 (245)
Q Consensus       183 iqCPnCGE~L~Vd~~~F~R~~  203 (245)
                      +.||+|++.+.+++.+...++
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~   23 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANG   23 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCC
Confidence            689999999999987765443

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.

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=86.25  E-value=0.36  Score=52.97  Aligned_cols=11  Identities=36%  Similarity=1.213  Sum_probs=7.1

Q ss_pred             eccCCCCCcee
Q 025946          161 QDSCPNCGNDF  171 (245)
Q Consensus       161 E~tCPnCG~eF  171 (245)
                      .+.||.||.+.
T Consensus       667 ~rkCPkCG~~t  677 (1337)
T PRK14714        667 RRRCPSCGTET  677 (1337)
T ss_pred             EEECCCCCCcc
Confidence            34777777653

>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=86.15  E-value=0.38  Score=48.88  Aligned_cols=23  Identities=26%  Similarity=0.654  Sum_probs=18.2

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCC
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      -+.||+||+++..       ..-.||.||+
T Consensus       568 ~~~C~~CG~~~~g-------~~~~CP~CGs  590 (625)
T PRK08579        568 ITVCNKCGRSTTG-------LYTRCPRCGS  590 (625)
T ss_pred             CccCCCCCCccCC-------CCCcCcCCCC
Confidence            3499999997654       3679999997

>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins

Probab=86.05  E-value=0.46  Score=45.64  Aligned_cols=24  Identities=38%  Similarity=0.863  Sum_probs=21.5

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      +||+||..++-       +..+|-+||..|-
T Consensus         1 ~C~~Cg~~v~F-------eNt~C~~Cg~~LG   24 (343)
T PF10005_consen    1 SCPNCGQPVFF-------ENTRCLSCGSALG   24 (343)
T ss_pred             CCCCCCCccee-------CCCccccCCcccc
Confidence            69999999998       7889999999774

>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.96  E-value=0.24  Score=46.02  Aligned_cols=13  Identities=31%  Similarity=0.835  Sum_probs=10.8

Q ss_pred             eccCCCCCceeee
Q 025946          161 QDSCPNCGNDFQI  173 (245)
Q Consensus       161 E~tCPnCG~eF~~  173 (245)
                      +.+||+|+++|.-
T Consensus        19 ~ieCPvC~tkFkk   31 (267)
T COG1655          19 TIECPVCNTKFKK   31 (267)
T ss_pred             eeccCcccchhhh
Confidence            3599999999875

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

Probab=85.88  E-value=0.42  Score=31.84  Aligned_cols=27  Identities=30%  Similarity=0.742  Sum_probs=13.9

Q ss_pred             cCCCCCceeeeccccc---CCCcccCCCCCCc
Q 025946          163 SCPNCGNDFQIFKSTL---NDELQLCPYCSQP  191 (245)
Q Consensus       163 tCPnCG~eF~~~ed~L---n~d~iqCPnCGE~  191 (245)
                      -||+||.+...  .+.   +..-.+||.||..
T Consensus         2 fC~~CG~~l~~--~ip~gd~r~R~vC~~Cg~I   31 (34)
T PF14803_consen    2 FCPQCGGPLER--RIPEGDDRERLVCPACGFI   31 (34)
T ss_dssp             B-TTT--B-EE--E--TT-SS-EEEETTTTEE
T ss_pred             ccccccChhhh--hcCCCCCccceECCCCCCE
Confidence            49999988654  122   3346789999864

>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]

Probab=85.74  E-value=0.25  Score=48.71  Aligned_cols=43  Identities=21%  Similarity=0.541  Sum_probs=33.9

Q ss_pred             cCCCCCceeeecccc--cCC--CcccCCCCCCceeeeCCeeEEeccc
Q 025946          163 SCPNCGNDFQIFKST--LND--ELQLCPYCSQPFSVVDDKFVRESVR  205 (245)
Q Consensus       163 tCPnCG~eF~~~ed~--Ln~--d~iqCPnCGE~L~Vd~~~F~R~~~~  205 (245)
                      .||+|.++|..+|-.  +..  +...|-+|+..|..|+..-..+.++
T Consensus       130 ~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~~~~e~~  176 (436)
T KOG2593|consen  130 VCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKLPSKESR  176 (436)
T ss_pred             cCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccCchHHHH
Confidence            899999999987665  443  6999999999999888766554443

>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases

Probab=85.40  E-value=0.62  Score=38.67  Aligned_cols=34  Identities=21%  Similarity=0.573  Sum_probs=23.3

Q ss_pred             ceeccCCCCCceeeeccc---ccCCCcccCCCCCCce
Q 025946          159 IVQDSCPNCGNDFQIFKS---TLNDELQLCPYCSQPF  192 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed---~Ln~d~iqCPnCGE~L  192 (245)
                      +.+..|+.|++++...+.   .-++..-.||.||..+
T Consensus       103 l~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~l  139 (178)
T PF02146_consen  103 LFRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGLL  139 (178)
T ss_dssp             EEEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCBE
T ss_pred             hceeeecCCCccccchhhcccccccccccccccCccC
Confidence            444599999998865321   1234566999999855

This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....

>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length

Probab=85.28  E-value=0.91  Score=38.53  Aligned_cols=32  Identities=31%  Similarity=0.904  Sum_probs=23.5

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEec
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRES  203 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~  203 (245)
                      .|-+||.+.....   -.--..||.||      +..|+|.+
T Consensus       114 ~C~~Cg~~~~~~~---~~~l~~Cp~C~------~~~F~R~~  145 (146)
T PF07295_consen  114 VCENCGHEVELTH---PERLPPCPKCG------HTEFTRQP  145 (146)
T ss_pred             ecccCCCEEEecC---CCcCCCCCCCC------CCeeeeCC
Confidence            8999999988721   11356799998      55677765

Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.

>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised

Probab=85.25  E-value=0.94  Score=32.97  Aligned_cols=27  Identities=41%  Similarity=0.710  Sum_probs=20.5

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEe
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRE  202 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~  202 (245)
                      .||+||+....     |        =+-.|.|+|+-|.|.
T Consensus        15 ~Cp~CGN~~vG-----n--------gEG~liV~edtfkRt   41 (49)
T PF12677_consen   15 KCPKCGNDKVG-----N--------GEGTLIVEEDTFKRT   41 (49)
T ss_pred             cCcccCCcEee-----c--------CcceEEEeccceeee
Confidence            79999988877     2        123568999999885

This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.

>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]

Probab=84.76  E-value=0.36  Score=45.60  Aligned_cols=29  Identities=31%  Similarity=0.896  Sum_probs=23.8

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .||.|+...|.  ..|.....+||+|+--+.
T Consensus        30 KCp~c~~~~y~--~eL~~n~~vcp~c~~h~r   58 (294)
T COG0777          30 KCPSCGEMLYR--KELESNLKVCPKCGHHMR   58 (294)
T ss_pred             ECCCccceeeH--HHHHhhhhcccccCcccc
Confidence            79999999997  346778999999987543

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=84.45  E-value=0.73  Score=39.25  Aligned_cols=30  Identities=17%  Similarity=0.478  Sum_probs=23.0

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .+...||.||....-    ..-++..||+||..-
T Consensus       147 vv~a~~~~~g~~~~~----~~~~~~~c~~~~~~e  176 (189)
T PRK09521        147 VIYAMCSRCRTPLVK----KGENELKCPNCGNIE  176 (189)
T ss_pred             EEEEEccccCCceEE----CCCCEEECCCCCCEE
Confidence            345589999998876    455789999998643

>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=84.45  E-value=0.51  Score=48.64  Aligned_cols=25  Identities=36%  Similarity=0.709  Sum_probs=17.3

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      +.--+.||+||+..-.        .-.||.||.
T Consensus       677 n~~~~~C~~CG~~~~~--------~~~CP~CG~  701 (735)
T PRK07111        677 NHPVDRCPVCGYLGVI--------EDKCPKCGS  701 (735)
T ss_pred             CCCCeecCCCCCCCCc--------CccCcCCCC
Confidence            3334499999954322        479999996

>COG4031 Predicted metal-binding protein [General function prediction only]

Probab=84.26  E-value=0.54  Score=42.81  Aligned_cols=21  Identities=24%  Similarity=0.803  Sum_probs=18.0

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .| -||+++..        |..||+||++=
T Consensus         2 ~C-rCG~~l~~--------p~~Cl~Cg~~~   22 (227)
T COG4031           2 IC-RCGAELSS--------PAFCLNCGRRH   22 (227)
T ss_pred             cc-ccCCcccc--------cchhcccCCcc
Confidence            58 99999775        79999999983

>COG4640 Predicted membrane protein [Function unknown]

Probab=84.24  E-value=0.46  Score=47.04  Aligned_cols=24  Identities=29%  Similarity=0.886  Sum_probs=18.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      -||.||..       =++|..+||-||.++.
T Consensus         3 fC~kcG~q-------k~Ed~~qC~qCG~~~t   26 (465)
T COG4640           3 FCPKCGSQ-------KAEDDVQCTQCGHKFT   26 (465)
T ss_pred             cccccccc-------cccccccccccCCcCC
Confidence            69999943       1346788999999874

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

Probab=84.18  E-value=0.65  Score=41.46  Aligned_cols=27  Identities=19%  Similarity=0.646  Sum_probs=21.5

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      +-..|++|+....-     ......||+||..
T Consensus       148 I~A~CsrC~~~L~~-----~~~~l~Cp~Cg~t  174 (188)
T COG1096         148 IYARCSRCRAPLVK-----KGNMLKCPNCGNT  174 (188)
T ss_pred             EEEEccCCCcceEE-----cCcEEECCCCCCE
Confidence            44599999988775     4568999999974

>PRK06450 threonine synthase; Validated

Probab=84.14  E-value=0.6  Score=43.30  Aligned_cols=31  Identities=26%  Similarity=0.627  Sum_probs=23.2

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      .-.|+.||+++..      .....||.||.+|.++-+
T Consensus         3 ~~~C~~Cg~~~~~------~~~~~C~~cg~~l~~~~d   33 (338)
T PRK06450          3 KEVCMKCGKERES------IYEIRCKKCGGPFEILID   33 (338)
T ss_pred             eeEECCcCCcCCC------cccccCCcCCCEeEEeec
Confidence            3489999998532      235789999999988743

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

Probab=83.83  E-value=0.44  Score=41.57  Aligned_cols=34  Identities=26%  Similarity=0.661  Sum_probs=20.9

Q ss_pred             cCCCCCceeeecc---cc--c---CCCcccCCCCCCceeeeC
Q 025946          163 SCPNCGNDFQIFK---ST--L---NDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       163 tCPnCG~eF~~~e---d~--L---n~d~iqCPnCGE~L~Vd~  196 (245)
                      .||+|++...+..   ++  |   ..-|..|-+||.+++-.+
T Consensus        41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~   82 (158)
T PF10083_consen   41 SCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTE   82 (158)
T ss_pred             HCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHH
Confidence            6888887765532   11  1   113777888888877544

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.

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

Probab=83.82  E-value=2  Score=35.90  Aligned_cols=73  Identities=12%  Similarity=0.200  Sum_probs=40.1

Q ss_pred             hHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcceeccCCCCCceeeecccc--cCCCcccC
Q 025946          108 LGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKST--LNDELQLC  185 (245)
Q Consensus       108 lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~~~Gf~WWl~rnLIE~tCPnCG~eF~~~ed~--Ln~d~iqC  185 (245)
                      +++|+..+.++-..+-. +|.++...-++..+.+++++|...+..                 -.|..=..  .+--+++|
T Consensus        11 ~R~~al~lif~g~~vmy-~gi~f~~~~~im~ifmllG~L~~l~S~-----------------~VYfwIGmlStkav~V~C   72 (114)
T PF11023_consen   11 IRTFALSLIFIGMIVMY-IGIFFKASPIIMVIFMLLGLLAILAST-----------------AVYFWIGMLSTKAVQVEC   72 (114)
T ss_pred             HHHHHHHHHHHHHHHHh-hhhhhcccHHHHHHHHHHHHHHHHHHH-----------------HHHHHhhhhcccceeeEC
Confidence            34555444333332222 245556667778888888877755544                 12211011  12248889


Q ss_pred             CCCCCceeeeCCe
Q 025946          186 PYCSQPFSVVDDK  198 (245)
Q Consensus       186 PnCGE~L~Vd~~~  198 (245)
                      |+|+.+-..-++.
T Consensus        73 P~C~K~TKmLGr~   85 (114)
T PF11023_consen   73 PNCGKQTKMLGRV   85 (114)
T ss_pred             CCCCChHhhhchh
Confidence            9999887655544

; GO: 0005887 integral to plasma membrane

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

Probab=83.77  E-value=0.62  Score=35.22  Aligned_cols=29  Identities=21%  Similarity=0.474  Sum_probs=20.9

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      -.|-.||..+...|   .-..-.||||||..-
T Consensus        10 ~~CtSCg~~i~p~e---~~v~F~CPnCGe~~I   38 (61)
T COG2888          10 PVCTSCGREIAPGE---TAVKFPCPNCGEVEI   38 (61)
T ss_pred             ceeccCCCEeccCC---ceeEeeCCCCCceee
Confidence            38999999985421   225788999997653

>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose

Probab=83.75  E-value=0.52  Score=40.65  Aligned_cols=31  Identities=23%  Similarity=0.613  Sum_probs=21.3

Q ss_pred             ccCCCCCceeeeccc---ccCCCcccCCCCCCce
Q 025946          162 DSCPNCGNDFQIFKS---TLNDELQLCPYCSQPF  192 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed---~Ln~d~iqCPnCGE~L  192 (245)
                      ..|+.|++++...+.   ..+.....||.||.++
T Consensus       110 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~l  143 (218)
T cd01407         110 VRCTKCGKEYPRDELQADIDREEVPRCPKCGGLL  143 (218)
T ss_pred             ceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCcc
Confidence            389999998765321   1233467899999774

Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=83.63  E-value=0.98  Score=29.37  Aligned_cols=13  Identities=23%  Similarity=0.759  Sum_probs=9.8

Q ss_pred             cccCCCCCCceee
Q 025946          182 LQLCPYCSQPFSV  194 (245)
Q Consensus       182 ~iqCPnCGE~L~V  194 (245)
                      -.+||.|||.+..
T Consensus        32 ~~~C~~CGE~~~~   44 (46)
T TIGR03831        32 ALVCPQCGEEYLD   44 (46)
T ss_pred             ccccccCCCEeeC
Confidence            3479999998753

This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=83.48  E-value=0.37  Score=31.93  Aligned_cols=21  Identities=24%  Similarity=0.657  Sum_probs=17.3

Q ss_pred             ccCCCCCCceeeeCCeeEEec
Q 025946          183 QLCPYCSQPFSVVDDKFVRES  203 (245)
Q Consensus       183 iqCPnCGE~L~Vd~~~F~R~~  203 (245)
                      ++||+|+..+.++|.+.-..+
T Consensus         3 i~Cp~C~~~y~i~d~~ip~~g   23 (36)
T PF13717_consen    3 ITCPNCQAKYEIDDEKIPPKG   23 (36)
T ss_pred             EECCCCCCEEeCCHHHCCCCC
Confidence            689999999999998755443

>PRK10445 endonuclease VIII; Provisional

Probab=83.47  E-value=0.77  Score=41.32  Aligned_cols=27  Identities=22%  Similarity=0.680  Sum_probs=21.0

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCC
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCS  189 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCG  189 (245)
                      ..||+||.+... ..+-..+...||+|-
T Consensus       236 ~~Cp~Cg~~I~~-~~~~gR~t~~CP~CQ  262 (263)
T PRK10445        236 EACERCGGIIEK-TTLSSRPFYWCPGCQ  262 (263)
T ss_pred             CCCCCCCCEeEE-EEECCCCcEECCCCc
Confidence            489999988875 344566899999994

>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]

Probab=83.40  E-value=0.49  Score=42.69  Aligned_cols=32  Identities=22%  Similarity=0.599  Sum_probs=20.6

Q ss_pred             eeccCCCCCceeeecccccCC----CcccCCCCCCce
Q 025946          160 VQDSCPNCGNDFQIFKSTLND----ELQLCPYCSQPF  192 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~----d~iqCPnCGE~L  192 (245)
                      +...||+||.+=+. -.+++.    -...|++||+..
T Consensus         5 iy~~Cp~Cg~eev~-hEVik~~g~~~lvrC~eCG~V~   40 (201)
T COG1326           5 IYIECPSCGSEEVS-HEVIKERGREPLVRCEECGTVH   40 (201)
T ss_pred             EEEECCCCCcchhh-HHHHHhcCCceEEEccCCCcEe
Confidence            44589999933221 122333    268999999987

>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.85  E-value=0.73  Score=34.93  Aligned_cols=17  Identities=29%  Similarity=0.854  Sum_probs=13.7

Q ss_pred             cCCCcccCCCCCCceee
Q 025946          178 LNDELQLCPYCSQPFSV  194 (245)
Q Consensus       178 Ln~d~iqCPnCGE~L~V  194 (245)
                      =+++++.||||++.+..
T Consensus        44 g~~gev~CPYC~t~y~l   60 (62)
T COG4391          44 GDEGEVVCPYCSTRYRL   60 (62)
T ss_pred             CCCCcEecCccccEEEe
Confidence            34579999999998764

>PRK11032 hypothetical protein; Provisional

Probab=82.83  E-value=1.3  Score=38.42  Aligned_cols=31  Identities=35%  Similarity=0.892  Sum_probs=23.5

Q ss_pred             cCCCCCceeeecccccCCC-cccCCCCCCceeeeCCeeEEec
Q 025946          163 SCPNCGNDFQIFKSTLNDE-LQLCPYCSQPFSVVDDKFVRES  203 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d-~iqCPnCGE~L~Vd~~~F~R~~  203 (245)
                      .|-+||.+...    -..+ -..||.||      +.+|+|.+
T Consensus       126 vC~~Cg~~~~~----~~p~~i~pCp~C~------~~~F~R~~  157 (160)
T PRK11032        126 VCEKCHHHLAF----YTPEVLPLCPKCG------HDQFQRRP  157 (160)
T ss_pred             EecCCCCEEEe----cCCCcCCCCCCCC------CCeeeeCC
Confidence            89999999876    2223 56799998      56788875

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=82.79  E-value=0.59  Score=51.38  Aligned_cols=9  Identities=44%  Similarity=1.401  Sum_probs=5.4

Q ss_pred             cCCCCCcee
Q 025946          163 SCPNCGNDF  171 (245)
Q Consensus       163 tCPnCG~eF  171 (245)
                      .||.||...
T Consensus       681 fCP~CGs~t  689 (1337)
T PRK14714        681 RCPDCGTHT  689 (1337)
T ss_pred             cCcccCCcC
Confidence            566666553

>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A

Probab=82.71  E-value=0.51  Score=46.82  Aligned_cols=25  Identities=36%  Similarity=0.683  Sum_probs=11.4

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .--+.|++||+.--        ..-.||.||++
T Consensus       489 ~~~~~C~~CG~~~~--------~~~~CP~CGs~  513 (546)
T PF13597_consen  489 PPIDICPDCGYIGG--------EGDKCPKCGSE  513 (546)
T ss_dssp             --EEEETTT---S----------EEE-CCC---
T ss_pred             cCcccccCCCcCCC--------CCCCCCCCCCc
Confidence            33459999997422        26789999998

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

Probab=82.47  E-value=0.88  Score=40.97  Aligned_cols=27  Identities=22%  Similarity=0.646  Sum_probs=20.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      .||+||.++.- ..+-..+...||.|-.
T Consensus       247 pC~~Cg~~I~~-~~~~gR~t~~CP~CQ~  273 (274)
T PRK01103        247 PCRRCGTPIEK-IKQGGRSTFFCPRCQK  273 (274)
T ss_pred             CCCCCCCeeEE-EEECCCCcEECcCCCC
Confidence            79999988765 3333458999999953

>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT)

Probab=82.44  E-value=1.1  Score=35.84  Aligned_cols=36  Identities=19%  Similarity=0.590  Sum_probs=25.8

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      ..+...|+.|+.++.-...+ +.....||.|+.+|..
T Consensus       120 ~~~~~~C~~C~~~~~r~~~~-~~~~~~C~~C~~~l~~  155 (157)
T PF10263_consen  120 KKYVYRCPSCGREYKRHRRS-KRKRYRCGRCGGPLVQ  155 (157)
T ss_pred             cceEEEcCCCCCEeeeeccc-chhhEECCCCCCEEEE
Confidence            34555999999998773333 4456789999988753

SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.

>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=82.18  E-value=0.71  Score=47.04  Aligned_cols=26  Identities=19%  Similarity=0.515  Sum_probs=18.8

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      |.--+.||+||+....       ..-.||.||.
T Consensus       563 n~~~~iC~~CG~~~~g-------~~~~CP~CGs  588 (623)
T PRK08271        563 NVKITICNDCHHIDKR-------TGKRCPICGS  588 (623)
T ss_pred             CCCCccCCCCCCcCCC-------CCcCCcCCCC
Confidence            3444599999976333       4689999996

>TIGR03844 cysteate_syn cysteate synthase

Probab=82.15  E-value=0.88  Score=43.33  Aligned_cols=31  Identities=19%  Similarity=0.336  Sum_probs=23.5

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      .-.|+.||+++-+  +    ....||.|+.+|.++-+
T Consensus         2 ~l~C~~Cg~~~~~--~----~~~~C~~c~g~l~~~y~   32 (398)
T TIGR03844         2 TLRCPGCGEVLPD--H----YTLSCPLDCGLLRAEYA   32 (398)
T ss_pred             EEEeCCCCCccCC--c----cccCCCCCCCceEEeec
Confidence            4579999999742  1    25789999999888744

Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.

>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=82.13  E-value=0.43  Score=40.60  Aligned_cols=31  Identities=29%  Similarity=0.507  Sum_probs=14.8

Q ss_pred             eccCCCCCceeeecccccCC---------CcccCCCCCCce
Q 025946          161 QDSCPNCGNDFQIFKSTLND---------ELQLCPYCSQPF  192 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~---------d~iqCPnCGE~L  192 (245)
                      |+.||+||..-..- -.+-+         ....||+||-..
T Consensus         1 ~s~Cp~C~~~~~~~-~~~~~IP~F~evii~sf~C~~CGyk~   40 (161)
T PF03367_consen    1 ESLCPNCGENGTTR-ILLTDIPYFKEVIIMSFECEHCGYKN   40 (161)
T ss_dssp             -EE-TTTSSCCEEE-EEEEEETTTEEEEEEEEE-TTT--EE
T ss_pred             CCcCCCCCCCcEEE-EEEEcCCCCceEEEEEeECCCCCCEe
Confidence            56899999875430 01111         145899998643

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.

>COG1656 Uncharacterized conserved protein [Function unknown]

Probab=81.91  E-value=0.64  Score=40.73  Aligned_cols=34  Identities=21%  Similarity=0.704  Sum_probs=22.9

Q ss_pred             eccCCCCCceeeecccccCCC----------------cccCCCCCCceeeeCCee
Q 025946          161 QDSCPNCGNDFQIFKSTLNDE----------------LQLCPYCSQPFSVVDDKF  199 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d----------------~iqCPnCGE~L~Vd~~~F  199 (245)
                      -..||.|+.++..    +..+                -..||+||..+ -.+.||
T Consensus        97 ~~RCp~CN~~L~~----vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY-W~GsHw  146 (165)
T COG1656          97 FSRCPECNGELEK----VSREEVKEKVPEKVYRNYEEFYRCPKCGKIY-WKGSHW  146 (165)
T ss_pred             cccCcccCCEecc----CcHHHHhhccchhhhhcccceeECCCCcccc-cCchHH
Confidence            3489999998876    2222                33499999876 334444

>PF14311 DUF4379: Domain of unknown function (DUF4379)

Probab=81.90  E-value=1  Score=31.51  Aligned_cols=26  Identities=31%  Similarity=0.925  Sum_probs=18.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYC  188 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnC  188 (245)
                      .||.||.++...=+.--.....||+|
T Consensus        30 ~C~~Cgh~w~~~v~~R~~~~~~CP~C   55 (55)
T PF14311_consen   30 KCPKCGHEWKASVNDRTRRGKGCPYC   55 (55)
T ss_pred             ECCCCCCeeEccHhhhccCCCCCCCC
Confidence            79999999887211111358899998

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=81.67  E-value=0.96  Score=34.80  Aligned_cols=27  Identities=19%  Similarity=0.765  Sum_probs=13.8

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      |..||.|..++.-     ..+...|+.|.+.+
T Consensus         1 e~~CP~C~~~L~~-----~~~~~~C~~C~~~~   27 (70)
T PF07191_consen    1 ENTCPKCQQELEW-----QGGHYHCEACQKDY   27 (70)
T ss_dssp             --B-SSS-SBEEE-----ETTEEEETTT--EE
T ss_pred             CCcCCCCCCccEE-----eCCEEECccccccc
Confidence            3467777777554     33677777775543

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation

Probab=81.62  E-value=0.78  Score=39.83  Aligned_cols=29  Identities=17%  Similarity=0.592  Sum_probs=19.5

Q ss_pred             cCCCCCceeeeccccc-----CCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTL-----NDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~L-----n~d~iqCPnCGE~L  192 (245)
                      .|+.|+..+.. ++..     .+....||.||.++
T Consensus        97 ~C~~C~~~~~~-~~~~~~~~~~~~~p~C~~Cgg~l  130 (206)
T cd01410          97 VCKSCGPEYVR-DDVVETRGDKETGRRCHACGGIL  130 (206)
T ss_pred             cCCCCCCccch-HHHHHHhhcCCCCCcCCCCcCcc
Confidence            89999977543 3322     12346799998764

Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.

>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases []

Probab=81.59  E-value=1.4  Score=29.38  Aligned_cols=26  Identities=23%  Similarity=0.572  Sum_probs=18.0

Q ss_pred             CcccCCCCCCceeeeCCeeEEecccc
Q 025946          181 ELQLCPYCSQPFSVVDDKFVRESVRF  206 (245)
Q Consensus       181 d~iqCPnCGE~L~Vd~~~F~R~~~~f  206 (245)
                      ++..||.||..|..-+..++|+-..+
T Consensus         1 e~~~C~~Cg~~l~~ig~~~~~q~l~~   26 (47)
T PF13005_consen    1 EPRACPDCGGELKEIGEEKVRQVLDL   26 (47)
T ss_pred             CCCcCCCCCceeeECCceeeEEEEee
Confidence            35678888888887777766654443

>KOG1088 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.23  E-value=0.73  Score=38.92  Aligned_cols=19  Identities=21%  Similarity=0.471  Sum_probs=12.8

Q ss_pred             CCCcccCCCCCCceeeeCC
Q 025946          179 NDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       179 n~d~iqCPnCGE~L~Vd~~  197 (245)
                      -+++.+||+||..+++.+|
T Consensus        95 ~EG~l~CpetG~vfpI~~G  113 (124)
T KOG1088|consen   95 IEGELVCPETGRVFPISDG  113 (124)
T ss_pred             ccceEecCCCCcEeecccC
Confidence            4456777777777776665

>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=81.19  E-value=0.81  Score=47.07  Aligned_cols=33  Identities=21%  Similarity=0.448  Sum_probs=19.3

Q ss_pred             cCcceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          156 SRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       156 ~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .-|.--+.||+||++  + |-......-.||+||..
T Consensus       636 ~in~~~~~C~~CG~~--G-e~~~~~~~~~CP~CG~~  668 (711)
T PRK09263        636 GTNTPIDECYECGFT--G-EFECTEKGFTCPKCGNH  668 (711)
T ss_pred             EeCCCCcccCCCCCC--c-cccCCCCCCcCcCCCCC
Confidence            334444699999973  2 00011123689999964

>PF14353 CpXC: CpXC protein

Probab=81.11  E-value=0.85  Score=36.22  Aligned_cols=18  Identities=28%  Similarity=0.947  Sum_probs=15.8

Q ss_pred             cCcceeccCCCCCceeee
Q 025946          156 SRDIVQDSCPNCGNDFQI  173 (245)
Q Consensus       156 ~rnLIE~tCPnCG~eF~~  173 (245)
                      ...+...+||+||++++.
T Consensus        33 ~g~l~~~~CP~Cg~~~~~   50 (128)
T PF14353_consen   33 DGSLFSFTCPSCGHKFRL   50 (128)
T ss_pred             cCCcCEEECCCCCCceec
Confidence            567778899999999988

>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]

Probab=81.11  E-value=1  Score=33.81  Aligned_cols=33  Identities=36%  Similarity=0.879  Sum_probs=23.5

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccccccc
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE  209 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~~  209 (245)
                      +.||+|| ..+.        .-.||.||+...+      -.+++||-.
T Consensus         6 rkC~~cg-~YTL--------ke~Cp~CG~~t~~------~~PprFSPe   38 (59)
T COG2260           6 RKCPKCG-RYTL--------KEKCPVCGGDTKV------PHPPRFSPE   38 (59)
T ss_pred             hcCcCCC-ceee--------cccCCCCCCcccc------CCCCCCCcc
Confidence            4799999 3333        3679999987654      457888763

>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase

Probab=80.82  E-value=0.95  Score=45.87  Aligned_cols=26  Identities=27%  Similarity=0.736  Sum_probs=17.2

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      +.--+.||+||+ +..      .-.-.||.||+
T Consensus       529 n~~~siC~~CGy-~~g------~~~~~CP~CGs  554 (586)
T TIGR02827       529 NIKITICNDCHH-IDK------RTLHRCPVCGS  554 (586)
T ss_pred             CCCCeecCCCCC-cCC------CcCCcCcCCCC
Confidence            333459999997 211      11369999996

Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)

Probab=80.64  E-value=1.1  Score=40.36  Aligned_cols=25  Identities=24%  Similarity=0.713  Sum_probs=19.7

Q ss_pred             cCCCCCceeeecccccCCCcccCCCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYC  188 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnC  188 (245)
                      .||.||.++.- ..+-..+...||.|
T Consensus       247 pC~~Cg~~I~~-~~~~gR~t~~CP~C  271 (272)
T TIGR00577       247 PCRRCGTPIEK-IKVGGRGTHFCPQC  271 (272)
T ss_pred             CCCCCCCeeEE-EEECCCCCEECCCC
Confidence            89999998876 23345689999999

All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]

Probab=80.38  E-value=1.2  Score=36.89  Aligned_cols=31  Identities=19%  Similarity=0.626  Sum_probs=21.3

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCC-CceeeeCC
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCS-QPFSVVDD  197 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCG-E~L~Vd~~  197 (245)
                      -.|+.|+.++..     ..-...||.|| -.+.+.+|
T Consensus        71 ~~C~~C~~~~~~-----e~~~~~CP~C~s~~~~i~~G  102 (115)
T COG0375          71 CWCLDCGQEVEL-----EELDYRCPKCGSINLRIIGG  102 (115)
T ss_pred             EEeccCCCeecc-----hhheeECCCCCCCceEEecC
Confidence            389999988776     23334499999 45665554

>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=80.04  E-value=0.71  Score=34.99  Aligned_cols=38  Identities=21%  Similarity=0.488  Sum_probs=23.2

Q ss_pred             ceeccCCCCCceeee--cccccCCC--cccCCCCCCceeeeC
Q 025946          159 IVQDSCPNCGNDFQI--FKSTLNDE--LQLCPYCSQPFSVVD  196 (245)
Q Consensus       159 LIE~tCPnCG~eF~~--~ed~Ln~d--~iqCPnCGE~L~Vd~  196 (245)
                      +++-||..|+.+..-  .+...+++  -++||.|...--+.|
T Consensus         2 ~l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlIaD   43 (66)
T PF05180_consen    2 QLTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIAD   43 (66)
T ss_dssp             EEEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES--
T ss_pred             eEEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeehh
Confidence            356799999988764  34445555  789999987655443

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. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	245
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	96.62
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	96.29
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	96.22
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	96.21
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	95.97
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	95.85
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	95.75
2aus_D	60	NOP10, ribosome biogenesis protein NOP10; isomeras	95.72
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	95.69
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	95.5
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	95.47
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	95.21
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	95.07
1vd4_A	62	Transcription initiation factor IIE, alpha subunit	94.94
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	94.81
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	94.81
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	94.71
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	94.37
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	94.3
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	94.27
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	93.44
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	92.71
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	92.71
1yuz_A	202	Nigerythrin; rubrythrin, rubredoxin, hemerythrin,	92.62
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	92.43
1wge_A	83	Hypothetical protein 2610018L09RIK; diphthamide,CS	92.25
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	92.21
2jr7_A	89	DPH3 homolog; DESR1, CSL zinc finger, metal bindin	91.98
2k5r_A	97	Uncharacterized protein XF2673; solution structure	91.42
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	91.09
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	90.99
2zjr_Z	60	50S ribosomal protein L32; ribosome, large ribosom	90.95
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	90.89
3v2d_5	60	50S ribosomal protein L32; ribosome associated inh	90.65
1yop_A	83	KTI11P; zinc finger, metal binding protein; NMR {S	90.6
3ir9_A	166	Peptide chain release factor subunit 1; structural	90.5
2l6l_A	155	DNAJ homolog subfamily C member 24; DPH4, Zn-CSL,	90.04
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	89.91
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	89.16
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	88.98
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	88.96
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	88.79
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	88.64
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	88.6
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	88.48
3uk3_C	57	Zinc finger protein 217; transcription factor, DNA	88.21
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	88.11
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	87.99
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	87.95
1m2k_A	249	Silent information regulator 2; protein-ligand com	87.46
2ctu_A	73	Zinc finger protein 483; zinc finger domain, struc	87.04
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	86.79
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	86.66
1bbo_A	57	Human enhancer-binding protein MBP-1; DNA-binding	86.07
1ltl_A	279	DNA replication initiator (CDC21/CDC54); HET: DNA;	86.03
1ma3_A	253	SIR2-AF2, transcriptional regulatory protein, SIR2	85.76
2epq_A	45	POZ-, at HOOK-, and zinc finger-containing protein	85.46
1x6e_A	72	Zinc finger protein 24; ZNF24, KOX17, ZNF191, zsca	85.36
2drp_A	66	Protein (tramtrack DNA-binding domain); protein-DN	85.0
1s5p_A	235	NAD-dependent deacetylase; protein deacetylase, SI	84.93
3flo_B	206	DNA polymerase alpha catalytic subunit A; protein-	84.86
2lv2_A	85	Insulinoma-associated protein 1; structural genomi	84.52
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	84.44
2adr_A	60	ADR1; transcription regulation, zinc finger,; NMR	84.08
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	83.87
3u50_C	172	Telomerase-associated protein 82; TEB1, processivi	83.47
1x5w_A	70	Zinc finger protein 64, isoforms 1; ZNF338, nuclea	83.4
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	83.29
3irb_A	145	Uncharacterized protein from DUF35 family; 1381535	83.28
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	82.87
2d9h_A	78	Zinc finger protein 692; ZF-C2H2 domain, structura	82.57
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	82.44
2kmk_A	82	Zinc finger protein GFI-1; tandem repeat zinc fing	82.3
1s24_A	87	Rubredoxin 2; electron transport; NMR {Pseudomonas	82.16
2f9y_B	304	Acetyl-coenzyme A carboxylase carboxyl transferas	82.01
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	81.66
2ctd_A	96	Zinc finger protein 512; zinc binding, two ZF-C2H2	81.6
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	81.47
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	81.15
2cot_A	77	Zinc finger protein 435; ADK_LID domain, zinc fing	81.12
1yc5_A	246	NAD-dependent deacetylase; SIR2, sirtuin, SIR2TM,	80.87
2jrr_A	67	Uncharacterized protein; solution structure, SIR90	80.67
3bvo_A	207	CO-chaperone protein HSCB, mitochondrial precurso;	80.1

>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=96.62  E-value=0.0009  Score=49.46  Aligned_cols=31  Identities=13%  Similarity=0.497  Sum_probs=25.4

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      +-++..|+.||.+|..    ...+++.||+||..+
T Consensus        25 ~~v~Y~C~~CG~~~e~----~~~d~irCp~CG~RI   55 (70)
T 1twf_L           25 ATLKYICAECSSKLSL----SRTDAVRCKDCGHRI   55 (70)
T ss_dssp             CCCCEECSSSCCEECC----CTTSTTCCSSSCCCC
T ss_pred             ceEEEECCCCCCccee----CCCCCccCCCCCceE
Confidence            4567799999999987    456899999999943

>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1

Probab=96.29  E-value=0.002  Score=47.19  Aligned_cols=39  Identities=18%  Similarity=0.362  Sum_probs=31.1

Q ss_pred             Ccceec-cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          157 RDIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       157 rnLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      .++++. .||+|+.++...+   .++..+||.||..|++.||-
T Consensus         3 ~~LL~iL~CP~ck~~L~~~~---~~~~LiC~~cg~~YPI~dGI   42 (68)
T 2hf1_A            3 AKFLEILVCPLCKGPLVFDK---SKDELICKGDRLAFPIKDGI   42 (68)
T ss_dssp             CCCEEECBCTTTCCBCEEET---TTTEEEETTTTEEEEEETTE
T ss_pred             hHHhhheECCCCCCcCeEeC---CCCEEEcCCCCcEecCCCCe
Confidence            345555 9999999887632   25789999999999999985

>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1

Probab=96.22  E-value=0.0019  Score=47.42  Aligned_cols=38  Identities=11%  Similarity=0.336  Sum_probs=30.4

Q ss_pred             cceec-cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          158 DIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       158 nLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      ++++. .||+|+.++...+   .++..+||.||..|++.+|-
T Consensus         4 ~LLeiL~CP~ck~~L~~~~---~~~~LiC~~cg~~YPI~dGI   42 (69)
T 2pk7_A            4 KLLDILACPICKGPLKLSA---DKTELISKGAGLAYPIRDGI   42 (69)
T ss_dssp             CGGGTCCCTTTCCCCEECT---TSSEEEETTTTEEEEEETTE
T ss_pred             HHHhheeCCCCCCcCeEeC---CCCEEEcCCCCcEecCcCCe
Confidence            44555 8999999887632   24789999999999999985

>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}

Probab=96.21  E-value=0.0021  Score=47.35  Aligned_cols=38  Identities=18%  Similarity=0.406  Sum_probs=30.5

Q ss_pred             cceec-cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          158 DIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       158 nLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      ++++. .||+|+.++...+   .++..+||+||..|++.||-
T Consensus         4 ~LL~iL~CP~ck~~L~~~~---~~~~LiC~~cg~~YPI~dGI   42 (70)
T 2js4_A            4 RLLDILVCPVCKGRLEFQR---AQAELVCNADRLAFPVRDGV   42 (70)
T ss_dssp             CCCCCCBCTTTCCBEEEET---TTTEEEETTTTEEEEEETTE
T ss_pred             HHhhheECCCCCCcCEEeC---CCCEEEcCCCCceecCCCCe
Confidence            44555 8999999888732   24789999999999999985

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=95.97  E-value=0.0031  Score=46.22  Aligned_cols=38  Identities=8%  Similarity=0.220  Sum_probs=30.2

Q ss_pred             cceec-cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          158 DIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       158 nLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      ++++. .||+|+.++...+   .++..+||+||..|++.||-
T Consensus         4 ~LL~iL~CP~ck~~L~~~~---~~~~LiC~~cg~~YPI~dGI   42 (68)
T 2jr6_A            4 KFLDILVCPVTKGRLEYHQ---DKQELWSRQAKLAYPIKDGI   42 (68)
T ss_dssp             SSSCCCBCSSSCCBCEEET---TTTEEEETTTTEEEEEETTE
T ss_pred             HHhhheECCCCCCcCeEeC---CCCEEEcCCCCcEecCCCCe
Confidence            44555 8999999887632   34789999999999999985

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=95.85  E-value=0.0032  Score=45.71  Aligned_cols=33  Identities=33%  Similarity=0.868  Sum_probs=24.3

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccccccc
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE  209 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~~  209 (245)
                      +.||+||  .|.    |   ..+||+||++..+      -.+++||-.
T Consensus         7 r~C~~Cg--vYT----L---k~~CP~CG~~T~~------~hParfSp~   39 (60)
T 2apo_B            7 KKCPKCG--LYT----L---KEICPKCGEKTVI------PKPPKFSLE   39 (60)
T ss_dssp             EECTTTC--CEE----S---SSBCSSSCSBCBC------CCCCCCCTT
T ss_pred             eeCCCCC--CEe----c---cccCcCCCCcCCC------CCCCCCCCC
Confidence            4899998  344    3   5679999998754      468888864

>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1

Probab=95.75  E-value=0.0037  Score=45.83  Aligned_cols=38  Identities=11%  Similarity=0.335  Sum_probs=30.2

Q ss_pred             cceec-cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946          158 DIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       158 nLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      ++++. .||.|..++...+   .++..+||.||..|++.||-
T Consensus         6 ~LLeiL~CP~ck~~L~~~~---~~g~LvC~~c~~~YPI~dGI   44 (67)
T 2jny_A            6 QLLEVLACPKDKGPLRYLE---SEQLLVNERLNLAYRIDDGI   44 (67)
T ss_dssp             GGTCCCBCTTTCCBCEEET---TTTEEEETTTTEEEEEETTE
T ss_pred             HHHHHhCCCCCCCcCeEeC---CCCEEEcCCCCccccCCCCE
Confidence            44555 8999999887632   34789999999999999985

>2aus_D NOP10, ribosome biogenesis protein NOP10; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_B 3lwo_B* 3lwq_B* 3lwp_B 3lwv_B 3hax_C* 2hvy_C* 3hay_C* 2ey4_E 3hjw_B* 2rfk_B* 3hjy_B 3mqk_B

Probab=95.72  E-value=0.0048  Score=44.88  Aligned_cols=33  Identities=39%  Similarity=0.827  Sum_probs=24.2

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccccccc
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE  209 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~~  209 (245)
                      ..||+||  .|.    |   ..+||+||++..      +..+++||-.
T Consensus         6 r~C~~Cg--~YT----L---k~~CP~CG~~t~------~ahParfSP~   38 (60)
T 2aus_D            6 RKCPKCG--RYT----L---KETCPVCGEKTK------VAHPPRFSPE   38 (60)
T ss_dssp             EECTTTC--CEE----S---SSBCTTTCSBCE------ESSCCCCCSC
T ss_pred             eECCCCC--CEE----c---cccCcCCCCccC------CCCCCCCCCC
Confidence            4899998  344    2   567999999874      4568888864

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

Probab=95.69  E-value=0.0057  Score=49.13  Aligned_cols=34  Identities=21%  Similarity=0.475  Sum_probs=24.5

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      ..+.-.|+.||+.|-.     ......||.||.++....
T Consensus       129 ~~~~y~C~~Cg~~~~~-----~~~~~~Cp~CG~~~~~~~  162 (165)
T 2lcq_A          129 IKWRYVCIGCGRKFST-----LPPGGVCPDCGSKVKLIP  162 (165)
T ss_dssp             CCCCEEESSSCCEESS-----CCGGGBCTTTCCBEEECC
T ss_pred             ccEEEECCCCCCcccC-----CCCCCcCCCCCCcceeCC
Confidence            3345599999998875     133469999999875443

>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A*

Probab=95.50  E-value=0.0049  Score=49.66  Aligned_cols=44  Identities=18%  Similarity=0.576  Sum_probs=28.9

Q ss_pred             ccCCCCCceeeecc------cccCCC----------cccCCCCCCc-ee-eeCCeeEEeccc
Q 025946          162 DSCPNCGNDFQIFK------STLNDE----------LQLCPYCSQP-FS-VVDDKFVRESVR  205 (245)
Q Consensus       162 ~tCPnCG~eF~~~e------d~Ln~d----------~iqCPnCGE~-L~-Vd~~~F~R~~~~  205 (245)
                      ..|++||+++...+      +...+.          +..||.||.+ +. +.++.+.=++..
T Consensus        71 ~~C~~CG~~~~~~~~~~~~~~~~~~~~h~~p~~~~~~~~CP~Cgs~~~~i~~G~el~I~~ie  132 (139)
T 3a43_A           71 FKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGVYVAGIK  132 (139)
T ss_dssp             EEETTTCCEEEGGGCTTCCSCCCGGGCCCCGGGCGGGCSCSSSSCCCEEEEESSCEEEEEEE
T ss_pred             EECCCCCCEEecccccccccccccccccccccccccCCcCccccCCccEEecCCeEEEEEEE
Confidence            38999999998743      011113          6889999997 44 466666655443

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

Probab=95.47  E-value=0.0074  Score=46.78  Aligned_cols=36  Identities=17%  Similarity=0.313  Sum_probs=25.9

Q ss_pred             ccCCCCCceeeecccccCCCcc-cCCCCCCce-e-eeCCeeEEe
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQ-LCPYCSQPF-S-VVDDKFVRE  202 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~i-qCPnCGE~L-~-Vd~~~F~R~  202 (245)
                      ..|++||++|..     .+.+. .||.||.+- . +.++.+.-.
T Consensus        74 ~~C~~CG~~~e~-----~~~~~~~CP~Cgs~~~~i~~G~el~i~  112 (119)
T 2kdx_A           74 LECKDCSHVFKP-----NALDYGVCEKCHSKNVIITQGNEMRLL  112 (119)
T ss_dssp             EECSSSSCEECS-----CCSTTCCCSSSSSCCCEEEESSCCEEE
T ss_pred             EEcCCCCCEEeC-----CCCCCCcCccccCCCcEEecCCeEEEE
Confidence            389999999886     34467 899999873 2 455555543

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

Probab=95.21  E-value=0.0078  Score=40.33  Aligned_cols=29  Identities=17%  Similarity=0.477  Sum_probs=22.0

Q ss_pred             ccCCCCCc-eeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGN-DFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~-eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ..||+||. ++.-+   -..++..|++||..++
T Consensus         6 ~~CP~C~~~~l~~d---~~~gelvC~~CG~v~~   35 (50)
T 1pft_A            6 KVCPACESAELIYD---PERGEIVCAKCGYVIE   35 (50)
T ss_dssp             CSCTTTSCCCEEEE---TTTTEEEESSSCCBCC
T ss_pred             EeCcCCCCcceEEc---CCCCeEECcccCCccc
Confidence            47999998 55432   3457899999999885

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

Probab=95.07  E-value=0.0099  Score=43.47  Aligned_cols=33  Identities=21%  Similarity=0.420  Sum_probs=25.5

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      -+...|..||.++...    ..+++.||+||-.+-..
T Consensus        19 ~v~Y~C~~Cg~~~~l~----~~~~iRC~~CG~RILyK   51 (63)
T 3h0g_L           19 TMIYLCADCGARNTIQ----AKEVIRCRECGHRVMYK   51 (63)
T ss_dssp             CCCCBCSSSCCBCCCC----SSSCCCCSSSCCCCCBC
T ss_pred             CeEEECCCCCCeeecC----CCCceECCCCCcEEEEE
Confidence            4566999999998862    34799999999866443

>1vd4_A Transcription initiation factor IIE, alpha subunit; zinc finger; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=94.94  E-value=0.011  Score=39.31  Aligned_cols=38  Identities=16%  Similarity=0.457  Sum_probs=26.8

Q ss_pred             cCCCCCceeeecccc----cCCCcccCCCCCCceeeeCCeeE
Q 025946          163 SCPNCGNDFQIFKST----LNDELQLCPYCSQPFSVVDDKFV  200 (245)
Q Consensus       163 tCPnCG~eF~~~ed~----Ln~d~iqCPnCGE~L~Vd~~~F~  200 (245)
                      .||.||+.|......    ..+.+..|+.||..+...+...+
T Consensus        16 ~C~~C~k~F~~~~~l~~~H~~~k~~~C~~C~k~f~~~~~~~~   57 (62)
T 1vd4_A           16 KCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEEDESAMP   57 (62)
T ss_dssp             ECSSSCCEEEHHHHHHHEETTTTEEBCSSSCCBCEECTTCSC
T ss_pred             cCCCCCchhccHHHhHhhcCCCCCEECCCCCCccccCccccc
Confidence            799999999863322    12357899999988776655443

>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}

Probab=94.81  E-value=0.014  Score=41.15  Aligned_cols=36  Identities=22%  Similarity=0.570  Sum_probs=29.1

Q ss_pred             cceec-cCCCCCceeeecccccCCCcccCC--CCCCceeeeCCe
Q 025946          158 DIVQD-SCPNCGNDFQIFKSTLNDELQLCP--YCSQPFSVVDDK  198 (245)
Q Consensus       158 nLIE~-tCPnCG~eF~~~ed~Ln~d~iqCP--nCGE~L~Vd~~~  198 (245)
                      ++++. .||.|..++...     +++.+|+  .||..|++.+|-
T Consensus         6 ~lL~iL~CP~c~~~L~~~-----~~~L~C~~~~c~~~YPI~dGI   44 (56)
T 2kpi_A            6 GLLEILACPACHAPLEER-----DAELICTGQDCGLAYPVRDGI   44 (56)
T ss_dssp             SCTTSCCCSSSCSCEEEE-----TTEEEECSSSCCCEEEEETTE
T ss_pred             HHHhheeCCCCCCcceec-----CCEEEcCCcCCCcEEeeECCE
Confidence            34444 899999987762     3889999  999999999884

>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=94.81  E-value=0.014  Score=41.07  Aligned_cols=34  Identities=21%  Similarity=0.487  Sum_probs=23.5

Q ss_pred             cceec-cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          158 DIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       158 nLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ++++. .||.||.+-...  .-..++++|+.||..+.
T Consensus         7 ~ll~~~~Cp~C~~~~lv~--D~~~ge~vC~~CGlVl~   41 (58)
T 1dl6_A            7 DALPRVTCPNHPDAILVE--DYRAGDMICPECGLVVG   41 (58)
T ss_dssp             CCCSCCSBTTBSSSCCEE--CSSSCCEECTTTCCEEC
T ss_pred             hccccccCcCCCCCceeE--eCCCCeEEeCCCCCEEe
Confidence            34444 899999732221  13558999999999884

>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=94.71  E-value=0.01  Score=53.53  Aligned_cols=39  Identities=38%  Similarity=0.859  Sum_probs=25.6

Q ss_pred             HhcCcceeccCCCCCce-eeecccccCCC---cccCCCCCCceeeeCCe
Q 025946          154 WASRDIVQDSCPNCGND-FQIFKSTLNDE---LQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       154 Wl~rnLIE~tCPnCG~e-F~~~ed~Ln~d---~iqCPnCGE~L~Vd~~~  198 (245)
                      |+.+|.   -||+||.. +.-+   -|+.   .-.||+|.|.++....+
T Consensus        30 Wv~~n~---yCPnCG~~~l~~f---~nN~PVaDF~C~~C~EeyELKSk~   72 (257)
T 4esj_A           30 WVYRQS---YCPNCGNNPLNHF---ENNRPVADFYCNHCSEEFELKSKK   72 (257)
T ss_dssp             HHHHHC---CCTTTCCSSCEEC-------CCCEEECTTTCCEEEEEEEE
T ss_pred             HHHHCC---cCCCCCChhhhhc---cCCCcccccccCCcchhheecccc
Confidence            555544   69999984 5442   2333   45799999999987654

>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=94.37  E-value=0.013  Score=48.79  Aligned_cols=25  Identities=36%  Similarity=0.793  Sum_probs=19.2

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      -.|++||+...+.     +-|-.||.||.+
T Consensus       156 ~~C~~CG~~~~g~-----~~p~~CP~C~~~  180 (191)
T 1lko_A          156 WRCRNCGYVHEGT-----GAPELCPACAHP  180 (191)
T ss_dssp             EEETTTCCEEEEE-----ECCSBCTTTCCB
T ss_pred             EEECCCCCEeeCC-----CCCCCCCCCcCC
Confidence            3799999987651     235599999986

>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=94.30  E-value=0.02  Score=47.49  Aligned_cols=24  Identities=33%  Similarity=0.836  Sum_probs=18.7

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      -.||+||+....      +-|-.||.||.+
T Consensus       139 ~~C~~CG~i~~~------~~p~~CP~Cg~~  162 (170)
T 3pwf_A          139 YICPICGYTAVD------EAPEYCPVCGAP  162 (170)
T ss_dssp             EECTTTCCEEES------CCCSBCTTTCCB
T ss_pred             eEeCCCCCeeCC------CCCCCCCCCCCC
Confidence            379999987653      346699999975

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=94.27  E-value=0.02  Score=40.38  Aligned_cols=31  Identities=26%  Similarity=0.525  Sum_probs=23.6

Q ss_pred             cCCCCCceeeecccccCC-CcccCCCCCCceeee
Q 025946          163 SCPNCGNDFQIFKSTLND-ELQLCPYCSQPFSVV  195 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~-d~iqCPnCGE~L~Vd  195 (245)
                      .|-.||++|...  .|+. ..+.|||||-.+-..
T Consensus         5 ~C~rCg~~fs~~--el~~lP~IrCpyCGyrii~K   36 (48)
T 4ayb_P            5 RCGKCWKTFTDE--QLKVLPGVRCPYCGYKIIFM   36 (48)
T ss_dssp             CCCCTTTTCCCC--CSCCCSSSCCTTTCCSCEEC
T ss_pred             EeeccCCCccHH--HHhhCCCcccCccCcEEEEE
Confidence            699999999873  3333 689999999766543

>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=93.44  E-value=0.024  Score=42.04  Aligned_cols=37  Identities=19%  Similarity=0.491  Sum_probs=27.9

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEE
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVR  201 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R  201 (245)
                      +=.-|| ||.-.+..+   .....+|| ||+.+.++.-.---
T Consensus         3 ~vv~C~-C~~~~~~~~---~~kT~~C~-CG~~~~~~k~rif~   39 (71)
T 1gh9_A            3 IIFRCD-CGRALYSRE---GAKTRKCV-CGRTVNVKDRRIFG   39 (71)
T ss_dssp             EEEEET-TSCCEEEET---TCSEEEET-TTEEEECCSSSCBS
T ss_pred             EEEECC-CCCEEEEcC---CCcEEECC-CCCeeeeceEEEEE
Confidence            345799 999988842   33688999 99999988765433

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=92.71  E-value=0.044  Score=41.80  Aligned_cols=24  Identities=46%  Similarity=1.172  Sum_probs=17.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      .|+.|++.|..        ...||.||++|++
T Consensus        20 ~C~~C~~~~~~--------~afCPeCgq~Le~   43 (81)
T 2jrp_A           20 HCETCAKDFSL--------QALCPDCRQPLQV   43 (81)
T ss_dssp             ECTTTCCEEEE--------EEECSSSCSCCCE
T ss_pred             ECccccccCCC--------cccCcchhhHHHH
Confidence            46666666555        4489999999877

>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=92.71  E-value=0.049  Score=41.25  Aligned_cols=28  Identities=36%  Similarity=0.825  Sum_probs=20.1

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .+||+||....-.   ...+...||+||..+
T Consensus        28 y~Cp~CG~~~v~r---~atGiW~C~~Cg~~~   55 (83)
T 1vq8_Z           28 HACPNCGEDRVDR---QGTGIWQCSYCDYKF   55 (83)
T ss_dssp             EECSSSCCEEEEE---EETTEEEETTTCCEE
T ss_pred             CcCCCCCCcceec---cCCCeEECCCCCCEe
Confidence            4899999854432   223678899998865

>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIR center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A

Probab=92.62  E-value=0.055  Score=45.79  Aligned_cols=25  Identities=32%  Similarity=0.866  Sum_probs=19.7

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .-.|++||+...+      ..|-.||.||.+
T Consensus       171 ~~~C~~CG~i~~g------~~p~~CP~C~~~  195 (202)
T 1yuz_A          171 FHLCPICGYIHKG------EDFEKCPICFRP  195 (202)
T ss_dssp             EEECSSSCCEEES------SCCSBCTTTCCB
T ss_pred             EEEECCCCCEEcC------cCCCCCCCCCCC
Confidence            3489999988543      357899999986

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

Probab=92.43  E-value=0.064  Score=44.26  Aligned_cols=28  Identities=21%  Similarity=0.695  Sum_probs=23.1

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .+...||.||...+-    .. .+.+||+||..
T Consensus       138 vv~a~~~~~g~~m~~----~~-~~~~cp~~g~~  165 (179)
T 3m7n_A          138 VLRALCSNCKTEMVR----EG-DILKCPECGRV  165 (179)
T ss_dssp             EEECBCTTTCCBCEE----CS-SSEECSSSCCE
T ss_pred             EEEecccccCCceEE----CC-CEEECCCCCCE
Confidence            456699999999877    44 89999999874

>1wge_A Hypothetical protein 2610018L09RIK; diphthamide,CSL zinc finger, ADP-ribosylating toxin, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.17.1

Probab=92.25  E-value=0.059  Score=41.03  Aligned_cols=35  Identities=37%  Similarity=0.806  Sum_probs=29.5

Q ss_pred             ceeccCCCCCceeeecccccCCC--cccCCCCCCceee
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDE--LQLCPYCSQPFSV  194 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d--~iqCPnCGE~L~V  194 (245)
                      .+...|| ||..|...++.|.++  -++||.|--.+.|
T Consensus        28 ~y~y~Cr-CGd~F~it~edL~~ge~iv~C~sCSL~I~V   64 (83)
T 1wge_A           28 TYFYPCP-CGDNFAITKEDLENGEDVATCPSCSLIIKV   64 (83)
T ss_dssp             EEEECCS-SSSCEEEEHHHHHTTCCEEECTTTCCEEEE
T ss_pred             EEEEeCC-CCCEEEECHHHHhCCCEEEECCCCceEEEE
Confidence            4667999 999999988888775  5899999887765

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

Probab=92.21  E-value=0.088  Score=39.07  Aligned_cols=35  Identities=23%  Similarity=0.625  Sum_probs=27.8

Q ss_pred             CcceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          157 RDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       157 rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      -.++.+.||.|+++-.+|.  =.+..+.|..||+.|.
T Consensus         3 S~Fm~VKCp~C~niq~VFS--hA~tvV~C~~Cg~~L~   37 (66)
T 1qxf_A            3 SRFVKVKCPDCEHEQVIFD--HPSTIVKCIICGRTVA   37 (66)
T ss_dssp             CCEEEEECTTTCCEEEEES--SCSSCEECSSSCCEEE
T ss_pred             ceeEEEECCCCCCceEEEe--cCceEEEcccCCCEEe
Confidence            3578889999999888831  2346999999999984

>2jr7_A DPH3 homolog; DESR1, CSL zinc finger, metal binding protein; NMR {Homo sapiens}

Probab=91.98  E-value=0.048  Score=42.13  Aligned_cols=35  Identities=37%  Similarity=0.810  Sum_probs=29.4

Q ss_pred             ceeccCCCCCceeeecccccCCC--cccCCCCCCceee
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDE--LQLCPYCSQPFSV  194 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d--~iqCPnCGE~L~V  194 (245)
                      .+...|| ||..|...++.|.++  -++||.|.-.+.|
T Consensus        21 ~y~ypCr-CGd~F~IteedLe~ge~iv~C~sCSL~IkV   57 (89)
T 2jr7_A           21 TYFYPCP-CGDNFSITKEDLENGEDVATCPSCSLIIKV   57 (89)
T ss_dssp             EEEEECT-TSSEEEEEHHHHHHTCCEEECTTTCCEEEE
T ss_pred             EEEEcCC-CCCEEEECHHHHhCCCEEEECCCCccEEEE
Confidence            4667999 999999988888765  5899999987766

>2k5r_A Uncharacterized protein XF2673; solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Xylella fastidiosa TEMECULA1}

Probab=91.42  E-value=0.086  Score=41.20  Aligned_cols=42  Identities=17%  Similarity=0.245  Sum_probs=31.5

Q ss_pred             Ccceec-cCCCCCceeeecccc------------------------cCCCcccCCCCCCceeeeCCe
Q 025946          157 RDIVQD-SCPNCGNDFQIFKST------------------------LNDELQLCPYCSQPFSVVDDK  198 (245)
Q Consensus       157 rnLIE~-tCPnCG~eF~~~ed~------------------------Ln~d~iqCPnCGE~L~Vd~~~  198 (245)
                      .++++. .||.|..++..+++.                        ..++..+||.||..|++.+|-
T Consensus         3 ~~LLdILaCP~cK~pL~l~~~~~~~~~~ca~~~~~~~~~~~~~~~e~~~~~LvC~~c~~~YPI~dGI   69 (97)
T 2k5r_A            3 RKLLHLLCSPDTRQPLSLLESKGLEALNKAIVSGTVQRADGSIQNQSLHEALITRDRKQVFRIEDSI   69 (97)
T ss_dssp             TTTCSSCCCCTTSSCCEECCHHHHHHHHHHHHHTCCBCTTSCBCCCCCSEEEECTTSCEEEEEETTE
T ss_pred             hHHhhheECCCCCCcccccccchhhhhhhhhhccccccccccccccccCCeEEcCCCCCCccccCCC
Confidence            345555 899999988775441                        114578999999999999984

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

Probab=91.09  E-value=0.14  Score=37.60  Aligned_cols=34  Identities=21%  Similarity=0.553  Sum_probs=27.0

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .++...||.|+++-.+|  .=.+..+.|..||+.|-
T Consensus        12 ~Fm~VkCp~C~~~q~VF--Sha~t~V~C~~Cgt~L~   45 (63)
T 3j20_W           12 RFLRVKCIDCGNEQIVF--SHPATKVRCLICGATLV   45 (63)
T ss_dssp             CEEEEECSSSCCEEEEE--SSCSSCEECSSSCCEEE
T ss_pred             cEEEEECCCCCCeeEEE--ecCCeEEEccCcCCEEe
Confidence            46778999999988883  12346999999999885

>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1

Probab=90.99  E-value=0.13  Score=35.35  Aligned_cols=29  Identities=21%  Similarity=0.660  Sum_probs=18.2

Q ss_pred             cCCCCCceeeeccc---ccCC--CcccCCCCCCc
Q 025946          163 SCPNCGNDFQIFKS---TLND--ELQLCPYCSQP  191 (245)
Q Consensus       163 tCPnCG~eF~~~ed---~Ln~--d~iqCPnCGE~  191 (245)
                      .|++||+.+--.+.   .+.+  +.-+||.||.+
T Consensus         6 ~C~vCGyvyd~~~Gd~t~f~~lP~dw~CP~Cg~~   39 (46)
T 6rxn_A            6 VCNVCGYEYDPAEHDNVPFDQLPDDWCCPVCGVS   39 (46)
T ss_dssp             EETTTCCEECGGGGTTCCGGGSCTTCBCTTTCCB
T ss_pred             ECCCCCeEEeCCcCCCcchhhCCCCCcCcCCCCc
Confidence            79999977652111   1122  23499999975

>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M* 1jzz_M* 1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5 2b9n_5 2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y* 3pio_Z* 3pip_Z* 1nwy_Z* 1nwx_Z* ...

Probab=90.95  E-value=0.087  Score=37.76  Aligned_cols=19  Identities=32%  Similarity=1.177  Sum_probs=16.0

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCS  189 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCG  189 (245)
                      .||+||.. ..       ..-.||+||
T Consensus        32 ~c~~cG~~-~~-------pH~vc~~CG   50 (60)
T 2zjr_Z           32 ECPQCHGK-KL-------SHHICPNCG   50 (60)
T ss_dssp             ECTTTCCE-EC-------TTBCCTTTC
T ss_pred             ECCCCCCE-eC-------CceEcCCCC
Confidence            89999966 33       689999999

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=90.89  E-value=0.11  Score=41.40  Aligned_cols=30  Identities=27%  Similarity=0.608  Sum_probs=22.6

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      ++...|-.||++|..    -.+.|..||.|+..-
T Consensus        65 v~p~~C~~CG~~F~~----~~~kPsrCP~CkSe~   94 (105)
T 2gmg_A           65 IKPAQCRKCGFVFKA----EINIPSRCPKCKSEW   94 (105)
T ss_dssp             ECCCBBTTTCCBCCC----CSSCCSSCSSSCCCC
T ss_pred             EECcChhhCcCeecc----cCCCCCCCcCCCCCc
Confidence            445599999999932    234689999998764

>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=90.65  E-value=0.096  Score=37.61  Aligned_cols=20  Identities=30%  Similarity=0.813  Sum_probs=15.8

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCC
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCS  189 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCG  189 (245)
                      ..||+||..-.        ..-.||+||
T Consensus        31 ~~c~~cGe~~~--------~H~vc~~CG   50 (60)
T 3v2d_5           31 VPCPECKAMKP--------PHTVCPECG   50 (60)
T ss_dssp             EECTTTCCEEC--------TTSCCTTTC
T ss_pred             eECCCCCCeec--------ceEEcCCCC
Confidence            38999996332        588999999

>1yop_A KTI11P; zinc finger, metal binding protein; NMR {Saccharomyces cerevisiae} SCOP: g.41.17.1 PDB: 1yws_A

Probab=90.60  E-value=0.074  Score=40.49  Aligned_cols=35  Identities=34%  Similarity=0.888  Sum_probs=29.3

Q ss_pred             ceeccCCCCCceeeecccccCCC--cccCCCCCCceee
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDE--LQLCPYCSQPFSV  194 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d--~iqCPnCGE~L~V  194 (245)
                      .+...|| ||..|...++.|.++  -++||.|.-.+.|
T Consensus        21 ~y~ypCr-CGd~F~it~edL~~ge~iv~C~sCSL~I~V   57 (83)
T 1yop_A           21 MFTYPCP-CGDRFQIYLDDMFEGEKVAVCPSCSLMIDV   57 (83)
T ss_dssp             EEEEEET-TTEEEEEEHHHHHTTCCEEECSSSCCEEEC
T ss_pred             EEEEeCC-CCCeEEECHHHHhCCCEEEECCCCccEEEE
Confidence            4667999 999999988888775  6899999887765

>3ir9_A Peptide chain release factor subunit 1; structural genomics, APC36528.1, C-terminal domain, PSI-2, protein structure initiative; 2.21A {Methanosarcina mazei}

Probab=90.50  E-value=0.14  Score=42.31  Aligned_cols=40  Identities=23%  Similarity=0.454  Sum_probs=24.4

Q ss_pred             cceeccCCCCCceeee----cccccCCCcccCCCCCCceeeeCC
Q 025946          158 DIVQDSCPNCGNDFQI----FKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~----~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      ..+...||+||+.-..    ....-..+...||.||+++++.+.
T Consensus        75 ~r~~~~c~~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~e~  118 (166)
T 3ir9_A           75 ERVTTKCSVCGYENKWTRRWKPGEPAPAAGNCPKCGSSLEVTDV  118 (166)
T ss_dssp             EEEEEEESSSSCEEEEEECCCC--CCCCCCBCTTTCCBEEEEEE
T ss_pred             eEEEEECCCCCceeEEEeecChhhcccccccccccCccchhhhH
Confidence            3445689999975322    001011234579999999987764

>2l6l_A DNAJ homolog subfamily C member 24; DPH4, Zn-CSL, J-domain, chaperone; NMR {Homo sapiens}

Probab=90.04  E-value=0.096  Score=41.62  Aligned_cols=35  Identities=26%  Similarity=0.549  Sum_probs=28.3

Q ss_pred             ceeccCCCCCceeeecccccCC-CcccCCCCCCceee
Q 025946          159 IVQDSCPNCGNDFQIFKSTLND-ELQLCPYCSQPFSV  194 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~-d~iqCPnCGE~L~V  194 (245)
                      .+...|| ||..|...++.+++ ..+.||+|...+.|
T Consensus       110 ~f~~~Cr-CG~~f~i~~~~l~~~~~v~C~sCSl~~~v  145 (155)
T 2l6l_A          110 SFYLSCR-CGGKYSVSKDEAEEVSLISCDTCSLIIEL  145 (155)
T ss_dssp             EEEEECS-SSCEEEEETTHHHHCCEEECSSSSCEEEE
T ss_pred             EEEEcCC-CCCeEEecHHHhCCCCEEECCCCceEEEE
Confidence            4556999 99999998777764 47999999988765

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=89.91  E-value=0.11  Score=41.43  Aligned_cols=35  Identities=29%  Similarity=0.669  Sum_probs=21.8

Q ss_pred             eeccCCCCCceeeeccccc-----CC---CcccCCCCCCceee
Q 025946          160 VQDSCPNCGNDFQIFKSTL-----ND---ELQLCPYCSQPFSV  194 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~L-----n~---d~iqCPnCGE~L~V  194 (245)
                      |+..||.|..+..-.....     ++   -+..||.|+++|++
T Consensus        31 M~~~CP~Cq~eL~~~g~~~hC~~C~~~f~~~a~CPdC~q~Lev   73 (101)
T 2jne_A           31 MELHCPQCQHVLDQDNGHARCRSCGEFIEMKALCPDCHQPLQV   73 (101)
T ss_dssp             CCCBCSSSCSBEEEETTEEEETTTCCEEEEEEECTTTCSBCEE
T ss_pred             ccccCccCCCcceecCCEEECccccchhhccccCcchhhHHHH
Confidence            7788999988865421111     11   15678888888865

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=89.16  E-value=0.17  Score=45.28  Aligned_cols=30  Identities=20%  Similarity=0.452  Sum_probs=22.4

Q ss_pred             eccCCCCCce---eeecccccCCCcccCCCCCCcee
Q 025946          161 QDSCPNCGND---FQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       161 E~tCPnCG~e---F~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ...||+||.+   +..+   ...++.+|..||.+++
T Consensus        21 ~~~Cp~Cg~~~~~iv~D---~~~G~~vC~~CG~Vl~   53 (345)
T 3k7a_M           21 VLTCPECKVYPPKIVER---FSEGDVVCALCGLVLS   53 (345)
T ss_dssp             CCCCSTTCCSCCCCCCC---SSSCSCCCSSSCCCCC
T ss_pred             CCcCcCCCCCCCceEEE---CCCCCEecCCCCeEcc
Confidence            3479999985   2221   3568999999999985

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

Probab=88.98  E-value=0.26  Score=37.82  Aligned_cols=39  Identities=23%  Similarity=0.422  Sum_probs=29.7

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCe
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDK  198 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~  198 (245)
                      .++.+.||.|+++-.++.  =..+.+.|..||+.|- ..+|+
T Consensus        29 ~Fm~VkCp~C~n~q~VFS--hA~t~V~C~~Cg~~L~~PTGGK   68 (81)
T 2xzm_6           29 YFMDVKCAQCQNIQMIFS--NAQSTIICEKCSAILCKPTGGK   68 (81)
T ss_dssp             CEEEEECSSSCCEEEEET--TCSSCEECSSSCCEEEEECSSC
T ss_pred             cEEEeECCCCCCeeEEEe--cCccEEEccCCCCEEeecCCCC
Confidence            567789999999988842  2347999999999985 44554

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

Probab=88.96  E-value=0.2  Score=34.47  Aligned_cols=27  Identities=22%  Similarity=0.491  Sum_probs=19.0

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .||.||....-.   -+.+-..||.||-..
T Consensus        21 ~CP~CG~~~fm~---~~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           21 FCPRCGPGVFMA---DHGDRWACGKCGYTE   47 (50)
T ss_dssp             ECSSSCSSCEEE---ECSSEEECSSSCCEE
T ss_pred             cCCCCCCceEEe---cCCCeEECCCCCCEE
Confidence            799999753331   345788999998654

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=88.79  E-value=0.25  Score=37.59  Aligned_cols=31  Identities=26%  Similarity=0.703  Sum_probs=21.9

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      |+.+||.|..+..-     +....+|+.|++.+...
T Consensus         1 M~~~CP~C~~~l~~-----~~~~~~C~~C~~~~~~~   31 (81)
T 2jrp_A            1 MEITCPVCHHALER-----NGDTAHCETCAKDFSLQ   31 (81)
T ss_dssp             CCCCCSSSCSCCEE-----CSSEEECTTTCCEEEEE
T ss_pred             CCCCCCCCCCcccc-----CCCceECccccccCCCc
Confidence            45789999988765     33466799997755443

>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=88.64  E-value=0.27  Score=37.79  Aligned_cols=39  Identities=23%  Similarity=0.439  Sum_probs=29.3

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCe
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDK  198 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~  198 (245)
                      .++.+.||.|+++-.++.  =.+..+.|..||+.|- ..+|+
T Consensus        31 ~Fm~VkCp~C~~~q~VFS--ha~t~V~C~~Cg~~L~~PTGGK   70 (82)
T 3u5c_b           31 YFLDVKCPGCLNITTVFS--HAQTAVTCESCSTILCTPTGGK   70 (82)
T ss_dssp             CEEEEECTTSCSCEEEES--BCSSCCCCSSSCCCCEECCSSB
T ss_pred             cEEEEECCCCCCeeEEEe--cCCeEEEccccCCEEeccCCCC
Confidence            457789999999888841  2347999999999886 44444

>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=88.60  E-value=0.31  Score=37.76  Aligned_cols=39  Identities=21%  Similarity=0.452  Sum_probs=29.1

Q ss_pred             cceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCe
Q 025946          158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDK  198 (245)
Q Consensus       158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~  198 (245)
                      .++.+.||.|+++-.++.  =....+.|..||+.|- ..+|+
T Consensus        33 ~Fm~VkCp~C~~~~~VFS--hA~t~V~C~~CgtvL~~PTGGK   72 (86)
T 3iz6_X           33 FFMDVKCQGCFNITTVFS--HSQTVVVCPGCQTVLCQPTGGK   72 (86)
T ss_dssp             CEEEEECTTTCCEEEEET--TCSSCCCCSSSCCCCSCCCSSS
T ss_pred             cEeEEECCCCCCeeEEEe--cCCcEEEccCCCCEeecCCCCC
Confidence            567789999999888831  2346999999999885 34443

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

Probab=88.48  E-value=0.27  Score=33.68  Aligned_cols=38  Identities=26%  Similarity=0.573  Sum_probs=23.8

Q ss_pred             CcceeccCCCCCceeeecccc-c--CCCc----ccCCCCCCceee
Q 025946          157 RDIVQDSCPNCGNDFQIFKST-L--NDEL----QLCPYCSQPFSV  194 (245)
Q Consensus       157 rnLIE~tCPnCG~eF~~~ed~-L--n~d~----iqCPnCGE~L~V  194 (245)
                      -+..+..||.||..-..+.++ +  .+.+    ..|++||..+..
T Consensus        11 ~~~~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~~   55 (57)
T 1qyp_A           11 LPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             SCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             CCceEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEecc
Confidence            344567899999765543332 1  2223    589999987654

>3uk3_C Zinc finger protein 217; transcription factor, DNA binding, DNA-metal BI protein complex; 2.10A {Homo sapiens}

Probab=88.21  E-value=0.14  Score=31.89  Aligned_cols=31  Identities=19%  Similarity=0.490  Sum_probs=22.4

Q ss_pred             cCCCCCceeeecccc-------cCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKST-------LNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~-------Ln~d~iqCPnCGE~L~  193 (245)
                      .|+.||+.|....++       ..+.+..||.|+..+.
T Consensus         6 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~   43 (57)
T 3uk3_C            6 ECSYCGKFFRSNYYLNIHLRTHTGEKPYKCEFCEYAAA   43 (57)
T ss_dssp             BCTTTCCBCSCHHHHHHHHHHHHCCCCEECSSSSCEES
T ss_pred             cCCCCcchhCChHHHHHHHHHcCCCCCcCCCCCcchhC
Confidence            799999998763322       1245789999988664

>2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5

Probab=88.11  E-value=0.13  Score=42.91  Aligned_cols=27  Identities=30%  Similarity=0.978  Sum_probs=22.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .||.|+.+++-    -..+..+||.|+-.+.
T Consensus        29 ~CP~C~seytY----eDg~l~vCPeC~hEW~   55 (138)
T 2akl_A           29 PCPQCNSEYTY----EDGALLVCPECAHEWS   55 (138)
T ss_dssp             CCTTTCCCCCE----ECSSSEEETTTTEEEC
T ss_pred             CCCCCCCcceE----ecCCeEECCccccccC
Confidence            89999988876    2346899999998885

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=87.99  E-value=0.18  Score=45.56  Aligned_cols=35  Identities=17%  Similarity=0.441  Sum_probs=21.9

Q ss_pred             cCcce-eccCCCCCc---eeeecccccCCCcccCCCCCCcee
Q 025946          156 SRDIV-QDSCPNCGN---DFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       156 ~rnLI-E~tCPnCG~---eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      +-|+. ...||.||.   .+..+   ...++.+|..||-+++
T Consensus        15 ~~~l~~~~~Cp~C~~~~~~lv~D---~~~G~~vC~~CGlVl~   53 (345)
T 4bbr_M           15 GPNLNIVLTCPECKVYPPKIVER---FSEGDVVCALCGLVLS   53 (345)
T ss_dssp             -------CCCSSCCCSSCCEEEE---GGGTEEEETTTCBEEE
T ss_pred             CcccccCCcCCCCCCCCCceeEE---CCCCcEEeCCCCCCcc
Confidence            34444 348999995   33221   4668999999999885

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

Probab=87.95  E-value=0.15  Score=44.46  Aligned_cols=29  Identities=21%  Similarity=0.485  Sum_probs=21.8

Q ss_pred             ccCCCCCce---eeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGND---FQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~e---F~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ..||.||..   +..+   -..++.+|.+||.+++
T Consensus        22 ~~CPECGs~~t~IV~D---~erGE~VCsdCGLVLE   53 (197)
T 3k1f_M           22 LTCPECKVYPPKIVER---FSEGDVVCALCGLVLS   53 (197)
T ss_dssp             CCCTTTCCSSCCEEEE---GGGTEEEETTTCBBCC
T ss_pred             eECcCCCCcCCeEEEe---CCCCEEEEcCCCCCcC
Confidence            389999972   3221   4568999999999884

>1m2k_A Silent information regulator 2; protein-ligand complex, gene regulation; HET: APR; 1.47A {Archaeoglobus fulgidus} SCOP: c.31.1.5 PDB: 1m2g_A* 1m2h_A* 1m2j_A* 1m2n_A* 1ici_A*

Probab=87.46  E-value=0.39  Score=41.19  Aligned_cols=31  Identities=26%  Similarity=0.632  Sum_probs=21.2

Q ss_pred             cCCCCCceeeecccccCCC-cccCCCCCCceee
Q 025946          163 SCPNCGNDFQIFKSTLNDE-LQLCPYCSQPFSV  194 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d-~iqCPnCGE~L~V  194 (245)
                      .|..|++++.. ++.+..+ .-.||.||..+..
T Consensus       123 ~C~~C~~~~~~-~~~~~~~~~p~C~~Cgg~lrP  154 (249)
T 1m2k_A          123 RCTSCNNSFEV-ESAPKIPPLPKCDKCGSLLRP  154 (249)
T ss_dssp             EESSSSCEEEC-SSCCCSSSCCBCSSSSSBEEE
T ss_pred             EeCCCCCcccc-hhhccCCCCCCCCCCCCCcCC
Confidence            89999986543 3334433 5699999977643

>2ctu_A Zinc finger protein 483; zinc finger domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.04  E-value=0.093  Score=33.90  Aligned_cols=31  Identities=19%  Similarity=0.461  Sum_probs=22.9

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .|+.||+.|....++..+.+..|+.||..+.
T Consensus        20 ~C~~C~k~f~~~~~l~~~~~~~C~~C~~~f~   50 (73)
T 2ctu_A           20 KCSKCGIIFIRRSTLSRRKTPMCEKCRKDSC   50 (73)
T ss_dssp             ECSSSCCEEECCCCCCCSSSCCCHHHHHTCS
T ss_pred             eCCcccchhCCHHHhCcCCCCCCCCCChhhc
Confidence            7999999998744443456788999976553

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=86.79  E-value=0.35  Score=35.49  Aligned_cols=27  Identities=30%  Similarity=0.664  Sum_probs=19.5

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      -||.|++-+....+   ...++||.|+..+
T Consensus        27 wCP~C~~~~~~~~~---~~~v~C~~C~~~F   53 (86)
T 2ct7_A           27 WCAQCSFGFIYERE---QLEATCPQCHQTF   53 (86)
T ss_dssp             CCSSSCCCEECCCS---CSCEECTTTCCEE
T ss_pred             ECcCCCchheecCC---CCceEeCCCCCcc
Confidence            39999987766322   3468899998765

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=86.66  E-value=0.077  Score=40.07  Aligned_cols=33  Identities=18%  Similarity=0.400  Sum_probs=20.9

Q ss_pred             cCCCCCce-ee----------eccc-ccCC-CcccCCCCCCceeee
Q 025946          163 SCPNCGND-FQ----------IFKS-TLND-ELQLCPYCSQPFSVV  195 (245)
Q Consensus       163 tCPnCG~e-F~----------~~ed-~Ln~-d~iqCPnCGE~L~Vd  195 (245)
                      .||.||.. ..          ..+. ++.+ .-..||.||+.+...
T Consensus         4 ~Cp~Cg~~~~~~~~~~~~~~~kg~~~~v~~v~~~~C~~CGE~~~d~   49 (133)
T 3o9x_A            4 KCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNK   49 (133)
T ss_dssp             BCTTTSSSBEEEEEEEEEEEETTEEEEEEEEEEEEESSSSCEECCH
T ss_pred             CCCcCCCCceeeceEEEEEEECCEEEEECCCceeECCCCCCEeecH
Confidence            69999975 11          1111 2333 467899999988543

>1bbo_A Human enhancer-binding protein MBP-1; DNA-binding protein; HET: ABA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 PDB: 3znf_A 4znf_A

Probab=86.07  E-value=0.26  Score=30.70  Aligned_cols=31  Identities=23%  Similarity=0.513  Sum_probs=21.7

Q ss_pred             cCCCCCceeeecccc-------cCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKST-------LNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~-------Ln~d~iqCPnCGE~L~  193 (245)
                      .|+.||+.|....++       ..+.+..|+.||..+.
T Consensus         3 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~   40 (57)
T 1bbo_A            3 ICEECGIRXKKPSMLKKHIRTHTDVRPYHCTYCNFSFK   40 (57)
T ss_dssp             BCTTTCCBCSSHHHHHHHHHHTSSCCCEECSSSSCEES
T ss_pred             cCCCCcCcCCCHHHHHHHHHhcCCCCCccCCCCCchhc
Confidence            699999998763222       1234789999987663

>1ltl_A DNA replication initiator (CDC21/CDC54); HET: DNA; 3.00A {Methanothermobacterthermautotrophicus} SCOP: b.40.4.11

Probab=86.03  E-value=1  Score=39.00  Aligned_cols=48  Identities=21%  Similarity=0.538  Sum_probs=28.5

Q ss_pred             cCCCCCceeeecccc-cCCCcccCCCCCCc-eeeeCCeeEEecccccc-ccccccc
Q 025946          163 SCPNCGNDFQIFKST-LNDELQLCPYCSQP-FSVVDDKFVRESVRFSN-ESTTFGQ  215 (245)
Q Consensus       163 tCPnCG~eF~~~ed~-Ln~d~iqCPnCGE~-L~Vd~~~F~R~~~~f~~-~~~~~~~  215 (245)
                      .|+.||.+.+..-+. --..|..||+|+.. +.+     ..+...|.+ |.-.-++
T Consensus       136 ~C~~C~~~~~v~~~~~~~~~P~~Cp~C~~~~f~l-----~~~~s~f~D~Q~ikiQE  186 (279)
T 1ltl_A          136 ECRGCMRHHAVTQSTNMITEPSLCSECGGRSFRL-----LQDESEFLDTQTLKLQE  186 (279)
T ss_dssp             EETTTCCEEEEECSSSSCCCCSCCTTTCCCCEEE-----CGGGCEEEEEEEEEEEC
T ss_pred             EcCCCCCEEEEEecCCcccCCCcCCCCCCCCcEE-----eccccEEEeeEEEEEec
Confidence            899999987763211 11247899999975 222     223455666 4444444

>1ma3_A SIR2-AF2, transcriptional regulatory protein, SIR2 family; enzyme-substrate complex, protein binding, transcription; HET: ALY MES; 2.00A {Archaeoglobus fulgidus} SCOP: c.31.1.5 PDB: 1s7g_A* 1yc2_A*

Probab=85.76  E-value=0.52  Score=40.54  Aligned_cols=31  Identities=16%  Similarity=0.499  Sum_probs=20.5

Q ss_pred             ccCCCCCceeeeccccc----CCCcccCCCCCC-cee
Q 025946          162 DSCPNCGNDFQIFKSTL----NDELQLCPYCSQ-PFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~L----n~d~iqCPnCGE-~L~  193 (245)
                      ..|+.|++++ ..++.+    ....-.||.||. .+.
T Consensus       124 ~~C~~C~~~~-~~~~~~~~~~~~~~p~C~~Cgg~~lr  159 (253)
T 1ma3_A          124 LDCLDCHETY-DWSEFVEDFNKGEIPRCRKCGSYYVK  159 (253)
T ss_dssp             EEETTTCCEE-EGGGTHHHHHTTCCCCCTTTCCSCEE
T ss_pred             eeeCCCCCcC-cHHHHHHHhccCCCCCCCCCCCcccc
Confidence            3899999874 434433    223568999997 553

>2epq_A POZ-, at HOOK-, and zinc finger-containing protein 1; C2H2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1

Probab=85.46  E-value=0.25  Score=29.73  Aligned_cols=27  Identities=26%  Similarity=0.379  Sum_probs=19.0

Q ss_pred             cCCCCCceeeecccc-------cCCCcccCCCCC
Q 025946          163 SCPNCGNDFQIFKST-------LNDELQLCPYCS  189 (245)
Q Consensus       163 tCPnCG~eF~~~ed~-------Ln~d~iqCPnCG  189 (245)
                      .|+.||+.|.....+       ..+.+..||.||
T Consensus        12 ~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~cg   45 (45)
T 2epq_A           12 SCPVCGLRFKRKDRMSYHVRSHDGSVGKSGPSSG   45 (45)
T ss_dssp             EETTTTEECSCHHHHHHHHHHHSCCCCCCCCCCC
T ss_pred             cCCCCCcccCCHHHHHHHHHHccCCCCCCCcCCC
Confidence            799999998763222       123478899997

>1x6e_A Zinc finger protein 24; ZNF24, KOX17, ZNF191, zscan3, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=85.36  E-value=0.2  Score=33.14  Aligned_cols=32  Identities=25%  Similarity=0.543  Sum_probs=22.6

Q ss_pred             ccCCCCCceeeecccc-------cCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKST-------LNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~-------Ln~d~iqCPnCGE~L~  193 (245)
                      -.|+.|++.|....++       ..+.+..|+.|+..+.
T Consensus        15 ~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~   53 (72)
T 1x6e_A           15 YGCVECGKAFSRSSILVQHQRVHTGEKPYKCLECGKAFS   53 (72)
T ss_dssp             EECSSSCCEESSHHHHHHHHHGGGCSCCEECSSSCCEES
T ss_pred             ccCCCCCCccCCHHHHHHHHHhcCCCCCeECCCCCcccC
Confidence            3799999999763222       1235789999987653

>2drp_A Protein (tramtrack DNA-binding domain); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 2.80A {Drosophila melanogaster} SCOP: g.37.1.1 g.37.1.1

Probab=85.00  E-value=0.35  Score=31.10  Aligned_cols=31  Identities=23%  Similarity=0.652  Sum_probs=22.1

Q ss_pred             cCCCCCceeeecccc---------cCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKST---------LNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~---------Ln~d~iqCPnCGE~L~  193 (245)
                      .|+.||+.|....+.         -.+.+..||.||..+.
T Consensus        12 ~C~~C~k~f~~~~~l~~H~~~~H~~~~~~~~C~~C~k~f~   51 (66)
T 2drp_A           12 RCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEFT   51 (66)
T ss_dssp             ECTTTCCEESSHHHHHHHHHHHSSSSCCCEECTTTCCEES
T ss_pred             ECCCCcchhCCHHHHHHHHHHHcCCCCcCeECCCCCCccC
Confidence            799999999763221         1235789999987664

>1s5p_A NAD-dependent deacetylase; protein deacetylase, SIR2 homologue, hydrolase; HET: ALY; 1.96A {Escherichia coli} SCOP: c.31.1.5

Probab=84.93  E-value=0.47  Score=40.37  Aligned_cols=32  Identities=13%  Similarity=0.269  Sum_probs=14.9

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      .|..|++++...+++.......||.||..+..
T Consensus       115 ~C~~C~~~~~~~~~~~~~~~p~c~~Cgg~lrP  146 (235)
T 1s5p_A          115 RCSQSGQVLDWTGDVTPEDKCHCCQFPAPLRP  146 (235)
T ss_dssp             EETTTCCEEECCSCCCSSCCC-------CEEE
T ss_pred             EeCCCCCcccchhhccCCCCCCCCCCCCeecC
Confidence            79999986554332333345689999876654

>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=84.86  E-value=0.34  Score=41.73  Aligned_cols=33  Identities=30%  Similarity=0.695  Sum_probs=22.7

Q ss_pred             eeccCCCCCceeeecccccC-------CCcccCCCCCCcee
Q 025946          160 VQDSCPNCGNDFQIFKSTLN-------DELQLCPYCSQPFS  193 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln-------~d~iqCPnCGE~L~  193 (245)
                      +.-+||.|+.++. ++.+..       .+.++||+|+++++
T Consensus        21 l~l~Cp~C~~~~~-F~gv~~~~~~~~~~sg~~C~~C~~~~~   60 (206)
T 3flo_B           21 LELSCPSCDKRFP-FGGIVSSNYYRVSYNGLQCKHCEQLFT   60 (206)
T ss_dssp             EEEECTTTCCEEE-ECSSSCCSSEEEETTEEEETTTCCBCC
T ss_pred             eEEECCCCCCccC-CCCcccCCCcccccccccCCCCCCcCC
Confidence            4459999998765 444432       23578999999753

>2lv2_A Insulinoma-associated protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=84.52  E-value=0.34  Score=35.26  Aligned_cols=31  Identities=29%  Similarity=0.728  Sum_probs=22.7

Q ss_pred             cCCCCCceeeecccc-------cCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKST-------LNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~-------Ln~d~iqCPnCGE~L~  193 (245)
                      .||.||+.|..-..+       -.+-+..|+.|+..|.
T Consensus        30 ~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~k~F~   67 (85)
T 2lv2_A           30 LCPVCGESFASKGAQERHLRLLHAAQVFPCKYCPATFY   67 (85)
T ss_dssp             ECTTSCCEESSHHHHHHHHHTTSCSSSEECTTSSCEES
T ss_pred             ECCCCCCCcCcHHHHhhhhhhccCCCccCCCCCCCEeC
Confidence            799999999873332       1224789999988764

>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis}

Probab=84.44  E-value=0.53  Score=35.77  Aligned_cols=36  Identities=22%  Similarity=0.510  Sum_probs=21.5

Q ss_pred             ccCCCCCceeeeccc----------ccCC--CcccCCCCCCceeeeCCeeEE
Q 025946          162 DSCPNCGNDFQIFKS----------TLND--ELQLCPYCSQPFSVVDDKFVR  201 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed----------~Ln~--d~iqCPnCGE~L~Vd~~~F~R  201 (245)
                      -.|++||+.+...+.          .+++  +.-.||.||.+    ..+|+.
T Consensus        28 y~C~vCGyvYD~~~Gdp~~gI~pGT~fedlPddW~CPvCga~----K~~F~~   75 (81)
T 2kn9_A           28 FRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAA----KSDFEM   75 (81)
T ss_dssp             EEETTTCCEEETTTCBTTTTBCTTCCTTTSCTTCCCTTTCCC----GGGEEE
T ss_pred             EEeCCCCEEEcCCcCCcccCcCCCCChhHCCCCCcCCCCCCC----HHHcEE
Confidence            489999988442110          0122  23489999985    445554

>2adr_A ADR1; transcription regulation, zinc finger,; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 g.37.1.1

Probab=84.08  E-value=0.39  Score=30.25  Aligned_cols=31  Identities=23%  Similarity=0.564  Sum_probs=21.7

Q ss_pred             cCCCCCceeeecccc-------cCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKST-------LNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~-------Ln~d~iqCPnCGE~L~  193 (245)
                      .|+.|++.|....++       ..+.+..||.|+..+.
T Consensus         4 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~   41 (60)
T 2adr_A            4 VCEVCTRAFARQEHLKRHYRSHTNEKPYPCGLCNRAFT   41 (60)
T ss_dssp             CCTTTCCCBSCHHHHHHHHHTTTSSCSEECTTTCCEES
T ss_pred             cCCCCccccCCHHHHHHHHHHhCCCCCccCCCCCCccC
Confidence            799999999763322       1234789999987653

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=83.87  E-value=0.6  Score=34.26  Aligned_cols=37  Identities=24%  Similarity=0.619  Sum_probs=22.1

Q ss_pred             ccCCCCCceeeeccc----------ccC--CCcccCCCCCCceeeeCCeeEEe
Q 025946          162 DSCPNCGNDFQIFKS----------TLN--DELQLCPYCSQPFSVVDDKFVRE  202 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed----------~Ln--~d~iqCPnCGE~L~Vd~~~F~R~  202 (245)
                      -.|++||+...-.+-          .+.  .+.-.||.||.+    ..+|+..
T Consensus         8 y~C~vCGyiYd~~~Gdp~~gi~pGT~f~~lPddw~CP~Cga~----K~~F~~~   56 (70)
T 1dx8_A            8 YECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSP----KNQFKSI   56 (70)
T ss_dssp             EEETTTCCEECTTTCCTTTTCCSSCCGGGSCTTCBCTTTCCB----GGGEEEC
T ss_pred             EEeCCCCEEEcCCCCCcccCcCCCCchhhCCCCCcCCCCCCC----HHHceEc
Confidence            489999987432110          011  233489999985    4566654

>1x5w_A Zinc finger protein 64, isoforms 1; ZNF338, nuclear protein, DNA binding, transcription, C2H2 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=83.40  E-value=0.39  Score=31.44  Aligned_cols=31  Identities=23%  Similarity=0.446  Sum_probs=21.9

Q ss_pred             cCCCCCceeeecccc-------cCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKST-------LNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~-------Ln~d~iqCPnCGE~L~  193 (245)
                      .|+.|++.|....++       -.+.+..|+.|+..+.
T Consensus        11 ~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~   48 (70)
T 1x5w_A           11 KCSECSYSCSSKAALRIHERIHCTDRPFKCNYCSFDTK   48 (70)
T ss_dssp             ECSSSSCEESSHHHHHHHHGGGCCSCSEECSSSSCEES
T ss_pred             ECCCCCcccCCHHHHHHHHHHcCCCCCEeCCCCCCccC
Confidence            799999998763322       1234789999987653

>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=83.29  E-value=0.46  Score=36.17  Aligned_cols=34  Identities=21%  Similarity=0.567  Sum_probs=23.4

Q ss_pred             cCCCCCcee--ee-cccccCCCcccCCCCCCceeeeC
Q 025946          163 SCPNCGNDF--QI-FKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       163 tCPnCG~eF--~~-~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      +||.|+.+-  .. .+-.-+-..+.|-+||+.++..=
T Consensus        25 ~CPfCnh~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i   61 (85)
T 1wii_A           25 TCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPI   61 (85)
T ss_dssp             CCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEEEC
T ss_pred             cCCCCCCCCeEEEEEEccCCEEEEEcccCCCeEEecc
Confidence            899999982  22 11112336999999999887643

>3irb_A Uncharacterized protein from DUF35 family; 13815350, protein with unknown function from DUF35 family, S genomics; 1.80A {Sulfolobus solfataricus}

Probab=83.28  E-value=0.41  Score=38.46  Aligned_cols=29  Identities=24%  Similarity=0.590  Sum_probs=23.7

Q ss_pred             cCcceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          156 SRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       156 ~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      ..+++=..|+.||+.++-       ....||.||..
T Consensus        42 ~grL~~~rC~~CG~~~~P-------Pr~~Cp~C~s~   70 (145)
T 3irb_A           42 QNKIIGSKCSKCGRIFVP-------ARSYCEHCFVK   70 (145)
T ss_dssp             TTCCEEEECTTTCCEEES-------CCSEETTTTEE
T ss_pred             cCeEEEEEeCCCCcEEcC-------chhhCcCCCCC
Confidence            446777799999998887       67889999963

>1e8j_A Rubredoxin; iron-sulfur-protein, zinc-substitution, thermostability; NMR {Desulfovibrio gigas} SCOP: g.41.5.1 PDB: 1rdg_A 2dsx_A 1spw_A

Probab=82.87  E-value=0.7  Score=32.05  Aligned_cols=30  Identities=23%  Similarity=0.633  Sum_probs=17.8

Q ss_pred             ccCCCCCceeeeccc----------ccC--CCcccCCCCCCc
Q 025946          162 DSCPNCGNDFQIFKS----------TLN--DELQLCPYCSQP  191 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed----------~Ln--~d~iqCPnCGE~  191 (245)
                      -.|++||+..--.+.          .++  .+.-.||.||.+
T Consensus         4 y~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cg~~   45 (52)
T 1e8j_A            4 YVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGAS   45 (52)
T ss_dssp             EECSSSCCCCCTTTCCTTTTCCSSCCTTSSCTTCCCSSSCCC
T ss_pred             EEeCCCCeEEcCCcCCcccCcCCCCchHHCCCCCcCCCCCCc
Confidence            379999987432110          011  223389999985

>2d9h_A Zinc finger protein 692; ZF-C2H2 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=82.57  E-value=0.33  Score=32.35  Aligned_cols=31  Identities=23%  Similarity=0.449  Sum_probs=21.7

Q ss_pred             cCCCCCceeeeccccc----------CCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTL----------NDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~L----------n~d~iqCPnCGE~L~  193 (245)
                      .|+.|++.|.....+.          .+.+..|+.||..+.
T Consensus         9 ~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~k~f~   49 (78)
T 2d9h_A            9 QCEICGFTCRQKASLNWHQRKHAETVAALRFPCEFCGKRFE   49 (78)
T ss_dssp             ECSSSCCEESSHHHHHHHHHHHHHHTTTCCEECTTTCCEES
T ss_pred             ECCCCCCeeCCHHHHHHHHHHhhccCCCcccCCCCCCchhC
Confidence            7999999997632221          135789999987653

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=82.44  E-value=1  Score=34.88  Aligned_cols=39  Identities=18%  Similarity=0.259  Sum_probs=28.5

Q ss_pred             cCCCCCceeeeccccc-CCCcccCCCCCCceeeeCCeeEE
Q 025946          163 SCPNCGNDFQIFKSTL-NDELQLCPYCSQPFSVVDDKFVR  201 (245)
Q Consensus       163 tCPnCG~eF~~~ed~L-n~d~iqCPnCGE~L~Vd~~~F~R  201 (245)
                      -||.||.-++..++.- +.....|++||-..++++..-.+
T Consensus         6 FCp~Cgn~L~~~~~~~~~~~~~~C~~C~y~~~~~~~~v~~   45 (113)
T 3h0g_I            6 YCIECNNMLYPREDKVDRVLRLACRNCDYSEIAATSKVYR   45 (113)
T ss_dssp             CCSSSCCCCEECCCTTTCCCCEECSSSCCEECCSCSEEEE
T ss_pred             eCcCCCCEeeEcccCCCCeeEEECCCCCCeEEcCCCeEEE
Confidence            5999999999843321 22379999999999888754443

>2kmk_A Zinc finger protein GFI-1; tandem repeat zinc finger domain, protein-DNA complex, DNA-B metal-binding, nucleus; HET: DNA; NMR {Rattus norvegicus}

Probab=82.30  E-value=0.43  Score=31.33  Aligned_cols=11  Identities=36%  Similarity=1.066  Sum_probs=5.9

Q ss_pred             cCCCCCceeee
Q 025946          163 SCPNCGNDFQI  173 (245)
Q Consensus       163 tCPnCG~eF~~  173 (245)
                      .|+.|++.|..
T Consensus        31 ~C~~C~~~f~~   41 (82)
T 2kmk_A           31 PCQYCGKRFHQ   41 (82)
T ss_dssp             ECSSSCCEESS
T ss_pred             eCCcCChhhCC
Confidence            45555555543

>1s24_A Rubredoxin 2; electron transport; NMR {Pseudomonas oleovorans} SCOP: g.41.5.1

Probab=82.16  E-value=0.57  Score=36.02  Aligned_cols=30  Identities=23%  Similarity=0.418  Sum_probs=18.4

Q ss_pred             eccCCCCCceeeeccc-----------ccCC--CcccCCCCCCc
Q 025946          161 QDSCPNCGNDFQIFKS-----------TLND--ELQLCPYCSQP  191 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed-----------~Ln~--d~iqCPnCGE~  191 (245)
                      .-.|++||+. |+-+.           .+.+  +.-.||.||.+
T Consensus        35 ~y~C~vCGyv-YD~~~Gdp~~gI~pGT~fedlPddW~CPvCga~   77 (87)
T 1s24_A           35 KWICITCGHI-YDEALGDEAEGFTPGTRFEDIPDDWCCPDCGAT   77 (87)
T ss_dssp             EEEETTTTEE-EETTSCCTTTTCCSCCCGGGCCTTCCCSSSCCC
T ss_pred             eEECCCCCeE-ecCCcCCcccCcCCCCChhHCCCCCCCCCCCCC
Confidence            3489999977 44210           0112  33489999974

>2f9y_B Acetyl-coenzyme A carboxylase carboxyl transferas beta; zinc ribbon, crotonase superfamily, spiral domain, ligase; 3.20A {Escherichia coli} SCOP: c.14.1.4

Probab=82.01  E-value=1.1  Score=40.14  Aligned_cols=31  Identities=26%  Similarity=0.725  Sum_probs=23.5

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ...||+|+...|.  ..|.+...+||.|+-...
T Consensus        24 ~~kc~~~~~~~~~--~~l~~~~~v~~~~~~~~r   54 (304)
T 2f9y_B           24 WTKCDSCGQVLYR--AELERNLEVCPKCDHHMR   54 (304)
T ss_dssp             EECCTTTCCCEET--THHHHTTTBCTTTCCBCC
T ss_pred             HHhhhhccchhhH--HHHHHHhCCCCCCCCCCC
Confidence            4589999999997  123456799999987543

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=81.66  E-value=0.82  Score=32.00  Aligned_cols=28  Identities=21%  Similarity=0.488  Sum_probs=18.1

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      ..||.||......   -..+-..|+.||-..
T Consensus        19 ~fCPkCG~~~~ma---~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           19 RFCPRCGPGVFLA---EHADRYSCGRCGYTE   46 (55)
T ss_dssp             CCCTTTTTTCCCE---ECSSEEECTTTCCCE
T ss_pred             ccCcCCCCceeEe---ccCCEEECCCCCCEE
Confidence            4788888743320   234688888888764

>2ctd_A Zinc finger protein 512; zinc binding, two ZF-C2H2 domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=81.60  E-value=0.61  Score=33.66  Aligned_cols=31  Identities=26%  Similarity=0.575  Sum_probs=22.0

Q ss_pred             ccCCCCCcee-eeccccc-------CCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDF-QIFKSTL-------NDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF-~~~ed~L-------n~d~iqCPnCGE~L~  193 (245)
                      ..|+.||+.| ... ..|       .+.+..|+.||..+.
T Consensus        35 ~~C~~C~k~F~~~~-~~L~~H~~~h~~k~~~C~~Cgk~F~   73 (96)
T 2ctd_A           35 VSCPTCQAVGRKTI-EGLKKHMENCKQEMFTCHHCGKQLR   73 (96)
T ss_dssp             EECTTTCSCEESSH-HHHHHHHHHHCCCCCCCSSSCCCCS
T ss_pred             cCCCCCCCCcccCH-HHHHHHHHHHCCCCeECCCCCCeeC
Confidence            3899999999 431 111       345889999988763

>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa}

Probab=81.47  E-value=0.69  Score=32.44  Aligned_cols=30  Identities=20%  Similarity=0.363  Sum_probs=18.1

Q ss_pred             ccCCCCCceeeeccc----------ccC--CCcccCCCCCCc
Q 025946          162 DSCPNCGNDFQIFKS----------TLN--DELQLCPYCSQP  191 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed----------~Ln--~d~iqCPnCGE~  191 (245)
                      -.|++||+...-.+.          .+.  .+.-.||.||.+
T Consensus         4 y~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cga~   45 (55)
T 2v3b_B            4 WQCVVCGFIYDEALGLPEEGIPAGTRWEDIPADWVCPDCGVG   45 (55)
T ss_dssp             EEETTTCCEEETTTCBTTTTBCTTCCGGGSCTTCCCTTTCCC
T ss_pred             EEeCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCCCCCCC
Confidence            379999987433110          011  233489999985

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=81.15  E-value=0.79  Score=36.45  Aligned_cols=21  Identities=14%  Similarity=0.273  Sum_probs=16.8

Q ss_pred             cccCCCCCCceeeeCCeeEEe
Q 025946          182 LQLCPYCSQPFSVVDDKFVRE  202 (245)
Q Consensus       182 ~iqCPnCGE~L~Vd~~~F~R~  202 (245)
                      +..||.|.++++.+++.|.-+
T Consensus        32 ~~~CP~Cq~eL~~~g~~~hC~   52 (101)
T 2jne_A           32 ELHCPQCQHVLDQDNGHARCR   52 (101)
T ss_dssp             CCBCSSSCSBEEEETTEEEET
T ss_pred             cccCccCCCcceecCCEEECc
Confidence            378999999998888877544

>2cot_A Zinc finger protein 435; ADK_LID domain, zinc finger and SCAN domain containing protein 16, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=81.12  E-value=0.37  Score=32.10  Aligned_cols=32  Identities=22%  Similarity=0.561  Sum_probs=22.3

Q ss_pred             ccCCCCCceeeecccc-------cCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKST-------LNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~-------Ln~d~iqCPnCGE~L~  193 (245)
                      -.|+.|++.|....++       ..+.+..|+.|+..+.
T Consensus        19 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~   57 (77)
T 2cot_A           19 YKCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAFI   57 (77)
T ss_dssp             SBCSSSCCBCSCHHHHHHHHTTTCCSCSEECSSSCCEES
T ss_pred             EECCCCCcccCCHHHHHHHHHHcCCCcCeeCCCCCCccC
Confidence            4899999999763222       1234789999987653

>1yc5_A NAD-dependent deacetylase; SIR2, sirtuin, SIR2TM, SIRT1, nicotinamide, hydrolase; HET: ALY; 1.40A {Thermotoga maritima} SCOP: c.31.1.5 PDB: 2h2d_A* 2h2f_A 2h2g_A* 2h2h_A* 2h2i_A* 2h4f_A* 2h4j_A* 3d4b_A* 3d81_A* 3pdh_A* 2h4h_A* 3jr3_A* 2h59_A*

Probab=80.87  E-value=0.79  Score=39.15  Aligned_cols=32  Identities=16%  Similarity=0.557  Sum_probs=21.1

Q ss_pred             ccCCCCCceeeeccccc---CC-CcccCCCCCCceee
Q 025946          162 DSCPNCGNDFQIFKSTL---ND-ELQLCPYCSQPFSV  194 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~L---n~-d~iqCPnCGE~L~V  194 (245)
                      ..|..|++++ ..++..   .. ..-.||.||..+..
T Consensus       122 ~~C~~C~~~~-~~~~~~~~~~~~~~p~C~~Cgg~lrP  157 (246)
T 1yc5_A          122 YYCVRCEKKY-TVEDVIKKLESSDVPLCDDCNSLIRP  157 (246)
T ss_dssp             EEETTTCCEE-EHHHHHHHTTTCSSCBCTTTCCBEEE
T ss_pred             eEcCCCCCCC-cHHHHHHHhccCCCCCCCCCCCccCc
Confidence            3899999874 433322   22 35699999976643

>2jrr_A Uncharacterized protein; solution structure, SIR90, structural genomics, PSI-2, protein structure initiative; NMR {Silicibacter pomeroyi}

Probab=80.67  E-value=0.43  Score=35.20  Aligned_cols=18  Identities=22%  Similarity=0.647  Sum_probs=14.7

Q ss_pred             CCcccCCCCCCceeeeCC
Q 025946          180 DELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       180 ~d~iqCPnCGE~L~Vd~~  197 (245)
                      .++..|||||+.|..++.
T Consensus        38 ~g~~~CpYCg~~f~l~~~   55 (67)
T 2jrr_A           38 TGWVECPYCDCKYVLKGS   55 (67)
T ss_dssp             TSEEEETTTTEEEEETTS
T ss_pred             CCeEECCCCCCEEEECCC
Confidence            479999999998877653

>3bvo_A CO-chaperone protein HSCB, mitochondrial precurso; structural genomics medical relev protein structure initiative, PSI-2; 3.00A {Homo sapiens}

Probab=80.10  E-value=0.9  Score=38.56  Aligned_cols=31  Identities=23%  Similarity=0.474  Sum_probs=22.5

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      ...|++|+.....    +......||+|+...+++
T Consensus        10 ~~~Cw~C~~~~~~----~~~~~~fC~~c~~~q~~~   40 (207)
T 3bvo_A           10 YPRCWNCGGPWGP----GREDRFFCPQCRALQAPD   40 (207)
T ss_dssp             -CBCSSSCCBCCS----SCSCCCBCTTTCCBCCCC
T ss_pred             CCCCCCCCCCccc----ccccccccccccccCCCC
Confidence            4589999976322    344789999999877665

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	245
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	95.22
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	95.21
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	94.99
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	94.94
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	94.46
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	94.42
d1vd4a_	62	Transcription initiation factor TFIIE-alpha {Human	94.02
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	93.95
d2f9yb1	263	Acetyl-coenzyme A carboxylase carboxyl transferase	93.67
d1lkoa2	44	Rubrerythrin, C-terminal domain {Desulfovibrio vul	93.3
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	93.23
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	93.17
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	93.14
d1wgea1	70	DelGEF-interacting protein 1, DelGIP1 {Mouse (Mus	93.11
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	92.88
d2ey4e1	52	Ribosome biogenesis protein Nop10 {Archaeon Pyroco	92.63
d2apob1	55	Ribosome biogenesis protein Nop10 {Archaeon Methan	92.02
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	91.68
d2j0151	59	Ribosomal protein L32p {Thermus thermophilus [TaxI	91.6
d1ywsa1	82	Diphthamide biosynthesis protein 3, DPH3 {Baker's	91.24
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	90.82
d2zjrz1	58	Ribosomal protein L32p {Deinococcus radiodurans [T	90.64
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	90.17
d1m2ka_	249	AF1676, Sir2 homolog (Sir2-AF1?) {Archaeon Archaeo	90.13
d1ltla_	239	DNA replication initiator (cdc21/cdc54) N-terminal	89.81
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	89.81
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	89.41
d2gmga1	105	Hypothetical protein PF0610 {Pyrococcus furiosus [	89.18
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	88.92
d1s5pa_	235	NAD-dependent deacetylase CobB {Escherichia coli [	88.55
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	88.05
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	87.04
d2gnra1	137	Hypothetical protein SSO2064 {Sulfolobus solfatari	86.24
d1twfl_	46	RBP12 subunit of RNA polymerase II {Baker's yeast	85.81
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	85.2
d2qam01	56	Ribosomal protein L32p {Escherichia coli [TaxId: 5	84.65
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	82.81
d1fqta_	109	Rieske-type ferredoxin associated with biphenyl di	80.99
d1vm9a_	109	Toluene-4-monooxygenase system protein C, TmoC {Ps	80.33

>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=95.22  E-value=0.0052  Score=39.12  Aligned_cols=23  Identities=35%  Similarity=0.973  Sum_probs=19.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .||+||+...+      +-|-.||.||.+
T Consensus         7 vC~vCGyi~~g------~~Pe~CPvCg~~   29 (36)
T d1yuza2           7 LCPICGYIHKG------EDFEKCPICFRP   29 (36)
T ss_dssp             ECSSSCCEEES------SCCSBCTTTCCB
T ss_pred             ECCCCCCEeeC------CCCCcCCCCCCc
Confidence            79999998776      257899999976

>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=95.21  E-value=0.0052  Score=39.24  Aligned_cols=23  Identities=35%  Similarity=0.912  Sum_probs=19.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .||+||+...+      +-|-.||.||.+
T Consensus         7 ~C~vCG~i~~g------~~P~~CPvCg~~   29 (37)
T d1nnqa2           7 ICPICGYTAVD------EAPEYCPVCGAP   29 (37)
T ss_dssp             ECTTTCCEEES------CCCSBCTTTCCB
T ss_pred             ECCCCCCEecC------CCCCcCCCCCCc
Confidence            79999998876      257899999976

>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=94.99  E-value=0.0051  Score=39.15  Aligned_cols=29  Identities=28%  Similarity=0.666  Sum_probs=21.7

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      ++.+||.|+++=.-        --+|..||..+...+
T Consensus         1 V~G~CP~C~~~~a~--------GDqCe~CG~~~~p~e   29 (35)
T d1pfva3           1 VKGTCPKCKSPDQY--------GDNCEVCGATYSPTE   29 (35)
T ss_dssp             EEEECTTTCCSSEE--------TTBCTTTCCBCCGGG
T ss_pred             CeeECCCCCCcccc--------cccHHHcCCcCCHHH
Confidence            57899999987322        358999999886543

>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=94.94  E-value=0.0042  Score=39.54  Aligned_cols=28  Identities=29%  Similarity=0.738  Sum_probs=21.3

Q ss_pred             eeccCCCCCce-eeecccccCCCcccCCCCCCceeeeC
Q 025946          160 VQDSCPNCGND-FQIFKSTLNDELQLCPYCSQPFSVVD  196 (245)
Q Consensus       160 IE~tCPnCG~e-F~~~ed~Ln~d~iqCPnCGE~L~Vd~  196 (245)
                      ++.+||.||++ -|         --||.+||..+...+
T Consensus         1 V~G~CP~C~~~~a~---------GDqCe~CG~~~~p~e   29 (35)
T d1rqga3           1 VIGTCPYCGAEDQK---------GDQCEVCGRPLTPEI   29 (35)
T ss_dssp             CCSBCSSSCCSCCC---------TTTCSSSCCCCCTTS
T ss_pred             CeEECCCCCCCccc---------CcchhhcCCccCHHH
Confidence            46799999975 33         358999999886543

>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=94.46  E-value=0.0069  Score=40.34  Aligned_cols=31  Identities=23%  Similarity=0.461  Sum_probs=23.0

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      |..||.||.+-..  ..-..+++.|.+||.+++
T Consensus         5 ~~~Cp~Cgs~~iv--~D~~~Ge~vC~~CG~Vie   35 (50)
T d1pfta_           5 QKVCPACESAELI--YDPERGEIVCAKCGYVIE   35 (50)
T ss_dssp             CCSCTTTSCCCEE--EETTTTEEEESSSCCBCC
T ss_pred             cccCcCCCCCcEE--EECCCCeEecccCCcEec
Confidence            5689999976433  114568999999999873

>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein Cgl1405/cg1592
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=94.42  E-value=0.0073  Score=41.56  Aligned_cols=38  Identities=11%  Similarity=0.345  Sum_probs=30.3

Q ss_pred             Ccceec-cCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          157 RDIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       157 rnLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      .++++. .||.|+.++...+   .+...+|+.|+..|++.+|
T Consensus         5 ~~LL~iL~CP~ck~~L~~~~---~~~~Lvc~~~~~~YPI~dg   43 (59)
T d2jnya1           5 PQLLEVLACPKDKGPLRYLE---SEQLLVNERLNLAYRIDDG   43 (59)
T ss_dssp             GGGTCCCBCTTTCCBCEEET---TTTEEEETTTTEEEEEETT
T ss_pred             HHHHHHhcCCCCCCEeEEeC---CCCEEEcCccCccccccCC
Confidence            345555 8999999987632   3468999999999999987

>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.02  E-value=0.01  Score=41.48  Aligned_cols=37  Identities=16%  Similarity=0.436  Sum_probs=29.1

Q ss_pred             eccCCCCCceeeecccc----cCCCcccCCCCCCceeeeCC
Q 025946          161 QDSCPNCGNDFQIFKST----LNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~----Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      .-.||.|+++|..+|-.    ...+...|-+|+++|.-|+.
T Consensus        14 ~y~Cp~C~~~ys~Lda~~L~d~~~~~F~C~~C~~el~eD~s   54 (62)
T d1vd4a_          14 SFKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEEDES   54 (62)
T ss_dssp             EEECSSSCCEEEHHHHHHHEETTTTEEBCSSSCCBCEECTT
T ss_pred             ceECCCCCCCcchhhHHHhcCcCCCeEEecCCCCEEecCCc
Confidence            34899999999987654    23468899999999976654

>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=93.95  E-value=0.011  Score=40.45  Aligned_cols=33  Identities=18%  Similarity=0.445  Sum_probs=24.8

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      +.+..||+||.+-...  .-.+++++|.+||.+++
T Consensus         9 ~~~~~Cp~Cgs~~ii~--D~~~Ge~vC~~CG~Vle   41 (58)
T d1dl6a_           9 LPRVTCPNHPDAILVE--DYRAGDMICPECGLVVG   41 (58)
T ss_dssp             CSCCSBTTBSSSCCEE--CSSSCCEECTTTCCEEC
T ss_pred             ccccCCCCCCCCCEEE--ECCCCcEecccCCCEec
Confidence            4567999999874431  14568999999999873

>d2f9yb1 c.14.1.4 (B:23-285) Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Biotin dependent carboxylase carboxyltransferase domain
domain: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD
species: Escherichia coli [TaxId: 562]

Probab=93.67  E-value=0.021  Score=47.68  Aligned_cols=40  Identities=23%  Similarity=0.620  Sum_probs=29.5

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee----------eeCCeeEEecc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS----------VVDDKFVRESV  204 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~----------Vd~~~F~R~~~  204 (245)
                      +||+|++.+|.  ..|.+.-.+||+|+--+.          +|++.|+--+.
T Consensus         4 ~C~~C~~~~~~--~~l~~~~~vC~~C~~h~~ltaReRi~~L~D~gsf~Ei~~   53 (263)
T d2f9yb1           4 KCDSCGQVLYR--AELERNLEVCPKCDHHMRMTARNRLHSLLDEGSLVELGS   53 (263)
T ss_dssp             CCTTTCCCEET--THHHHTTTBCTTTCCBCCCCHHHHHHHHSCSSCCEECSC
T ss_pred             cCCCCcceeeH--HHHHHhCCCCcCCCCCCCcCHHHHHHHHccCCceEEeCC
Confidence            89999988876  345666779999998554          46666766554

>d1lkoa2 g.41.5.1 (A:148-191) Rubrerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

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

Probab=93.30  E-value=0.015  Score=38.39  Aligned_cols=26  Identities=35%  Similarity=0.816  Sum_probs=21.0

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .-.|.+||+...+     .+-|..||.|+.+
T Consensus         8 ~W~C~~CGyi~~g-----~~aP~~CPvC~~p   33 (44)
T d1lkoa2           8 KWRCRNCGYVHEG-----TGAPELCPACAHP   33 (44)
T ss_dssp             EEEETTTCCEEEE-----EECCSBCTTTCCB
T ss_pred             EEEcCCCCcEEEC-----CCCCCcCCCCCCc
Confidence            3389999999887     3358899999975

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=93.23  E-value=0.01  Score=38.38  Aligned_cols=29  Identities=28%  Similarity=0.865  Sum_probs=22.9

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV  195 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd  195 (245)
                      .||.|+.+++-    -..+..+||.||-.++.+
T Consensus         5 ~CP~C~seytY----edg~l~vCPeC~hEW~~~   33 (38)
T d2akla2           5 PCPQCNSEYTY----EDGALLVCPECAHEWSPN   33 (38)
T ss_dssp             CCTTTCCCCCE----ECSSSEEETTTTEEECTT
T ss_pred             cCCCCCCcceE----cCCCEEECCcccCcCCcc
Confidence            69999988876    344689999999877544

>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=93.17  E-value=0.026  Score=39.15  Aligned_cols=35  Identities=23%  Similarity=0.625  Sum_probs=27.7

Q ss_pred             CcceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          157 RDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       157 rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      -.++...||.|+++-.++.  =...++.|..||+.|.
T Consensus         3 S~F~~VkC~~C~n~~ivFs--ha~t~V~C~~Cg~~L~   37 (58)
T d1qxfa_           3 SRFVKVKCPDCEHEQVIFD--HPSTIVKCIICGRTVA   37 (58)
T ss_dssp             CCEEEEECTTTCCEEEEES--SCSSCEECSSSCCEEE
T ss_pred             ceeEEeECCCCCCeEEEEe--cCceEEEccccCCEEe
Confidence            3578889999999988831  2236999999999885

>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]

Probab=93.14  E-value=0.023  Score=39.12  Aligned_cols=36  Identities=19%  Similarity=0.412  Sum_probs=29.2

Q ss_pred             ceec-cCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          159 IVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       159 LIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      +++. .||.|+.++...+   ++++.+|+.|+-.|++.+|
T Consensus         4 LL~iL~CP~ck~~L~~~~---~~~~Lvc~~~~l~YPI~dG   40 (59)
T d2hf1a1           4 FLEILVCPLCKGPLVFDK---SKDELICKGDRLAFPIKDG   40 (59)
T ss_dssp             CEEECBCTTTCCBCEEET---TTTEEEETTTTEEEEEETT
T ss_pred             HhhhhcCCCCCCeeeEeC---CCCEEecCCcCccccccCC
Confidence            4444 8999999988632   3468999999999999987

>d1wgea1 g.41.17.1 (A:8-77) DelGEF-interacting protein 1, DelGIP1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: CSL zinc finger
family: CSL zinc finger
domain: DelGEF-interacting protein 1, DelGIP1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.11  E-value=0.019  Score=41.07  Aligned_cols=35  Identities=37%  Similarity=0.763  Sum_probs=28.6

Q ss_pred             ceeccCCCCCceeeecccccCCCc--ccCCCCCCceee
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDEL--QLCPYCSQPFSV  194 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~--iqCPnCGE~L~V  194 (245)
                      .+...|| ||..|...++.|.+++  ++||.|.-.+.|
T Consensus        21 ~~~ypCp-CGd~F~it~~dLe~ge~V~~C~sCSL~ikV   57 (70)
T d1wgea1          21 TYFYPCP-CGDNFAITKEDLENGEDVATCPSCSLIIKV   57 (70)
T ss_dssp             EEEECCS-SSSCEEEEHHHHHTTCCEEECTTTCCEEEE
T ss_pred             EEEeCCC-CCCeEEECHHHHhCCCeEEeCCCCceEEEE
Confidence            3556999 9999999988888864  479999887765

>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein PFL1779
species: Pseudomonas fluorescens [TaxId: 294]

Probab=92.88  E-value=0.022  Score=39.28  Aligned_cols=32  Identities=13%  Similarity=0.398  Sum_probs=27.2

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD  197 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~  197 (245)
                      .||.|..++.-++   ++.+.+|+.|+-.|++.+|
T Consensus         8 ~CP~ck~~L~~~~---~~~~Lvc~~~~laYPI~dG   39 (59)
T d2pk7a1           8 ACPICKGPLKLSA---DKTELISKGAGLAYPIRDG   39 (59)
T ss_dssp             CCTTTCCCCEECT---TSSEEEETTTTEEEEEETT
T ss_pred             ECCCCCCcceEeC---CCCEEecCCcCccccccCC
Confidence            7999999988743   3467999999999999987

>d2ey4e1 g.41.16.1 (E:4-55) Ribosome biogenesis protein Nop10 {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Nop10-like SnoRNP
family: Nucleolar RNA-binding protein Nop10-like
domain: Ribosome biogenesis protein Nop10
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.63  E-value=0.03  Score=38.20  Aligned_cols=32  Identities=41%  Similarity=0.924  Sum_probs=23.1

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccccccc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE  209 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~~  209 (245)
                      .||.||.  |.    |   .-.||.||+.-.      ..-+++||-.
T Consensus         4 kC~~C~~--YT----L---~~~CP~CG~~t~------~a~ParfSPe   35 (52)
T d2ey4e1           4 KCPKCGR--YT----L---KEVCPVCGEKTK------VAHPPRFSPE   35 (52)
T ss_dssp             ECTTTCC--EE----S---SSBCTTTCCBCE------ESSCCCCCTT
T ss_pred             cCCcccc--ee----c---cccCcCCCCccc------ccCCCCCCCC
Confidence            6999994  44    2   457999998764      4457777753

>d2apob1 g.41.16.1 (B:403-457) Ribosome biogenesis protein Nop10 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Nop10-like SnoRNP
family: Nucleolar RNA-binding protein Nop10-like
domain: Ribosome biogenesis protein Nop10
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=92.02  E-value=0.031  Score=38.48  Aligned_cols=33  Identities=33%  Similarity=0.818  Sum_probs=23.6

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccccccc
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE  209 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~~  209 (245)
                      ..||.||.  |.    |   .-.||.||++-..      .-+++||-.
T Consensus         5 rkC~~C~~--YT----L---~~~CP~CG~~t~~------a~P~rfSPe   37 (55)
T d2apob1           5 KKCPKCGL--YT----L---KEICPKCGEKTVI------PKPPKFSLE   37 (55)
T ss_dssp             EECTTTCC--EE----S---SSBCSSSCSBCBC------CCCCCCCTT
T ss_pred             eeCCcccc--ee----c---cccCcCCCCccCc------cCCCCCCCC
Confidence            37999994  44    2   5689999987643      457777753

>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=91.68  E-value=0.062  Score=34.13  Aligned_cols=31  Identities=10%  Similarity=0.027  Sum_probs=21.9

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ++||+||..+-.. .---+.+-.|-.||++|.
T Consensus         3 r~C~~cG~~Yh~~-~~ppk~~g~CD~cg~~L~   33 (38)
T d1akya2           3 LIHPASGRSYHKI-FNPPKEDMKDDVTGEALV   33 (38)
T ss_dssp             EECTTTCCEEETT-TBCCSSTTBCTTTCCBCB
T ss_pred             cCCcCccchhhhh-ccCcCcCCccCCCCCEee
Confidence            5899999877662 111224779999999875

>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=91.60  E-value=0.034  Score=38.27  Aligned_cols=21  Identities=29%  Similarity=0.748  Sum_probs=16.5

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCC
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      +.||+||+.-.        ..-.||+||.
T Consensus        30 ~~C~~CG~~~~--------pHrvC~~CG~   50 (59)
T d2j0151          30 VPCPECKAMKP--------PHTVCPECGY   50 (59)
T ss_dssp             BCCSSSSSCBC--------TTCBCTTTCC
T ss_pred             eECCCCCCccc--------ceeECCCCCe
Confidence            48999996433        5889999994

>d1ywsa1 g.41.17.1 (A:1-82) Diphthamide biosynthesis protein 3, DPH3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: CSL zinc finger
family: CSL zinc finger
domain: Diphthamide biosynthesis protein 3, DPH3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.24  E-value=0.03  Score=41.03  Aligned_cols=35  Identities=34%  Similarity=0.844  Sum_probs=28.2

Q ss_pred             ceeccCCCCCceeeecccccCCCc--ccCCCCCCceee
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDEL--QLCPYCSQPFSV  194 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~--iqCPnCGE~L~V  194 (245)
                      .+...|| ||..|...++.|.+++  .+||.|.-.+.|
T Consensus        20 ~~~ypCr-CGd~F~it~~dLe~ge~v~~C~sCSL~IrV   56 (82)
T d1ywsa1          20 MFTYPCP-CGDRFQIYLDDMFEGEKVAVCPSCSLMIDV   56 (82)
T ss_dssp             EEEECCS-SSSCEEEEHHHHHTTCCEEEETTTTEEEEE
T ss_pred             EEEeccc-cCCeEEEcHHHHhCCCeEEeCCCCceEEEE
Confidence            4556899 9999999888888864  469999877665

>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=90.82  E-value=0.077  Score=33.07  Aligned_cols=31  Identities=6%  Similarity=0.006  Sum_probs=21.9

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ++||+||..+-. +..--+-+-.|-.||++|-
T Consensus         3 r~c~~cG~~Yh~-~~~PPk~~g~CD~cg~~L~   33 (35)
T d1e4va2           3 RVHAPSGRVYHV-KFNPPKVEGKDDVTGEELT   33 (35)
T ss_dssp             EEETTTTEEEET-TTBCCSSTTBCTTTCCBCB
T ss_pred             cCCcCcCChhhh-ccCccccCCcccCCCCEee
Confidence            589999977666 1112224789999999873

>d2zjrz1 g.41.8.5 (Z:2-59) Ribosomal protein L32p {Deinococcus radiodurans [TaxId: 1299]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Deinococcus radiodurans [TaxId: 1299]

Probab=90.64  E-value=0.046  Score=37.51  Aligned_cols=19  Identities=32%  Similarity=1.017  Sum_probs=15.7

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCS  189 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCG  189 (245)
                      +||+||+.-.        ..-.||+||
T Consensus        31 ~C~~CG~~~l--------pHrvC~~CG   49 (58)
T d2zjrz1          31 ECPQCHGKKL--------SHHICPNCG   49 (58)
T ss_dssp             ECTTTCCEEC--------TTBCCTTTC
T ss_pred             ECCCCCCCcc--------ceeeCCCCC
Confidence            7999996433        588999998

>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=90.17  E-value=0.097  Score=32.65  Aligned_cols=31  Identities=19%  Similarity=0.532  Sum_probs=21.8

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      ++||+||..+-+ +..--+.+-.|-.||++|.
T Consensus         3 r~C~~CG~~Yh~-~~~pPk~~g~CD~cG~~L~   33 (35)
T d1zina2           3 RICRNCGATYHL-IFHPPAKPGVCDKCGGELY   33 (35)
T ss_dssp             EEETTTCCEEET-TTBCCSSTTBCTTTCCBEE
T ss_pred             cCCcCcCchhcc-ccCCCCCCCcCCCCCCCcc
Confidence            489999987665 1112224889999999873

>d1m2ka_ c.31.1.5 (A:) AF1676, Sir2 homolog (Sir2-AF1?) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: DHS-like NAD/FAD-binding domain
superfamily: DHS-like NAD/FAD-binding domain
family: Sir2 family of transcriptional regulators
domain: AF1676, Sir2 homolog (Sir2-AF1?)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=90.13  E-value=0.096  Score=42.42  Aligned_cols=31  Identities=23%  Similarity=0.548  Sum_probs=22.1

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      ..|+.|++.+...+..-.+..-.||.||..+
T Consensus       122 ~~C~~c~~~~~~~~~~~~~~~p~C~~Cgg~l  152 (249)
T d1m2ka_         122 VRCTSCNNSFEVESAPKIPPLPKCDKCGSLL  152 (249)
T ss_dssp             EEESSSSCEEECSSCCCSSSCCBCSSSSSBE
T ss_pred             eeeccCCCcccccccccCCCCCCcccCCCEe
Confidence            4999999887764333333566899998665

>d1ltla_ b.40.4.11 (A:) DNA replication initiator (cdc21/cdc54) N-terminal domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: DNA replication initiator (cdc21/cdc54) N-terminal domain
domain: DNA replication initiator (cdc21/cdc54) N-terminal domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=89.81  E-value=0.14  Score=41.44  Aligned_cols=71  Identities=20%  Similarity=0.445  Sum_probs=41.0

Q ss_pred             cCCCCCceeeecccc-cCCCcccCCCCCCceeeeCCeeE--Eecccccc-ccccccccccccCCCCCCCCCCCceeEEee
Q 025946          163 SCPNCGNDFQIFKST-LNDELQLCPYCSQPFSVVDDKFV--RESVRFSN-ESTTFGQAFSDFFPGSRKGRESSTSVVDVE  238 (245)
Q Consensus       163 tCPnCG~eF~~~ed~-Ln~d~iqCPnCGE~L~Vd~~~F~--R~~~~f~~-~~~~~~~af~~~~~~~~~~~~~~~~vvdve  238 (245)
                      .|+.||.+.+...+. .-..|..||+|+..      .|.  .+..+|.+ |.-.-++...+    ...|..|....|-+|
T Consensus       128 ~C~~C~~~~~~~~~~~~~~~p~~C~~C~~~------~f~~~~~~s~~~d~Q~i~iQE~~e~----~~~G~~Pr~i~v~l~  197 (239)
T d1ltla_         128 ECRGCMRHHAVTQSTNMITEPSLCSECGGR------SFRLLQDESEFLDTQTLKLQEPLEN----LSGGEQPRQITVVLE  197 (239)
T ss_dssp             EETTTCCEEEEECSSSSCCCCSCCTTTCCC------CEEECGGGCEEEEEEEEEEECCSTT----CCSSCCCCEEEEEEE
T ss_pred             ECCCCCceEEEEecCCeecCCccCCCCCCc------ccEEccCcceEeeeEEEEEeccccc----CCCCCCCcEEEEEEe
Confidence            899999999884433 22358999999862      243  44455665 44444443322    233455655445455


Q ss_pred             eeeec
Q 025946          239 AEIKD  243 (245)
Q Consensus       239 aev~d  243 (245)
                      .+..|
T Consensus       198 ~dlvd  202 (239)
T d1ltla_         198 DDLVD  202 (239)
T ss_dssp             GGGTT
T ss_pred             ccccC
Confidence            44443

>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=89.81  E-value=0.1  Score=32.90  Aligned_cols=31  Identities=13%  Similarity=0.169  Sum_probs=22.0

Q ss_pred             ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      .+||.||..+-.. .---+-+-.|-.||++|-
T Consensus         3 ~vc~~cG~~Yh~~-~~pPk~~g~CD~cg~~L~   33 (37)
T d2ak3a2           3 WIHPGSGRVYNIE-FNPPKTMGIDDLTGEPLV   33 (37)
T ss_dssp             EEETTTTEEEETT-TBCCSSTTBCTTTCCBCB
T ss_pred             eeeCCcCChhhhc-cCCccccCCccCCCCcCE
Confidence            4899999777661 111224889999999874

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.41  E-value=0.046  Score=34.35  Aligned_cols=31  Identities=13%  Similarity=0.337  Sum_probs=23.8

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      +|-.|+..+..--..-.++++.||.||.-..
T Consensus         1 ncgkcsvslvg~gfltq~~~i~c~~cgsg~d   31 (34)
T d1x68a2           1 NCGKCSVSLVGKGFLTQNKEIFCQKCGSGMD   31 (34)
T ss_dssp             BCTTTCCBCSSSCEEEETTEEEETTTTCCCC
T ss_pred             CCccceEEEEeeeeeeccCcEEehhcCCCcC
Confidence            4888888877744455678999999998654

>d2gmga1 a.4.5.82 (A:1-105) Hypothetical protein PF0610 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF0610-like
domain: Hypothetical protein PF0610
species: Pyrococcus furiosus [TaxId: 2261]

Probab=89.18  E-value=0.13  Score=39.09  Aligned_cols=33  Identities=24%  Similarity=0.731  Sum_probs=23.7

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeE
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFV  200 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~  200 (245)
                      .|-+||+.|.+   -+ +-|..||.|.... +++=.|.
T Consensus        69 ~CrkCGfvFr~---~~-kkPSRCP~CKSE~-Ie~P~F~  101 (105)
T d2gmga1          69 QCRKCGFVFKA---EI-NIPSRCPKCKSEW-IEEPRFK  101 (105)
T ss_dssp             BBTTTCCBCCC---CS-SCCSSCSSSCCCC-BCCCCEE
T ss_pred             hhhhcCCeecc---cC-CCCCCCCCCCCcc-ccCCcee
Confidence            99999998732   23 5689999998876 4444443

>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=88.92  E-value=0.13  Score=31.98  Aligned_cols=29  Identities=17%  Similarity=0.445  Sum_probs=21.9

Q ss_pred             ccCCCCCceeeecccccCC--CcccCCCCCCcee
Q 025946          162 DSCPNCGNDFQIFKSTLND--ELQLCPYCSQPFS  193 (245)
Q Consensus       162 ~tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~  193 (245)
                      ++||+||..+-+.   .+.  .+-.|-.||++|.
T Consensus         3 ~~C~~CG~~Yh~~---~~pPk~~g~CD~cg~~L~   33 (35)
T d1s3ga2           3 RICKVCGTSYHLL---FNPPQVEGKCDKDGGELY   33 (35)
T ss_dssp             EEETTTCCEEETT---TBCCSBTTBCTTTCCBEE
T ss_pred             cCCcCcCchhccc---cCCCCCCCccCCCCCCce
Confidence            4899999877662   333  4789999999873

>d1s5pa_ c.31.1.5 (A:) NAD-dependent deacetylase CobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: DHS-like NAD/FAD-binding domain
superfamily: DHS-like NAD/FAD-binding domain
family: Sir2 family of transcriptional regulators
domain: NAD-dependent deacetylase CobB
species: Escherichia coli [TaxId: 562]

Probab=88.55  E-value=0.11  Score=42.13  Aligned_cols=34  Identities=12%  Similarity=0.240  Sum_probs=20.2

Q ss_pred             eccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      +..|++|++.+....+...++...||.||..+..
T Consensus       113 ~~~C~~C~~~~~~~~~~~~~~~~~c~~Cgg~lrP  146 (235)
T d1s5pa_         113 KVRCSQSGQVLDWTGDVTPEDKCHCCQFPAPLRP  146 (235)
T ss_dssp             EEEETTTCCEEECCSCCCSSCCC-------CEEE
T ss_pred             EEEECCCCCccccccccccccccccccccccccc
Confidence            3399999998877666666778899999987643

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=88.05  E-value=0.082  Score=37.97  Aligned_cols=13  Identities=54%  Similarity=1.157  Sum_probs=9.0

Q ss_pred             cccCCCCCCceee
Q 025946          182 LQLCPYCSQPFSV  194 (245)
Q Consensus       182 ~iqCPnCGE~L~V  194 (245)
                      +..||.|+++|++
T Consensus        31 ~a~CPdC~~~Le~   43 (71)
T d2jnea1          31 KALCPDCHQPLQV   43 (71)
T ss_dssp             EEECTTTCSBCEE
T ss_pred             EEeCCccccHHHH
Confidence            5677777777764

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=87.04  E-value=0.15  Score=36.54  Aligned_cols=30  Identities=17%  Similarity=0.548  Sum_probs=22.0

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV  194 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V  194 (245)
                      ||.+||.|..++--     +++...|..|...+..
T Consensus         1 m~~~CP~C~~eL~~-----~~~~~~C~~C~~~~~~   30 (71)
T d2jnea1           1 MELHCPQCQHVLDQ-----DNGHARCRSCGEFIEM   30 (71)
T ss_dssp             CCCBCSSSCSBEEE-----ETTEEEETTTCCEEEE
T ss_pred             CCCcCCCccCcccc-----cCCCEehhhhhhhhee
Confidence            46789999888654     4578889999665544

>d2gnra1 b.40.4.15 (A:8-144) Hypothetical protein SSO2064 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: SSO2064-like
domain: Hypothetical protein SSO2064
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=86.24  E-value=0.13  Score=39.15  Aligned_cols=29  Identities=24%  Similarity=0.590  Sum_probs=24.2

Q ss_pred             cCcceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          156 SRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       156 ~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      ..+++-..|+.||+.++-       ....||.|++.
T Consensus        34 egrL~~~~C~~CG~v~~P-------pr~~Cp~C~s~   62 (137)
T d2gnra1          34 QNKIIGSKCSKCGRIFVP-------ARSYCEHCFVK   62 (137)
T ss_dssp             TTCCEEEECTTTCCEEES-------CCSEETTTTEE
T ss_pred             cCeEEEEEcCCCCCEEeC-------ccccCCCCCCC
Confidence            457777899999998887       67789999874

>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RBP12 subunit of RNA polymerase II
domain: RBP12 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.81  E-value=0.2  Score=33.27  Aligned_cols=30  Identities=13%  Similarity=0.500  Sum_probs=23.9

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS  193 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~  193 (245)
                      +.-.|-.||.++..    -..++++|-+||--+-
T Consensus         3 v~YiCgeCg~~~~l----~~~d~irCreCG~RIl   32 (46)
T d1twfl_           3 LKYICAECSSKLSL----SRTDAVRCKDCGHRIL   32 (46)
T ss_dssp             CCEECSSSCCEECC----CTTSTTCCSSSCCCCC
T ss_pred             eEEEcccCCCceEe----CCCCcEEeccCCcEEE
Confidence            45589999999886    4558999999997553

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.20  E-value=0.22  Score=33.99  Aligned_cols=27  Identities=30%  Similarity=0.673  Sum_probs=19.9

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF  192 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L  192 (245)
                      .||.|++.+..++   ....++||.||..+
T Consensus        20 ~CP~C~~~~~~~~---~~~~~~C~~C~~~f   46 (73)
T d2ct7a1          20 WCAQCSFGFIYER---EQLEATCPQCHQTF   46 (73)
T ss_dssp             CCSSSCCCEECCC---SCSCEECTTTCCEE
T ss_pred             CCCCCCCEeEECC---CCCEEEcCCCCCeE
Confidence            7999998776532   23578999998765

>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=84.65  E-value=0.17  Score=34.28  Aligned_cols=19  Identities=5%  Similarity=0.001  Sum_probs=14.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCC
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ  190 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE  190 (245)
                      .||+||..-.        ..-+|| ||.
T Consensus        29 ~c~~CG~~~l--------pH~vC~-cG~   47 (56)
T d2qam01          29 VDKTSGEKHL--------RHHITA-DGY   47 (56)
T ss_dssp             ECSSSCCEEC--------TTSCCT-TSC
T ss_pred             ECCCCCCCcc--------CcEECC-CCC
Confidence            6899996544        478899 983

>d1x4la2 g.39.1.3 (A:37-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.81  E-value=0.044  Score=33.59  Aligned_cols=29  Identities=21%  Similarity=0.446  Sum_probs=21.3

Q ss_pred             cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946          163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP  191 (245)
Q Consensus       163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~  191 (245)
                      .|..|...+.+--..-.++.+.||.||..
T Consensus         1 nc~kcsvslvgrgflterddilc~dcgkd   29 (30)
T d1x4la2           1 NCKKCSLSLVGRGFLTERDDILCPDCGKD   29 (30)
T ss_dssp             BCSSSCCBCTTSCCEECSSSEECHHHHHT
T ss_pred             CcceeeEEEEeeeccccccceeccccCcC
Confidence            47888777666444456789999999864

>d1fqta_ b.33.1.1 (A:) Rieske-type ferredoxin associated with biphenyl dioxygenase {Burkholderia cepacia [TaxId: 292]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Rieske-type ferredoxin associated with biphenyl dioxygenase
species: Burkholderia cepacia [TaxId: 292]

Probab=80.99  E-value=0.41  Score=34.00  Aligned_cols=44  Identities=18%  Similarity=0.242  Sum_probs=33.4

Q ss_pred             eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEecc
Q 025946          160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESV  204 (245)
Q Consensus       160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~  204 (245)
                      ++..||.-|..+.. ...+.++.++||..+..+.+++|+-...++
T Consensus        39 ~~~~CpH~g~~l~~-g~~~~~~~i~Cp~H~~~F~l~tG~~~~~p~   82 (109)
T d1fqta_          39 TQDRCTHGDWSLSD-GGYLEGDVVECSLHMGKFCVRTGKVKSPPP   82 (109)
T ss_dssp             EESBCTTSSCBSST-TCCEETTEEECTTTCCEEETTTCCEEESSC
T ss_pred             EEeeccccCccccc-ceeecCCEEEccccCCEEECCCccCccCCC
Confidence            45599999988642 222455688999999999999999777654

>d1vm9a_ b.33.1.1 (A:) Toluene-4-monooxygenase system protein C, TmoC {Pseudomonas mendocina [TaxId: 300]}

class: All beta proteins
fold: ISP domain
superfamily: ISP domain
family: Rieske iron-sulfur protein (ISP)
domain: Toluene-4-monooxygenase system protein C, TmoC
species: Pseudomonas mendocina [TaxId: 300]

Probab=80.33  E-value=0.31  Score=34.61  Aligned_cols=39  Identities=13%  Similarity=0.114  Sum_probs=30.2

Q ss_pred             ceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCee
Q 025946          159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKF  199 (245)
Q Consensus       159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F  199 (245)
                      -++..||.-|..+.  +..++++.++||+.|..|.+++|+-
T Consensus        39 A~~~~CpH~g~~l~--~g~~~~~~i~Cp~Hg~~F~l~~G~~   77 (109)
T d1vm9a_          39 AYQAMCPHQEILLS--EGSYEGGVITCRAHLWTFNDGTGHG   77 (109)
T ss_dssp             EEESBCSSSSCBGG--GSEEETTEEECTTTCCEEETTTCBB
T ss_pred             EEEeeCCCCCccce--eEeccCCEEEcccCCceEECCCccC
Confidence            35669999987653  2335678999999999999988864