Citrus Sinensis ID: 024592

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-----
Protein Sequence
MYSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccEEEEEHHHHHcccccccccEEEccEEEEEEEEEEEEEEEEEcccEEEEEEEccccEEEEEEccccccccccccccccccEEEEEEEEEEEccEEEEEEEEEEEcccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccHHHHHHHccccHHHHHHHHHHHHHccEEEEEEcccEEEcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccEEEEEHHHHHHccccccccEEEccEEEEEEEEEEEEEEEcccccEEEEEEEccccEEEEEEEEccccccccccccccccEEEEEEEEEEccccEEEEEEEEEEcccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccHHHHHHHccccHHHHHHHHHHHHHcccEEEEccccccccccc
Coil and Loop (DISEMBL)
mysgefdgaaafagggfmpsqattvpdpsssfsknrnvrtLLPMTVKQLSelssndessasidgadvnTITVVGIVcdmqdkepqfifliddgtgriecSRWAHEQMefnevnqiskGMYVRVYGHLKafqdkrslnayslrpiidfneITSHFVECIYVQLYntrlrggssnqpqmtnsnhlkeynaissnhysfdegksIDQMVLDFLrrpeflannngvhrnVISQQLNLPMDKLMEALESLNENSLVYSIDEFhyksavna
Flexible Loop (DISEMBL)
MYSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSndessasidgadvNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLrggssnqpqMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA
Low Complexity Region (SEG)
MYSGEFDgaaafagggfMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQlselssndessasIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA
Disordered region (IsUnstruct)
****************************************************************ADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRL*************************HYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHY******
Disordered Region (DISOPRED)
**********AF******************************PMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYN***************************************QMVLDFL***************VISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVN*
Disordered Region (DISEMBL)
MYSGEFDGAAAFAGGGFMPSQA***********KNRNVRTLLPMTVKQL***********SIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA
Disordered Region (DISPRO)
**************************************RTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRL********************************KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFH*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MYSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	265	2.2.26 [Sep-21-2011]
Q8LFJ8	278	Replication protein A 32	yes	no	1.0	0.953	0.482	1e-71
Q9ZQ19	279	Replication protein A 32	no	no	0.947	0.899	0.394	8e-53
Q92373	279	Replication factor A prot	yes	no	0.803	0.763	0.303	2e-21
Q63528	270	Replication protein A 32	yes	no	0.913	0.896	0.279	9e-19
Q62193	270	Replication protein A 32	yes	no	0.867	0.851	0.263	2e-18
P26754	273	Replication factor A prot	yes	no	0.860	0.835	0.273	2e-16
Q5RC43	270	Replication protein A 32	yes	no	0.867	0.851	0.255	2e-15
P15927	270	Replication protein A 32	yes	no	0.867	0.851	0.255	2e-15
Q13156	261	Replication protein A 30	no	no	0.935	0.950	0.229	2e-09

>sp|Q8LFJ8|RFA2B_ARATH Replication protein A 32 kDa subunit B OS=Arabidopsis thaliana GN=RPA2B PE=2 SV=1

 Score =  269 bits (688), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 134/278 (48%), Positives = 184/278 (66%), Gaps = 13/278 (4%)

Query: 1   MYSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDESSA 60
           MY G+FDG AAFAGGGFMPSQATT    SSS  KNR+VRTLLP+T+KQLS  S+  ES+ 
Sbjct: 1   MYGGDFDGNAAFAGGGFMPSQATTQAHESSSSLKNRDVRTLLPLTLKQLSSASTTGESNF 60

Query: 61  SIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMY 120
           SIDG D+ T+ +VG +  M+++  Q  F++DDGTG ++C RW H + E  E+  +  GMY
Sbjct: 61  SIDGVDIKTVVIVGRISRMENRITQVDFVVDDGTGWVDCVRWCHARQETEEMEAVKLGMY 120

Query: 121 VRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQ------ 174
           VR++GHLK FQ KRS+N +S+RP+ DFNEI  HF EC+YV +YNT+LRGGS  Q      
Sbjct: 121 VRLHGHLKIFQGKRSVNVFSVRPVTDFNEIVHHFTECMYVHMYNTKLRGGSITQDTATPR 180

Query: 175 PQM---TNSNHLKEYNAISSNHYS---FDEGKSIDQMVLDFLRRPEFLANNNGVHRNVIS 228
           PQM   T     K Y    SN +     D    + Q VL++L +P  + +  GVH ++I+
Sbjct: 181 PQMPYSTMPTPAKPYQTGPSNQFPNQFNDSMHGVKQTVLNYLNQPMHIVSEAGVHCDIIA 240

Query: 229 QQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA 265
           ++L +P+ ++ EALE L+ +  +YS +DE  +KS  NA
Sbjct: 241 RELRIPLLQVKEALEQLSNDGCIYSTLDETCFKSTANA 278

Component of the replication protein A complex (RP-A) required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions. Required fo cell division in meristems. Involved in the maintenance of transcriptional epigenetic gene silencing (TGS) at specific loci (including some transposons) by regulating histone H3 acetylation, 'Lys-4' and 'Lys-9' methylation.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZQ19|RFA2A_ARATH Replication protein A 32 kDa subunit A OS=Arabidopsis thaliana GN=RPA2A PE=1 SV=2

 Score =  207 bits (526), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 110/279 (39%), Positives = 169/279 (60%), Gaps = 28/279 (10%)

Query: 3   SGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSEL--SSNDESSA 60
           S +F+  + F+GGGFM SQ +   + SSS +KNR+ + L+P+TVKQ++E   SS ++S  
Sbjct: 4   SSQFEPNSGFSGGGFMSSQPSQAYESSSSTAKNRDFQGLVPVTVKQITECFQSSGEKSGL 63

Query: 61  SIDGADVNTITVVGIVCDM-QDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGM 119
            I+G  +  +++VG+VCD  + K  +  F +DDGTGRI+C RW  E  +  E+  +  G 
Sbjct: 64  VINGISLTNVSLVGLVCDKDESKVTEVRFTLDDGTGRIDCKRWVSETFDAREMESVRDGT 123

Query: 120 YVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIY----------------VQLY 163
           YVR+ GHLK FQ K  L  +S+RPI+DFNE+T H++ECI+                 Q  
Sbjct: 124 YVRLSGHLKTFQGKTQLLVFSVRPIMDFNEVTFHYIECIHFYSQNSESQRQQVGDVTQSV 183

Query: 164 NTRLRGGS-SNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGV 222
           NT  +GGS +NQ  + N         +SS +   +  K++D M+LD+L++P   A   G+
Sbjct: 184 NTTFQGGSNTNQATLLNP-------VVSSQNNDGNGRKNLDDMILDYLKQPACTARQQGI 236

Query: 223 HRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYK 260
           H + I+QQL +P +KL   ++SL  + L+YS IDE+H+K
Sbjct: 237 HIDEIAQQLKIPKNKLEGVVQSLEGDGLIYSTIDEYHFK 275

Component of the replication protein A complex (RP-A) required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions. Required fo cell division in meristems. Involved in the maintenance of transcriptional epigenetic gene silencing (TGS) at specific loci (including some transposons) by regulating histone H3 acetylation, 'Lys-4' and 'Lys-9' methylation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q92373|RFA2_SCHPO Replication factor A protein 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ssb2 PE=1 SV=1

 Score =  102 bits (255), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 120/237 (50%), Gaps = 24/237 (10%)

Query: 41  LLPMTVKQLSELSS-NDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIEC 99
           L P+T+KQ+   S  + ++   IDG +V  +T VG++ ++  +     + I+DGTG IE 
Sbjct: 50  LRPVTIKQILNASQVHADAEFKIDGVEVGQVTFVGVLRNIHAQTTNTTYQIEDGTGMIEV 109

Query: 100 SRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIY 159
             W H     + +++++   YVRVYG++K F  K  + +  +R I D NE+  HF+E I 
Sbjct: 110 RHWEH----IDALSELATDTYVRVYGNIKIFSGKIYIASQYIRTIKDHNEVHFHFLEAIA 165

Query: 160 VQLYNTRLRGG--SSNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLA 217
           V L+ T+       +N P    SN L  YN ISSN        S++Q + ++   P  + 
Sbjct: 166 VHLHFTQKANAVNGANAPGYGTSNALG-YNNISSN----GAANSLEQKLAEYSLTPAQMT 220

Query: 218 ----------NNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY-SIDEFHYKSAV 263
                      N GVH   ++Q +   +D L    + L +  ++Y +IDE H+KS +
Sbjct: 221 VMQAIHSAPETNEGVHVRQLAQSVGPGID-LTAVTDFLQQEGIIYTTIDENHFKSVL 276

Binds to single-stranded sequences.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q63528|RFA2_RAT Replication protein A 32 kDa subunit OS=Rattus norvegicus GN=Rpa2 PE=2 SV=2

 Score = 94.0 bits (232), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 72/258 (27%), Positives = 132/258 (51%), Gaps = 16/258 (6%)

Query: 13  AGGGFMPSQAT-TVPDPSSSFSKNR-NVRTLLPMTVKQLSELSSNDESSASIDGADVNTI 70
           A GG+  S      P PS +  K+R   + ++P T+ QL   +  DE    I   +++ +
Sbjct: 16  AAGGYTQSPGGFGSPTPSQAEKKSRARAQHIVPCTISQLLSATLTDEV-FKIGDVEISQV 74

Query: 71  TVVGIVCDMQDKEPQFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA 129
           T+VGI+   +      ++ IDD T   ++  +W        E   +    YV+V GHL++
Sbjct: 75  TIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSGENTVVPPETYVKVAGHLRS 134

Query: 130 FQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSS-NQPQMTNSNHLKEYNA 188
           FQ+K+SL A+ + P+ D NE T+H +E +   L  ++    +S  +P M+N   + E   
Sbjct: 135 FQNKKSLVAFKIIPLEDMNEFTAHILEVVNSHLMLSKANSQASVGRPSMSNPG-MGEPGN 193

Query: 189 ISSNHYSFDEGKSIDQ-MVLDFLR---RPEFLANNNGVHRNVISQQLNLPMDKLMEALES 244
            S N++    G ++ Q  VL+ ++   RPE L       +++ SQ  ++P+  + +A++ 
Sbjct: 194 FSGNNFMPANGLTVVQNQVLNLIKACPRPEGLN-----FQDLRSQLQHMPVASIKQAVDF 248

Query: 245 L-NENSLVYSIDEFHYKS 261
           L NE  +  ++D+ H+KS
Sbjct: 249 LCNEGHIYSTVDDDHFKS 266

Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions. Required for the efficient recruitment of the DNA double-strand break repair factor RAD51 to chromatin in response to DNA damage (By similarity). Required for simian virus 40 DNA replication in vitro. It participates in a very early step in initiation.

Rattus norvegicus (taxid: 10116)

>sp|Q62193|RFA2_MOUSE Replication protein A 32 kDa subunit OS=Mus musculus GN=Rpa2 PE=1 SV=1

 Score = 92.8 bits (229), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 124/243 (51%), Gaps = 13/243 (5%)

Query: 26  PDPSSSFSKNR-NVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEP 84
           P PS +  K+R   + ++P T+ QL   +  DE    I   +++ +T+VGI+   +    
Sbjct: 30  PTPSQAEKKSRVRAQHIVPCTISQLLSATLTDEV-FRIGDVEISQVTIVGIIRHAEKAPT 88

Query: 85  QFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143
             ++ IDD T   ++  +W        E   +    YV+V GHL++FQ+K+SL A+ + P
Sbjct: 89  NIVYKIDDMTAPPMDVRQWVDTDDASGENAVVPPETYVKVAGHLRSFQNKKSLVAFKIIP 148

Query: 144 IIDFNEITSHFVECIYVQLYNTRLRG-GSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSI 202
           + D NE T+H +E +   +  ++     S+ +P M+N    + +N   +N    +    +
Sbjct: 149 LEDMNEFTAHILEVVNSHMMLSKPNSQASAGRPSMSNPGMSESFNFSGNNFMPANRLTVV 208

Query: 203 DQMVLDFLR---RPEFLANNNGVHRNVISQQLNLPMDKLMEALESL-NENSLVYSIDEFH 258
              VL+ ++   RPE L       +++ SQ  ++P+  + +A++ L NE  +  ++D+ H
Sbjct: 209 QNQVLNLIKACPRPEGLN-----FQDLRSQLQHMPVPSIKQAVDFLCNEGHIYSTVDDDH 263

Query: 259 YKS 261
           +KS
Sbjct: 264 FKS 266

Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions. Required for the efficient recruitment of the DNA double-strand break repair factor RAD51 to chromatin in response to DNA damage.

Mus musculus (taxid: 10090)

>sp|P26754|RFA2_YEAST Replication factor A protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFA2 PE=1 SV=1

 Score = 86.3 bits (212), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/267 (27%), Positives = 122/267 (45%), Gaps = 39/267 (14%)

Query: 10  AAFAGGGFMPSQATTVPDPSSSFSK-NRNVRTLLPMTVKQLSELSSNDESSASID-GADV 67
           ++  GGGF  S++     P S  S+ N  V TL P+T+KQ+ E   + +    +    ++
Sbjct: 11  SSVTGGGFENSESR----PGSGESETNTRVNTLTPVTIKQILESKQDIQDGPFVSHNQEL 66

Query: 68  NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVN-------------- 113
           + +  VG+V ++ D        I+DGTG+IE  +W+ +  +    N              
Sbjct: 67  HHVCFVGVVRNITDHTANIFLTIEDGTGQIEVRKWSEDANDLAAGNDDSSGKGYGSQVAQ 126

Query: 114 QISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSN 173
           Q   G YV+V+G LK F  K+++    ++PI  FNE+ +H +E I        +  G   
Sbjct: 127 QFEIGGYVKVFGALKEFGGKKNIQYAVIKPIDSFNEVLTHHLEVIKCH----SIASGMMK 182

Query: 174 QPQMTNSNH------LKEYNAISSNHYSFDEGKSIDQMVLDFLRR--PEFLANNNGVHRN 225
           QP  + SN+      +K+ N  SS       G S  Q +L+F ++      AN+  V   
Sbjct: 183 QPLESASNNNGQSLFVKDDNDTSS-------GSSPLQRILEFCKKQCEGKDANSFAVPIP 235

Query: 226 VISQQLNLPMDKLMEALESLNENSLVY 252
           +ISQ LNL    +     +L +   +Y
Sbjct: 236 LISQSLNLDETTVRNCCTTLTDQGFIY 262

Binds to single-stranded sequences participating in DNA replication in addition to those mediating transcriptional repression (URS1) and activation (CAR1). Stimulates the activity of a cognate strand exchange protein (SEP1). It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the simian virus 40 origin of DNA replication.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q5RC43|RFA2_PONAB Replication protein A 32 kDa subunit OS=Pongo abelii GN=RPA2 PE=2 SV=1

 Score = 83.2 bits (204), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 121/243 (49%), Gaps = 13/243 (5%)

Query: 26  PDPSSSFSKNR-NVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEP 84
           P PS +  K+R   + ++P T+ QL   +  DE    I   +++ +T+VGI+   +    
Sbjct: 30  PAPSQAEKKSRARAQHIVPCTISQLLSATLVDEV-FRIGNVEISQVTIVGIIRHAEKAPT 88

Query: 85  QFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143
             ++ IDD T   ++  +W       +E   +    YV+V GHL++FQ+K+SL A+ + P
Sbjct: 89  NIVYKIDDMTAAPMDVRQWVDTDDASSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMP 148

Query: 144 IIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSID 203
           + D NE T+H +E I   +  ++     S      ++  + E      N +    G ++ 
Sbjct: 149 LEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAGNFGGNSFMPANGLTVA 208

Query: 204 Q-MVLDFLR---RPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFH 258
           Q  VL+ ++   RPE L       +++ +Q  ++ +  + +A++ L+    +YS +D+ H
Sbjct: 209 QNQVLNLIKACPRPEGLN-----FQDLKNQLKHMSVSSVKQAMDFLSNEGHIYSTVDDDH 263

Query: 259 YKS 261
           +KS
Sbjct: 264 FKS 266

Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions (By similarity). Required for the efficient recruitment of the DNA double-strand break repair factor RAD51 to chromatin in response to DNA damage.

Pongo abelii (taxid: 9601)

>sp|P15927|RFA2_HUMAN Replication protein A 32 kDa subunit OS=Homo sapiens GN=RPA2 PE=1 SV=1

 Score = 83.2 bits (204), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 121/243 (49%), Gaps = 13/243 (5%)

Query: 26  PDPSSSFSKNR-NVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEP 84
           P PS +  K+R   + ++P T+ QL   +  DE    I   +++ +T+VGI+   +    
Sbjct: 30  PAPSQAEKKSRARAQHIVPCTISQLLSATLVDEV-FRIGNVEISQVTIVGIIRHAEKAPT 88

Query: 85  QFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143
             ++ IDD T   ++  +W       +E   +    YV+V GHL++FQ+K+SL A+ + P
Sbjct: 89  NIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMP 148

Query: 144 IIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSID 203
           + D NE T+H +E I   +  ++     S      ++  + E      N +    G ++ 
Sbjct: 149 LEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAGNFGGNSFMPANGLTVA 208

Query: 204 Q-MVLDFLR---RPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFH 258
           Q  VL+ ++   RPE L       +++ +Q  ++ +  + +A++ L+    +YS +D+ H
Sbjct: 209 QNQVLNLIKACPRPEGLN-----FQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDH 263

Query: 259 YKS 261
           +KS
Sbjct: 264 FKS 266

Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.

Homo sapiens (taxid: 9606)

>sp|Q13156|RFA4_HUMAN Replication protein A 30 kDa subunit OS=Homo sapiens GN=RPA4 PE=1 SV=2

 Score = 62.8 bits (151), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 60/262 (22%), Positives = 115/262 (43%), Gaps = 14/262 (5%)

Query: 4   GEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSND-ESSASI 62
           G    A   +GG     +    P   +   K R ++ ++P  V QL  LSS   +    +
Sbjct: 10  GSISAADGASGGSDQLCERDATPAIKTQRPKVR-IQDVVPCNVNQL--LSSTVFDPVFKV 66

Query: 63  DGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYV 121
            G  V+ +++VG++   +       + IDD T + IE  +W   + +  +V  +S G+YV
Sbjct: 67  RGIIVSQVSIVGVIRGAEKASNHICYKIDDMTAKPIEARQWFGRE-KVKQVTPLSVGVYV 125

Query: 122 RVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSN 181
           +V+G LK     +SL    +  + D NE T H +E +   +   + R  ++ +    + +
Sbjct: 126 KVFGILKCPTGTKSLEVLKIHVLEDMNEFTVHILETVNAHMMLDKARRDTTVESVPVSPS 185

Query: 182 HLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEA 241
            + +      +H +F     I   VL  +           +H  + +Q  +L +  + EA
Sbjct: 186 EVNDAGDNDESHRNF-----IQDEVLRLIHECPH-QEGKSIH-ELRAQLCDLSVKAIKEA 238

Query: 242 LESLNENSLVY-SIDEFHYKSA 262
           ++ L     +Y ++D  H+KSA
Sbjct: 239 IDYLTVEGHIYPTVDREHFKSA 260

Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.

Homo sapiens (taxid: 9606)

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	265
359485014	275	PREDICTED: replication protein A 32 kDa	1.0	0.963	0.516	1e-75
297735401	277	unnamed protein product [Vitis vinifera]	1.0	0.956	0.512	1e-74
449457165	277	PREDICTED: replication protein A 32 kDa	0.996	0.953	0.517	4e-74
224143708	272	predicted protein [Populus trichocarpa]	0.992	0.966	0.518	1e-71
297832926	278	hypothetical protein ARALYDRAFT_477538 [	1.0	0.953	0.489	2e-70
18396383	278	replication factor A2 [Arabidopsis thali	1.0	0.953	0.482	8e-70
6728969	282	putative replication factor A [Arabidops	1.0	0.939	0.478	2e-69
68299229	299	putative replication factor A [Capsicum	1.0	0.886	0.489	2e-66
334185046	298	replication factor A2 [Arabidopsis thali	1.0	0.889	0.453	2e-66
224126075	275	predicted protein [Populus trichocarpa]	0.992	0.956	0.494	1e-65

>gi|359485014|ref|XP_002268721.2| PREDICTED: replication protein A 32 kDa subunit [Vitis vinifera]

 Score =  289 bits (739), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 142/275 (51%), Positives = 196/275 (71%), Gaps = 10/275 (3%)

Query: 1   MYS-GEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSE--LSSNDE 57
           MYS  +FDG AAF+GGGFMPSQAT   +P  S ++NR+ + LLP+TVKQ+SE  LSS+D+
Sbjct: 1   MYSHSQFDGNAAFSGGGFMPSQATQAAEPGFSPARNRDTQALLPLTVKQISEAFLSSDDK 60

Query: 58  SSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISK 117
           S+  IDG +VN +T+VG+V +  ++     F++DDGTGRI+C+RW +E ++  E+  I  
Sbjct: 61  SNFLIDGVEVNNVTLVGMVFNKAERVTDVGFMLDDGTGRIDCNRWVNEAVDTKEMEGILD 120

Query: 118 GMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQM 177
           GMYVRV+GHLK FQ KR LN +S+RP+ DFNEI SHF+ECIYV +YNT+ R G   Q  +
Sbjct: 121 GMYVRVHGHLKGFQGKRHLNVFSIRPVTDFNEIASHFIECIYVHIYNTKSRAGGPTQSHV 180

Query: 178 TN---SNHLKEYNAISSNHYSFDEG---KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL 231
           TN      LK Y A   N +S   G   K +DQ+V+D+L++P+ LA + GV R+ ++QQL
Sbjct: 181 TNPAIGTPLKGYQASQPNQFSGQYGAGLKGVDQLVIDYLQQPQSLARDQGVGRDELAQQL 240

Query: 232 NLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA 265
           N+P+DK+ME++ SL E  L+YS IDE+HYKS  N 
Sbjct: 241 NVPVDKIMESIRSLEEEGLIYSTIDEWHYKSTGNG 275

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297735401|emb|CBI17841.3| unnamed protein product [Vitis vinifera]

 Score =  285 bits (729), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 142/277 (51%), Positives = 197/277 (71%), Gaps = 12/277 (4%)

Query: 1   MYS-GEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSE--LSSNDE 57
           MYS  +FDG AAF+GGGFMPSQAT   +P  S ++NR+ + LLP+TVKQ+SE  LSS+D+
Sbjct: 1   MYSHSQFDGNAAFSGGGFMPSQATQAAEPGFSPARNRDTQALLPLTVKQISEAFLSSDDK 60

Query: 58  SSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISK 117
           S+  IDG +VN +T+VG+V +  ++     F++DDGTGRI+C+RW +E ++  E+  I  
Sbjct: 61  SNFLIDGVEVNNVTLVGMVFNKAERVTDVGFMLDDGTGRIDCNRWVNEAVDTKEMEGILD 120

Query: 118 GMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNT--RLRGGSSNQP 175
           GMYVRV+GHLK FQ KR LN +S+RP+ DFNEI SHF+ECIYV +YNT  R++ G   Q 
Sbjct: 121 GMYVRVHGHLKGFQGKRHLNVFSIRPVTDFNEIASHFIECIYVHIYNTKSRVQAGGPTQS 180

Query: 176 QMTN---SNHLKEYNAISSNHYSFDEG---KSIDQMVLDFLRRPEFLANNNGVHRNVISQ 229
            +TN      LK Y A   N +S   G   K +DQ+V+D+L++P+ LA + GV R+ ++Q
Sbjct: 181 HVTNPAIGTPLKGYQASQPNQFSGQYGAGLKGVDQLVIDYLQQPQSLARDQGVGRDELAQ 240

Query: 230 QLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA 265
           QLN+P+DK+ME++ SL E  L+YS IDE+HYKS  N 
Sbjct: 241 QLNVPVDKIMESIRSLEEEGLIYSTIDEWHYKSTGNG 277

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457165|ref|XP_004146319.1| PREDICTED: replication protein A 32 kDa subunit B-like [Cucumis sativus] gi|449500253|ref|XP_004161048.1| PREDICTED: replication protein A 32 kDa subunit B-like [Cucumis sativus]

 Score =  283 bits (725), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 144/278 (51%), Positives = 197/278 (70%), Gaps = 14/278 (5%)

Query: 1   MYSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSE--LSSNDES 58
           MY+ +FDG AAF+GGGFMPSQ T  PD S S +KNR+V+ LLP+TVKQ+++  LSS+D+S
Sbjct: 1   MYASQFDGNAAFSGGGFMPSQTTQAPDHSFSPAKNRDVQALLPLTVKQINDAFLSSDDKS 60

Query: 59  SASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKG 118
           +  IDG DVN + +VG+V +   +     F +DDGTGRI+CS+W +E  + NEV  I  G
Sbjct: 61  NFVIDGVDVNNVKLVGMVRNRAGRITDVTFALDDGTGRIDCSKWVNEAADSNEVEGILDG 120

Query: 119 MYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSN----Q 174
           MYVRV+GHLK+FQ KR+LN +S+RP+ D+NEIT+HF+E IYV  YNTRLR   S+    Q
Sbjct: 121 MYVRVHGHLKSFQGKRTLNVFSIRPVTDYNEITNHFIESIYVHFYNTRLRKQQSSSMTTQ 180

Query: 175 PQMTN--SNHLKEYNAISSNHYSFDEG----KSIDQMVLDFLRRPEFLANNNGVHRNVIS 228
           PQMTN  +  +K Y A  +N Y+   G    KS++QMVLDFL+ P    +  G HR+VI+
Sbjct: 181 PQMTNLSNTPMKVYQAPIANQYTGQAGGDSWKSLEQMVLDFLQLPS-CDSERGAHRDVIA 239

Query: 229 QQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA 265
           QQL +P++KL+ A+++L E  L+YS  D+FH+KS  N 
Sbjct: 240 QQLKVPLEKLIPAMKNLEEEGLIYSTTDDFHFKSTANG 277

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224143708|ref|XP_002325047.1| predicted protein [Populus trichocarpa] gi|222866481|gb|EEF03612.1| predicted protein [Populus trichocarpa]

 Score =  275 bits (703), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 142/274 (51%), Positives = 193/274 (70%), Gaps = 11/274 (4%)

Query: 1   MY-SGEFDG-AAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDES 58
           MY S +FDG AAAF GGGFMP+Q    P  SSS SKNR  R L P+TVKQ+S L+SN+ES
Sbjct: 1   MYGSSQFDGSAAAFMGGGFMPTQTAHPPSDSSSISKNREARCLFPLTVKQISNLASNNES 60

Query: 59  SASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKG 118
           +  IDGA+VN +T+VG V   +DK  ++ FL+DDGTG+IEC++W  E ++  ++ +I  G
Sbjct: 61  NFIIDGAEVNNVTIVGRVSHKEDKASEYTFLVDDGTGQIECTKWVQESLDTEQMGEILVG 120

Query: 119 MYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMT 178
           MYVRV+GHL+  Q +R LN +S+RP+ DFNEI  HF+ECIYV  YNTRL+G +S QP + 
Sbjct: 121 MYVRVHGHLRGLQGRRFLNVFSIRPVTDFNEIPGHFIECIYVHFYNTRLQGVTS-QPPVA 179

Query: 179 NSNH--LKEYNAI----SSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN 232
           NS    LK Y       SS + S D   ++ QM+L+FL++P +L N  G H +VI++QLN
Sbjct: 180 NSTSIPLKGYQTAPPYQSSVYSSADGLNNVSQMILNFLQQPAYL-NTEGAHYDVIARQLN 238

Query: 233 LPMDKLMEALESLNENSLVY-SIDEFHYKSAVNA 265
           +PM+KL E L+ L +N LVY +I++ +YKS VNA
Sbjct: 239 IPMNKLKEELQMLVDNGLVYTTINDDYYKSTVNA 272

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297832926|ref|XP_002884345.1| hypothetical protein ARALYDRAFT_477538 [Arabidopsis lyrata subsp. lyrata] gi|297330185|gb|EFH60604.1| hypothetical protein ARALYDRAFT_477538 [Arabidopsis lyrata subsp. lyrata]

 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 136/278 (48%), Positives = 184/278 (66%), Gaps = 13/278 (4%)

Query: 1   MYSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDESSA 60
           MY GEFDG AAFAGGGFMPSQATT    SSS  KNR+VRTLLP+T+KQLS  S+  ES+ 
Sbjct: 1   MYGGEFDGNAAFAGGGFMPSQATTQAHDSSSSLKNRDVRTLLPLTLKQLSSASTTGESNF 60

Query: 61  SIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMY 120
           SIDG D+NT+ +VG +  M+++  Q  F++DDGTG ++C RW  E+ E  E+  +  GMY
Sbjct: 61  SIDGVDINTVAIVGRISRMENRITQVEFVVDDGTGWVDCVRWCQERQETEEMEAVKLGMY 120

Query: 121 VRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQ------ 174
           VR++GHLK FQ KRS+N +S+RP+ DFNEI  HF EC+YV +YNT+LRGGS  Q      
Sbjct: 121 VRLHGHLKIFQGKRSVNVFSIRPVTDFNEIVHHFTECMYVHMYNTKLRGGSITQATTTPR 180

Query: 175 PQM---TNSNHLKEYNAISSNHYS---FDEGKSIDQMVLDFLRRPEFLANNNGVHRNVIS 228
           PQM   T     K Y    SN +     D    + Q VL++L +P  L +  GVH ++I+
Sbjct: 181 PQMPYSTMPTPAKPYQTGPSNQFPNQFNDPMHGVKQTVLNYLNQPMHLVSEAGVHCDIIA 240

Query: 229 QQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA 265
           + L +P+ ++ +ALE L+ +  +YS +DE  +KS  NA
Sbjct: 241 RDLRIPLPQVKDALEQLSNDGCIYSTMDETCFKSTANA 278

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18396383|ref|NP_566188.1| replication factor A2 [Arabidopsis thaliana] gi|75330048|sp|Q8LFJ8.1|RFA2B_ARATH RecName: Full=Replication protein A 32 kDa subunit B; Short=AtRPA32B; Short=RP-A p32 B; AltName: Full=DNA replication protein A2 subunit B; AltName: Full=Replication factor A protein 2 B; Short=AtRPA2 B; Short=RF-A protein 2 B; AltName: Full=Replicon protein A2 B gi|21537031|gb|AAM61372.1| putative replication factor A [Arabidopsis thaliana] gi|26450657|dbj|BAC42439.1| putative replication factor A [Arabidopsis thaliana] gi|90186248|gb|ABD91500.1| At3g02920 [Arabidopsis thaliana] gi|332640358|gb|AEE73879.1| replication factor A2 [Arabidopsis thaliana]

 Score =  269 bits (688), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 134/278 (48%), Positives = 184/278 (66%), Gaps = 13/278 (4%)

Query: 1   MYSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDESSA 60
           MY G+FDG AAFAGGGFMPSQATT    SSS  KNR+VRTLLP+T+KQLS  S+  ES+ 
Sbjct: 1   MYGGDFDGNAAFAGGGFMPSQATTQAHESSSSLKNRDVRTLLPLTLKQLSSASTTGESNF 60

Query: 61  SIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMY 120
           SIDG D+ T+ +VG +  M+++  Q  F++DDGTG ++C RW H + E  E+  +  GMY
Sbjct: 61  SIDGVDIKTVVIVGRISRMENRITQVDFVVDDGTGWVDCVRWCHARQETEEMEAVKLGMY 120

Query: 121 VRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQ------ 174
           VR++GHLK FQ KRS+N +S+RP+ DFNEI  HF EC+YV +YNT+LRGGS  Q      
Sbjct: 121 VRLHGHLKIFQGKRSVNVFSVRPVTDFNEIVHHFTECMYVHMYNTKLRGGSITQDTATPR 180

Query: 175 PQM---TNSNHLKEYNAISSNHYS---FDEGKSIDQMVLDFLRRPEFLANNNGVHRNVIS 228
           PQM   T     K Y    SN +     D    + Q VL++L +P  + +  GVH ++I+
Sbjct: 181 PQMPYSTMPTPAKPYQTGPSNQFPNQFNDSMHGVKQTVLNYLNQPMHIVSEAGVHCDIIA 240

Query: 229 QQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA 265
           ++L +P+ ++ EALE L+ +  +YS +DE  +KS  NA
Sbjct: 241 RELRIPLLQVKEALEQLSNDGCIYSTLDETCFKSTANA 278

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6728969|gb|AAF26967.1|AC018363_12 putative replication factor A [Arabidopsis thaliana]

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 135/282 (47%), Positives = 184/282 (65%), Gaps = 17/282 (6%)

Query: 1   MYSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDESSA 60
           MY G+FDG AAFAGGGFMPSQATT    SSS  KNR+VRTLLP+T+KQLS  S+  ES+ 
Sbjct: 1   MYGGDFDGNAAFAGGGFMPSQATTQAHESSSSLKNRDVRTLLPLTLKQLSSASTTGESNF 60

Query: 61  SIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMY 120
           SIDG D+ T+ +VG +  M+++  Q  F++DDGTG ++C RW H + E  E+  +  GMY
Sbjct: 61  SIDGVDIKTVVIVGRISRMENRITQVDFVVDDGTGWVDCVRWCHARQETEEMEAVKLGMY 120

Query: 121 VRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQ------ 174
           VR++GHLK FQ KRS+N +S+RP+ DFNEI  HF EC+YV +YNT+LRGGS  Q      
Sbjct: 121 VRLHGHLKIFQGKRSVNVFSVRPVTDFNEIVHHFTECMYVHMYNTKLRGGSITQDTATPR 180

Query: 175 PQM---TNSNHLKEYNAISSNHYSF-------DEGKSIDQMVLDFLRRPEFLANNNGVHR 224
           PQM   T     K Y    SN   F       D    + Q VL++L +P  + +  GVH 
Sbjct: 181 PQMPYSTMPTPAKPYQTGPSNQNLFQFPNQFNDSMHGVKQTVLNYLNQPMHIVSEAGVHC 240

Query: 225 NVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA 265
           ++I+++L +P+ ++ EALE L+ +  +YS +DE  +KS  NA
Sbjct: 241 DIIARELRIPLLQVKEALEQLSNDGCIYSTLDETCFKSTANA 282

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|68299229|emb|CAJ13715.1| putative replication factor A [Capsicum chinense]

 Score =  258 bits (659), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 137/280 (48%), Positives = 190/280 (67%), Gaps = 15/280 (5%)

Query: 1   MYSG--EFDGAAAFAGGGFMPSQAT-TVPDPSSSFSKNRNVRTLLPMTVKQLSEL--SSN 55
           MY G  +FDG AAF+GGGFMPSQAT T  D S S +KNR+ +TL+P+TVKQ+SE   SS+
Sbjct: 20  MYGGNNQFDGNAAFSGGGFMPSQATQTASDHSFSPTKNRDSQTLIPLTVKQISEAFQSSD 79

Query: 56  DESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQI 115
           D+++  IDG DVN + +VGI+ +  +      F++DDGTGR++C RW +E ++  E+  +
Sbjct: 80  DKTNFLIDGVDVNNVKLVGILFNKAEMLTAVSFVVDDGTGRLDCFRWVNEAVDTKEMEAL 139

Query: 116 SKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGG----- 170
           + G+YVRV+GHLK FQ K+ L AYS+RP+ D+NEI SHF E IYV  YN+RLR       
Sbjct: 140 TNGIYVRVHGHLKGFQGKKQLMAYSVRPVDDYNEIASHFAEVIYVHSYNSRLRKQQDSSF 199

Query: 171 -SSNQPQMTNSNHLKEYNAISSNH---YSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNV 226
            S+  P  + +  LK Y A +SN    ++ D    + +MVLD+L++P  LA   GVHRN 
Sbjct: 200 MSAQVPSSSFNTPLKGYQASASNQFPGFNMDGIGGVHKMVLDYLQQPSCLALEKGVHRNE 259

Query: 227 ISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA 265
           ++QQL +P +K+M A+E+L    LVYS ID+FHYKS  NA
Sbjct: 260 LAQQLRVPSEKIMGAMEALESEGLVYSTIDDFHYKSTGNA 299

Source: Capsicum chinense

Species: Capsicum chinense

Genus: Capsicum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334185046|ref|NP_001189796.1| replication factor A2 [Arabidopsis thaliana] gi|332640359|gb|AEE73880.1| replication factor A2 [Arabidopsis thaliana]

 Score =  258 bits (659), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 135/298 (45%), Positives = 186/298 (62%), Gaps = 33/298 (11%)

Query: 1   MYSGEFDGAAAFAGGGFMPSQATTVPDPSSS-----------FS---------KNRNVRT 40
           MY G+FDG AAFAGGGFMPSQATT    SSS           FS         +NR+VRT
Sbjct: 1   MYGGDFDGNAAFAGGGFMPSQATTQAHESSSSLKVYVSDSRRFSGISAAKSSIRNRDVRT 60

Query: 41  LLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECS 100
           LLP+T+KQLS  S+  ES+ SIDG D+ T+ +VG +  M+++  Q  F++DDGTG ++C 
Sbjct: 61  LLPLTLKQLSSASTTGESNFSIDGVDIKTVVIVGRISRMENRITQVDFVVDDGTGWVDCV 120

Query: 101 RWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYV 160
           RW H + E  E+  +  GMYVR++GHLK FQ KRS+N +S+RP+ DFNEI  HF EC+YV
Sbjct: 121 RWCHARQETEEMEAVKLGMYVRLHGHLKIFQGKRSVNVFSVRPVTDFNEIVHHFTECMYV 180

Query: 161 QLYNTRLRGGSSNQ------PQM---TNSNHLKEYNAISSNHYS---FDEGKSIDQMVLD 208
            +YNT+LRGGS  Q      PQM   T     K Y    SN +     D    + Q VL+
Sbjct: 181 HMYNTKLRGGSITQDTATPRPQMPYSTMPTPAKPYQTGPSNQFPNQFNDSMHGVKQTVLN 240

Query: 209 FLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA 265
           +L +P  + +  GVH ++I+++L +P+ ++ EALE L+ +  +YS +DE  +KS  NA
Sbjct: 241 YLNQPMHIVSEAGVHCDIIARELRIPLLQVKEALEQLSNDGCIYSTLDETCFKSTANA 298

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224126075|ref|XP_002329655.1| predicted protein [Populus trichocarpa] gi|222870536|gb|EEF07667.1| predicted protein [Populus trichocarpa]

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 137/277 (49%), Positives = 189/277 (68%), Gaps = 14/277 (5%)

Query: 1   MYSG-EFDG-AAAFAGGGFMPSQATTVPDPSSSFS---KNRNVRTLLPMTVKQLSELSSN 55
           M+ G EFDG AAAF GGGFMP+Q+       SS     KNR  R L P+TVKQ++ L+SN
Sbjct: 1   MHGGSEFDGSAAAFMGGGFMPTQSALPSSSDSSSFSISKNREARCLFPLTVKQINNLTSN 60

Query: 56  DESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQI 115
           DES+  IDGA+VN +T+VG V   +DK  ++ FLIDDGTG+IEC++W  E ++  ++ +I
Sbjct: 61  DESNLIIDGAEVNNVTIVGRVSHKEDKASEYSFLIDDGTGQIECTQWVQESLDTEQMGEI 120

Query: 116 SKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQP 175
             GMYVRV+GHL+  Q +R LN +S+RP+ DFNE+ +HF+ECIYV  YNTR+RG ++ QP
Sbjct: 121 LVGMYVRVHGHLRGLQGRRFLNVFSIRPVTDFNEVPNHFIECIYVHFYNTRIRGVTA-QP 179

Query: 176 QMTNSNH--LKEYNAI----SSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQ 229
            + NS +  LK Y A     SS + S D   +  QM+L+FL++P +L    G H + I+ 
Sbjct: 180 PVANSTNTSLKGYQAAPPYQSSAYSSADGLNNASQMILNFLQQPSYLY-TEGAHYDAIAG 238

Query: 230 QLNLPMDKLMEALESLNENSLVY-SIDEFHYKSAVNA 265
           QLN+P DKL E L+ L +N LVY +I++ +YKS VNA
Sbjct: 239 QLNIPTDKLKEVLQVLVDNGLVYTTINDDYYKSTVNA 275

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	265
TAIR|locus:2061072	279	RPA2 "replicon protein A2" [Ar	0.973	0.924	0.367	2.2e-43
UNIPROTKB|Q6H7J5	298	OJ1643_A10.19 "Putative replic	0.932	0.828	0.325	4.7e-32
UNIPROTKB|Q9AVM2	279	OsRPA32 "Replication protein A	0.928	0.881	0.322	6e-32
POMBASE|SPCC1753.01c	279	ssb2 "single-stranded DNA bind	0.856	0.813	0.299	1.9e-21
RGD|619714	270	Rpa2 "replication protein A2"	0.864	0.848	0.270	3.5e-20
MGI|MGI:1339939	270	Rpa2 "replication protein A2"	0.867	0.851	0.255	5.7e-20
UNIPROTKB|G4MT45	275	MGG_07124 "Replication protein	0.807	0.778	0.300	8.3e-19
UNIPROTKB|P15927	270	RPA2 "Replication protein A 32	0.860	0.844	0.248	2.8e-18
UNIPROTKB|Q5RC43	270	RPA2 "Replication protein A 32	0.860	0.844	0.248	2.8e-18
ASPGD|ASPL0000062650	278	AN0582 [Emericella nidulans (t	0.875	0.834	0.279	4.6e-18

TAIR|locus:2061072 RPA2 "replicon protein A2" [Arabidopsis thaliana (taxid:3702)]

 Score = 458 (166.3 bits), Expect = 2.2e-43, P = 2.2e-43
 Identities = 100/272 (36%), Positives = 153/272 (56%)

Query:     3 SGEFDXXXXXXXXXXMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQXXX--XXXXXXXXX 60
             S +F+          M SQ +   + SSS +KNR+ + L+P+TVKQ              
Sbjct:     4 SSQFEPNSGFSGGGFMSSQPSQAYESSSSTAKNRDFQGLVPVTVKQITECFQSSGEKSGL 63

Query:    61 XIDGADVNTITVVGIVCDMQD-KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGM 119
              I+G  +  +++VG+VCD  + K  +  F +DDGTGRI+C RW  E  +  E+  +  G 
Sbjct:    64 VINGISLTNVSLVGLVCDKDESKVTEVRFTLDDGTGRIDCKRWVSETFDAREMESVRDGT 123

Query:   120 YVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNT---RLRGGSSNQPQ 176
             YVR+ GHLK FQ K  L  +S+RPI+DFNE+T H++ECI+    N+   R + G   Q  
Sbjct:   124 YVRLSGHLKTFQGKTQLLVFSVRPIMDFNEVTFHYIECIHFYSQNSESQRQQVGDVTQSV 183

Query:   177 MT------NSNHLKEYNAISSNHYSFDEG-KSIDQMVLDFLRRPEFLANNNGVHRNVISQ 229
              T      N+N     N + S+  +   G K++D M+LD+L++P   A   G+H + I+Q
Sbjct:   184 NTTFQGGSNTNQATLLNPVVSSQNNDGNGRKNLDDMILDYLKQPACTARQQGIHIDEIAQ 243

Query:   230 QLNLPMDKLMEALESLNENSLVYS-IDEFHYK 260
             QL +P +KL   ++SL  + L+YS IDE+H+K
Sbjct:   244 QLKIPKNKLEGVVQSLEGDGLIYSTIDEYHFK 275

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006260 "DNA replication" evidence=IGI;ISS;RCA

GO:0005515 "protein binding" evidence=IPI

GO:0006281 "DNA repair" evidence=IMP

GO:0016458 "gene silencing" evidence=RCA;IMP

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0000724 "double-strand break repair via homologous recombination" evidence=RCA

GO:0000911 "cytokinesis by cell plate formation" evidence=RCA

GO:0006261 "DNA-dependent DNA replication" evidence=RCA

GO:0006270 "DNA replication initiation" evidence=RCA

GO:0006275 "regulation of DNA replication" evidence=RCA

GO:0006306 "DNA methylation" evidence=RCA

GO:0008283 "cell proliferation" evidence=RCA

GO:0009555 "pollen development" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0010389 "regulation of G2/M transition of mitotic cell cycle" evidence=RCA

GO:0016444 "somatic cell DNA recombination" evidence=RCA

GO:0016568 "chromatin modification" evidence=RCA

GO:0031047 "gene silencing by RNA" evidence=RCA

GO:0034968 "histone lysine methylation" evidence=RCA

GO:0051567 "histone H3-K9 methylation" evidence=RCA

GO:0051726 "regulation of cell cycle" evidence=RCA

UNIPROTKB|Q6H7J5 OJ1643_A10.19 "Putative replication protein A2" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 87/267 (32%), Positives = 145/267 (54%)

Query:    18 MPSQATTVPDPSSS----FSKNRNVRTLLPMTVKQXXXXXXXXXXXX--XIDGADVNTIT 71
             MPSQAT   + +S     F K+RN + LLP+TVKQ               ++G +V+T+ 
Sbjct:    31 MPSQATNAAEGTSGGGGGFPKSRNAQALLPLTVKQIMDASQTNDDKSNFAVNGMEVSTVR 90

Query:    72 VVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ 131
             +VG + +  D+     F +DDGTGR+  +RW ++  +  E+  I  G YV V G LK FQ
Sbjct:    91 LVGRMLNKLDRVTDVSFTLDDGTGRVPVNRWENDSTDTKEMADIQNGDYVIVNGGLKGFQ 150

Query:   132 DKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRG--------GSSNQ--PQMT--- 178
              KR + AYS+R I +FN++T HF+ C++V L  TR +         G+ NQ  P+ +   
Sbjct:   151 GKRQVVAYSVRRITNFNDVTHHFLHCVHVHLELTRPKSQVNANTATGTPNQTMPRDSMAY 210

Query:   179 NSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKL 238
             N + L    +  S   +   G ++  +VL+    P  + +++GV  + +S++LNLP + +
Sbjct:   211 NQSPLTNQASTFSAPQNTGTGTNMIDLVLNVFHDPAVMNDDHGVGVDYVSRRLNLPEETV 270

Query:   239 MEAL-ESLNENSLVYSIDEFHYKSAVN 264
              + + + ++   L  +ID+ HYKS +N
Sbjct:   271 GKIIIDQVDLGHLYATIDDHHYKSTMN 297

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q9AVM2 OsRPA32 "Replication protein A 30kDa" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 86/267 (32%), Positives = 140/267 (52%)

Query:    19 PSQATTVPDP---SSSFSKNRNVRTLLPMTVKQXXXXXXXXXXXXX-----IDGADVNTI 70
             PSQ T+  +    S++ SK+R   + +P+TVKQ                  +DG +   +
Sbjct:    12 PSQFTSSQNAAADSTTPSKSRGASSTMPLTVKQISEAQQSGITGEKGAPFVVDGVETANV 71

Query:    71 TVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF 130
              +VG+V    ++     F+IDDGTGR++  RW ++  +  E   +  GMYV V G LK  
Sbjct:    72 RLVGLVSGKTERNTDVSFMIDDGTGRLDFIRWVNDGADSAETAAVQNGMYVSVIGSLKGL 131

Query:   131 QDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQM----TNSNHLKEY 186
             Q+++   A+++RP+ D+NE+T HF++C+ + L NT+ + GS  +       ++SN   E 
Sbjct:   132 QERKRATAFAIRPVTDYNEVTLHFIQCVRMHLENTKSQIGSPAKTYSAMGSSSSNGFSEM 191

Query:   187 N---AISSNH---YSFDEGKSID--QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKL 238
                 ++ SN     S   G   D    VL+  R P  + + +GVH + I ++L LP  K+
Sbjct:   192 TTPTSVKSNPAPVLSVTNGSKTDLNTEVLNVFREPANVESEHGVHIDEIVKRLRLPEAKI 251

Query:   239 MEALESLNENSLVYS-IDEFHYKSAVN 264
               A++ L +   +YS IDE HYKSA N
Sbjct:   252 KVAIDYLADIGHIYSTIDESHYKSAFN 278

GO:0005515 "protein binding" evidence=IPI

POMBASE|SPCC1753.01c ssb2 "single-stranded DNA binding protein Ssb2" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 251 (93.4 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 76/254 (29%), Positives = 121/254 (47%)

Query:    27 DPSSSFSKNRNV---RTLLPMTVKQXXXXXXXXXXXXX-IDGADVNTITVVGIVCDMQDK 82
             D SS  S +R       L P+T+KQ              IDG +V  +T VG++ ++  +
Sbjct:    33 DQSSQPSVDRQQGAGNKLRPVTIKQILNASQVHADAEFKIDGVEVGQVTFVGVLRNIHAQ 92

Query:    83 EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR 142
                  + I+DGTG IE   W H     + +++++   YVRVYG++K F  K  + +  +R
Sbjct:    93 TTNTTYQIEDGTGMIEVRHWEH----IDALSELATDTYVRVYGNIKIFSGKIYIASQYIR 148

Query:   143 PIIDFNEITSHFVECIYVQLYNTRLRGG--SSNQPQMTNSNHLKEYNAISSNHYSFDEGK 200
              I D NE+  HF+E I V L+ T+       +N P    SN L  YN ISSN        
Sbjct:   149 TIKDHNEVHFHFLEAIAVHLHFTQKANAVNGANAPGYGTSNALG-YNNISSN----GAAN 203

Query:   201 SIDQMVLDFLRRPEFLA----------NNNGVHRNVISQQLNLPMDKLMEALESLNENSL 250
             S++Q + ++   P  +            N GVH   ++Q +   +D L    + L +  +
Sbjct:   204 SLEQKLAEYSLTPAQMTVMQAIHSAPETNEGVHVRQLAQSVGPGID-LTAVTDFLQQEGI 262

Query:   251 VYS-IDEFHYKSAV 263
             +Y+ IDE H+KS +
Sbjct:   263 IYTTIDENHFKSVL 276

GO:0005634 "nucleus" evidence=IDA

GO:0005662 "DNA replication factor A complex" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006269 "DNA replication, synthesis of RNA primer" evidence=ISO

GO:0006281 "DNA repair" evidence=ISO

GO:0006310 "DNA recombination" evidence=ISO

GO:0065007 "biological regulation" evidence=NAS

GO:0003697 "single-stranded DNA binding" evidence=IDA

RGD|619714 Rpa2 "replication protein A2" [Rattus norvegicus (taxid:10116)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 66/244 (27%), Positives = 124/244 (50%)

Query:    26 PDPSSSFSKNR-NVRTLLPMTVKQXXXXXXXXXXXXXIDGADVNTITVVGIVCDMQDKEP 84
             P PS +  K+R   + ++P T+ Q             I   +++ +T+VGI+   +    
Sbjct:    30 PTPSQAEKKSRARAQHIVPCTISQLLSATLTDEVFK-IGDVEISQVTIVGIIRHAEKAPT 88

Query:    85 QFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143
               ++ IDD T   ++  +W        E   +    YV+V GHL++FQ+K+SL A+ + P
Sbjct:    89 NIVYKIDDMTAAPMDVRQWVDTDDTSGENTVVPPETYVKVAGHLRSFQNKKSLVAFKIIP 148

Query:   144 IIDFNEITSHFVECIYVQLYNTRLRGGSS-NQPQMTNSNHLKEYNAISSNHYSFDEGKSI 202
             + D NE T+H +E +   L  ++    +S  +P M+N   + E    S N++    G ++
Sbjct:   149 LEDMNEFTAHILEVVNSHLMLSKANSQASVGRPSMSNPG-MGEPGNFSGNNFMPANGLTV 207

Query:   203 DQ-MVLDFLR---RPEFLANNNGVHRNVISQQLNLPMDKLMEALESL-NENSLVYSIDEF 257
              Q  VL+ ++   RPE L N     +++ SQ  ++P+  + +A++ L NE  +  ++D+ 
Sbjct:   208 VQNQVLNLIKACPRPEGL-N----FQDLRSQLQHMPVASIKQAVDFLCNEGHIYSTVDDD 262

Query:   258 HYKS 261
             H+KS
Sbjct:   263 HFKS 266

GO:0003677 "DNA binding" evidence=ISO

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=ISO

GO:0005662 "DNA replication factor A complex" evidence=ISO;IDA

GO:0006260 "DNA replication" evidence=IC

GO:0006284 "base-excision repair" evidence=NAS

GO:0006310 "DNA recombination" evidence=IEA

GO:0010569 "regulation of double-strand break repair via homologous recombination" evidence=ISO;ISS

GO:0016605 "PML body" evidence=IEA

GO:0019903 "protein phosphatase binding" evidence=IEA;ISO

GO:0047485 "protein N-terminus binding" evidence=IMP

GO:0005730 "nucleolus" evidence=ISO

MGI|MGI:1339939 Rpa2 "replication protein A2" [Mus musculus (taxid:10090)]

 Score = 237 (88.5 bits), Expect = 5.7e-20, P = 5.7e-20
 Identities = 62/243 (25%), Positives = 121/243 (49%)

Query:    26 PDPSSSFSKNR-NVRTLLPMTVKQXXXXXXXXXXXXXIDGADVNTITVVGIVCDMQDKEP 84
             P PS +  K+R   + ++P T+ Q             I   +++ +T+VGI+   +    
Sbjct:    30 PTPSQAEKKSRVRAQHIVPCTISQLLSATLTDEVFR-IGDVEISQVTIVGIIRHAEKAPT 88

Query:    85 QFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143
               ++ IDD T   ++  +W        E   +    YV+V GHL++FQ+K+SL A+ + P
Sbjct:    89 NIVYKIDDMTAPPMDVRQWVDTDDASGENAVVPPETYVKVAGHLRSFQNKKSLVAFKIIP 148

Query:   144 IIDFNEITSHFVECIYVQLYNTRLRG-GSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSI 202
             + D NE T+H +E +   +  ++     S+ +P M+N    + +N   +N    +    +
Sbjct:   149 LEDMNEFTAHILEVVNSHMMLSKPNSQASAGRPSMSNPGMSESFNFSGNNFMPANRLTVV 208

Query:   203 DQMVLDFLR---RPEFLANNNGVHRNVISQQLNLPMDKLMEALESL-NENSLVYSIDEFH 258
                VL+ ++   RPE L N     +++ SQ  ++P+  + +A++ L NE  +  ++D+ H
Sbjct:   209 QNQVLNLIKACPRPEGL-N----FQDLRSQLQHMPVPSIKQAVDFLCNEGHIYSTVDDDH 263

Query:   259 YKS 261
             +KS
Sbjct:   264 FKS 266

GO:0003677 "DNA binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005662 "DNA replication factor A complex" evidence=ISO

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0010569 "regulation of double-strand break repair via homologous recombination" evidence=ISO

GO:0019903 "protein phosphatase binding" evidence=ISO

GO:0047485 "protein N-terminus binding" evidence=ISO

UNIPROTKB|G4MT45 MGG_07124 "Replication protein A 32 kDa subunit" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 226 (84.6 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 67/223 (30%), Positives = 105/223 (47%)

Query:    41 LLPMTVKQXXXXXXXX-XXXXXIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIEC 99
             L P+TVKQ              +DG  +  IT+VG V  +  +     + IDDGTG I+ 
Sbjct:    47 LKPVTVKQLLDVQAPYPDADFLLDGRAITQITLVGQVRSINPQPTNITYRIDDGTGTIDV 106

Query:   100 SRWAH-EQME-FNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVEC 157
              RW   E+ E  +  +Q     YVRV+G LKAF ++R + A  +RP+ DFNE+  H +E 
Sbjct:   107 KRWIDPEKAEDADAASQHQPDSYVRVWGKLKAFNNRRHVGALFVRPVEDFNEVNYHMLEV 166

Query:   158 IYVQLYNTRLR-GGSSNQPQMTNSN-HLKEYNAISSNHYSFDEGKSID-QMVLDFLRRPE 214
              YV L   R   GG        + N  +  Y        S     S + Q + + L+   
Sbjct:   167 AYVHLDAVRQSSGGGGGAGGGGDDNMFVDSYGGGGGGGGSKAANCSTNAQRLFNHLQNSS 226

Query:   215 FLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY-SIDE 256
               A N G+  N+I++ +N+ +  +  A + L    L+Y ++D+
Sbjct:   227 --AGNEGLEANIIARGINMSVRDVEAAADELLSAGLIYPTVDD 267

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|P15927 RPA2 "Replication protein A 32 kDa subunit" [Homo sapiens (taxid:9606)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 61/245 (24%), Positives = 120/245 (48%)

Query:    26 PDPSSSFSKNR-NVRTLLPMTVKQXXXXXXXXXXXXXIDGADVNTITVVGIVCDMQDKEP 84
             P PS +  K+R   + ++P T+ Q             I   +++ +T+VGI+   +    
Sbjct:    30 PAPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFR-IGNVEISQVTIVGIIRHAEKAPT 88

Query:    85 QFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143
               ++ IDD T   ++  +W       +E   +    YV+V GHL++FQ+K+SL A+ + P
Sbjct:    89 NIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMP 148

Query:   144 IIDFNEITSHFVECIYVQLYNTRLRGG-SSNQPQMTNSNHLKEYNAISSNHYSFDEGKSI 202
             + D NE T+H +E I   +  ++     S+ +  ++N   + E      N +    G ++
Sbjct:   149 LEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPG-MSEAGNFGGNSFMPANGLTV 207

Query:   203 DQ-MVLDFLR---RPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDE 256
              Q  VL+ ++   RPE      G++   +  QL ++ +  + +A++ L+    +YS +D+
Sbjct:   208 AQNQVLNLIKACPRPE------GLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDD 261

Query:   257 FHYKS 261
              H+KS
Sbjct:   262 DHFKS 266

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0047485 "protein N-terminus binding" evidence=IEA

GO:0016605 "PML body" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0019903 "protein phosphatase binding" evidence=IPI

GO:0010569 "regulation of double-strand break repair via homologous recombination" evidence=IMP

GO:0006261 "DNA-dependent DNA replication" evidence=TAS

GO:0005662 "DNA replication factor A complex" evidence=IPI

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0000718 "nucleotide-excision repair, DNA damage removal" evidence=TAS

GO:0000722 "telomere maintenance via recombination" evidence=TAS

GO:0000723 "telomere maintenance" evidence=TAS

GO:0000724 "double-strand break repair via homologous recombination" evidence=TAS

GO:0000730 "DNA recombinase assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006260 "DNA replication" evidence=TAS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006297 "nucleotide-excision repair, DNA gap filling" evidence=TAS

GO:0006302 "double-strand break repair" evidence=TAS

GO:0032201 "telomere maintenance via semi-conservative replication" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q5RC43 RPA2 "Replication protein A 32 kDa subunit" [Pongo abelii (taxid:9601)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 61/245 (24%), Positives = 120/245 (48%)

Query:    26 PDPSSSFSKNR-NVRTLLPMTVKQXXXXXXXXXXXXXIDGADVNTITVVGIVCDMQDKEP 84
             P PS +  K+R   + ++P T+ Q             I   +++ +T+VGI+   +    
Sbjct:    30 PAPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFR-IGNVEISQVTIVGIIRHAEKAPT 88

Query:    85 QFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143
               ++ IDD T   ++  +W       +E   +    YV+V GHL++FQ+K+SL A+ + P
Sbjct:    89 NIVYKIDDMTAAPMDVRQWVDTDDASSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMP 148

Query:   144 IIDFNEITSHFVECIYVQLYNTRLRGG-SSNQPQMTNSNHLKEYNAISSNHYSFDEGKSI 202
             + D NE T+H +E I   +  ++     S+ +  ++N   + E      N +    G ++
Sbjct:   149 LEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPG-MSEAGNFGGNSFMPANGLTV 207

Query:   203 DQ-MVLDFLR---RPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDE 256
              Q  VL+ ++   RPE      G++   +  QL ++ +  + +A++ L+    +YS +D+
Sbjct:   208 AQNQVLNLIKACPRPE------GLNFQDLKNQLKHMSVSSVKQAMDFLSNEGHIYSTVDD 261

Query:   257 FHYKS 261
              H+KS
Sbjct:   262 DHFKS 266

GO:0010569 "regulation of double-strand break repair via homologous recombination" evidence=ISS

ASPGD|ASPL0000062650 AN0582 [Emericella nidulans (taxid:162425)]

 Score = 219 (82.2 bits), Expect = 4.6e-18, P = 4.6e-18
 Identities = 72/258 (27%), Positives = 120/258 (46%)

Query:    18 MPSQATTVPDPSSSFSKNRNVRTLLPMTVKQXXXXXXXX-XXXXXIDGADVNTITVVGIV 76
             MP + T+   PS    +  N  TL P+T+KQ              IDG DV++I  +G V
Sbjct:    20 MPGETTS---PSGGRQEWNNT-TLRPVTIKQILDATQPYPEANFTIDGQDVSSIVFIGQV 75

Query:    77 CDMQDKEPQFIFLIDDGTGRIECSRWAH--EQMEFNE--------VNQISKGMYVRVYGH 126
              ++  +     + +DDGTG +E  +W +  E M+  E        +N +    Y +V+G 
Sbjct:    76 RNISTQATNVTYKLDDGTGEVEAKQWINPSEAMDTTEDFGKEGKDLNGVEINGYAKVFGK 135

Query:   127 LKA-FQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTR-LRGGSSNQPQMTNSNHLK 184
             LK+ F D++ +N + +RP+ D NE+  HF+E   V L++TR   G ++      +     
Sbjct:   136 LKSLFGDRKVVNTHCVRPLTDINELHVHFLEAAAVHLFHTRGAPGPAAGATGKIDGGDAA 195

Query:   185 EYN---AISSNHYSFDEGKSID-QMVLDFLR-RPEFLANNNGVHRNVISQQLNLPMDKLM 239
                   A       F    S   + V + LR  P+   NN G+H   I+ +L LP   ++
Sbjct:   196 MGGLDGAGVGGGGGFPANMSATARRVYNLLRTEPQ---NNEGLHAQFIAAKLGLPPQDVV 252

Query:   240 EALESLNENSLVYS-IDE 256
              A + L    +V+S +D+
Sbjct:   253 RAGDELINAGMVFSTVDD 270

GO:0045184 "establishment of protein localization" evidence=IEA

GO:0000722 "telomere maintenance via recombination" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

GO:0006268 "DNA unwinding involved in replication" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0007131 "reciprocal meiotic recombination" evidence=IEA

GO:0030491 "heteroduplex formation" evidence=IEA

GO:0007004 "telomere maintenance via telomerase" evidence=IEA

GO:0000724 "double-strand break repair via homologous recombination" evidence=IEA

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005662 "DNA replication factor A complex" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003690 "double-stranded DNA binding" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8LFJ8	RFA2B_ARATH	No assigned EC number	0.4820	1.0	0.9532	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	265
COG5235	258	COG5235, RFA2, Single-stranded DNA-binding replica	1e-37
cd04478	95	cd04478, RPA2_DBD_D, RPA2_DBD_D: A subfamily of OB	1e-34
pfam01336	75	pfam01336, tRNA_anti, OB-fold nucleic acid binding	5e-09
pfam08784	103	pfam08784, RPA_C, Replication protein A C terminal	3e-07
cd03524	75	cd03524, RPA2_OBF_family, RPA2_OBF_family: A famil	3e-06
cd04483	92	cd04483, hOBFC1_like, hOBFC1_like: A subfamily of	1e-05

>gnl|CDD|227560 COG5235, RFA2, Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]

 Score =  132 bits (334), Expect = 1e-37
 Identities = 65/254 (25%), Positives = 118/254 (46%), Gaps = 14/254 (5%)

Query: 14  GGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDESSAS--IDGADVNTIT 71
            G    + +    D S        V TL P+T+KQ+      DE+ ++  +D A+V  + 
Sbjct: 15  RGQIFGTGSPPPMDRSEG---GYIVNTLRPVTIKQILS-CDQDETDSTFLVDSAEVTNVQ 70

Query: 72  VVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ 131
            VG+V +++      +F+I+DGTG IE   W     E  +   + +  YV+V G LK F 
Sbjct: 71  FVGVVRNIKTSTTNSMFVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFN 130

Query: 132 DKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISS 191
            KRS++A  +  I D NE+T HF+ECIY  L+ TR       +P      +  +      
Sbjct: 131 GKRSISASHISAIEDSNEVTYHFLECIYQHLFYTRQ----LQRPLEEEVKNDGQSLFAKL 186

Query: 192 NHYSFDEGKSIDQMVLDFLRRPEFL-ANNNGVHRNVISQQLNLPMDKLMEALESLNENSL 250
           ++ +      + + +L+  RR +     +  V   ++SQ  +   D+    ++ L  +  
Sbjct: 187 DNDTSSGSSRLQEDILECYRRNQDENGLHINVVIKMLSQSYSE--DETRVNIDVLLRDGH 244

Query: 251 VY-SIDEFHYKSAV 263
           +Y ++D   +K+ +
Sbjct: 245 IYPTVDGNEFKTTI 258

Length = 258

>gnl|CDD|239924 cd04478, RPA2_DBD_D, RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

 Score =  119 bits (301), Expect = 1e-34
 Identities = 43/95 (45%), Positives = 67/95 (70%), Gaps = 1/95 (1%)

Query: 69  TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQ-MEFNEVNQISKGMYVRVYGHL 127
            +T+VG+V +++++     + IDDGTG IE  +W  +   + +EV  I +G YVRV+G+L
Sbjct: 1   QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNL 60

Query: 128 KAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQL 162
           K+FQ K+S+ A+S+RP+ DFNE+T H +E IYV L
Sbjct: 61  KSFQGKKSIMAFSIRPVTDFNEVTYHLLEVIYVHL 95

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro. Length = 95

>gnl|CDD|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain

 Score = 51.5 bits (124), Expect = 5e-09
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 70  ITVVGIVCDMQDKEPQFIFL-IDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK 128
           +TV G V  ++    +  FL + DGTG I+   +  E  +  +  ++ +G  V V G +K
Sbjct: 1   VTVAGRVTSVRRSGGKVAFLTLRDGTGSIQVVLFKEEAEKLAK--KLKEGDVVLVTGKVK 58

Query: 129 AFQDKR-SLNAYSLRPI 144
                   L    +  +
Sbjct: 59  KRPGGELELVVEEIEVL 75

This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. Length = 75

>gnl|CDD|220015 pfam08784, RPA_C, Replication protein A C terminal

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 24/104 (23%), Positives = 45/104 (43%), Gaps = 10/104 (9%)

Query: 162 LYNTRLR-GGSSNQPQMTNSNHLKEYNAI---SSNHYS--FDEGKSIDQMVLDFLRRPEF 215
           L  T+ R G S+     + +N           S    S        +   VL+ ++  + 
Sbjct: 2   LRLTKGRSGSSAGGAGPSVANTGSAMGTQGAFSGGDASVANPGLTPLQDQVLNLIK--QS 59

Query: 216 LANNNGVHRNVISQQLN-LPMDKLMEALESLNENSLVYS-IDEF 257
                GVH + ++ QLN LP++ + +A++ L+    +YS ID+ 
Sbjct: 60  CPGEEGVHVDELAAQLNGLPVNDIRQAVDFLSNEGHIYSTIDDD 103

This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. Length = 103

>gnl|CDD|239601 cd03524, RPA2_OBF_family, RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

 Score = 43.9 bits (104), Expect = 3e-06
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 6/77 (7%)

Query: 71  TVVGIVCDMQDKEPQ---FIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGH 126
           T+VGIV  +++   +    IF + DGTG  I  + +     E    N + +G  V + G 
Sbjct: 1   TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELE--NLLKEGQVVYIKGK 58

Query: 127 LKAFQDKRSLNAYSLRP 143
           +K F+ +  L   S+  
Sbjct: 59  VKKFRGRLQLIVESIEL 75

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1). Length = 75

>gnl|CDD|239929 cd04483, hOBFC1_like, hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1)

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 19/88 (21%), Positives = 38/88 (43%), Gaps = 18/88 (20%)

Query: 72  VVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHE------------------QMEFNEVN 113
           ++G V   +++E  + F +DDGTG + C  W +                    M   +  
Sbjct: 2   ILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAK 61

Query: 114 QISKGMYVRVYGHLKAFQDKRSLNAYSL 141
            +  G  +RV G ++ ++ +R +NA  +
Sbjct: 62  VLEIGDLLRVRGSIRTYRGEREINASVV 89

Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization. Length = 92

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	265
COG5235	258	RFA2 Single-stranded DNA-binding replication prote	100.0
KOG3108	265	consensus Single-stranded DNA-binding replication	100.0
cd04478	95	RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor	99.93
cd04483	92	hOBFC1_like hOBFC1_like: A subfamily of OB folds s	99.71
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	99.67
PF10451	256	Stn1: Telomere regulation protein Stn1; InterPro:	99.46
PF01336	75	tRNA_anti-codon: OB-fold nucleic acid binding doma	99.2
cd04492	83	YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol	98.78
PRK13480	314	3'-5' exoribonuclease YhaM; Provisional	98.6
cd03524	75	RPA2_OBF_family RPA2_OBF_family: A family of oligo	98.57
cd04485	84	DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp	98.49
cd04489	78	ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol	98.42
COG3390	196	Uncharacterized protein conserved in archaea [Func	98.31
PRK06461	129	single-stranded DNA-binding protein; Reviewed	98.31
cd04491	82	SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil	98.29
cd04482	91	RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara	98.25
cd04487	73	RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f	98.19
PF13742	99	tRNA_anti_2: OB-fold nucleic acid binding domain	98.05
cd04484	82	polC_OBF polC_OBF: A subfamily of OB folds corresp	98.01
cd04488	75	RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f	97.94
cd04321	86	ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, a	97.74
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	97.67
cd04100	85	Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, ant	97.67
cd04323	84	AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, a	97.64
cd04317	135	EcAspRS_like_N EcAspRS_like_N: N-terminal, anticod	97.62
COG4085	204	Predicted RNA-binding protein, contains TRAM domai	97.52
cd04320	102	AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r	97.44
cd04316	108	ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, a	97.43
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.42
cd04322	108	LysRS_N LysRS_N: N-terminal, anticodon recognition	97.4
cd04319	103	PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticod	97.35
cd04490	79	PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds	97.28
cd04318	82	EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticod	97.23
COG1570	440	XseA Exonuclease VII, large subunit [DNA replicati	97.22
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.19
PF04076	103	BOF: Bacterial OB fold (BOF) protein; InterPro: IP	97.15
PRK03932	450	asnC asparaginyl-tRNA synthetase; Validated	97.1
PRK05673	1135	dnaE DNA polymerase III subunit alpha; Validated	97.02
PRK00286	438	xseA exodeoxyribonuclease VII large subunit; Revie	96.96
TIGR00237	432	xseA exodeoxyribonuclease VII, large subunit. This	96.9
TIGR00457	453	asnS asparaginyl-tRNA synthetase. In a multiple se	96.89
PRK07211	485	replication factor A; Reviewed	96.89
TIGR00156	126	conserved hypothetical protein TIGR00156. As of th	96.87
PRK07373	449	DNA polymerase III subunit alpha; Reviewed	96.83
PRK10053	130	hypothetical protein; Provisional	96.79
PRK07217	311	replication factor A; Reviewed	96.64
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	96.56
PRK07218	423	replication factor A; Provisional	96.55
COG0017	435	AsnS Aspartyl/asparaginyl-tRNA synthetases [Transl	96.49
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	96.48
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	96.47
PF13730	55	HTH_36: Helix-turn-helix domain	96.46
TIGR00458	428	aspS_arch aspartyl-tRNA synthetase, archaeal type.	96.33
PRK12445	505	lysyl-tRNA synthetase; Reviewed	96.32
PRK14699	484	replication factor A; Provisional	96.29
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.24
TIGR01405	1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	96.23
cd04497	138	hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f	96.21
COG3481	287	Predicted HD-superfamily hydrolase [General functi	96.2
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	96.18
PRK00448	1437	polC DNA polymerase III PolC; Validated	96.17
PRK08402	355	replication factor A; Reviewed	96.15
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	96.13
PRK05159	437	aspC aspartyl-tRNA synthetase; Provisional	96.12
KOG3416	134	consensus Predicted nucleic acid binding protein [	96.09
PRK14699	484	replication factor A; Provisional	96.06
PRK07211	485	replication factor A; Reviewed	96.05
TIGR00459	583	aspS_bact aspartyl-tRNA synthetase, bacterial type	96.01
PRK00484	491	lysS lysyl-tRNA synthetase; Reviewed	95.98
PRK05672	1046	dnaE2 error-prone DNA polymerase; Validated	95.94
PRK06920	1107	dnaE DNA polymerase III DnaE; Reviewed	95.94
PRK12366	637	replication factor A; Reviewed	95.89
PLN02903	652	aminoacyl-tRNA ligase	95.88
COG3111	128	Periplasmic protein with OB-fold [Function unknown	95.84
PRK00476	588	aspS aspartyl-tRNA synthetase; Validated	95.83
PRK07374	1170	dnaE DNA polymerase III subunit alpha; Validated	95.81
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	95.79
PRK12820	706	bifunctional aspartyl-tRNA synthetase/aspartyl/glu	95.75
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.73
PLN02221	572	asparaginyl-tRNA synthetase	95.67
TIGR00499	496	lysS_bact lysyl-tRNA synthetase, eukaryotic and no	95.65
PRK06386	358	replication factor A; Reviewed	95.62
PLN02502	553	lysyl-tRNA synthetase	95.62
PRK15491	374	replication factor A; Provisional	95.6
PRK07218	423	replication factor A; Provisional	95.59
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.59
PRK06826	1151	dnaE DNA polymerase III DnaE; Reviewed	95.54
PRK11169	164	leucine-responsive transcriptional regulator; Prov	95.47
PLN02603	565	asparaginyl-tRNA synthetase	95.45
PRK12366	637	replication factor A; Reviewed	95.44
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	95.43
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	95.43
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.41
PLN02850	530	aspartate-tRNA ligase	95.36
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	95.34
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	95.34
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	95.33
PRK07279	1034	dnaE DNA polymerase III DnaE; Reviewed	95.13
PTZ00401	550	aspartyl-tRNA synthetase; Provisional	95.13
COG3355	126	Predicted transcriptional regulator [Transcription	95.1
cd04479	101	RPA3 RPA3: A subfamily of OB folds similar to huma	95.05
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	95.01
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	94.98
COG1571	421	Predicted DNA-binding protein containing a Zn-ribb	94.91
cd04475	101	RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor	94.8
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	94.75
COG2176	1444	PolC DNA polymerase III, alpha subunit (gram-posit	94.72
PRK15491	374	replication factor A; Provisional	94.68
COG1522	154	Lrp Transcriptional regulators [Transcription]	94.67
cd04481	106	RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of unc	94.65
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	94.64
PF08661	109	Rep_fac-A_3: Replication factor A protein 3; Inter	94.6
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	94.58
PRK06386	358	replication factor A; Reviewed	94.55
PF02765	146	POT1: Telomeric single stranded DNA binding POT1/C	94.52
PRK08402	355	replication factor A; Reviewed	94.45
PF03100	131	CcmE: CcmE; InterPro: IPR004329 CcmE is the produc	94.44
PTZ00385	659	lysyl-tRNA synthetase; Provisional	94.4
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	94.39
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	94.36
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	94.3
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	94.25
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	94.23
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	94.13
PTZ00425	586	asparagine-tRNA ligase; Provisional	93.95
cd04486	78	YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fol	93.79
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	93.69
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	93.69
cd04474	104	RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor	93.64
PRK02983	1094	lysS lysyl-tRNA synthetase; Provisional	93.57
PRK12423	202	LexA repressor; Provisional	93.49
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	93.45
PRK13254	148	cytochrome c-type biogenesis protein CcmE; Reviewe	93.33
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	93.21
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	93.18
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	93.07
PRK08486	182	single-stranded DNA-binding protein; Provisional	92.86
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.85
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	92.85
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	92.81
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	92.73
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	92.7
COG2345	218	Predicted transcriptional regulator [Transcription	92.64
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	92.62
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	92.57
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	92.53
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	92.4
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	92.35
PTZ00417	585	lysine-tRNA ligase; Provisional	92.33
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	92.3
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	92.24
PRK05813	219	single-stranded DNA-binding protein; Provisional	92.23
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	92.23
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	92.22
PF10771	65	DUF2582: Protein of unknown function (DUF2582); In	92.22
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	92.2
COG1190	502	LysU Lysyl-tRNA synthetase (class II) [Translation	92.16
PRK14999	241	histidine utilization repressor; Provisional	92.07
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	92.05
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	92.01
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	91.99
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	91.94
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	91.93
PRK10079	241	phosphonate metabolism transcriptional regulator P	91.93
COG1414	246	IclR Transcriptional regulator [Transcription]	91.83
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	91.67
COG2188	236	PhnF Transcriptional regulators [Transcription]	91.48
PRK11569	274	transcriptional repressor IclR; Provisional	91.36
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	91.35
PRK03573	144	transcriptional regulator SlyA; Provisional	91.27
PRK07459	121	single-stranded DNA-binding protein; Provisional	91.26
PF06969	66	HemN_C: HemN C-terminal domain; InterPro: IPR01072	91.14
PRK06751	173	single-stranded DNA-binding protein; Provisional	91.12
PRK07275	162	single-stranded DNA-binding protein; Provisional	91.02
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	90.88
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	90.8
PRK02801	101	primosomal replication protein N; Provisional	90.74
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	90.67
PRK06863	168	single-stranded DNA-binding protein; Provisional	90.58
PRK03902	142	manganese transport transcriptional regulator; Pro	90.57
PF10264	80	Stork_head: Winged helix Storkhead-box1 domain; In	90.41
PF02295	66	z-alpha: Adenosine deaminase z-alpha domain; Inter	90.35
PRK13509	251	transcriptional repressor UlaR; Provisional	90.32
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	90.3
KOG0555	545	consensus Asparaginyl-tRNA synthetase [Translation	90.23
PF08679	67	DsrD: Dissimilatory sulfite reductase D (DsrD); In	90.01
PRK09954	362	putative kinase; Provisional	89.99
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	89.88
PRK13159	155	cytochrome c-type biogenesis protein CcmE; Reviewe	89.78
PRK06752	112	single-stranded DNA-binding protein; Validated	89.73
PRK08763	164	single-stranded DNA-binding protein; Provisional	89.72
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	89.71
COG1725	125	Predicted transcriptional regulators [Transcriptio	89.7
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	89.65
PRK06293	161	single-stranded DNA-binding protein; Provisional	89.58
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	89.47
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	89.41
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	89.37
PHA02943	165	hypothetical protein; Provisional	89.3
TIGR00617	608	rpa1 replication factor-a protein 1 (rpa1). This f	89.29
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	89.26
PRK06958	182	single-stranded DNA-binding protein; Provisional	89.06
PF14502	48	HTH_41: Helix-turn-helix domain	88.89
TIGR03337	231	phnR transcriptional regulator protein. This famil	88.73
PRK00215	205	LexA repressor; Validated	88.57
PRK09462	148	fur ferric uptake regulator; Provisional	88.23
PF08646	146	Rep_fac-A_C: Replication factor-A C terminal domai	87.96
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	87.93
smart00753	88	PAM PCI/PINT associated module.	87.93
PRK09010	177	single-stranded DNA-binding protein; Provisional	87.93
PRK10870	176	transcriptional repressor MprA; Provisional	87.92
TIGR00621	164	ssb single stranded DNA-binding protein (ssb). Thi	87.86
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	87.64
PRK11050	152	manganese transport regulator MntR; Provisional	87.56
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	87.38
TIGR03338	212	phnR_burk phosphonate utilization associated trans	87.28
PRK13165	160	cytochrome c-type biogenesis protein CcmE; Reviewe	87.15
PRK06266	178	transcription initiation factor E subunit alpha; V	87.05
PF15072	86	DUF4539: Domain of unknown function (DUF4539)	86.97
PRK04984	239	fatty acid metabolism regulator; Provisional	86.89
PRK05733	172	single-stranded DNA-binding protein; Provisional	86.89
PRK11014	141	transcriptional repressor NsrR; Provisional	86.64
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	86.63
PRK14165	217	winged helix-turn-helix domain-containing protein/	86.62
PRK10681	252	DNA-binding transcriptional repressor DeoR; Provis	86.39
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	86.35
PRK11639	169	zinc uptake transcriptional repressor; Provisional	86.35
PRK13150	159	cytochrome c-type biogenesis protein CcmE; Reviewe	86.29
PRK13777	185	transcriptional regulator Hpr; Provisional	86.15
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	86.14
PRK07274	131	single-stranded DNA-binding protein; Provisional	85.87
PHA03103	183	double-strand RNA-binding protein; Provisional	85.78
PRK07217	311	replication factor A; Reviewed	85.68
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	85.65
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	85.61
PF09202	82	Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This	85.61
COG1654	79	BirA Biotin operon repressor [Transcription]	85.58
PRK08182	148	single-stranded DNA-binding protein; Provisional	85.58
COG3888	321	Predicted transcriptional regulator [Transcription	85.13
PF00436	104	SSB: Single-strand binding protein family; InterPr	85.13
cd04476	166	RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds cor	85.03
PRK13732	175	single-stranded DNA-binding protein; Provisional	85.01
COG0173	585	AspS Aspartyl-tRNA synthetase [Translation, riboso	85.0
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	84.89
PRK07772	186	single-stranded DNA-binding protein; Provisional	84.71
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	84.59
COG2512	258	Predicted membrane-associated trancriptional regul	84.45
PRK10046	225	dpiA two-component response regulator DpiA; Provis	84.13
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	84.03
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	83.87
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	83.86
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	83.51
PRK07135	973	dnaE DNA polymerase III DnaE; Validated	83.17
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	83.16
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	83.07
PF02760	170	HIN: HIN-200/IF120x domain; InterPro: IPR004021 Th	83.02
PRK04036	504	DNA polymerase II small subunit; Validated	82.98
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	82.96
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	82.86
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	82.77
cd04496	100	SSB_OBF SSB_OBF: A subfamily of OB folds similar t	82.69
PF05331	114	DUF742: Protein of unknown function (DUF742); Inte	82.62
COG4189	308	Predicted transcriptional regulator [Transcription	82.41
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	82.4
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	82.37
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	82.21
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	82.02
PRK05813	219	single-stranded DNA-binding protein; Provisional	81.67
PRK03837	241	transcriptional regulator NanR; Provisional	81.65
PF01399	105	PCI: PCI domain; InterPro: IPR000717 A homology do	81.6
COG1497	260	Predicted transcriptional regulator [Transcription	81.58
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	81.52
PRK06642	152	single-stranded DNA-binding protein; Provisional	81.52
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	81.45
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	81.39
PF04492	100	Phage_rep_O: Bacteriophage replication protein O ;	81.2
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	81.06
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	81.04
PRK04214	412	rbn ribonuclease BN/unknown domain fusion protein;	80.91
PHA00738	108	putative HTH transcription regulator	80.62
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	80.57
PF09106	59	SelB-wing_2: Elongation factor SelB, winged helix	80.29

>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]

Probab=100.00  E-value=3.3e-50  Score=334.77  Aligned_cols=240  Identities=26%  Similarity=0.407  Sum_probs=188.0

Q ss_pred             cCCcccCCCCCCCCCCCCCCcCcCCcccceeeeeHHHHhcC-CCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEE
Q 024592           12 FAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSEL-SSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLI   90 (265)
Q Consensus        12 ~~gGGf~~~~~~~~~~~~~~~~k~~~~~~~~PvtIkqi~~a-~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~L   90 (265)
                      ..+|||.+++++++   ...........+|||||||||+++ +.+.++.|.+++.++.+|++||+||+++.+.++.+|+|
T Consensus        13 it~g~~~~~~s~p~---~drseg~~~vntLrpvTIKQIl~~~qd~~d~~f~vd~~Ev~~V~fVGvvrni~~~ttn~~~~i   89 (258)
T COG5235          13 ITRGQIFGTGSPPP---MDRSEGGYIVNTLRPVTIKQILSCDQDETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVI   89 (258)
T ss_pred             eeccceecCCCCCC---CCccccCceeeeeeeeEHHHhhcccccccCCceeecceEEeeEEEEEEEEeeeecccceEEEE
Confidence            45789986555422   112223456899999999999999 77788999999999999999999999999999999999


Q ss_pred             EcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHHHHhccCCCC
Q 024592           91 DDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGG  170 (265)
Q Consensus        91 dDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~~~~~~~  170 (265)
                      +||||.|+|++|...+.+.+.....+++.||||+|.||.|+||++|.+.+|++|+|+||+++|+||||+.||.+++....
T Consensus        90 EDGTG~Ievr~W~~~~~~~e~~~d~~~~~yvkV~G~lk~F~GK~~I~~~~i~~I~d~NeV~~HfLe~I~~Hl~~t~~~~~  169 (258)
T COG5235          90 EDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTRQLQR  169 (258)
T ss_pred             ecCCceEEEEecCCCchHHHhccccccccEEEEecceeeeCCeeEEehhheeeccccchhHHHHHHHHHHHHHHHHHhcc
Confidence            99999999999987766666677889999999999999999999999999999999999999999999999999876432


Q ss_pred             C--CCCCCCCCCCCccccccccCCCCCCCCCChhHHHHHHHhcCcC-CCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592          171 S--SNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPE-FLANNNGVHRNVISQQLNLPMDKLMEALESLNE  247 (265)
Q Consensus       171 ~--~~~~~~~~~~~~~~~~~~~~n~~~~~~l~~~~~~Vl~~i~~~~-~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~  247 (265)
                      .  .+.+..+.+. ...+    .|-. +.+.++||+.++.+.|.+. ......+|++..|++.++.++  .+..++.|.+
T Consensus       170 ple~~~~n~GqSl-f~k~----dNdt-Ssgss~lq~~~~~c~~~~~~~~~~~~~V~I~~lsqs~~~de--t~v~~d~L~~  241 (258)
T COG5235         170 PLEEEVKNDGQSL-FAKL----DNDT-SSGSSRLQEDILECYRRNQDENGLHINVVIKMLSQSYSEDE--TRVNIDVLLR  241 (258)
T ss_pred             hhhhhcCCCccce-eeec----cCcc-ccccccccHHHHHHHHHhcCCCCcccceeehHhhhhcCccc--eeeeeeeehh
Confidence            1  1111111110 0011    1111 1345689999999998763 112346777777777777554  4444999999


Q ss_pred             CCeEEe-ecCCceeec
Q 024592          248 NSLVYS-IDEFHYKSA  262 (265)
Q Consensus       248 eG~IYs-iDd~hyk~t  262 (265)
                      +|+||. +|++|||++
T Consensus       242 ~g~iYpTvD~n~fkt~  257 (258)
T COG5235         242 DGHIYPTVDGNEFKTT  257 (258)
T ss_pred             CceEEeeecCcceeec
Confidence            999999 999999987

>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]

Probab=100.00  E-value=3.6e-48  Score=340.38  Aligned_cols=258  Identities=34%  Similarity=0.514  Sum_probs=203.2

Q ss_pred             CCCCCCCCCccCCcccCCCCCCCCCCCCCCcCcCCcccceeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeee
Q 024592            2 YSGEFDGAAAFAGGGFMPSQATTVPDPSSSFSKNRNVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQD   81 (265)
Q Consensus         2 ~~~~~~~~~~~~gGGf~~~~~~~~~~~~~~~~k~~~~~~~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~   81 (265)
                      ++..|.+..++.+||+++++.+....++......+..+.++|+||+||+++....+..|++++.++.+|++||+|+++++
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~v~~~ti~qi~s~~~~~~~~~~i~~~~v~~v~~VGivr~~e~   82 (265)
T KOG3108|consen    3 SSYTFEDYNGQSSGGQGPGQFTTSRPPSSQSITNRRVQGVVPLTIKQILSSTQDDDSVFKIGGVEVSAVSIVGIVRNIEK   82 (265)
T ss_pred             ccccceecccccccccCCCcccccCCccccccccceeccccccceeeeccccccccccEEEccEEEEEEEEEEEEEecee
Confidence            34466677777888888766532111111222357889999999999999944333399999999999999999999999


Q ss_pred             CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHH
Q 024592           82 KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQ  161 (265)
Q Consensus        82 ~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~  161 (265)
                      .+++++|+|+|+||.|+|++|..+..+..+.+.+++|.||||+|.||.|+|+++|.+++|+||+|+||+++|+|||+++|
T Consensus        83 ~~t~i~y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~~yVkv~G~Lk~f~Gk~sl~~fkI~pv~D~Nevt~h~LE~i~~h  162 (265)
T KOG3108|consen   83 SATNITYEIEDGTGQIDVRQWFHDNAESEEMPALETGTYVKVYGHLKPFQGKKSLQVFKIRPVEDFNEVTTHFLEVINAH  162 (265)
T ss_pred             cCcceEEEEecCcccEEEEEeccccchhhhCcccccCcEEEeeecccCCCCceeEEEEeeeeeecCCceeEEeehhhHHH
Confidence            99999999999999999999998776666778999999999999999999999999999999999999999999999999


Q ss_pred             HHhccCCCCCCCCCCCCCCCCcccccc--ccCCCCC-CCCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC-CCHHH
Q 024592          162 LYNTRLRGGSSNQPQMTNSNHLKEYNA--ISSNHYS-FDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN-LPMDK  237 (265)
Q Consensus       162 l~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~n~~~-~~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~-~~~~~  237 (265)
                      |.+++......+.... .+.+.+....  ..++... ...|..+++.|++.++++.+   .+|+|+.+|+++|+ .....
T Consensus       163 l~~s~~~~~~sa~~~~-~~~~~~s~~~~~~~~~~s~~~~~l~~i~~~v~~~~~~~~h---~eGv~~~~i~~~l~~~~~~~  238 (265)
T KOG3108|consen  163 LSLSKSPSQSSAGNDP-VGFPGMSEAADSGYSQESGQSSQLERIQQRVLQAIESGLH---IEGVHIKEIAAQLREPSVSE  238 (265)
T ss_pred             HHhhhcccccccccCC-CCCcccccccccccCcccccchhhhHHHHHHHHhhhcCcc---cccccHHHHHHHhcccchhh
Confidence            9999876543222111 1111110000  0011110 12367899999999998753   48999999999997 56678


Q ss_pred             HHHHHHHHhhCCeEEe-ecCCceeecc
Q 024592          238 LMEALESLNENSLVYS-IDEFHYKSAV  263 (265)
Q Consensus       238 v~~al~~L~~eG~IYs-iDd~hyk~t~  263 (265)
                      +++++++|.+|||||+ +||+|||+|+
T Consensus       239 ~~~~~~~l~~eG~iy~TvD~~hFks~~  265 (265)
T KOG3108|consen  239 LREAVDFLLNEGHIYSTVDEEHFKSTN  265 (265)
T ss_pred             HHHHHHHHhcCCeEEEeechhheeecC
Confidence            9999999999999999 9999999984

>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

Probab=99.93  E-value=3.7e-25  Score=167.80  Aligned_cols=94  Identities=46%  Similarity=0.893  Sum_probs=86.2

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCCh
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDF  147 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~  147 (265)
                      +|++||+|++++..++++.|+|+|+||+|+|++|.+++.+ ....+.+++|+||+|.|+++.|+++++|.++.++|++|+
T Consensus         1 ~v~~vG~V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~i~~i~~v~d~   80 (95)
T cd04478           1 QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTDF   80 (95)
T ss_pred             CEEEEEEEEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEEEEEEEEeCCc
Confidence            4899999999999999999999999999999999876421 124677999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHH
Q 024592          148 NEITSHFVECIYVQL  162 (265)
Q Consensus       148 Nei~~H~Levi~~~l  162 (265)
                      ||+++|+|||+++||
T Consensus        81 ne~~~h~l~~~~~~l   95 (95)
T cd04478          81 NEVTYHLLEVIYVHL   95 (95)
T ss_pred             cHHHHhHhhhhhhhC
Confidence            999999999999985

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam

>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1)

Probab=99.71  E-value=7.1e-17  Score=121.85  Aligned_cols=73  Identities=25%  Similarity=0.545  Sum_probs=64.3

Q ss_pred             EEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc------------------ccccccCCCCEEEEEEEeeeeCC
Q 024592           71 TVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF------------------NEVNQISKGMYVRVYGHLKAFQD  132 (265)
Q Consensus        71 ~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~------------------~~~~~~~~g~yVrV~G~i~~f~~  132 (265)
                      .|||+|+++++.++++.|+|+|+||+|+|++|.+...+.                  +..+.+++|+||||.|+|+.|++
T Consensus         1 ~ivG~V~sv~~~~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~G~i~~frg   80 (92)
T cd04483           1 DILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRG   80 (92)
T ss_pred             CeEEEEEEEEecCCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEEEEEeccCC
Confidence            389999999999999999999999999999998754221                  34567999999999999999999


Q ss_pred             ccEEEEEEeee
Q 024592          133 KRSLNAYSLRP  143 (265)
Q Consensus       133 ~~~i~~~~i~~  143 (265)
                      +++|++..+..
T Consensus        81 ~~ql~i~~~~~   91 (92)
T cd04483          81 EREINASVVYK   91 (92)
T ss_pred             eeEEEEEEEEe
Confidence            99999998764

Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=99.67  E-value=6.9e-17  Score=124.16  Aligned_cols=58  Identities=29%  Similarity=0.510  Sum_probs=49.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      ++++++++||++||+.  ..+++|||+++|+++|++++++||++|++|++||+||+ |||+
T Consensus        44 ~~~~~~~~Vl~~i~~~--~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  102 (102)
T PF08784_consen   44 GLSPLQDKVLNFIKQQ--PNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDDD  102 (102)
T ss_dssp             -S-HHHHHHHHHHHC------TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSSTT
T ss_pred             CCCHHHHHHHHHHHhc--CCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCCC
Confidence            6889999999999993  26789999999999999999999999999999999999 9996

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA

Probab=99.46  E-value=1.7e-12  Score=115.08  Aligned_cols=120  Identities=21%  Similarity=0.369  Sum_probs=92.6

Q ss_pred             eeeeHHHHhcC--CC----------CCCCCeEECCeEEeEEEEEEEEEEeeeC----CCeEEEEEEcCCC--eEEEEEec
Q 024592           42 LPMTVKQLSEL--SS----------NDESSASIDGADVNTITVVGIVCDMQDK----EPQFIFLIDDGTG--RIECSRWA  103 (265)
Q Consensus        42 ~PvtIkqi~~a--~~----------~~~~~f~i~g~~v~~V~iVG~V~~v~~~----~t~~~y~LdDgTG--~I~~~~w~  103 (265)
                      .||.|++|+..  .+          ...+.|.+.++||..|+|||.|+.+...    ..++.|+|||+||  .|.|+.|.
T Consensus        29 ~PlfI~DI~~~~~~Sr~~~~~y~~~~~~~~~f~~NhPI~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~~~~  108 (256)
T PF10451_consen   29 VPLFISDIHKRLKQSRKVCENYYAPQQQNIYFYNNHPIRWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECKCSK  108 (256)
T ss_dssp             -E--HHHHCT----C--THHHHGGGG-TT-EEETTEEE-EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEEEEH
T ss_pred             CcEEHHHhhhhcccccchhhhhhhhccCCEEEECCcccEEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEEEEc
Confidence            39999999993  11          2245788999999999999999999865    7899999999999  89999997


Q ss_pred             cccccc-ccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHHHHh
Q 024592          104 HEQMEF-NEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYN  164 (265)
Q Consensus       104 ~~~~~~-~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~  164 (265)
                      +..... .....+ .|..|+|.|.++  ++.++|.+..|..+.|+++...||.+++..+-.+
T Consensus       109 ~~~~~~~l~~~~~-~G~~V~VkG~vs--r~~~ql~ve~i~~~~~l~~Ei~fW~~~~~~R~~L  167 (256)
T PF10451_consen  109 SSYLSMGLPINDL-IGKVVEVKGTVS--RNERQLDVERIELVRDLNAEIEFWKERMRFRKEL  167 (256)
T ss_dssp             HHHHCCCHHCTT--TT-EEEEEEEEE--SSSEEEEEEEEEEETSCCHHHHHHHHHHHHHHHC
T ss_pred             ccccccCCCccCC-CCcEEEEEEEEc--cCcEEEEEEEEEccCChHHHHHHHHHHHHHHHHc
Confidence            632211 123344 999999999999  8899999999999999999999999999986544

Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.

>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands

Probab=99.20  E-value=1.5e-10  Score=82.83  Aligned_cols=73  Identities=25%  Similarity=0.367  Sum_probs=63.2

Q ss_pred             EEEEEEEEEe-eeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCc-cEEEEEEeeeC
Q 024592           70 ITVVGIVCDM-QDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDK-RSLNAYSLRPI  144 (265)
Q Consensus        70 V~iVG~V~~v-~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~-~~i~~~~i~~v  144 (265)
                      |+|.|+|.++ ......+.|+|+|+||.|+|+.|.+..  ......+++|+.|+|.|+++.+++. .+|.+..+++|
T Consensus         1 V~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~--~~~~~~l~~g~~v~v~G~v~~~~~~~~~l~~~~i~~l   75 (75)
T PF01336_consen    1 VTVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEY--ERFREKLKEGDIVRVRGKVKRYNGGELELIVPKIEIL   75 (75)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHH--HHHHHTS-TTSEEEEEEEEEEETTSSEEEEEEEEEEE
T ss_pred             CEEEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHh--hHHhhcCCCCeEEEEEEEEEEECCccEEEEECEEEEC
Confidence            7899999999 777899999999999999999998322  1346789999999999999999987 99999998764

The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....

>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1)

Probab=98.78  E-value=8.5e-08  Score=69.77  Aligned_cols=65  Identities=20%  Similarity=0.464  Sum_probs=56.7

Q ss_pred             CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHH
Q 024592           83 EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEI  150 (265)
Q Consensus        83 ~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei  150 (265)
                      ..++.++|+|+||.|+|++|.+..   .....+++|.+|.|.|+++.+++..++.+..+.+++|.|+.
T Consensus        18 ~~~~~~~l~D~tg~i~~~~f~~~~---~~~~~l~~g~~v~v~G~v~~~~~~~~l~~~~i~~l~~~~~~   82 (83)
T cd04492          18 KPYLALTLQDKTGEIEAKLWDASE---EDEEKFKPGDIVHVKGRVEEYRGRLQLKIQRIRLVTEEDGV   82 (83)
T ss_pred             CcEEEEEEEcCCCeEEEEEcCCCh---hhHhhCCCCCEEEEEEEEEEeCCceeEEEEEEEECCcccCC
Confidence            368999999999999999997543   12467899999999999999999899999999999998864

Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.

>PRK13480 3'-5' exoribonuclease YhaM; Provisional

Probab=98.60  E-value=2.8e-07  Score=84.28  Aligned_cols=62  Identities=18%  Similarity=0.397  Sum_probs=54.9

Q ss_pred             CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592           82 KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID  146 (265)
Q Consensus        82 ~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d  146 (265)
                      ...|+.++|.|.||+|+|++|...+.   ....+++|++|+|.|++..|+++.|+.+..+++++.
T Consensus        31 G~~yl~l~l~D~tG~I~ak~W~~~~~---~~~~~~~g~vv~v~G~v~~y~g~~Ql~i~~i~~~~~   92 (314)
T PRK13480         31 GKPFLTLILQDKSGDIEAKLWDVSPE---DEATYVPETIVHVKGDIINYRGRKQLKVNQIRLATE   92 (314)
T ss_pred             CCeEEEEEEEcCCcEEEEEeCCCChh---hHhhcCCCCEEEEEEEEEEECCcceEEEEEeEECCC
Confidence            34699999999999999999986542   357799999999999999999999999999998754

>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

Probab=98.57  E-value=4.2e-07  Score=63.51  Aligned_cols=70  Identities=29%  Similarity=0.465  Sum_probs=57.7

Q ss_pred             EEEEEEEEeeeCC---CeEEEEEEcCC-CeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592           71 TVVGIVCDMQDKE---PQFIFLIDDGT-GRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus        71 ~iVG~V~~v~~~~---t~~~y~LdDgT-G~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~  142 (265)
                      +++|.|.+++...   .+..++|+|+| |.|+|..|.+...  .....++.|..|.|.|+++.++++.++.+..++
T Consensus         1 ~v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~--~~~~~~~~g~~v~v~g~v~~~~~~~~l~~~~~~   74 (75)
T cd03524           1 TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAE--ELENLLKEGQVVYIKGKVKKFRGRLQLIVESIE   74 (75)
T ss_pred             CeEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHH--HHHhhccCCCEEEEEEEEEecCCeEEEEeeeec
Confidence            4789999997665   68999999999 9999999976432  123568999999999999999988888887654

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco

>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE)

Probab=98.49  E-value=3.6e-07  Score=66.02  Aligned_cols=72  Identities=17%  Similarity=0.215  Sum_probs=56.6

Q ss_pred             EEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCC
Q 024592           72 VVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPII  145 (265)
Q Consensus        72 iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~  145 (265)
                      ++|.|.++...     ..++.++|+|+||.++|++|.+.-.  .....+++|.+|.|.|+++.|++..++.+..+.++.
T Consensus         2 i~g~v~~~~~~~~k~g~~~~~~~l~D~tg~~~~~~f~~~~~--~~~~~l~~g~~v~v~G~v~~~~~~~~l~~~~i~~~~   78 (84)
T cd04485           2 VAGLVTSVRRRRTKKGKRMAFVTLEDLTGSIEVVVFPETYE--KYRDLLKEDALLLVEGKVERRDGGLRLIAERIEDLE   78 (84)
T ss_pred             EEEEEEEeEEEEcCCCCEEEEEEEEeCCCeEEEEECHHHHH--HHHHHhcCCCEEEEEEEEEecCCceEEEeeccccHH
Confidence            67788775421     2369999999999999999964311  124568999999999999999988999998887765

The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.

>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit

Probab=98.42  E-value=4.9e-06  Score=60.05  Aligned_cols=73  Identities=19%  Similarity=0.368  Sum_probs=59.1

Q ss_pred             EEEEEEEEEeee-CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC--CccEEEEEEeeeC
Q 024592           70 ITVVGIVCDMQD-KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ--DKRSLNAYSLRPI  144 (265)
Q Consensus        70 V~iVG~V~~v~~-~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~--~~~~i~~~~i~~v  144 (265)
                      +.+.|.|.+++. ......++|+|.||.|+|..|.+...  .....+++|+.|.|.|++..+.  +..++.+..+.|.
T Consensus         2 ~~v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~~~--~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v~~i~~~   77 (78)
T cd04489           2 VWVEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSNAR--RLGFPLEEGMEVLVRGKVSFYEPRGGYQLIVEEIEPA   77 (78)
T ss_pred             EEEEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcchhh--hCCCCCCCCCEEEEEEEEEEECCCCEEEEEEEEEEEC
Confidence            578899988875 33478999999999999999986432  2346789999999999999874  7789999888764

E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.

>COG3390 Uncharacterized protein conserved in archaea [Function unknown]

Probab=98.31  E-value=3.9e-06  Score=70.05  Aligned_cols=123  Identities=19%  Similarity=0.255  Sum_probs=91.0

Q ss_pred             eeeeHHHHhcCC---CC-C---CCCeE--ECCeEEeEEEEEEEEEEeee---CCCeEEEEEEcCCCeEEEE--Eeccccc
Q 024592           42 LPMTVKQLSELS---SN-D---ESSAS--IDGADVNTITVVGIVCDMQD---KEPQFIFLIDDGTGRIECS--RWAHEQM  107 (265)
Q Consensus        42 ~PvtIkqi~~a~---~~-~---~~~f~--i~g~~v~~V~iVG~V~~v~~---~~t~~~y~LdDgTG~I~~~--~w~~~~~  107 (265)
                      +-|.++.|.++.   .. +   .-+|.  --|..+++|-|||.|.+...   ..+...+.+.|+||.+-|-  ++..++ 
T Consensus        11 ~rVFa~El~e~~~s~~e~~e~~sp~yliTPlG~k~nRifivGtltek~~i~ed~~~~R~rVvDpTGsF~Vyag~yqPEa-   89 (196)
T COG3390          11 YRVFAKELRESKFSKKEEDEERSPNYLITPLGLKVNRIFIVGTLTEKEGIGEDREYWRIRVVDPTGSFYVYAGQYQPEA-   89 (196)
T ss_pred             HHHHHHHHhhcceeccccccccCCcEEechhhhheeEEEEEEEEEeccCcCCcccEEEEEEecCCceEEEEcCCCChHH-
Confidence            347788888881   11 1   12344  36899999999999999764   3568999999999998871  122221 


Q ss_pred             ccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee----CCChhHHHHHHHHHHHHHHHhcc
Q 024592          108 EFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP----IIDFNEITSHFVECIYVQLYNTR  166 (265)
Q Consensus       108 ~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~----v~d~Nei~~H~Levi~~~l~~~~  166 (265)
                       ..-.+.++.+++|-|+|+++.|++.--...++|||    ..|++-..+|-+++.+..|..-+
T Consensus        90 -~a~l~~ve~~~~VaViGKi~~y~~d~g~~~~siRpE~vs~vde~~r~~Wv~eta~~tl~Ri~  151 (196)
T COG3390          90 -KAFLEDVEVPDLVAVIGKIRTYRTDEGVVLFSIRPELVSKVDEEARDLWVLETAEQTLERIK  151 (196)
T ss_pred             -HHHHHhccCCceEEEecccceeecCCCceEEEechhhhhhcCHHHHHHHHHHHHHHHHHHHH
Confidence             12356789999999999999999887777777877    44678888999999988775543

>PRK06461 single-stranded DNA-binding protein; Reviewed

Probab=98.31  E-value=5.5e-06  Score=66.28  Aligned_cols=84  Identities=19%  Similarity=0.273  Sum_probs=65.7

Q ss_pred             eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeee-------C--CCeEEEEEEcCCCeEEEEEeccccccccccc
Q 024592           43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQD-------K--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVN  113 (265)
Q Consensus        43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~-------~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~  113 (265)
                      ++.|++|....              ..|.++++|.++..       .  ..+..++|.|.||+|.++.|.+.      ..
T Consensus         4 ~~kI~dL~~g~--------------~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~I~~tlW~~~------a~   63 (129)
T PRK06461          4 ITKIKDLKPGM--------------ERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQ------AG   63 (129)
T ss_pred             ceEHHHcCCCC--------------CceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCEEEEEEeCCc------cc
Confidence            56788875321              35777788876532       1  23778899999999999999863      34


Q ss_pred             ccCCCCEEEEE-EEeeeeCCccEEEEE---EeeeCCC
Q 024592          114 QISKGMYVRVY-GHLKAFQDKRSLNAY---SLRPIID  146 (265)
Q Consensus       114 ~~~~g~yVrV~-G~i~~f~~~~~i~~~---~i~~v~d  146 (265)
                      .+++|+.|+|. |.++.|+++.+|++.   .|+++.+
T Consensus        64 ~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~  100 (129)
T PRK06461         64 SLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD  100 (129)
T ss_pred             cCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence            68999999999 889999999999998   5888875

>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB)

Probab=98.29  E-value=3.6e-06  Score=61.73  Aligned_cols=53  Identities=21%  Similarity=0.345  Sum_probs=46.8

Q ss_pred             CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeeeCCccEEEEEE
Q 024592           83 EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAFQDKRSLNAYS  140 (265)
Q Consensus        83 ~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f~~~~~i~~~~  140 (265)
                      ..+..++|.|.||+|.+++|.+.+     ...+++|+.|++. |.++.|++..+|.+..
T Consensus        22 ~~~~~~~l~D~TG~i~~~~W~~~~-----~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~   75 (82)
T cd04491          22 GKVQSGLVGDETGTIRFTLWDEKA-----ADDLEPGDVVRIENAYVREFNGRLELSVGK   75 (82)
T ss_pred             eEEEEEEEECCCCEEEEEEECchh-----cccCCCCCEEEEEeEEEEecCCcEEEEeCC
Confidence            368899999999999999998653     4678999999999 9999999999998754

SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating

>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

Probab=98.25  E-value=1.4e-05  Score=60.16  Aligned_cols=73  Identities=30%  Similarity=0.415  Sum_probs=59.6

Q ss_pred             EEEEEEEEeee--CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592           71 TVVGIVCDMQD--KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID  146 (265)
Q Consensus        71 ~iVG~V~~v~~--~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d  146 (265)
                      .|.|.|.++..  .+..+-|+|.|.++.|.|.+|............+++|+-|.|.|+++.|.   +|.+..++++--
T Consensus         2 ~v~GeVs~~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~v~~y~---ql~ve~l~~~gl   76 (91)
T cd04482           2 RVTGKVVEEPRTIEGGHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVRPGT---TLNLEKLRVIRL   76 (91)
T ss_pred             EEEEEEeCCeecCCCCCEEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEEEecCC---EEEEEEEEECCC
Confidence            57899998865  46789999999999999999976521112356789999999999999997   899999988654

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende

>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ

Probab=98.19  E-value=2e-05  Score=56.84  Aligned_cols=72  Identities=19%  Similarity=0.327  Sum_probs=59.4

Q ss_pred             EEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee
Q 024592           70 ITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP  143 (265)
Q Consensus        70 V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~  143 (265)
                      |.+-|.|.+....+..+-|+|.|.++.|.|.+|.....  .....+++|+-|.|.|++...+|+-++.+..|+.
T Consensus         1 v~v~GeVs~~~~~~GHvyfsLkD~~a~i~cv~f~~~~~--~~~~~l~~Gd~V~v~G~v~~~~G~~ql~v~~i~~   72 (73)
T cd04487           1 VHIEGEVVQIKQTSGPTIFTLRDETGTVWAAAFEEAGV--RAYPEVEVGDIVRVTGEVEPRDGQLQIEVESLEV   72 (73)
T ss_pred             CEEEEEEeccccCCCCEEEEEEcCCEEEEEEEEchhcc--CCcCCCCCCCEEEEEEEEecCCeEEEEEEeeEEE
Confidence            46788898876555679999999999999999976542  1346789999999999999888888999888764

RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.

>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain

Probab=98.05  E-value=5.3e-05  Score=57.81  Aligned_cols=75  Identities=17%  Similarity=0.294  Sum_probs=63.8

Q ss_pred             EeEEEEEEEEEEeee-CCCeEEEEEEcCCCeEEEEEecccccccccc-cccCCCCEEEEEEEeeeeC--CccEEEEEEee
Q 024592           67 VNTITVVGIVCDMQD-KEPQFIFLIDDGTGRIECSRWAHEQMEFNEV-NQISKGMYVRVYGHLKAFQ--DKRSLNAYSLR  142 (265)
Q Consensus        67 v~~V~iVG~V~~v~~-~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~-~~~~~g~yVrV~G~i~~f~--~~~~i~~~~i~  142 (265)
                      +..|.|.|.|.+++. .+..+-|+|-|+...|.|.+|.....  .-. ..+++|+-|.|.|++..|.  |+-++.+..|+
T Consensus        21 ~~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~--~i~~~~l~~G~~V~v~g~~~~y~~~G~~sl~v~~i~   98 (99)
T PF13742_consen   21 LPNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRAR--RIRGFDLKDGDKVLVRGRVSFYEPRGSLSLIVEDID   98 (99)
T ss_pred             cCCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHh--hCCCCCCCCCCEEEEEEEEEEECCCcEEEEEEEEeE
Confidence            478999999999988 67889999999999999999986542  112 5789999999999999985  67889999888


Q ss_pred             e
Q 024592          143 P  143 (265)
Q Consensus       143 ~  143 (265)
                      |
T Consensus        99 P   99 (99)
T PF13742_consen   99 P   99 (99)
T ss_pred             C
Confidence            7

>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC)

Probab=98.01  E-value=6.8e-05  Score=55.22  Aligned_cols=72  Identities=24%  Similarity=0.407  Sum_probs=55.1

Q ss_pred             EEEEEEEEEeeeCC-----CeEEEEEEcCCCeEEEEEecccccccccccccC-CCCEEEEEEEee--eeCCccEEEEEEe
Q 024592           70 ITVVGIVCDMQDKE-----PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQIS-KGMYVRVYGHLK--AFQDKRSLNAYSL  141 (265)
Q Consensus        70 V~iVG~V~~v~~~~-----t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~-~g~yVrV~G~i~--~f~~~~~i~~~~i  141 (265)
                      |.|-|.|-.++.+.     .-++|.|.|.|.+|.|+.|..  .+......++ +|++|+|.|++.  .|.....+.+..|
T Consensus         2 v~i~G~Vf~~e~re~k~g~~i~~~~itD~t~Si~~K~F~~--~~~~~~~~ik~~G~~v~v~G~v~~D~f~~e~~~~i~~i   79 (82)
T cd04484           2 VVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLR--KDEKDKEELKSKGDWVRVRGKVQYDTFSKELVLMINDI   79 (82)
T ss_pred             EEEEEEEEEEEEEEecCCCEEEEEEEEcCCCCEEEEEecc--CChhHHhhcccCCCEEEEEEEEEEccCCCceEEEeeeE
Confidence            77899998876422     356899999999999999985  1123346789 999999999987  4667777777666


Q ss_pred             ee
Q 024592          142 RP  143 (265)
Q Consensus       142 ~~  143 (265)
                      .+
T Consensus        80 ~~   81 (82)
T cd04484          80 EE   81 (82)
T ss_pred             EE
Confidence            54

Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.

>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG

Probab=97.94  E-value=8.1e-05  Score=52.46  Aligned_cols=64  Identities=23%  Similarity=0.348  Sum_probs=48.7

Q ss_pred             EEEEEEEeee----CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEE
Q 024592           72 VVGIVCDMQD----KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNA  138 (265)
Q Consensus        72 iVG~V~~v~~----~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~  138 (265)
                      +.|.|.++..    ....+.+.|.|+||.|+|+.|....   .....++.|+.+.|+|+++.|++..++.-
T Consensus         2 i~~~V~~~~~~~~~~~~~~~~~~~D~~g~i~~~~F~~~~---~~~~~~~~G~~~~v~Gkv~~~~~~~qi~~   69 (75)
T cd04488           2 VEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNFQP---YLKKQLPPGTRVRVSGKVKRFRGGLQIVH   69 (75)
T ss_pred             EEEEEEEEEeccCCCccEEEEEEEcCCCEEEEEEECCCH---HHHhcCCCCCEEEEEEEEeecCCeeEEeC
Confidence            5666666532    2357999999999999999996322   12457899999999999999988766653

RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha

>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS)

Probab=97.74  E-value=0.00046  Score=51.08  Aligned_cols=75  Identities=17%  Similarity=0.203  Sum_probs=54.4

Q ss_pred             EEEEEEEEEEeee-CCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeC-------CccEEEEE
Q 024592           69 TITVVGIVCDMQD-KEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ-------DKRSLNAY  139 (265)
Q Consensus        69 ~V~iVG~V~~v~~-~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~-------~~~~i~~~  139 (265)
                      .|++.|||.+++. ......+.|.|+|| .|.|.. ............+..|+-|.|.|.+..=.       +...|.+.
T Consensus         1 ~V~v~Gwv~~~R~~~~~~~Fi~LrD~~g~~iQvv~-~~~~~~~~~~~~l~~~s~V~V~G~v~~~~~~~~~~~~~~Ei~~~   79 (86)
T cd04321           1 KVTLNGWIDRKPRIVKKLSFADLRDPNGDIIQLVS-TAKKDAFSLLKSITAESPVQVRGKLQLKEAKSSEKNDEWELVVD   79 (86)
T ss_pred             CEEEEEeEeeEeCCCCceEEEEEECCCCCEEEEEE-CCCHHHHHHHhcCCCCcEEEEEEEEEeCCCcCCCCCCCEEEEEE
Confidence            3789999999998 56777889999999 588753 32211112235689999999999998743       45677777


Q ss_pred             EeeeC
Q 024592          140 SLRPI  144 (265)
Q Consensus       140 ~i~~v  144 (265)
                      .+..+
T Consensus        80 ~i~il   84 (86)
T cd04321          80 DIQTL   84 (86)
T ss_pred             EEEEe
Confidence            77655

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

Probab=97.67  E-value=0.00021  Score=69.23  Aligned_cols=77  Identities=17%  Similarity=0.307  Sum_probs=68.4

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID  146 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d  146 (265)
                      .+|+|.|.|+.++..+.-..|+|.|+||.|.|--|....-  ..-+.++.|++|+|.|.++.-.|+.||-+..+..++-
T Consensus       214 ~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGv--RAyP~IevGdiV~ViG~V~~r~g~lQiE~~~me~L~G  290 (715)
T COG1107         214 KTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGV--RAYPEIEVGDIVEVIGEVTRRDGRLQIEIEAMEKLTG  290 (715)
T ss_pred             ceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCc--ccCCCCCCCceEEEEEEEeecCCcEEEeehhhHHhhC
Confidence            6899999999999999999999999999999888875432  3357899999999999999999999999999888874

>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs)

Probab=97.67  E-value=0.00056  Score=50.31  Aligned_cols=76  Identities=22%  Similarity=0.282  Sum_probs=56.1

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeee------CCccEEEEEEe
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAF------QDKRSLNAYSL  141 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f------~~~~~i~~~~i  141 (265)
                      .|+|.|+|.+++.......+.|.|+||.+.|..-.+...+ ......+..|++|.|.|.+..-      .+...|.+..+
T Consensus         1 ~V~i~Gwv~~~R~~g~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~~~~~~~El~~~~i   80 (85)
T cd04100           1 EVTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQAEEL   80 (85)
T ss_pred             CEEEEEEEehhccCCCEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCCCCCCCEEEEEeEE
Confidence            3889999999998888788899999999998764332211 1234578999999999998863      34456666666


Q ss_pred             eeC
Q 024592          142 RPI  144 (265)
Q Consensus       142 ~~v  144 (265)
                      +.+
T Consensus        81 ~il   83 (85)
T cd04100          81 EVL   83 (85)
T ss_pred             EEE
Confidence            544

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A

>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs

Probab=97.64  E-value=0.00079  Score=49.49  Aligned_cols=76  Identities=22%  Similarity=0.353  Sum_probs=54.7

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCc------cEEEEEEee
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDK------RSLNAYSLR  142 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~------~~i~~~~i~  142 (265)
                      .|+|.|+|.+++.......+.|.|++|.|.|..-.+...+......+..|+.|.|.|.+..-...      ..|.+..++
T Consensus         1 ~V~v~Gwv~~~R~~g~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~Ei~~~~i~   80 (84)
T cd04323           1 RVKVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKEDPRAKQAPGGYELQVDYLE   80 (84)
T ss_pred             CEEEEEEEEEEecCCCcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEECCcccCCCCCEEEEEEEEE
Confidence            37899999999988888888999999999986533221111234568899999999999874332      456665554


Q ss_pred             eC
Q 024592          143 PI  144 (265)
Q Consensus       143 ~v  144 (265)
                      .+
T Consensus        81 vl   82 (84)
T cd04323          81 II   82 (84)
T ss_pred             EE
Confidence            43

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with

>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS

Probab=97.62  E-value=0.00044  Score=55.48  Aligned_cols=78  Identities=18%  Similarity=0.213  Sum_probs=57.3

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee----------CCccEEEE
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF----------QDKRSLNA  138 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f----------~~~~~i~~  138 (265)
                      .|+|.|||.+++.....+.+.|.|++|.+.|..-.+...+......+..|++|.|.|.+..-          .+...|.+
T Consensus        16 ~V~i~Gwv~~~R~~gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~~~~~~~~El~~   95 (135)
T cd04317          16 EVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVA   95 (135)
T ss_pred             EEEEEEeEehhcccCCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCCCCCCCcEEEEE
Confidence            49999999999988877888999999999987643322111234568999999999998852          23356777


Q ss_pred             EEeeeCCC
Q 024592          139 YSLRPIID  146 (265)
Q Consensus       139 ~~i~~v~d  146 (265)
                      ..++.+..
T Consensus        96 ~~i~vl~~  103 (135)
T cd04317          96 SELEVLNK  103 (135)
T ss_pred             eEEEEEEC
Confidence            66665553

These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh

>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]

Probab=97.52  E-value=0.0007  Score=57.02  Aligned_cols=83  Identities=20%  Similarity=0.268  Sum_probs=62.6

Q ss_pred             CeEEeEEEEEEEEEEeee--CCCeEEEEEEcCCCeEEEEEecccccc---cccccccCCCCEEEEEEEeeeeCCccEEEE
Q 024592           64 GADVNTITVVGIVCDMQD--KEPQFIFLIDDGTGRIECSRWAHEQME---FNEVNQISKGMYVRVYGHLKAFQDKRSLNA  138 (265)
Q Consensus        64 g~~v~~V~iVG~V~~v~~--~~t~~~y~LdDgTG~I~~~~w~~~~~~---~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~  138 (265)
                      |.-+.-|.+=|.|.+.+.  ........|+|+||.|++..+...+..   ..-.+-+.+|++|.|.|++..|+|+..|.+
T Consensus        48 G~l~e~v~vkg~V~~~~n~~~~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~~~eGe~veVtGrv~~yrG~~eVkv  127 (204)
T COG4085          48 GRLNEEVTVKGEVTADQNAIGGGIESLVLNDGTGTITVVASRSTEETLELNEGMPVTVEGEIVEVTGRVEEYRGSSEVKV  127 (204)
T ss_pred             ceeeccceeeeEEEeeecccccceEEEEEECCCCcEEEEEecChhHhHhhcCCCCccccCcEEEEEEEEEEeCCCceeec
Confidence            444566778888888763  457788899999999999999765432   122456789999999999999999988877


Q ss_pred             EE---eeeCCC
Q 024592          139 YS---LRPIID  146 (265)
Q Consensus       139 ~~---i~~v~d  146 (265)
                      ..   ++|+.-
T Consensus       128 nq~~d~~~l~k  138 (204)
T COG4085         128 NQPNDSRPLPK  138 (204)
T ss_pred             cCccccccccc
Confidence            43   444443

>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS)

Probab=97.44  E-value=0.0013  Score=50.07  Aligned_cols=79  Identities=13%  Similarity=0.083  Sum_probs=58.7

Q ss_pred             EEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccc--cc--cccccccCCCCEEEEEEEeeee-C-------CccE
Q 024592           69 TITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQ--ME--FNEVNQISKGMYVRVYGHLKAF-Q-------DKRS  135 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~--~~--~~~~~~~~~g~yVrV~G~i~~f-~-------~~~~  135 (265)
                      .|+|.|||.+++... ..+.+.|.|+||.|.|..-.+..  .+  ......+..|+.|.|.|.++.- .       +...
T Consensus         1 ~V~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~E   80 (102)
T cd04320           1 EVLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVE   80 (102)
T ss_pred             CEEEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEE
Confidence            378999999999887 77888999999999998864421  11  1123568999999999998863 1       3467


Q ss_pred             EEEEEeeeCCCh
Q 024592          136 LNAYSLRPIIDF  147 (265)
Q Consensus       136 i~~~~i~~v~d~  147 (265)
                      |.+..++.+...
T Consensus        81 l~~~~i~il~~~   92 (102)
T cd04320          81 LHIEKIYVVSEA   92 (102)
T ss_pred             EEEEEEEEEecC
Confidence            777777766543

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.

>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS)

Probab=97.43  E-value=0.0016  Score=50.26  Aligned_cols=80  Identities=19%  Similarity=0.266  Sum_probs=58.7

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-c-cccccccCCCCEEEEEEEeeeeCC---ccEEEEEEee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-E-FNEVNQISKGMYVRVYGHLKAFQD---KRSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~-~~~~~~~~~g~yVrV~G~i~~f~~---~~~i~~~~i~  142 (265)
                      ..|+|.|||.+++.......+.|.|+||.|.|..-..... + ......+..++.|.|.|.+..-..   ...|.+..++
T Consensus        13 ~~V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~Ei~~~~i~   92 (108)
T cd04316          13 EEVTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKAPNGVEIIPEEIE   92 (108)
T ss_pred             CEEEEEEEEEeeeccCCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCCCCCCEEEEEeEEE
Confidence            3599999999999888888889999999999865432111 0 123356899999999999886432   3567777777


Q ss_pred             eCCCh
Q 024592          143 PIIDF  147 (265)
Q Consensus       143 ~v~d~  147 (265)
                      .+...
T Consensus        93 il~~~   97 (108)
T cd04316          93 VLSEA   97 (108)
T ss_pred             EEeCC
Confidence            66543

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=97.42  E-value=0.00033  Score=45.89  Aligned_cols=47  Identities=17%  Similarity=0.385  Sum_probs=39.4

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      |+..+.+||++|.+.      .+++..+|++.++++...|...|..|.++|.|
T Consensus         1 l~~~~~~Il~~l~~~------~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I   47 (48)
T PF13412_consen    1 LDETQRKILNYLREN------PRITQKELAEKLGISRSTVNRYLKKLEEKGLI   47 (48)
T ss_dssp             --HHHHHHHHHHHHC------TTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             CCHHHHHHHHHHHHc------CCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence            356788999999874      47999999999999999999999999999987

...

>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS)

Probab=97.40  E-value=0.0014  Score=50.46  Aligned_cols=76  Identities=14%  Similarity=0.187  Sum_probs=53.6

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccc-cCCCCEEEEEEEeeee-CCccEEEEEEeeeC
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQ-ISKGMYVRVYGHLKAF-QDKRSLNAYSLRPI  144 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~-~~~g~yVrV~G~i~~f-~~~~~i~~~~i~~v  144 (265)
                      .|+|.|||.+++.....+.+.|.|+||.|.|..-.+...+  ...... +..|+.|.|.|.+..- .+...|.+..+.-+
T Consensus         1 ~v~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~~~~il   80 (108)
T cd04322           1 EVSVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVKEFTLL   80 (108)
T ss_pred             CEEEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeCEeEEe
Confidence            3789999999999888888899999999998764332111  112223 8999999999998753 34455555444443

These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein

>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS)

Probab=97.35  E-value=0.002  Score=49.24  Aligned_cols=79  Identities=19%  Similarity=0.228  Sum_probs=56.8

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeeeCC---ccEEEEEEeeeC
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAFQD---KRSLNAYSLRPI  144 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f~~---~~~i~~~~i~~v  144 (265)
                      .|+|.|||.+++.....+.+.|.|+||.+.|..-.+...+ ......+..|+.|.|.|.++.-..   ...|.+..+..+
T Consensus         1 ~V~v~Gwv~~~R~~gk~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~~~~~~Ei~~~~i~vl   80 (103)
T cd04319           1 KVTLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPRAPGGAEVHGEKLEII   80 (103)
T ss_pred             CEEEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEE
Confidence            3889999999998888888899999999998664321111 122356889999999999886322   245666666666


Q ss_pred             CCh
Q 024592          145 IDF  147 (265)
Q Consensus       145 ~d~  147 (265)
                      ...
T Consensus        81 ~~a   83 (103)
T cd04319          81 QNV   83 (103)
T ss_pred             ecC
Confidence            543

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.

>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit

Probab=97.28  E-value=0.0028  Score=46.25  Aligned_cols=68  Identities=22%  Similarity=0.340  Sum_probs=48.3

Q ss_pred             EEEEEEEEEee--eCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEE
Q 024592           70 ITVVGIVCDMQ--DKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYS  140 (265)
Q Consensus        70 V~iVG~V~~v~--~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~  140 (265)
                      |.++|.|.+++  ..... .++|+|.||+++|..|.+.-.--.....++++..|-|.|++.. ++. .+.+..
T Consensus         2 v~i~GiI~~v~~TK~g~~-~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~~-~~~-~l~~~~   71 (79)
T cd04490           2 VSIIGMVNDVRSTKNGHR-IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVSK-DGG-LIFADE   71 (79)
T ss_pred             EEEEEEEeEEEEcCCCCE-EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEec-CCC-EEEEEE
Confidence            67889998875  22234 9999999999999999754210012457899999999999966 444 444443

PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.

>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS

Probab=97.23  E-value=0.0066  Score=44.22  Aligned_cols=74  Identities=23%  Similarity=0.289  Sum_probs=54.9

Q ss_pred             EEEEEEEEEeeeCCCeEEEEEEcCCCe--EEEEEecccccccccccccCCCCEEEEEEEeeeeC---CccEEEEEEeeeC
Q 024592           70 ITVVGIVCDMQDKEPQFIFLIDDGTGR--IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ---DKRSLNAYSLRPI  144 (265)
Q Consensus        70 V~iVG~V~~v~~~~t~~~y~LdDgTG~--I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~---~~~~i~~~~i~~v  144 (265)
                      |++.|||.+++.......+.|.|+||.  |.|..-.+.. .......+..|+.|.|.|.+..-.   +...|.+..+..+
T Consensus         2 v~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~-~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~~~~i~il   80 (82)
T cd04318           2 VTVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELT-NFKEILKLSTGSSIRVEGVLVKSPGAKQPFELQAEKIEVL   80 (82)
T ss_pred             EEEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCccc-CHHHHhcCCCceEEEEEEEEEeCCCCCCCEEEEEEEEEEe
Confidence            789999999998888888899999994  9987543321 112345789999999999988743   3456666666544

This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial

>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]

Probab=97.22  E-value=0.0045  Score=58.80  Aligned_cols=96  Identities=17%  Similarity=0.218  Sum_probs=77.7

Q ss_pred             EeEEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC--CccEEEEEEeee
Q 024592           67 VNTITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ--DKRSLNAYSLRP  143 (265)
Q Consensus        67 v~~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~--~~~~i~~~~i~~  143 (265)
                      +.+|.|-|.|.+++... ...-|+|-|....|.|.+|.....  .-...+++|+.|-|.|+|..|.  |.-+|.+..++|
T Consensus        23 ~~~V~v~GEISn~t~~~sgH~YFtLKD~~A~i~c~mf~~~~~--~l~f~p~eG~~V~v~G~is~Y~~rG~YQi~~~~~~p  100 (440)
T COG1570          23 LGQVWVRGEISNFTRPASGHLYFTLKDERAQIRCVMFKGNNR--RLKFRPEEGMQVLVRGKISLYEPRGDYQIVAESMEP  100 (440)
T ss_pred             CCeEEEEEEecCCccCCCccEEEEEccCCceEEEEEEcCccc--ccCCCccCCCEEEEEEEEEEEcCCCceEEEEecCCc
Confidence            68999999999998544 478999999999999999986543  2234579999999999999995  678999999998


Q ss_pred             CCChhHHHHHHHHHHHHHHHhcc
Q 024592          144 IIDFNEITSHFVECIYVQLYNTR  166 (265)
Q Consensus       144 v~d~Nei~~H~Levi~~~l~~~~  166 (265)
                      .-.  --.+--+|.++..|..+.
T Consensus       101 ~G~--G~L~~~~E~lK~kL~aEG  121 (440)
T COG1570         101 AGL--GALYLAFEQLKAKLAAEG  121 (440)
T ss_pred             CCh--hHHHHHHHHHHHHHHhCC
Confidence            754  234667788888886653

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=97.19  E-value=0.0016  Score=46.16  Aligned_cols=59  Identities=20%  Similarity=0.312  Sum_probs=49.4

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC-Cceeec
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE-FHYKSA  262 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd-~hyk~t  262 (265)
                      ...+++||.+|++.+    +.|++..+|++.|+++...|+..|..|.++|.|.. -+. ..|..+
T Consensus         5 ~~~~~~IL~~L~~~g----~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~   65 (68)
T smart00550        5 DSLEEKILEFLENSG----DETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWKLT   65 (68)
T ss_pred             hHHHHHHHHHHHHCC----CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceEee
Confidence            467889999999742    34799999999999999999999999999999988 544 455543

Helix-turn-helix-containing domain. Also known as Zab.

>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif)

Probab=97.15  E-value=0.012  Score=45.30  Aligned_cols=83  Identities=18%  Similarity=0.229  Sum_probs=54.9

Q ss_pred             eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEE
Q 024592           42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYV  121 (265)
Q Consensus        42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yV  121 (265)
                      ...|++|++++..  +          ..|.|-|.|++....+   .|...|+||+|.+..=.+.-    ....+.+++.|
T Consensus        21 ~~~TV~~a~~~~D--d----------~~V~L~G~Iv~~l~~d---~Y~F~D~TG~I~VeId~~~w----~g~~vt~~~~V   81 (103)
T PF04076_consen   21 TVTTVAQAKNAKD--D----------TPVTLEGNIVKQLGDD---KYLFRDATGEIEVEIDDDVW----RGQTVTPDDKV   81 (103)
T ss_dssp             ----HHHHTTS-S--S----------EEEEEEEEEEEEEETT---EEEEEETTEEEEEE--GGGS----TT----TTSEE
T ss_pred             CeEeHHHHhhCcC--C----------CeEEEEEEEEEEecCC---EEEEECCCCcEEEEEChhhc----CCcccCCCCEE
Confidence            4478999987632  3          7899999988866544   56899999999887532210    12456788999


Q ss_pred             EEEEEeeeeCCccEEEEEEeee
Q 024592          122 RVYGHLKAFQDKRSLNAYSLRP  143 (265)
Q Consensus       122 rV~G~i~~f~~~~~i~~~~i~~  143 (265)
                      +|+|.|..--.+..|-+.+|++
T Consensus        82 ri~GeVDk~~~~~~IdV~~I~K  103 (103)
T PF04076_consen   82 RISGEVDKDWNKTEIDVDRIEK  103 (103)
T ss_dssp             EEEEEEEEETTEEEEEEEEEEE
T ss_pred             EEEEEEeCCCCceEEEEEEEEC
Confidence            9999999655678888887764

Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.

>PRK03932 asnC asparaginyl-tRNA synthetase; Validated

Probab=97.10  E-value=0.0058  Score=58.84  Aligned_cols=94  Identities=19%  Similarity=0.222  Sum_probs=67.9

Q ss_pred             eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCE
Q 024592           42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMY  120 (265)
Q Consensus        42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~y  120 (265)
                      .+++|++|+..... +          ..|+|.|+|.+++.....+.+.|.|+||.|.+..-.+...+ ......+..|+.
T Consensus         2 ~~~~~~~~~~~~~~-~----------~~V~i~G~v~~~R~~g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~s~   70 (450)
T PRK03932          2 MRVSIKDILKGKYV-G----------QEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSS   70 (450)
T ss_pred             CcEEHHHhcccccC-C----------CEEEEEEEEEEEEeCCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcE
Confidence            46789998732111 1          67999999999998887788899999999877765433111 123456899999


Q ss_pred             EEEEEEeeeeC---CccEEEEEEeeeCCC
Q 024592          121 VRVYGHLKAFQ---DKRSLNAYSLRPIID  146 (265)
Q Consensus       121 VrV~G~i~~f~---~~~~i~~~~i~~v~d  146 (265)
                      |.|.|.+..-.   +...|.+..++.+..
T Consensus        71 v~v~G~v~~~~~~~~~~el~~~~i~vl~~   99 (450)
T PRK03932         71 VIVTGTVVESPRAGQGYELQATKIEVIGE   99 (450)
T ss_pred             EEEEEEEEcCCCCCCCEEEEEEEEEEccC
Confidence            99999998643   346777777766653

>PRK05673 dnaE DNA polymerase III subunit alpha; Validated

Probab=97.02  E-value=0.0018  Score=68.65  Aligned_cols=77  Identities=19%  Similarity=0.270  Sum_probs=61.8

Q ss_pred             eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592           68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~  142 (265)
                      ..|.++|.|.+++..     .....++|+|.||.|+++.|.+.-.  .....+.+|..|.|.|++..++++.++.+..+.
T Consensus       978 ~~V~v~G~I~~vk~~~TKkG~~mafltLeD~TG~iEvviFp~~ye--~~~~~L~~g~iV~V~GkVe~~~~~~qlii~~I~ 1055 (1135)
T PRK05673        978 SVVTVAGLVVSVRRRVTKRGNKMAIVTLEDLSGRIEVMLFSEALE--KYRDLLEEDRIVVVKGQVSFDDGGLRLTAREVM 1055 (1135)
T ss_pred             ceEEEEEEEEEEEecccCCCCeEEEEEEEeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeecc
Confidence            368899999887643     3478899999999999999975411  234568999999999999988888899998888


Q ss_pred             eCCC
Q 024592          143 PIID  146 (265)
Q Consensus       143 ~v~d  146 (265)
                      ++.+
T Consensus      1056 ~L~~ 1059 (1135)
T PRK05673       1056 DLEE 1059 (1135)
T ss_pred             cHHH
Confidence            7754

>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed

Probab=96.96  E-value=0.006  Score=58.40  Aligned_cols=112  Identities=16%  Similarity=0.253  Sum_probs=83.0

Q ss_pred             eeeHHHHhcC-CCCCCCCeEECCeEEeEEEEEEEEEEeeeC-CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCE
Q 024592           43 PMTVKQLSEL-SSNDESSASIDGADVNTITVVGIVCDMQDK-EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMY  120 (265)
Q Consensus        43 PvtIkqi~~a-~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~-~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~y  120 (265)
                      |+|+++|... ..      .++.. +..|.|.|.|.+++.. +..+=|+|-|.+..|.|.+|.....  .-...+++|+-
T Consensus         5 ~~svsel~~~ik~------~le~~-~~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~--~~~~~~~~G~~   75 (438)
T PRK00286          5 ILSVSELNRYVKS------LLERD-LGQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSAR--RLKFKPEEGMK   75 (438)
T ss_pred             cCcHHHHHHHHHH------HHHhh-CCcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhh--cCCCCCCCCCE
Confidence            5788888775 11      11111 5789999999999865 5678899999999999999986442  12356899999


Q ss_pred             EEEEEEeeeeC--CccEEEEEEeeeCCChhHHHHHHHHHHHHHHHhc
Q 024592          121 VRVYGHLKAFQ--DKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNT  165 (265)
Q Consensus       121 VrV~G~i~~f~--~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~~  165 (265)
                      |.|.|+|..|.  |.-+|.+..|.|.-- -++ +--+|-+...|..+
T Consensus        76 v~v~g~~~~y~~~g~~ql~v~~i~~~g~-G~l-~~~~~~lk~~L~~e  120 (438)
T PRK00286         76 VLVRGKVSLYEPRGDYQLIVEEIEPAGI-GAL-AAAFEQLKEKLAAE  120 (438)
T ss_pred             EEEEEEEEEECCCCCEEEEEEEeeeCCc-cHH-HHHHHHHHHHHHHC
Confidence            99999999885  668999999998654 343 55556666666544

>TIGR00237 xseA exodeoxyribonuclease VII, large subunit

Probab=96.90  E-value=0.0072  Score=57.89  Aligned_cols=95  Identities=12%  Similarity=0.201  Sum_probs=74.6

Q ss_pred             EeEEEEEEEEEEeeeC-CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC--CccEEEEEEeee
Q 024592           67 VNTITVVGIVCDMQDK-EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ--DKRSLNAYSLRP  143 (265)
Q Consensus        67 v~~V~iVG~V~~v~~~-~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~--~~~~i~~~~i~~  143 (265)
                      +..|.|.|-|.+++.. +..+=|+|-|....|.|.+|.....  .-...+++|+-|.|.|+|..|.  |+-+|.+..|.|
T Consensus        17 ~~~v~V~GEisn~~~~~sGH~YFtLkD~~a~i~~vmf~~~~~--~l~f~~~~G~~V~v~g~v~~y~~~G~~ql~v~~i~~   94 (432)
T TIGR00237        17 FLQVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNN--RLKFRPQNGQQVLVRGGISVYEPRGDYQIICFEMQP   94 (432)
T ss_pred             CCcEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhh--CCCCCCCCCCEEEEEEEEEEECCCCcEEEEEEEecc
Confidence            4689999999999764 4578899999999999999987542  1235679999999999999985  668999999998


Q ss_pred             CCChhHHHHHHHHHHHHHHHhc
Q 024592          144 IIDFNEITSHFVECIYVQLYNT  165 (265)
Q Consensus       144 v~d~Nei~~H~Levi~~~l~~~  165 (265)
                      .- .-+ .+--+|-+...|..+
T Consensus        95 ~G-~G~-l~~~~~~lk~~L~~e  114 (432)
T TIGR00237        95 AG-EGL-LQLAYEQLKEKLAAE  114 (432)
T ss_pred             CC-hHH-HHHHHHHHHHHHHHC
Confidence            74 334 355566666666554

This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.

>TIGR00457 asnS asparaginyl-tRNA synthetase

Probab=96.89  E-value=0.0088  Score=57.63  Aligned_cols=93  Identities=18%  Similarity=0.280  Sum_probs=63.8

Q ss_pred             eeeHHHHhcC-CCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCC--CeEEEEEecccccc-cccccccCCC
Q 024592           43 PMTVKQLSEL-SSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGT--GRIECSRWAHEQME-FNEVNQISKG  118 (265)
Q Consensus        43 PvtIkqi~~a-~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgT--G~I~~~~w~~~~~~-~~~~~~~~~g  118 (265)
                      |.+|+.++.. ...      + |   ..|+|.|||.+++.....+.+.|.|+|  |.|.|..-.....+ ......+..|
T Consensus         1 ~~~~~~~~~~~~~~------~-g---~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~g   70 (453)
T TIGR00457         1 SAAIKDLLQQVYKF------V-G---DEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTG   70 (453)
T ss_pred             CccHHHHHhcchhc------C-C---CEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCC
Confidence            5678888752 111      1 2   569999999999977777888999999  99999764331111 1234568999


Q ss_pred             CEEEEEEEeeee---CCccEEEEEEeeeCC
Q 024592          119 MYVRVYGHLKAF---QDKRSLNAYSLRPII  145 (265)
Q Consensus       119 ~yVrV~G~i~~f---~~~~~i~~~~i~~v~  145 (265)
                      +.|.|.|.+..-   .+...|.+..++.+.
T Consensus        71 s~V~v~G~v~~~~~~~~~~El~~~~i~vl~  100 (453)
T TIGR00457        71 SSVSVTGKVVESPGKGQPVELQVKKIEVVG  100 (453)
T ss_pred             cEEEEEEEEEcCCCCCCCEEEEEeEEEEEe
Confidence            999999998752   233556666555544

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.

>PRK07211 replication factor A; Reviewed

Probab=96.89  E-value=0.0062  Score=58.79  Aligned_cols=76  Identities=18%  Similarity=0.349  Sum_probs=60.7

Q ss_pred             eEEEEEEEEEEeee----------CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeeeCCccEE
Q 024592           68 NTITVVGIVCDMQD----------KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAFQDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~----------~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f~~~~~i  136 (265)
                      ..|.|.|+|.++..          ......+.|-|.||+|.+..|.+.+.   ..+.+++|+.|+|. ++++.|++...|
T Consensus       172 ~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG~IR~TlW~d~Ad---~~~~le~G~Vv~I~~a~Vre~~g~~EL  248 (485)
T PRK07211        172 SDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETGRVRVTLWDDRAD---LAEELDAGESVEIVDGYVRERDGSLEL  248 (485)
T ss_pred             CceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCCeEEEEEechhhh---hhccCCCCCEEEEEeeEEEecCCcEEE
Confidence            56889999987642          11347899999999999999987543   34568999999996 889999999999


Q ss_pred             EEE---EeeeCCC
Q 024592          137 NAY---SLRPIID  146 (265)
Q Consensus       137 ~~~---~i~~v~d  146 (265)
                      ++.   .|.++.+
T Consensus       249 sl~~~s~I~~~~d  261 (485)
T PRK07211        249 HVGDRGAVEEVDE  261 (485)
T ss_pred             EECCCceEEECCc
Confidence            885   6777765

>TIGR00156 conserved hypothetical protein TIGR00156

Probab=96.87  E-value=0.039  Score=43.87  Aligned_cols=82  Identities=15%  Similarity=0.159  Sum_probs=57.1

Q ss_pred             eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEE
Q 024592           42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYV  121 (265)
Q Consensus        42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yV  121 (265)
                      ...|++|++++..  +          ..|.|-|.|+..-..   =.|...|+||+|.+..=.+.-    .-..+.+++-|
T Consensus        44 ~~~tV~~a~~~~D--d----------t~V~L~G~Iv~~l~~---d~Y~F~D~TG~I~VeId~~~w----~G~~v~p~d~V  104 (126)
T TIGR00156        44 KKMTVDFAKSMHD--G----------ASVTLRGNIISHIGD---DRYVFRDKSGEINVVIPAAVW----NGREVQPKDMV  104 (126)
T ss_pred             ceEeHHHHhhCCC--C----------CEEEEEEEEEEEeCC---ceEEEECCCCCEEEEECHHHc----CCCcCCCCCEE
Confidence            3689999988632  3          678888888776543   457999999998887511100    12357789999


Q ss_pred             EEEEEeeeeCCccEEEEEEee
Q 024592          122 RVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus       122 rV~G~i~~f~~~~~i~~~~i~  142 (265)
                      +|.|.|..--....|-+.+|+
T Consensus       105 ~I~GeVDk~~~~~~IdV~~I~  125 (126)
T TIGR00156       105 NISGSLDKKSAPAEVDVTHIQ  125 (126)
T ss_pred             EEEEEECCCCCCeEEEEEEEE
Confidence            999999853334566666664

As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.

>PRK07373 DNA polymerase III subunit alpha; Reviewed

Probab=96.83  E-value=0.0046  Score=59.40  Aligned_cols=77  Identities=13%  Similarity=0.255  Sum_probs=60.0

Q ss_pred             eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592           68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~  142 (265)
                      ..|+++|+|.+++..     .....++|+|.||.++|..|.+.-.  .....++++..|.|.|++..-.+..++.+..|.
T Consensus       281 ~~v~vaG~I~~ik~~~TKkG~~maf~~leD~tG~ie~vvFp~~y~--~~~~~l~~~~~v~v~G~v~~~~~~~~liv~~i~  358 (449)
T PRK07373        281 TKVSAVVMLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPKSYE--RISELLQVDARLIIWGKVDRRDDQVQLIVEDAE  358 (449)
T ss_pred             CEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeEee
Confidence            368899999998643     2467889999999999999976321  224568999999999999864466788888888


Q ss_pred             eCCC
Q 024592          143 PIID  146 (265)
Q Consensus       143 ~v~d  146 (265)
                      ++.+
T Consensus       359 ~l~~  362 (449)
T PRK07373        359 PIEE  362 (449)
T ss_pred             cHhh
Confidence            7755

>PRK10053 hypothetical protein; Provisional

Probab=96.79  E-value=0.055  Score=43.28  Aligned_cols=82  Identities=16%  Similarity=0.253  Sum_probs=56.8

Q ss_pred             ccceeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEE----eccccccccccc
Q 024592           38 VRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSR----WAHEQMEFNEVN  113 (265)
Q Consensus        38 ~~~~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~----w~~~~~~~~~~~  113 (265)
                      +......|++|.+++..  +          ..|.|-|.|+.--..   =.|...|+||+|.+..    |..        .
T Consensus        44 p~~~~~~tV~~a~~~~D--d----------~~V~L~G~Iv~~lg~---d~Y~F~D~tG~I~VeID~~~w~G--------~  100 (130)
T PRK10053         44 TDDARKMTVEQAKTMHD--G----------ATVSLRGNLIDHKGD---DRYVFRDKSGEINVIIPAAVFDG--------R  100 (130)
T ss_pred             CcccceEEHHHhhcCcC--C----------CeEEEEEEEEEEeCC---ceEEEECCCCcEEEEeCHHHcCC--------C
Confidence            33334679999887632  3          567788887765443   3578999999988875    532        3


Q ss_pred             ccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592          114 QISKGMYVRVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus       114 ~~~~g~yVrV~G~i~~f~~~~~i~~~~i~  142 (265)
                      .+.+.+.||++|.+..-.....|-+.+|+
T Consensus       101 ~v~p~~kV~I~GevDk~~~~~~IdV~~i~  129 (130)
T PRK10053        101 EVQPDQMININGSLDKKSAPPVVRVTHLQ  129 (130)
T ss_pred             cCCCCCEEEEEEEECCCCCCeEEEEEEEe
Confidence            57889999999999753334566666554

>PRK07217 replication factor A; Reviewed

Probab=96.64  E-value=0.011  Score=53.76  Aligned_cols=73  Identities=18%  Similarity=0.304  Sum_probs=57.1

Q ss_pred             eEEEEEEEEEEeeeCC-CeEEE--EEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEEEEEEeee
Q 024592           68 NTITVVGIVCDMQDKE-PQFIF--LIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSLNAYSLRP  143 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~-t~~~y--~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i~~~~i~~  143 (265)
                      ..|+|.|+|..+-+.. ..+.+  .|.|.||+|....|.+++     .+.+++|+.|++.+- ++.|+|+.+|++..-..
T Consensus        83 ~~VsV~aKVl~l~e~~~~si~qvGllgDETG~IkfT~W~~s~-----~~~leeGd~~rI~na~v~ey~G~~~lnlg~~t~  157 (311)
T PRK07217         83 QWVDVTAKVVQLWEPSSDSIAQVGLLGDETGTIKFTKWAKSD-----LPELEEGKSYLLKNVVTDEYQGRFSVKLNRTTS  157 (311)
T ss_pred             CcEEEEEEEEEecCCCCCceEEEEEEEcCCceEEEEEccCCC-----CCcccCCCEEEEEeEEEeeECCEEEEEeCCceE
Confidence            5799999999985432 33333  699999999999998743     467999999999887 66899999999855444


Q ss_pred             CC
Q 024592          144 II  145 (265)
Q Consensus       144 v~  145 (265)
                      |+
T Consensus       158 I~  159 (311)
T PRK07217        158 IE  159 (311)
T ss_pred             EE
Confidence            43

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A

Probab=96.56  E-value=0.0024  Score=44.48  Aligned_cols=46  Identities=20%  Similarity=0.335  Sum_probs=39.5

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++|+++|++.     ..+++..||++.|+++..++|.-|+.|..+|.|-.
T Consensus         2 ke~Il~~i~~~-----~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~   47 (62)
T PF04703_consen    2 KEKILEYIKEQ-----NGPLKTREIADALGLSIYQARYYLEKLEKEGKVER   47 (62)
T ss_dssp             HHCHHHHHHHH-----TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE
T ss_pred             cHHHHHHHHHc-----CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            56799999873     35799999999999999999999999999999864

>PRK07218 replication factor A; Provisional

Probab=96.55  E-value=0.017  Score=55.10  Aligned_cols=72  Identities=19%  Similarity=0.346  Sum_probs=57.4

Q ss_pred             eEEEEEEEEEEeee-------CC-CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEE-EeeeeCCccEEEE
Q 024592           68 NTITVVGIVCDMQD-------KE-PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQDKRSLNA  138 (265)
Q Consensus        68 ~~V~iVG~V~~v~~-------~~-t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~~~~~i~~  138 (265)
                      ..|.|.|+|.++..       .. ......|.|.||+|.+..|.+.       +.+.+|+.|+|.+ .++.|+|..+|++
T Consensus       173 ~~V~v~g~Vl~~~~r~f~~~dg~~~v~~giigDeTG~Ir~tlW~~~-------~~l~~Gd~v~I~na~v~e~~G~~elnv  245 (423)
T PRK07218        173 RGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPL-------PEIEIGASIRIEDAYVREFRGVPSVNV  245 (423)
T ss_pred             CceEEEEEEEEecceeEEcCCCCeEEEEEEEECCCceEEEEEeccc-------ccCCCCCEEEEeeeEEeccCCeEEEEE
Confidence            45888999988743       11 2455689999999999999852       3589999999998 5889999999999


Q ss_pred             E---EeeeCCC
Q 024592          139 Y---SLRPIID  146 (265)
Q Consensus       139 ~---~i~~v~d  146 (265)
                      .   .|.++++
T Consensus       246 ~~~t~I~~~d~  256 (423)
T PRK07218        246 SEFTTVEALDR  256 (423)
T ss_pred             CCceEEEECCC
Confidence            7   6777654

>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]

Probab=96.49  E-value=0.033  Score=53.06  Aligned_cols=89  Identities=20%  Similarity=0.245  Sum_probs=64.6

Q ss_pred             eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-ccccccccCCCCE
Q 024592           42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-EFNEVNQISKGMY  120 (265)
Q Consensus        42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~~~~~~~~~~g~y  120 (265)
                      +.++|++|.+...         +   ..|+|-|||.+++.........|.|+||.|.|..-.+... +..+...+..++.
T Consensus         3 ~~~~i~di~~~~~---------~---~~V~v~GWV~~~R~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~es~   70 (435)
T COG0017           3 KRTYIKDIKPHVG---------G---QEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESS   70 (435)
T ss_pred             ceeeHHhhhccCC---------C---cEEEEEEEeeeecccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCccE
Confidence            3567778765321         1   7899999999999988888889999999999998754221 1111457899999


Q ss_pred             EEEEEEeeeeCC---ccEEEEEEee
Q 024592          121 VRVYGHLKAFQD---KRSLNAYSLR  142 (265)
Q Consensus       121 VrV~G~i~~f~~---~~~i~~~~i~  142 (265)
                      |.|.|.|+.-..   .-.|.+..|.
T Consensus        71 v~V~G~v~~~~~a~~g~El~v~~i~   95 (435)
T COG0017          71 VVVTGIVKASPKAPQGFELQVEKIE   95 (435)
T ss_pred             EEEEEEEEcCCCCCCCEEEEEEEEE
Confidence            999999997542   2345554443

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=96.48  E-value=0.0019  Score=45.47  Aligned_cols=52  Identities=23%  Similarity=0.352  Sum_probs=40.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCc--CHHHHHHhcCCC-HHHHHHHHHHHhhCCeEE
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGV--HRNVISQQLNLP-MDKLMEALESLNENSLVY  252 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv--~~~~I~~~l~~~-~~~v~~al~~L~~eG~IY  252 (265)
                      .|++.|.+||++|++-   ..+.|+  ++.||++.|++. ...|...|+-|.+.|+|=
T Consensus         3 ~LT~rQ~~vL~~I~~~---~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~   57 (65)
T PF01726_consen    3 ELTERQKEVLEFIREY---IEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR   57 (65)
T ss_dssp             ---HHHHHHHHHHHHH---HHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHHHHHH---HHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence            5788999999999863   223454  789999999975 999999999999999984

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=96.47  E-value=0.0061  Score=41.57  Aligned_cols=44  Identities=16%  Similarity=0.348  Sum_probs=39.3

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      +..|+++|++.      .-+++.++++.|+.++..||.-|..|.++|.|-
T Consensus         2 ~~~Il~~l~~~------~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~   45 (57)
T PF08220_consen    2 QQQILELLKEK------GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIK   45 (57)
T ss_pred             HHHHHHHHHHc------CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            46799999874      368999999999999999999999999999874

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>PF13730 HTH_36: Helix-turn-helix domain

Probab=96.46  E-value=0.0099  Score=39.78  Aligned_cols=54  Identities=13%  Similarity=0.183  Sum_probs=42.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      +|++....||-+|....+.....-.+.+.|++.++++...|+++|.+|++.|.|
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence            466778888888776542222233489999999999999999999999999986

>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type

Probab=96.33  E-value=0.027  Score=53.90  Aligned_cols=78  Identities=19%  Similarity=0.226  Sum_probs=57.7

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccccCCCCEEEEEEEeeeeC---CccEEEEEEee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQISKGMYVRVYGHLKAFQ---DKRSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~g~yVrV~G~i~~f~---~~~~i~~~~i~  142 (265)
                      ..|+|.|+|.+++.....+...|.|++|.|.|..-.+...+  -+....+..|+.|.|.|.+..-+   +...|.+..+.
T Consensus        13 ~~v~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~~~~~~el~~~~i~   92 (428)
T TIGR00458        13 QEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIVKIKEKAPGGFEIIPTKIE   92 (428)
T ss_pred             CEEEEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEEEecCCCCCcEEEEEeEEE
Confidence            45999999999998888888899999999999775432111  11235689999999999998643   44666666665


Q ss_pred             eCC
Q 024592          143 PII  145 (265)
Q Consensus       143 ~v~  145 (265)
                      .+.
T Consensus        93 vl~   95 (428)
T TIGR00458        93 VIN   95 (428)
T ss_pred             EEe
Confidence            544

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).

>PRK12445 lysyl-tRNA synthetase; Reviewed

Probab=96.32  E-value=0.03  Score=54.68  Aligned_cols=77  Identities=17%  Similarity=0.141  Sum_probs=56.5

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc---ccccccCCCCEEEEEEEeee-eCCccEEEEEEeeeC
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF---NEVNQISKGMYVRVYGHLKA-FQDKRSLNAYSLRPI  144 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~g~yVrV~G~i~~-f~~~~~i~~~~i~~v  144 (265)
                      .|+|.|+|.+++.....+.+.|.|++|.|.|..-.+...+.   .....+..|+.|.|.|.+.. -.+...|.+..+..+
T Consensus        67 ~v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~gelel~~~~~~ll  146 (505)
T PRK12445         67 EVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLL  146 (505)
T ss_pred             EEEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCCCcEEEEEeEEEEE
Confidence            49999999999988888888999999999986643321111   12346889999999999864 346666766665544


Q ss_pred             C
Q 024592          145 I  145 (265)
Q Consensus       145 ~  145 (265)
                      .
T Consensus       147 s  147 (505)
T PRK12445        147 T  147 (505)
T ss_pred             e
Confidence            3

>PRK14699 replication factor A; Provisional

Probab=96.29  E-value=0.015  Score=56.45  Aligned_cols=77  Identities=17%  Similarity=0.209  Sum_probs=55.3

Q ss_pred             eEEEEEEEEEEeee--------CC--CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEE
Q 024592           68 NTITVVGIVCDMQD--------KE--PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLN  137 (265)
Q Consensus        68 ~~V~iVG~V~~v~~--------~~--t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~  137 (265)
                      ..|+|.|+|.++..        .+  ....+.|.|.||+|.+..|.+.+. .-..-.|++|+.|+|.|.+|...+...|+
T Consensus        68 ~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~iaDeTG~ir~tlW~~~a~-~~~~g~l~~GDvv~I~~~~r~~~~g~el~  146 (484)
T PRK14699         68 GPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMAD-LIKAGKIKAGQTLQISGYAKQGYSGVEVN  146 (484)
T ss_pred             ceEEEEEEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCccc-hhhhcCCCCCCEEEEcceeccCCCCceEE
Confidence            46888888888741        12  345679999999999999986431 01112599999999999998866667888


Q ss_pred             EE---EeeeCC
Q 024592          138 AY---SLRPII  145 (265)
Q Consensus       138 ~~---~i~~v~  145 (265)
                      +.   .+++.+
T Consensus       147 ~~~~~~i~~~~  157 (484)
T PRK14699        147 IGNNGVLTESE  157 (484)
T ss_pred             eCCCceeeccC
Confidence            75   444443

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=96.24  E-value=0.0062  Score=42.77  Aligned_cols=50  Identities=24%  Similarity=0.247  Sum_probs=43.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++....+||..|-.      ..+++..+|++.++++...|..+|..|.+.|.|..
T Consensus         5 gLs~~E~~vy~~Ll~------~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~   54 (68)
T PF01978_consen    5 GLSENEAKVYLALLK------NGPATAEEIAEELGISRSTVYRALKSLEEKGLVER   54 (68)
T ss_dssp             CHHHHHHHHHHHHHH------HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred             CcCHHHHHHHHHHHH------cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            456778889888753      24789999999999999999999999999999987

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type

Probab=96.23  E-value=0.025  Score=60.47  Aligned_cols=78  Identities=15%  Similarity=0.286  Sum_probs=61.4

Q ss_pred             eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee--eeCCccEEEEEE
Q 024592           68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK--AFQDKRSLNAYS  140 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~--~f~~~~~i~~~~  140 (265)
                      ..|.|.|.|-.++..     ..-++|.|.|.|.+|.|+.|.....+.+....+++|++|+|.|++.  .|..+..+.+..
T Consensus         8 ~~~~~~g~i~~~~~~~~~~~~~~~~~~~~d~~~s~~~k~f~~~~~~~~~~~~~~~g~~~~~~g~~~~d~~~~~~~~~~~~   87 (1213)
T TIGR01405         8 NRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRARGKIELDNFSRDLQMIIKD   87 (1213)
T ss_pred             CeEEEEEEEEEEEeEeccCCCEEEEEEEEcCCCCEEEEEecccccchHHHhhcCCCcEEEEEEEEeccCCCCceEEEeee
Confidence            678899999887642     2456899999999999999986554334457899999999999987  466777888877


Q ss_pred             eeeCC
Q 024592          141 LRPII  145 (265)
Q Consensus       141 i~~v~  145 (265)
                      |.++.
T Consensus        88 ~~~~~   92 (1213)
T TIGR01405        88 IEEIP   92 (1213)
T ss_pred             eeecC
Confidence            77653

The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.

>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP)

Probab=96.21  E-value=0.074  Score=42.84  Aligned_cols=69  Identities=12%  Similarity=0.189  Sum_probs=54.1

Q ss_pred             eEEEEEEEEEEeee------CCCeEEEEEEcCCC---e-EEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEE
Q 024592           68 NTITVVGIVCDMQD------KEPQFIFLIDDGTG---R-IECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~------~~t~~~y~LdDgTG---~-I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i  136 (265)
                      ..|.++|+|+++..      ..-.++|+|-|.|+   . |.|.+|.+..+   ..+.+.+|+.|.+.+- |+.|+|+.+.
T Consensus        15 ~~v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~---~LP~v~~GDVIll~~~kv~~~~g~~~~   91 (138)
T cd04497          15 GSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEE---SLPIVKVGDIILLRRVKIQSYNGKPQG   91 (138)
T ss_pred             CeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCChh---hCCCCCCCCEEEEEEEEEEEECCceEE
Confidence            57889999999753      23468999999887   2 99999987653   4666799999999874 8889988666


Q ss_pred             EEE
Q 024592          137 NAY  139 (265)
Q Consensus       137 ~~~  139 (265)
                      ...
T Consensus        92 ~~~   94 (138)
T cd04497          92 ISN   94 (138)
T ss_pred             EEC
Confidence            554

POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB

>COG3481 Predicted HD-superfamily hydrolase [General function prediction only]

Probab=96.20  E-value=0.0038  Score=56.22  Aligned_cols=63  Identities=22%  Similarity=0.420  Sum_probs=55.9

Q ss_pred             eCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592           81 DKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID  146 (265)
Q Consensus        81 ~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d  146 (265)
                      ....++.++++|.||.|+++.|.....   ....+..|..|.+.|....+++.+|+.+..+|++++
T Consensus        18 ~~~~~l~l~~~d~~gei~~~~wd~~~~---~~~~~~~~~Vv~~~g~~~~~~~~~q~ki~~~r~~~~   80 (287)
T COG3481          18 NGKDKLKLTLQDKTGEIEAKLWDALKN---DEEAFKPGMVVHVEGVKEVYRGRKQHKIIRIRLITD   80 (287)
T ss_pred             cCChhheeeeccccceecccccccccc---cHhhhCcCceeccccceecccccchheeeecccccc
Confidence            345789999999999999999986543   356799999999999999999999999999999887

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=96.18  E-value=0.017  Score=39.35  Aligned_cols=55  Identities=16%  Similarity=0.193  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...+    +.+++..+|++.++++...|...|..|++.|.|.. -|.
T Consensus         2 glt~~q~~vL~~l~~~~----~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~   57 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHP----GEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP   57 (62)
T ss_dssp             TSTHHHHHHHHHHHHST----TSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred             ccCHHHHHHHHHHHHCC----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence            46778889999998742    33599999999999999999999999999999998 654

...

>PRK00448 polC DNA polymerase III PolC; Validated

Probab=96.17  E-value=0.029  Score=60.89  Aligned_cols=79  Identities=25%  Similarity=0.431  Sum_probs=61.7

Q ss_pred             eEEEEEEEEEEeeeCC-----CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee--eCCccEEEEEE
Q 024592           68 NTITVVGIVCDMQDKE-----PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQDKRSLNAYS  140 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~-----t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~~~~~i~~~~  140 (265)
                      ..|.|-|.|-.++...     .-++|.|.|.|.+|.|+.|..+..+.+....++.|++|+|.|++..  |.....+.+..
T Consensus       237 ~~v~i~G~if~~e~~~~k~~~~~~~~~~td~~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~g~~~~d~~~~~~~~~~~~  316 (1437)
T PRK00448        237 RRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVRGSVQNDTFTRDLVMNAQD  316 (1437)
T ss_pred             CeEEEEEEEEEEEEEeccCCCEEEEEEEEcCCCCEEEEEEecCcchhHHHhcCCCCCEEEEEEEEeccCCCCceEEEeee
Confidence            5788999998876432     3568999999999999999865443344577999999999999975  66777777777


Q ss_pred             eeeCCC
Q 024592          141 LRPIID  146 (265)
Q Consensus       141 i~~v~d  146 (265)
                      |.++..
T Consensus       317 ~~~~~~  322 (1437)
T PRK00448        317 INEIKH  322 (1437)
T ss_pred             eeecCC
Confidence            776644

>PRK08402 replication factor A; Reviewed

Probab=96.15  E-value=0.031  Score=52.14  Aligned_cols=70  Identities=20%  Similarity=0.280  Sum_probs=53.1

Q ss_pred             eEEEEEEEEEEeee--------CCC--eEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeee-CCccE
Q 024592           68 NTITVVGIVCDMQD--------KEP--QFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAF-QDKRS  135 (265)
Q Consensus        68 ~~V~iVG~V~~v~~--------~~t--~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f-~~~~~  135 (265)
                      ..|.++|+|.++..        .++  -...+|.|.||.|.+..|.+...  ...+.+.+|+.|+|. +.++.| +|..+
T Consensus        73 ~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~ir~TlW~~~a~--~~~~~l~~Gdvi~I~~a~V~e~~~G~~e  150 (355)
T PRK08402         73 RGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVA--KYYNKINVGDVIKVIDAQVRESLSGLPE  150 (355)
T ss_pred             ceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEEEEechhhh--hhcccCCCCCEEEEECCEEeecCCCcEE
Confidence            57899999988742        111  23479999999999999987542  123568999999987 889975 88878


Q ss_pred             EEEE
Q 024592          136 LNAY  139 (265)
Q Consensus       136 i~~~  139 (265)
                      |++.
T Consensus       151 Lsvg  154 (355)
T PRK08402        151 LHIN  154 (355)
T ss_pred             EEEC
Confidence            8884

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=96.13  E-value=0.012  Score=39.14  Aligned_cols=45  Identities=22%  Similarity=0.310  Sum_probs=38.3

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      -.||++|.+.     ..++++.+|+++++++...+...|..|.+.|.|..
T Consensus         6 l~iL~~l~~~-----~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen    6 LRILEALAES-----GGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             HHHHHCHHCT-----BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHcC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence            3578888764     45789999999999999999999999999999864

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>PRK05159 aspC aspartyl-tRNA synthetase; Provisional

Probab=96.12  E-value=0.039  Score=52.92  Aligned_cols=78  Identities=18%  Similarity=0.265  Sum_probs=57.1

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeeeC---CccEEEEEEeee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAFQ---DKRSLNAYSLRP  143 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f~---~~~~i~~~~i~~  143 (265)
                      ..|+|.|+|.+++.....+.+.|.|++|.|.|..=.+...+ .+....|..|+.|.|.|.+..-+   +...|.+..+..
T Consensus        17 ~~V~i~GrV~~~R~~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~G~v~~~~~~~~~~el~~~~i~v   96 (437)
T PRK05159         17 EEVTLAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVVSVTGTVKANPKAPGGVEVIPEEIEV   96 (437)
T ss_pred             CEEEEEEEeEeeecCCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCCcEEEEEEEEEcCCCCCCCEEEEEeEEEE
Confidence            45889999999998887788899999999998763322111 12345789999999999998754   445677666555


Q ss_pred             CC
Q 024592          144 II  145 (265)
Q Consensus       144 v~  145 (265)
                      +.
T Consensus        97 ls   98 (437)
T PRK05159         97 LN   98 (437)
T ss_pred             Ee
Confidence            43

>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]

Probab=96.09  E-value=0.032  Score=43.97  Aligned_cols=82  Identities=22%  Similarity=0.220  Sum_probs=59.0

Q ss_pred             eeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEE
Q 024592           44 MTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRV  123 (265)
Q Consensus        44 vtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV  123 (265)
                      ..||||..+...    +    .....|...|.++.-.+......+.+-|.||+|.+-.|.+.      ...++.||.||.
T Consensus         5 i~ikdi~P~~kN----~----~v~fIvl~~g~~tkTkdg~~v~~~kVaD~TgsI~isvW~e~------~~~~~PGDIirL   70 (134)
T KOG3416|consen    5 IFIKDIKPGLKN----I----NVTFIVLEYGRATKTKDGHEVRSCKVADETGSINISVWDEE------GCLIQPGDIIRL   70 (134)
T ss_pred             hhHhhcChhhhc----c----eEEEEEEeeceeeeccCCCEEEEEEEecccceEEEEEecCc------CcccCCccEEEe
Confidence            357777665321    1    12344556677776667778999999999999999999853      367899999999


Q ss_pred             EEEeee-eCCccEEEEE
Q 024592          124 YGHLKA-FQDKRSLNAY  139 (265)
Q Consensus       124 ~G~i~~-f~~~~~i~~~  139 (265)
                      .|...+ |++...|-+.
T Consensus        71 t~Gy~Si~qg~LtL~~G   87 (134)
T KOG3416|consen   71 TGGYASIFQGCLTLYVG   87 (134)
T ss_pred             cccchhhhcCceEEEec
Confidence            988765 6776655553

>PRK14699 replication factor A; Provisional

Probab=96.06  E-value=0.027  Score=54.62  Aligned_cols=75  Identities=23%  Similarity=0.304  Sum_probs=55.5

Q ss_pred             EEEEEEEEEEeeeC-------C---CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-ee--eeCCccE
Q 024592           69 TITVVGIVCDMQDK-------E---PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LK--AFQDKRS  135 (265)
Q Consensus        69 ~V~iVG~V~~v~~~-------~---t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~--~f~~~~~  135 (265)
                      .|+|.|+|.++..-       .   .-....|-|.||+|.+..|.+...   ..+.|++|+.|+|.+. +|  .|++...
T Consensus       178 ~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG~ir~tlW~~~a~---~~~~l~~Gd~v~I~~a~vr~~~~~~~~e  254 (484)
T PRK14699        178 DLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETGTLRVTLWDDKTD---FLNQIEYGDTVELINAYARENAFTQKVE  254 (484)
T ss_pred             ceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCceEEEEEECcccc---cccccCCCCEEEEecceEeecccCCceE
Confidence            48899999886431       1   244579999999999999987532   3457999999998744 44  5888888


Q ss_pred             EEEEEeeeCCC
Q 024592          136 LNAYSLRPIID  146 (265)
Q Consensus       136 i~~~~i~~v~d  146 (265)
                      |++.....+..
T Consensus       255 l~~~~~s~i~~  265 (484)
T PRK14699        255 LQVGNRSIIRK  265 (484)
T ss_pred             EEecCceEeec
Confidence            88866555544

>PRK07211 replication factor A; Reviewed

Probab=96.05  E-value=0.034  Score=53.82  Aligned_cols=77  Identities=16%  Similarity=0.276  Sum_probs=57.6

Q ss_pred             eEEEEEEEEEEeee------C-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEE
Q 024592           68 NTITVVGIVCDMQD------K-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~------~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i  136 (265)
                      ..|+|.|+|.++..      .     ..-..+.|-|.||.|.+..|.+...  .....|++|+.++|.|+++...+...|
T Consensus        64 ~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG~Ir~TlW~d~ad--~~~~~Le~GdV~~I~~~~~~~ys~~El  141 (485)
T PRK07211         64 DEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETGSVRVAFWDEQAV--AAEEELEVGQVLRIKGRPKDGYNGLEV  141 (485)
T ss_pred             CceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCCeEEEEEechHhH--hhhcccCCCCEEEEeceEeccccceEE
Confidence            56888888877542      1     2457889999999999999986542  134679999999999998765555677


Q ss_pred             EEEEeeeCCC
Q 024592          137 NAYSLRPIID  146 (265)
Q Consensus       137 ~~~~i~~v~d  146 (265)
                      ++..+.+-.|
T Consensus       142 ~i~~ve~~~d  151 (485)
T PRK07211        142 SVDKVEPDPD  151 (485)
T ss_pred             EEeeEEEccc
Confidence            7777666544

>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type

Probab=96.01  E-value=0.041  Score=54.60  Aligned_cols=76  Identities=17%  Similarity=0.158  Sum_probs=56.8

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee----------eCCccEEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA----------FQDKRSLN  137 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~----------f~~~~~i~  137 (265)
                      ..|+|.|||.+++....-+.+.|.|+||.|.|..-.+ ....+....+..|+.|.|.|.+..          -.+...|.
T Consensus        16 ~~V~l~GwV~~~R~~Gkl~Fi~LrD~sg~iQvv~~~~-~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~~~tg~iEl~   94 (583)
T TIGR00459        16 QTVTLAGWVNRRRDLGGLIFIDLRDRSGIVQVVCDPD-ADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLDTGEIEIL   94 (583)
T ss_pred             CEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCC-HHHHHHHhcCCCCCEEEEEEEEEeCCccccCccCCCCcEEEE
Confidence            3699999999999888888889999999999875333 111123457899999999999974          23456777


Q ss_pred             EEEeeeC
Q 024592          138 AYSLRPI  144 (265)
Q Consensus       138 ~~~i~~v  144 (265)
                      +..+..+
T Consensus        95 ~~~i~iL  101 (583)
T TIGR00459        95 AESITLL  101 (583)
T ss_pred             EeEEEEe
Confidence            7776554

In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.

>PRK00484 lysS lysyl-tRNA synthetase; Reviewed

Probab=95.98  E-value=0.045  Score=53.29  Aligned_cols=100  Identities=18%  Similarity=0.152  Sum_probs=65.6

Q ss_pred             eeeeHHHHhcCCCC-CCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccccCCC
Q 024592           42 LPMTVKQLSELSSN-DESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQISKG  118 (265)
Q Consensus        42 ~PvtIkqi~~a~~~-~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~g  118 (265)
                      +..+|+++...-.. ......-   .-..|+|.|||.+++.....+.+.|.|+||.|.|..-.+...+  -.....+..|
T Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~---~~~~v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g  107 (491)
T PRK00484         31 RTHTAAELRAKYDDKEKEELEE---LEIEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLG  107 (491)
T ss_pred             CccCHHHHHHHhccccchhhcc---cCcEEEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCC
Confidence            34678888765211 1111100   0156999999999998888888899999999998754332111  1123358999


Q ss_pred             CEEEEEEEeee-eCCccEEEEEEeeeC
Q 024592          119 MYVRVYGHLKA-FQDKRSLNAYSLRPI  144 (265)
Q Consensus       119 ~yVrV~G~i~~-f~~~~~i~~~~i~~v  144 (265)
                      +.|.|.|.+.. -.+...|.+..++.+
T Consensus       108 ~~v~v~G~v~~t~~ge~el~~~~~~vl  134 (491)
T PRK00484        108 DIIGVEGTLFKTKTGELSVKATELTLL  134 (491)
T ss_pred             CEEEEEEEEEEcCCCcEEEEEeEEEEE
Confidence            99999999875 345566666665543

>PRK05672 dnaE2 error-prone DNA polymerase; Validated

Probab=95.94  E-value=0.025  Score=59.73  Aligned_cols=76  Identities=18%  Similarity=0.246  Sum_probs=59.0

Q ss_pred             EEEEEEEEEEeeeCCC---eEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCC
Q 024592           69 TITVVGIVCDMQDKEP---QFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPII  145 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t---~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~  145 (265)
                      .|+++|+|..+....|   ...++|+|.||.++|..|.+.-.  .....++++..|.|.|+++.-++..++.+..|.++.
T Consensus       955 ~v~v~g~i~~~~~~~TkkGmaf~~leD~~g~~e~~ifp~~~~--~~~~~l~~~~~~~v~g~v~~~~~~~~~~~~~i~~~~ 1032 (1046)
T PRK05672        955 RVRVAGVVTHRQRPGTASGVTFLTLEDETGMVNVVVWPGLWE--RQRREALGARLLLVRGRVQNAEGVRHLVADRLEDLS 1032 (1046)
T ss_pred             EEEEEEEEEEEEEecCCCceEEEEEecCCCCEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeeeechH
Confidence            4889999988765422   57789999999999999976321  123568999999999999976666788888887764


Q ss_pred             C
Q 024592          146 D  146 (265)
Q Consensus       146 d  146 (265)
                      +
T Consensus      1033 ~ 1033 (1046)
T PRK05672       1033 P 1033 (1046)
T ss_pred             H
Confidence            4

>PRK06920 dnaE DNA polymerase III DnaE; Reviewed

Probab=95.94  E-value=0.019  Score=60.74  Aligned_cols=75  Identities=12%  Similarity=0.148  Sum_probs=59.0

Q ss_pred             EEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee
Q 024592           69 TITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP  143 (265)
Q Consensus        69 ~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~  143 (265)
                      .|+++|.|.+++..     .....++|+|.||.+++..|.+.-.  .....+.++..|.|.|++..-++..++.+..+.|
T Consensus       945 ~v~v~g~i~~~~~~~tk~g~~maf~~leD~tg~~e~~vFp~~y~--~~~~~l~~~~~~~v~G~v~~~~~~~~~~~~~i~~ 1022 (1107)
T PRK06920        945 VQRAIVYITSVKVIRTKKGQKMAFITFCDQNDEMEAVVFPETYI--HFSDKLQEGAIVLVDGTIELRNHKLQWIVNGLYP 1022 (1107)
T ss_pred             EEEEEEEEEEeEeecCCCCCeEEEEEEeeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCcEEEEEeeccc
Confidence            68999999988532     3467889999999999999976321  2245689999999999998756667888888876


Q ss_pred             CC
Q 024592          144 II  145 (265)
Q Consensus       144 v~  145 (265)
                      +.
T Consensus      1023 l~ 1024 (1107)
T PRK06920       1023 LE 1024 (1107)
T ss_pred             HH
Confidence            64

>PRK12366 replication factor A; Reviewed

Probab=95.89  E-value=0.031  Score=56.14  Aligned_cols=73  Identities=23%  Similarity=0.345  Sum_probs=58.4

Q ss_pred             EEEEEEEEEEeeeC----------CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee-eCCccEEE
Q 024592           69 TITVVGIVCDMQDK----------EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA-FQDKRSLN  137 (265)
Q Consensus        69 ~V~iVG~V~~v~~~----------~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~-f~~~~~i~  137 (265)
                      .|.|+|.|.++...          .....+.|.|.||+|.+.+|.+.+.     ..+..|+.|+|.|..+. |++...|.
T Consensus       186 ~v~v~G~V~~~~~~~~f~rkdg~~~~~r~~~l~D~TG~irvTlW~~~a~-----~~~~~g~vv~i~g~~~~~~~~~~el~  260 (637)
T PRK12366        186 SATIEGEVTKAYPIKEFTRKDGSEGKLKSFILKDDTGSIRVTLWNDLTD-----IEVNKGDIVRVKGYVKQGYRTGLEIS  260 (637)
T ss_pred             eEEEEEEEEEccCcEEEEEcCCCeeEEEEEEEEcCCCcEEEEEEChhhc-----ccCCCCCEEEEEeEEecCcCCceEEE
Confidence            79999999887531          2467899999999999999987652     35899999999998554 77888888


Q ss_pred             EEEeeeCCC
Q 024592          138 AYSLRPIID  146 (265)
Q Consensus       138 ~~~i~~v~d  146 (265)
                      +.....|..
T Consensus       261 ~~~~~~i~~  269 (637)
T PRK12366        261 ANNIEILEK  269 (637)
T ss_pred             eCCceeecc
Confidence            877666654

>PLN02903 aminoacyl-tRNA ligase

Probab=95.88  E-value=0.056  Score=54.18  Aligned_cols=78  Identities=19%  Similarity=0.181  Sum_probs=56.5

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc-cccccccCCCCEEEEEEEeeee----------CCccEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME-FNEVNQISKGMYVRVYGHLKAF----------QDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~g~yVrV~G~i~~f----------~~~~~i  136 (265)
                      ..|+|.|||.+++....-+.+.|.|+||.|.|..-.+...+ ......+..++.|.|.|.|+.-          .+...|
T Consensus        73 k~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G~V~~r~~~~~n~~~~tGeiEl  152 (652)
T PLN02903         73 SRVTLCGWVDLHRDMGGLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEGTVRSRPQESPNKKMKTGSVEV  152 (652)
T ss_pred             CEEEEEEEEEEEecCCCcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCCCEEEEEEEEEeCCCcCcCCCCCCCCEEE
Confidence            36999999999998887788899999999998764332111 1123578999999999999852          144566


Q ss_pred             EEEEeeeCC
Q 024592          137 NAYSLRPII  145 (265)
Q Consensus       137 ~~~~i~~v~  145 (265)
                      .+..+..+.
T Consensus       153 ~~~~i~VL~  161 (652)
T PLN02903        153 VAESVDILN  161 (652)
T ss_pred             EEeEEEEEe
Confidence            666655543

>COG3111 Periplasmic protein with OB-fold [Function unknown]

Probab=95.84  E-value=0.2  Score=39.46  Aligned_cols=81  Identities=15%  Similarity=0.290  Sum_probs=57.2

Q ss_pred             eeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEE----EecccccccccccccC
Q 024592           41 LLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECS----RWAHEQMEFNEVNQIS  116 (265)
Q Consensus        41 ~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~----~w~~~~~~~~~~~~~~  116 (265)
                      ..-.|+++-+++..  +          ..|+|.|.|+..-...   .|...|+||+|.+-    .|..        ..+.
T Consensus        43 ~~~~TV~~Ak~~~D--d----------a~V~l~GnIv~qi~~D---~y~FrD~sGeI~VeIdd~~w~g--------~tv~   99 (128)
T COG3111          43 AKVTTVDQAKTLHD--D----------AWVSLEGNIVRQIGDD---RYVFRDASGEINVDIDDKVWNG--------QTVT   99 (128)
T ss_pred             cceeEHHHhhcccc--C----------CeEEEEeeEEEeeCCc---eEEEEcCCccEEEEecccccCC--------cccC
Confidence            44567888777632  3          6788999887754443   56889999987765    4543        3577


Q ss_pred             CCCEEEEEEEeeeeCCccEEEEEEeeeC
Q 024592          117 KGMYVRVYGHLKAFQDKRSLNAYSLRPI  144 (265)
Q Consensus       117 ~g~yVrV~G~i~~f~~~~~i~~~~i~~v  144 (265)
                      +.+.|++.|.+..=-.+..|-+.+|+++
T Consensus       100 P~dkV~I~GevDk~~~~~eIdV~~I~k~  127 (128)
T COG3111         100 PKDKVRIQGEVDKDWNSVEIDVKHIEKL  127 (128)
T ss_pred             cccEEEEEeEEcCCCccceeEhhheEec
Confidence            8899999999976445566766666654

>PRK00476 aspS aspartyl-tRNA synthetase; Validated

Probab=95.83  E-value=0.061  Score=53.49  Aligned_cols=76  Identities=17%  Similarity=0.229  Sum_probs=55.1

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee----------CCccEEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF----------QDKRSLN  137 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f----------~~~~~i~  137 (265)
                      ..|+|.|||.+++.....+.+.|.|+||.|.|..-. .....+....+..++.|.|.|.+..-          .+...|.
T Consensus        18 ~~V~l~GwV~~~R~~g~l~Fi~LrD~~g~iQ~v~~~-~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~n~~~~~g~~El~   96 (588)
T PRK00476         18 QTVTLCGWVHRRRDHGGLIFIDLRDREGIVQVVFDP-DAEAFEVAESLRSEYVIQVTGTVRARPEGTVNPNLPTGEIEVL   96 (588)
T ss_pred             CEEEEEEEEEEEEeCCCeEEEEEEeCCceEEEEEeC-CHHHHHHHhCCCCCCEEEEEEEEEecCCcccCccCCCCcEEEE
Confidence            359999999999988888888999999999887532 11111234578999999999999862          2345565


Q ss_pred             EEEeeeC
Q 024592          138 AYSLRPI  144 (265)
Q Consensus       138 ~~~i~~v  144 (265)
                      +..++.+
T Consensus        97 ~~~i~il  103 (588)
T PRK00476         97 ASELEVL  103 (588)
T ss_pred             EeEEEEE
Confidence            5555443

>PRK07374 dnaE DNA polymerase III subunit alpha; Validated

Probab=95.81  E-value=0.03  Score=59.69  Aligned_cols=77  Identities=16%  Similarity=0.239  Sum_probs=60.3

Q ss_pred             eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592           68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~  142 (265)
                      ..|+++|.|.+++..     .....++|+|.||.++|..|.+.-.  .....+.++..|.|.|++..-.+..++.+..+.
T Consensus      1001 ~~v~v~g~i~~~k~~~Tk~G~~maf~~leD~tg~~e~vvFp~~y~--~~~~~l~~~~~~~v~g~v~~~~~~~~~~~~~i~ 1078 (1170)
T PRK07374       1001 AKVSAIAMIPEMKQVTTRKGDRMAILQLEDLTGSCEAVVFPKSYE--RLSDHLMTDTRLLVWAKVDRRDDRVQLIIDDCR 1078 (1170)
T ss_pred             CEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeeee
Confidence            468999999988632     2357789999999999999975321  123568999999999999875567789998888


Q ss_pred             eCCC
Q 024592          143 PIID  146 (265)
Q Consensus       143 ~v~d  146 (265)
                      ++.+
T Consensus      1079 ~l~~ 1082 (1170)
T PRK07374       1079 EIDD 1082 (1170)
T ss_pred             cHhh
Confidence            7754

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=95.79  E-value=0.033  Score=40.94  Aligned_cols=55  Identities=20%  Similarity=0.217  Sum_probs=45.8

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      ...|+++|...     +.++++.+|++.++++...|...|..|.+.|.|.. -++..|..+
T Consensus         7 ~~~Il~~l~~~-----~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~   62 (91)
T smart00346        7 GLAVLRALAEE-----PGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLG   62 (91)
T ss_pred             HHHHHHHHHhC-----CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceeec
Confidence            34578888652     24799999999999999999999999999999998 566677654

>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional

Probab=95.75  E-value=0.06  Score=54.48  Aligned_cols=77  Identities=12%  Similarity=0.170  Sum_probs=56.3

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccccCCCCEEEEEEEeeee----------CCccE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQISKGMYVRVYGHLKAF----------QDKRS  135 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~g~yVrV~G~i~~f----------~~~~~  135 (265)
                      ..|+|.|||.+++....-+.+.|.|+||.|.|..-.+...+  ......+..++.|.|.|.++.-          .+...
T Consensus        19 ~~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G~v~~r~~~~~n~~~~tg~iE   98 (706)
T PRK12820         19 REVCLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVALQGEVQKRLEETENPHIETGDIE   98 (706)
T ss_pred             CEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEeEEeccCccccCCCCCCCcEE
Confidence            45999999999998888888899999999998764332111  1123578999999999998872          14456


Q ss_pred             EEEEEeeeC
Q 024592          136 LNAYSLRPI  144 (265)
Q Consensus       136 i~~~~i~~v  144 (265)
                      |.+..+..+
T Consensus        99 l~~~~i~iL  107 (706)
T PRK12820         99 VFVRELSIL  107 (706)
T ss_pred             EEeeEEEEE
Confidence            666655544

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.73  E-value=0.032  Score=36.27  Aligned_cols=45  Identities=20%  Similarity=0.326  Sum_probs=39.4

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +..|+++|.+.      .++++.+|++.++++...++..|..|.++|.|..
T Consensus         2 ~~~il~~l~~~------~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~   46 (53)
T smart00420        2 QQQILELLAQQ------GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR   46 (53)
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            45688888652      3699999999999999999999999999999986

>PLN02221 asparaginyl-tRNA synthetase

Probab=95.67  E-value=0.13  Score=51.07  Aligned_cols=94  Identities=15%  Similarity=0.201  Sum_probs=62.3

Q ss_pred             eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCC--eEEEEEEcCC--CeEEEEEecccccccccccccCC
Q 024592           42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEP--QFIFLIDDGT--GRIECSRWAHEQMEFNEVNQISK  117 (265)
Q Consensus        42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t--~~~y~LdDgT--G~I~~~~w~~~~~~~~~~~~~~~  117 (265)
                      ..++|+.|+..+.. +  -...|   ..|+|.|||.+++....  .+.+.|.|+|  |.|.|..-.+..   .....+..
T Consensus        31 ~~~~~~~~~~~~~~-~--~~~~g---~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~---~~~~~L~~  101 (572)
T PLN02221         31 DRVLIRSILDRPDG-G--AGLAG---QKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSLY---DLSTLVAT  101 (572)
T ss_pred             CceEHHHHhccccC-C--hhcCC---CEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCchh---hHHhcCCC
Confidence            56689999855211 1  11122   46999999999998764  5677999999  899997632211   11125788


Q ss_pred             CCEEEEEEEeeeeC------CccEEEEEEeeeC
Q 024592          118 GMYVRVYGHLKAFQ------DKRSLNAYSLRPI  144 (265)
Q Consensus       118 g~yVrV~G~i~~f~------~~~~i~~~~i~~v  144 (265)
                      ++.|+|.|.|+.-.      +...|.+..+..+
T Consensus       102 ES~V~V~G~V~~~~~~~~~~~~iEl~v~~i~vl  134 (572)
T PLN02221        102 GTCVTVDGVLKVPPEGKGTKQKIELSVEKVIDV  134 (572)
T ss_pred             ceEEEEEEEEEeCCccCCCCccEEEEEeEEEEE
Confidence            99999999998632      2345666555443

>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial

Probab=95.65  E-value=0.093  Score=51.18  Aligned_cols=75  Identities=13%  Similarity=0.106  Sum_probs=53.2

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc--ccc-cccCCCCEEEEEEEeeeeC-CccEEEEEEeee
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF--NEV-NQISKGMYVRVYGHLKAFQ-DKRSLNAYSLRP  143 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~--~~~-~~~~~g~yVrV~G~i~~f~-~~~~i~~~~i~~  143 (265)
                      .|+|.|+|.+++.......+.|.|+||.|.|..-.+...+.  ... ..+..|+.|.|.|.+..-+ +...|.+..+..
T Consensus        55 ~v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~gelel~~~~i~i  133 (496)
T TIGR00499        55 EVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKTGELSVHVTELQI  133 (496)
T ss_pred             EEEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCCCcEEEEeeEEEE
Confidence            48999999999987788888999999999987643321110  111 2379999999999987543 445565555443

This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.

>PRK06386 replication factor A; Reviewed

Probab=95.62  E-value=0.054  Score=50.55  Aligned_cols=70  Identities=16%  Similarity=0.310  Sum_probs=53.6

Q ss_pred             eEEEEEEEEEEeeeC--------CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEEEE
Q 024592           68 NTITVVGIVCDMQDK--------EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSLNA  138 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~--------~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i~~  138 (265)
                      ..|.+.|+|.++.+.        ..-....|.|.||+|....|.+         .+.+|+.|+|.+- ++.|++..+|++
T Consensus       118 ~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTGrIr~TlW~~---------~l~eGd~v~i~na~v~e~~G~~el~v  188 (358)
T PRK06386        118 PYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTARVRISSFGK---------PLEDNRFVRIENARVSQYNGYIEISV  188 (358)
T ss_pred             CceEEEEEEEEccCceEecCCCccEEEEEEEEcCCCeEEEEEccc---------cccCCCEEEEeeeEEEccCCeEEEEe
Confidence            457888888876431        1245789999999999999964         3789999999886 667999999998


Q ss_pred             EEeeeCCC
Q 024592          139 YSLRPIID  146 (265)
Q Consensus       139 ~~i~~v~d  146 (265)
                      .....|+.
T Consensus       189 ~~~t~I~~  196 (358)
T PRK06386        189 GNKSVIKE  196 (358)
T ss_pred             CCeEEEEE
Confidence            55544443

>PLN02502 lysyl-tRNA synthetase

Probab=95.62  E-value=0.099  Score=51.62  Aligned_cols=77  Identities=14%  Similarity=0.130  Sum_probs=55.0

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc----ccc-cccCCCCEEEEEEEeee-eCCccEEEEEEe
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF----NEV-NQISKGMYVRVYGHLKA-FQDKRSLNAYSL  141 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~----~~~-~~~~~g~yVrV~G~i~~-f~~~~~i~~~~i  141 (265)
                      ..|+|.|+|.+++.....+.+.|.|++|.|.|..-.+...+.    ... ..+..|+.|.|.|.+.. -.+...|.+..+
T Consensus       109 ~~V~v~GrV~~~R~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~~gelel~~~~i  188 (553)
T PLN02502        109 VSVSVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKKGELSIFPTSF  188 (553)
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecCCCCEEEEEeEE
Confidence            359999999999988888889999999999987543321110    111 35889999999998764 235566666555


Q ss_pred             eeC
Q 024592          142 RPI  144 (265)
Q Consensus       142 ~~v  144 (265)
                      ..+
T Consensus       189 ~vL  191 (553)
T PLN02502        189 EVL  191 (553)
T ss_pred             EEE
Confidence            443

>PRK15491 replication factor A; Provisional

Probab=95.60  E-value=0.05  Score=51.18  Aligned_cols=75  Identities=23%  Similarity=0.346  Sum_probs=55.8

Q ss_pred             EEEEEEEEEEeee-------CC---CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-ee--eeCCccE
Q 024592           69 TITVVGIVCDMQD-------KE---PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LK--AFQDKRS  135 (265)
Q Consensus        69 ~V~iVG~V~~v~~-------~~---t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~--~f~~~~~  135 (265)
                      .|.|.|+|.++..       ..   ......|.|.||.|.+..|.+.+.   ..+.|++|+.|++... +|  .|+++..
T Consensus       178 ~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG~Ir~t~W~~~a~---~~~~l~~Gd~V~i~~~~~r~~~~~g~~E  254 (374)
T PRK15491        178 DINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETGKIRVTLWDGKTD---LADKLENGDSVEIINGYARTNNYSQEVE  254 (374)
T ss_pred             cEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCCeEEEEEecchhc---ccccCCCCCEEEEEeceEEEeccCCCEE
Confidence            4888999988743       11   356689999999999999987542   3467999999999663 55  4667888


Q ss_pred             EEEE---EeeeCCC
Q 024592          136 LNAY---SLRPIID  146 (265)
Q Consensus       136 i~~~---~i~~v~d  146 (265)
                      |++.   .|.+..+
T Consensus       255 l~~~~~s~I~~~~~  268 (374)
T PRK15491        255 IQIGNHGSLRKTDR  268 (374)
T ss_pred             EEeCCCceEEECCc
Confidence            8863   5777655

>PRK07218 replication factor A; Provisional

Probab=95.59  E-value=0.06  Score=51.36  Aligned_cols=83  Identities=22%  Similarity=0.339  Sum_probs=62.8

Q ss_pred             eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeC--------CCeEEEEEEcCCCeEEEEEecccccccccccc
Q 024592           43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDK--------EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQ  114 (265)
Q Consensus        43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~--------~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~  114 (265)
                      ++.|++|....              ..|.|.|+|.++.+.        ..-....|-|.||+|....|.+.        .
T Consensus        58 ~~kI~Di~~~~--------------~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~~~--------~  115 (423)
T PRK07218         58 SKDIKELSTDD--------------KNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWKDF--------G  115 (423)
T ss_pred             CccHhhCCCCC--------------ceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEECCC--------C
Confidence            56688874321              578899999887521        24567799999999999999832        3


Q ss_pred             cCCCCEEEEEE-EeeeeCCccEEEE---EEeeeCCCh
Q 024592          115 ISKGMYVRVYG-HLKAFQDKRSLNA---YSLRPIIDF  147 (265)
Q Consensus       115 ~~~g~yVrV~G-~i~~f~~~~~i~~---~~i~~v~d~  147 (265)
                      +++|+.|+|.+ .++.|+++..|++   ..|..+++.
T Consensus       116 l~~Gdvv~I~na~vre~~g~~el~ig~~t~I~~~de~  152 (423)
T PRK07218        116 LSPGDTVTIGNAGVREWDGRPELNIGESTTVSLLDDS  152 (423)
T ss_pred             CCCCCEEEEeccEeeccCCceEEeccCcceEEEcCcc
Confidence            99999999995 6899999989986   456655553

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=95.59  E-value=0.014  Score=41.18  Aligned_cols=46  Identities=20%  Similarity=0.359  Sum_probs=37.8

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSID  255 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD  255 (265)
                      .+|.++|++.      .-++..+|+++|+.+++.|+..|+.|+..|+|-.++
T Consensus         3 ~~i~~~l~~~------~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~   48 (69)
T PF09012_consen    3 QEIRDYLRER------GRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVD   48 (69)
T ss_dssp             HHHHHHHHHS-------SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEE
T ss_pred             HHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence            3588888763      368999999999999999999999999999998833

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>PRK06826 dnaE DNA polymerase III DnaE; Reviewed

Probab=95.54  E-value=0.046  Score=58.29  Aligned_cols=77  Identities=14%  Similarity=0.256  Sum_probs=59.7

Q ss_pred             eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee-CCccEEEEEEe
Q 024592           68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF-QDKRSLNAYSL  141 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i  141 (265)
                      ..|+++|.|.+++..     .....++|+|.||.+++..|.+.-.  .....+.++..|.|.|++... ++..++.+..+
T Consensus       992 ~~v~v~g~i~~~~~~~tk~G~~maf~~leD~~g~~e~~vfp~~~~--~~~~~l~~~~~~~v~g~v~~~~~~~~~~~~~~~ 1069 (1151)
T PRK06826        992 DKVIIGGIITEVKRKTTRNNEMMAFLTLEDLYGTVEVIVFPKVYE--KYRSLLNEDNIVLIKGRVSLREDEEPKLICEEI 1069 (1151)
T ss_pred             cEEEEEEEEEEeEeeccCCCCeEEEEEEEECCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCCceEEEEeee
Confidence            368899999887642     2467889999999999999976321  123568999999999999864 46678999888


Q ss_pred             eeCCC
Q 024592          142 RPIID  146 (265)
Q Consensus       142 ~~v~d  146 (265)
                      .++.+
T Consensus      1070 ~~l~~ 1074 (1151)
T PRK06826       1070 EPLVI 1074 (1151)
T ss_pred             ecHhh
Confidence            87754

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=95.47  E-value=0.035  Score=45.99  Aligned_cols=51  Identities=18%  Similarity=0.375  Sum_probs=45.5

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE--Ee
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV--YS  253 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I--Ys  253 (265)
                      ..+..+..+||++|+.+      .-++..+|++++++++..|+.-++.|.++|.|  |.
T Consensus        10 ~~lD~~D~~IL~~Lq~d------~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~   62 (164)
T PRK11169         10 KDLDRIDRNILNELQKD------GRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYT   62 (164)
T ss_pred             hhHHHHHHHHHHHhccC------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            34778999999999874      35789999999999999999999999999998  66

>PLN02603 asparaginyl-tRNA synthetase

Probab=95.45  E-value=0.11  Score=51.50  Aligned_cols=96  Identities=18%  Similarity=0.309  Sum_probs=62.4

Q ss_pred             eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCC--eEEEEEeccccccccccc--ccCC
Q 024592           42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTG--RIECSRWAHEQMEFNEVN--QISK  117 (265)
Q Consensus        42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG--~I~~~~w~~~~~~~~~~~--~~~~  117 (265)
                      ..+.|++|+..+...  .-.+ |   ..|+|.|||++++.........|.|+||  .|.|..=.+ ........  .+..
T Consensus        88 ~~~~~~~~~~~~~~~--~~~~-g---~~V~v~GwV~~iR~~g~~~Fi~l~Dgs~~~~lQ~v~~~~-~~~~~~l~~~~l~~  160 (565)
T PLN02603         88 KKLRIADVKGGEDEG--LARV-G---KTLNVMGWVRTLRAQSSVTFIEVNDGSCLSNMQCVMTPD-AEGYDQVESGLITT  160 (565)
T ss_pred             CceEhhhcccccccc--cccC-C---CEEEEEEEEEEEEeCCCeEEEEEECCCCCEeEEEEEECc-HHHHHHHhhcCCCC
Confidence            456788887431110  1111 2   4699999999999888888889999997  488876322 11111122  3889


Q ss_pred             CCEEEEEEEeeeeCCc---cEEEEEEeeeC
Q 024592          118 GMYVRVYGHLKAFQDK---RSLNAYSLRPI  144 (265)
Q Consensus       118 g~yVrV~G~i~~f~~~---~~i~~~~i~~v  144 (265)
                      |+.|.|.|.++.-.+.   ..|.+..+..+
T Consensus       161 gs~V~V~G~v~~~~~~~~~~EL~v~~i~vl  190 (565)
T PLN02603        161 GASVLVQGTVVSSQGGKQKVELKVSKIVVV  190 (565)
T ss_pred             CCEEEEEEEEEecCCCCccEEEEEeEEEEE
Confidence            9999999999864332   46666665443

>PRK12366 replication factor A; Reviewed

Probab=95.44  E-value=0.11  Score=52.20  Aligned_cols=66  Identities=24%  Similarity=0.317  Sum_probs=50.9

Q ss_pred             eEEEEEEEEEEeeeCC----------CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEE
Q 024592           68 NTITVVGIVCDMQDKE----------PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~----------t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i  136 (265)
                      ..|.|+|+|.++.+..          ..-...|.|.||+|.+.+|.+.+.     ..+.+|+.|++.+- ++.|+|...|
T Consensus       409 ~~VdVig~V~~v~~~~~i~~k~G~~~~~r~i~l~D~TG~I~vtlWg~~a~-----~~~~~G~vi~i~~~~V~~~~g~~~L  483 (637)
T PRK12366        409 NDITVIARVVEDYPVNEFERSDGSKGKVRNIELADGTGSIRLTLWDDDAE-----IEIKEGDAIKILHPYVKENGDYLDL  483 (637)
T ss_pred             cEEEEEEEEEEccCceEEEecCCCEeEEEEEEEEeCCCEEEEEEeccccc-----cCCCCCCEEEEEeeEEEeCCCeeEE
Confidence            5788999998764321          245678999999999999987542     25788999998764 7789988777


Q ss_pred             EE
Q 024592          137 NA  138 (265)
Q Consensus       137 ~~  138 (265)
                      ++
T Consensus       484 s~  485 (637)
T PRK12366        484 SI  485 (637)
T ss_pred             Ee
Confidence            76

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=95.43  E-value=0.046  Score=36.43  Aligned_cols=42  Identities=12%  Similarity=0.294  Sum_probs=34.8

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCC
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENS  249 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG  249 (265)
                      +.+|+.+|.+.     +..++.++|++.|+++...|+..|..|.+.|
T Consensus         2 ~~~il~~L~~~-----~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    2 QKQILKLLLES-----KEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHHHT-----TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHc-----CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            45688888542     2349999999999999999999999999999

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=95.43  E-value=0.046  Score=40.34  Aligned_cols=62  Identities=11%  Similarity=0.109  Sum_probs=50.6

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC-----ceeeccC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF-----HYKSAVN  264 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~-----hyk~t~~  264 (265)
                      .+++..+-.||.+|...      .+++..+|++.++++...|..+|..|.+.|.|+. -+..     +|+.|..
T Consensus         6 ~~l~~~~~~il~~l~~~------~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~   73 (101)
T smart00347        6 LGLTPTQFLVLRILYEE------GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEE   73 (101)
T ss_pred             cCCCHHHHHHHHHHHHc------CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHh
Confidence            35777888899999763      2689999999999999999999999999999998 5532     5655543

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.41  E-value=0.079  Score=53.66  Aligned_cols=66  Identities=23%  Similarity=0.310  Sum_probs=50.8

Q ss_pred             eEEEEEEEEEEeeeC---CCeEEEEEEcCCCeEEEEEec-ccccccccccccCCCCEEEEEEEeeeeCCccEE
Q 024592           68 NTITVVGIVCDMQDK---EPQFIFLIDDGTGRIECSRWA-HEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~---~t~~~y~LdDgTG~I~~~~w~-~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i  136 (265)
                      ..|+++|.|.++...   ...+.+.+.|+||.|.+++|. +..   -....+++|..+.|+|+++.+++++++
T Consensus        60 ~~vtv~g~V~~~~~~~~~~~~~~v~l~D~tg~i~l~~F~~n~~---~~~~~l~~G~~~~v~Gkv~~~~~~~qm  129 (681)
T PRK10917         60 EKVTVEGEVLSAEVVFGKRRRLTVTVSDGTGNLTLRFFNFNQP---YLKKQLKVGKRVAVYGKVKRGKYGLEM  129 (681)
T ss_pred             CEEEEEEEEEEEEEccCCceEEEEEEEECCeEEEEEEEccCcH---HHHhhCCCCCEEEEEEEEEecCCeEEE
Confidence            478999999887533   357899999999999998773 221   123578999999999999998766554

>PLN02850 aspartate-tRNA ligase

Probab=95.36  E-value=0.13  Score=50.60  Aligned_cols=77  Identities=13%  Similarity=0.200  Sum_probs=56.2

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc----ccccccCCCCEEEEEEEeeee-------CCccEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF----NEVNQISKGMYVRVYGHLKAF-------QDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~----~~~~~~~~g~yVrV~G~i~~f-------~~~~~i  136 (265)
                      ..|+|.|+|.+++..+..+.+.|.|++|.|.|..-.....-+    +....|..|+.|.|.|.|+.-       .+...|
T Consensus        82 ~~V~v~Grv~~~R~~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~t~~~El  161 (530)
T PLN02850         82 SEVLIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRESVVDVEGVVSVPKKPVKGTTQQVEI  161 (530)
T ss_pred             CEEEEEEEEEEEccCCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCCCEEEEEEEEEccCcCCCCCCccEEE
Confidence            469999999999988887888999999999998754422101    124578999999999999842       123556


Q ss_pred             EEEEeeeC
Q 024592          137 NAYSLRPI  144 (265)
Q Consensus       137 ~~~~i~~v  144 (265)
                      .+..|..+
T Consensus       162 ~~~~i~vl  169 (530)
T PLN02850        162 QVRKIYCV  169 (530)
T ss_pred             EEeEEEEE
Confidence            66665544

>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities

Probab=95.34  E-value=0.073  Score=36.82  Aligned_cols=52  Identities=13%  Similarity=0.196  Sum_probs=38.6

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      +-..|.+.|.... ....+=+ +..+|+++++.+...|++||..|.++|.|+..
T Consensus         5 i~~~l~~~I~~g~-~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~   57 (64)
T PF00392_consen    5 IYDQLRQAILSGR-LPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERR   57 (64)
T ss_dssp             HHHHHHHHHHTTS-S-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCC-CCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence            3455666666542 2334567 89999999999999999999999999999873

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=95.34  E-value=0.039  Score=42.06  Aligned_cols=47  Identities=15%  Similarity=0.342  Sum_probs=42.4

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      ++++.+|+..|+..      ..++..+|++.+++++..++..+..|.++|.|.
T Consensus         2 d~~D~~il~~L~~~------~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~   48 (108)
T smart00344        2 DEIDRKILEELQKD------ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK   48 (108)
T ss_pred             CHHHHHHHHHHHHh------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            46788999999873      368999999999999999999999999999987

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators

Probab=95.33  E-value=0.13  Score=34.95  Aligned_cols=39  Identities=18%  Similarity=0.152  Sum_probs=33.5

Q ss_pred             CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceee
Q 024592          223 HRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKS  261 (265)
Q Consensus       223 ~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~  261 (265)
                      +..+|++.++++.+.|+++|..|.++|.|......+|..
T Consensus        27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~~~~~~l   65 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFV   65 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeEEe
Confidence            499999999999999999999999999987654445543

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

>PRK07279 dnaE DNA polymerase III DnaE; Reviewed

Probab=95.13  E-value=0.063  Score=56.52  Aligned_cols=75  Identities=5%  Similarity=0.177  Sum_probs=57.2

Q ss_pred             EEEEEEEEEEee----e--CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592           69 TITVVGIVCDMQ----D--KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus        69 ~V~iVG~V~~v~----~--~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~  142 (265)
                      .+.++|+|.++.    .  ......++|+|.||.|+|..|.+.-.  .....+.++..|.|.|++..-++..++.+..+.
T Consensus       886 ~~~~~~~i~~~~~~~tk~~g~~maf~~leD~~g~ie~~vFp~~y~--~~~~~l~~~~~~~v~G~v~~~~~~~~l~~~~i~  963 (1034)
T PRK07279        886 EATILVQIQSIRVIRTKTKGQQMAFLSVTDTKKKLDVTLFPETYR--QYKDELKEGKFYYLKGKIQERDGRLQMVLQQIQ  963 (1034)
T ss_pred             cceEEEEEEEEEEEEEcCCCCeEEEEEEeeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeeEEEEeeee
Confidence            356777776653    2  23468889999999999999976321  224568999999999999876677889998888


Q ss_pred             eCC
Q 024592          143 PII  145 (265)
Q Consensus       143 ~v~  145 (265)
                      ++.
T Consensus       964 ~l~  966 (1034)
T PRK07279        964 EAS  966 (1034)
T ss_pred             ccc
Confidence            875

>PTZ00401 aspartyl-tRNA synthetase; Provisional

Probab=95.13  E-value=0.17  Score=49.88  Aligned_cols=77  Identities=13%  Similarity=0.210  Sum_probs=56.1

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc---cccccccCCCCEEEEEEEeeee--------CCccEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME---FNEVNQISKGMYVRVYGHLKAF--------QDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~---~~~~~~~~~g~yVrV~G~i~~f--------~~~~~i  136 (265)
                      ..|+|.|+|.+++.....+.+.|.|++|.|.|..-.....+   .+....|..++.|.|.|.|+.-        .+...|
T Consensus        79 ~~V~v~Grv~~~R~~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l~~esiV~V~G~v~~~~~~~~~~~~~~~El  158 (550)
T PTZ00401         79 KTVLIRARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTESIVDVEATVCKVEQPITSTSHSDIEL  158 (550)
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcCCCCCEEEEEEEEEecCccCCCCCCccEEE
Confidence            45999999999998888888899999999999874332111   1123568999999999998862        233556


Q ss_pred             EEEEeeeC
Q 024592          137 NAYSLRPI  144 (265)
Q Consensus       137 ~~~~i~~v  144 (265)
                      .+..+..+
T Consensus       159 ~v~~i~vl  166 (550)
T PTZ00401        159 KVKKIHTV  166 (550)
T ss_pred             EeeEEEEE
Confidence            66555443

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=95.10  E-value=0.06  Score=42.79  Aligned_cols=52  Identities=21%  Similarity=0.191  Sum_probs=45.3

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      -+++.+.-.||..|-+.     +.++++++|++.|+.+.+.|..+|+.|++-|.|+-
T Consensus        23 ~GLs~~Dv~v~~~LL~~-----~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~R   74 (126)
T COG3355          23 YGLSELDVEVYKALLEE-----NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVER   74 (126)
T ss_pred             hCCcHHHHHHHHHHHhh-----cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeee
Confidence            36888888888877532     45889999999999999999999999999999987

>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14)

Probab=95.05  E-value=0.7  Score=35.17  Aligned_cols=64  Identities=17%  Similarity=0.239  Sum_probs=45.4

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID  146 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d  146 (265)
                      +.|+|||+|.+++..    .+++.+.-| .++|+.-.+        .....+.||.|+|++..   ...|.+......-|
T Consensus        16 k~V~ivGkV~~~~~~----~~~~~~~Dg~~v~v~l~~~--------~~~~~~~~vEViG~V~~---~~~I~~~~~~~~g~   80 (101)
T cd04479          16 KTVRIVGKVEKVDGD----SLTLISSDGVNVTVELNRP--------LDLPISGYVEVIGKVSP---DLTIRVLSYIDFGD   80 (101)
T ss_pred             CEEEEEEEEEEecCC----eEEEEcCCCCEEEEEeCCC--------CCcccCCEEEEEEEECC---CCeEEEEEEEECCC
Confidence            689999999998643    355555554 788875432        24577899999999974   46677766665544

RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=95.01  E-value=0.1  Score=33.84  Aligned_cols=46  Identities=20%  Similarity=0.285  Sum_probs=39.3

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+.+|+.+|.+.       -.++.+|++.++++.+.|..-|..|.+.|.|.+
T Consensus         2 ~~R~~Il~~L~~~-------~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen    2 PTRLRILKLLSEG-------PLTVSELAEELGLSQSTVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             HHHHHHHHHHTTS-------SEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHhC-------CCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence            4677889888752       478999999999999999999999999999864

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=94.98  E-value=0.056  Score=37.38  Aligned_cols=59  Identities=17%  Similarity=0.255  Sum_probs=43.6

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC-----Cceeecc
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE-----FHYKSAV  263 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd-----~hyk~t~  263 (265)
                      +.-+-.||.+|..     ....++..+|++.++++...+..+|+.|.+.|.|.. -|+     .+|..|.
T Consensus         2 t~~q~~vL~~l~~-----~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~   66 (68)
T PF13463_consen    2 TRPQWQVLRALAH-----SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTP   66 (68)
T ss_dssp             -HHHHHHHHHHT-------TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-H
T ss_pred             CHHHHHHHHHHHc-----cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCC
Confidence            4456778998872     246889999999999999999999999999999977 554     3566654

>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=94.91  E-value=0.1  Score=49.51  Aligned_cols=75  Identities=23%  Similarity=0.263  Sum_probs=58.2

Q ss_pred             EEeEEEEEEEEEEe--eeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee
Q 024592           66 DVNTITVVGIVCDM--QDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP  143 (265)
Q Consensus        66 ~v~~V~iVG~V~~v--~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~  143 (265)
                      +.+..+++|+|...  ......+.+.+.|++|.|.|..+............|..|+.|.++|.++...    |++.+++.
T Consensus       265 ~~~~~~v~g~v~~~p~~ieGghv~v~i~d~~G~I~~~A~eptk~fr~~a~~L~pGD~i~~~G~~~~~~----~n~ek~~v  340 (421)
T COG1571         265 DYSKYRVVGRVEAEPRAIEGGHVVVEITDGEGEIGAVAFEPTKEFRELARKLIPGDEITVYGSVKPGT----LNLEKFQV  340 (421)
T ss_pred             hccceEEEEEEecccEEeeCCEEEEEecCCCceEEEEEecccccchHHHHhcCCCCEEEEecCccccc----eeEEEEEE
Confidence            34678999988774  3456789999999999999999976554334467899999999999999865    66655554


Q ss_pred             C
Q 024592          144 I  144 (265)
Q Consensus       144 v  144 (265)
                      +
T Consensus       341 ~  341 (421)
T COG1571         341 L  341 (421)
T ss_pred             E
Confidence            3

>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70)

Probab=94.80  E-value=0.22  Score=37.53  Aligned_cols=64  Identities=19%  Similarity=0.337  Sum_probs=43.2

Q ss_pred             EEEEEEEEEeee-----------CCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEE-EeeeeCCccEE
Q 024592           70 ITVVGIVCDMQD-----------KEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQDKRSL  136 (265)
Q Consensus        70 V~iVG~V~~v~~-----------~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~~~~~i  136 (265)
                      |-|+|.|.++..           ......+.|.|.|| .|.|.+|.+.+..    ...+.|+.|.+.+ +++.|+ .+.+
T Consensus         2 vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~----~~~~~~~vv~~~~~~i~~~~-~~~l   76 (101)
T cd04475           2 VDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAEL----FDGSENPVIAIKGVKVSEFN-GKSL   76 (101)
T ss_pred             EeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhh----cccCCCCEEEEEeeEEEecC-CeEE
Confidence            567888876632           12578899999999 8999999875431    1112277777666 466787 4566


Q ss_pred             EE
Q 024592          137 NA  138 (265)
Q Consensus       137 ~~  138 (265)
                      +.
T Consensus        77 ~~   78 (101)
T cd04475          77 ST   78 (101)
T ss_pred             ee
Confidence            55

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=94.75  E-value=0.19  Score=33.42  Aligned_cols=39  Identities=21%  Similarity=0.229  Sum_probs=33.4

Q ss_pred             CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCc
Q 024592          220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFH  258 (265)
Q Consensus       220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~h  258 (265)
                      .-+ +..+|++.++++...|+++|..|.++|.|.......
T Consensus        18 ~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~~g   57 (60)
T smart00345       18 DKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSG   57 (60)
T ss_pred             CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCe
Confidence            356 899999999999999999999999999987644333

>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]

Probab=94.72  E-value=0.07  Score=56.07  Aligned_cols=78  Identities=17%  Similarity=0.322  Sum_probs=60.6

Q ss_pred             eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee--eCCccEEEEEE
Q 024592           68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQDKRSLNAYS  140 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~~~~~i~~~~  140 (265)
                      ..|.|.|.|-.++..     .+-+.|.+-|+|-++.|+.|..+..+.+....++.|++|||.|.|..  |....++.+..
T Consensus       240 ~~v~v~G~IF~~e~~~~ksGr~l~~i~vTD~t~Sl~~k~f~~~~ed~~~~~~ik~g~wvk~~g~v~~d~f~~~l~m~i~~  319 (1444)
T COG2176         240 TRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGIKKGMWVKARGNVQLDTFTRDLTMIIND  319 (1444)
T ss_pred             cceEEEEEEEEEeeeecccCcEEEEEEEecCchheeehhhccccccHHHHhhcccCcEEEEEEEEEecccccceEEEhhh
Confidence            459999999887643     24688999999999999999987666667788999999999999975  45555555555


Q ss_pred             eeeCC
Q 024592          141 LRPII  145 (265)
Q Consensus       141 i~~v~  145 (265)
                      |.+|.
T Consensus       320 I~ei~  324 (1444)
T COG2176         320 INEIE  324 (1444)
T ss_pred             hhhhh
Confidence            54443

>PRK15491 replication factor A; Provisional

Probab=94.68  E-value=0.18  Score=47.42  Aligned_cols=77  Identities=14%  Similarity=0.193  Sum_probs=55.0

Q ss_pred             eEEEEEEEEEEeee--------C--CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee-eeCCccEE
Q 024592           68 NTITVVGIVCDMQD--------K--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK-AFQDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~--------~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~-~f~~~~~i  136 (265)
                      ..|+|.|+|.++..        .  .....+.|-|.||+|.+..|.+.... -....|++|+.|+|.|..+ .|++ ..|
T Consensus        68 ~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~ir~tlW~~~a~~-~~~~~le~G~v~~I~~~~~~~y~g-~Ei  145 (374)
T PRK15491         68 SNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLADL-IKTGDIEVGKSLNISGYAKEGYSG-IEV  145 (374)
T ss_pred             CceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCeEEEEEECchhhh-hccCCcCCCCEEEEeeeeccCccc-EEE
Confidence            56889999987631        1  23455699999999999999865421 1124689999999999988 4555 677


Q ss_pred             EEE---EeeeCCC
Q 024592          137 NAY---SLRPIID  146 (265)
Q Consensus       137 ~~~---~i~~v~d  146 (265)
                      ++.   .+.+.++
T Consensus       146 ~i~~~~~i~~~~~  158 (374)
T PRK15491        146 NIGRYGGISESDE  158 (374)
T ss_pred             EeCCCceeeeccc
Confidence            775   4555544

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=94.67  E-value=0.068  Score=43.20  Aligned_cols=49  Identities=14%  Similarity=0.362  Sum_probs=44.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      .+..+..+||++|+..+      -++..+|++++++++..+...++.|.++|.|-
T Consensus         5 ~lD~~D~~IL~~L~~d~------r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~   53 (154)
T COG1522           5 KLDDIDRRILRLLQEDA------RISNAELAERVGLSPSTVLRRIKRLEEEGVIK   53 (154)
T ss_pred             cccHHHHHHHHHHHHhC------CCCHHHHHHHHCCCHHHHHHHHHHHHHCCcee
Confidence            47789999999999853      38999999999999999999999999999773

>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70)

Probab=94.65  E-value=0.23  Score=37.93  Aligned_cols=67  Identities=24%  Similarity=0.449  Sum_probs=42.6

Q ss_pred             EEEEEEEeee---------CCCeEEEEEEcCCC-eEEEEEeccccccccccc--ccCCCCEEEE--EEEeeeeCCccEEE
Q 024592           72 VVGIVCDMQD---------KEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVN--QISKGMYVRV--YGHLKAFQDKRSLN  137 (265)
Q Consensus        72 iVG~V~~v~~---------~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~--~~~~g~yVrV--~G~i~~f~~~~~i~  137 (265)
                      ++|.|.++..         ......|+|.|.+| +|+|..|-+.+.+-....  ....+-.|-|  ..+|+.|+|.+.+.
T Consensus         2 viG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls   81 (106)
T cd04481           2 VIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLS   81 (106)
T ss_pred             eeEEEEEecceEecccCCccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEE
Confidence            4566655532         34589999999998 699999976443211110  2344555544  36899999876664


Q ss_pred             E
Q 024592          138 A  138 (265)
Q Consensus       138 ~  138 (265)
                      -
T Consensus        82 ~   82 (106)
T cd04481          82 N   82 (106)
T ss_pred             c
Confidence            3

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=94.64  E-value=0.072  Score=43.54  Aligned_cols=50  Identities=10%  Similarity=0.210  Sum_probs=44.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE--Ee
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV--YS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I--Ys  253 (265)
                      .+..+..+||++|+.+      .=.+..+|++++++++..|+.-++.|.++|.|  |.
T Consensus         6 ~lD~~D~~Il~~Lq~d------~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~   57 (153)
T PRK11179          6 QIDNLDRGILEALMEN------ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTR   57 (153)
T ss_pred             ccCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEE
Confidence            4678999999999874      24699999999999999999999999999999  65

>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair

Probab=94.60  E-value=0.65  Score=35.73  Aligned_cols=70  Identities=21%  Similarity=0.270  Sum_probs=40.0

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID  146 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d  146 (265)
                      ..|+|||+|.++...+..++..-.|+ |.|.|..-.+        ..+..+.||.|+|++..-.+-..|....+.+..|
T Consensus        19 k~VrivGkv~~~~~~g~~~~l~~~d~-~~V~v~l~~~--------~~~~~~~~vEviG~V~~~~~~~~i~~~~~~~~g~   88 (109)
T PF08661_consen   19 KTVRIVGKVESVDPDGGSATLSTSDG-GQVTVSLNPP--------SDEELSKYVEVIGKVNDDGTVLSIRYFSFTDFGD   88 (109)
T ss_dssp             SEEEEEEEEEEE-TTSSEEEEE-TTS--EEEEEESS----------SS---SEEEEEEEE-TTS-EEEEEEEE---SSS
T ss_pred             CeEEEEEEEeeEcCCCCEEEEEcCCC-CEEEEEeCCC--------CCCCCCCEEEEEEEEcCCCCceEEEEEEeccCCC
Confidence            58999999999985555444433343 3566654422        2345689999999998765545777777777665

; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]

Probab=94.58  E-value=0.24  Score=49.60  Aligned_cols=74  Identities=19%  Similarity=0.248  Sum_probs=58.1

Q ss_pred             eEEEEEEEEEEeeeC----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeee
Q 024592           68 NTITVVGIVCDMQDK----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP  143 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~  143 (265)
                      ..|+++|.|.++...    .....+.+.|+||.|.+++|.-...   -...+++|.-|.|+|+++.|++..++.--.+..
T Consensus        61 ~~vti~g~V~~~~~~~~~~~~~l~v~~~d~~~~l~l~fFn~~~~---l~~~~~~G~~v~v~Gk~~~~~~~~~~~hpe~~~  137 (677)
T COG1200          61 EIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNFPAY---LKKKLKVGERVIVYGKVKRFKGGLQITHPEYIV  137 (677)
T ss_pred             ceEEEEEEEEeeeccCCCCCceEEEEEecCcEEEEEEEECccHH---HHhhCCCCCEEEEEEEEeeccCceEEEcceEEe
Confidence            578999999887644    3678999999999999998865421   346789999999999999999877666544444


Q ss_pred             C
Q 024592          144 I  144 (265)
Q Consensus       144 v  144 (265)
                      .
T Consensus       138 ~  138 (677)
T COG1200         138 N  138 (677)
T ss_pred             c
Confidence            3

>PRK06386 replication factor A; Reviewed

Probab=94.55  E-value=0.23  Score=46.39  Aligned_cols=65  Identities=14%  Similarity=0.250  Sum_probs=50.4

Q ss_pred             eEEEEEEEEEEeee------C--CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEEEE
Q 024592           68 NTITVVGIVCDMQD------K--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSLNA  138 (265)
Q Consensus        68 ~~V~iVG~V~~v~~------~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i~~  138 (265)
                      ..|.|.|+|.++..      .  .....=.|-|.||+|....|..       .+.+++|+.|++..- ++.|+|+..|++
T Consensus        13 ~~V~v~akVl~~~~r~i~~~~g~~~~~~gllgDeTG~I~fT~W~~-------~~~l~~Gd~v~i~na~v~~~~G~~~Lnv   85 (358)
T PRK06386         13 QNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEF-------PDAVKSGDVIEIKYCYSKEYNGKIRIYF   85 (358)
T ss_pred             CcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcceEEEEecCC-------cccCCCCCEEEEEeEEEeeECCEEEEEE
Confidence            46788888876642      1  2344447999999999999973       246899999999876 679999988888


Q ss_pred             E
Q 024592          139 Y  139 (265)
Q Consensus       139 ~  139 (265)
                      .
T Consensus        86 ~   86 (358)
T PRK06386         86 D   86 (358)
T ss_pred             c
Confidence            4

>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []

Probab=94.52  E-value=0.51  Score=38.28  Aligned_cols=71  Identities=14%  Similarity=0.237  Sum_probs=55.0

Q ss_pred             eEEEEEEEEEEeeeC--------CCeEEEEEEcCCC--------eEEEEEecccccccccccccCC-CCEEEEE-EEeee
Q 024592           68 NTITVVGIVCDMQDK--------EPQFIFLIDDGTG--------RIECSRWAHEQMEFNEVNQISK-GMYVRVY-GHLKA  129 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~--------~t~~~y~LdDgTG--------~I~~~~w~~~~~~~~~~~~~~~-g~yVrV~-G~i~~  129 (265)
                      ..|.|+|+|++...-        .-.++++|-|.|-        .|.|.+|.+..+   ..+.+.. ||.|++. -+|+.
T Consensus        13 ~~vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~---~LP~v~~~GDii~l~r~kv~~   89 (146)
T PF02765_consen   13 KFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKE---SLPNVKSVGDIIRLRRVKVQS   89 (146)
T ss_dssp             EEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHH---HSCTTCSTTHEEEEEEEEEEE
T ss_pred             CEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHH---HCCCCCCCCCEEEEEEEEEEE
Confidence            678999999887532        2268899999883        599999976542   4677777 9999998 78999


Q ss_pred             eCCccEEEEEEe
Q 024592          130 FQDKRSLNAYSL  141 (265)
Q Consensus       130 f~~~~~i~~~~i  141 (265)
                      |+++.++....-
T Consensus        90 ~~~~~~~~~~~~  101 (146)
T PF02765_consen   90 YNGKPQGLSNST  101 (146)
T ss_dssp             ETTEEEEEEECE
T ss_pred             ECCEEEEEecCC
Confidence            999988766433

It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....

>PRK08402 replication factor A; Reviewed

Probab=94.45  E-value=0.14  Score=47.86  Aligned_cols=75  Identities=23%  Similarity=0.250  Sum_probs=53.9

Q ss_pred             eEEEEEEcCCCeEEEEEecccccc-----------c-c---c----ccc-----------cCCCCEEEEEEEee--eeCC
Q 024592           85 QFIFLIDDGTGRIECSRWAHEQME-----------F-N---E----VNQ-----------ISKGMYVRVYGHLK--AFQD  132 (265)
Q Consensus        85 ~~~y~LdDgTG~I~~~~w~~~~~~-----------~-~---~----~~~-----------~~~g~yVrV~G~i~--~f~~  132 (265)
                      .+.+.|+|+||.+.|..|.+....           . .   +    .+.           -..|.+..+.|+++  .|++
T Consensus       246 il~~~l~D~TG~~~vt~f~e~ae~llG~sa~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~~  325 (355)
T PRK08402        246 ILDFGLDDGTGYIRVTLFGDDAAELLGVEPEEIAEKLKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFLG  325 (355)
T ss_pred             EEEEEEEcCCCcEEEEEecHHHHHHhCCCHHHHHHHHHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccCC
Confidence            467789999999999999764321           0 0   0    011           23489999999998  4777


Q ss_pred             ccEEEEEEeeeCCChhHHHHHHHHHHHHH
Q 024592          133 KRSLNAYSLRPIIDFNEITSHFVECIYVQ  161 (265)
Q Consensus       133 ~~~i~~~~i~~v~d~Nei~~H~Levi~~~  161 (265)
                      .. +.+..+.|| |+....-|+++-|...
T Consensus       326 ~~-~~v~~~~~v-d~~~e~~~l~~~i~~~  352 (355)
T PRK08402        326 LI-LKASSWDEV-DYKREIERVRAELEEL  352 (355)
T ss_pred             eE-EEEEEcccC-CHHHHHHHHHHHHHHh
Confidence            55 888889888 6777778888877543

>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria

Probab=94.44  E-value=0.67  Score=37.00  Aligned_cols=65  Identities=23%  Similarity=0.278  Sum_probs=44.6

Q ss_pred             eEEEEEEEEE--Eeee--CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEe
Q 024592           68 NTITVVGIVC--DMQD--KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSL  141 (265)
Q Consensus        68 ~~V~iVG~V~--~v~~--~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i  141 (265)
                      ..|++-|.|.  +++.  ....++|.|.|+...|.|.+--.      .++.|++|.-|-|.|++.   ....+.|..|
T Consensus        51 ~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~------~Pd~F~eg~~VVv~G~~~---~~g~F~A~~l  119 (131)
T PF03100_consen   51 RKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGP------LPDLFREGQGVVVEGRLG---EDGVFEATEL  119 (131)
T ss_dssp             SEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--------CTT--TTSEEEEEEEEC---CTSEEEEEEE
T ss_pred             ceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCC------CCccccCCCeEEEEEEEC---CCCEEEEEEE
Confidence            6788899998  5655  46899999999988898886532      467899999999999882   2334555443

Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.

>PTZ00385 lysyl-tRNA synthetase; Provisional

Probab=94.40  E-value=0.33  Score=48.84  Aligned_cols=77  Identities=14%  Similarity=0.152  Sum_probs=56.8

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccc-cc--ccc-ccccCCCCEEEEEEEeeee-CCccEEEEEEeee
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQ-ME--FNE-VNQISKGMYVRVYGHLKAF-QDKRSLNAYSLRP  143 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~-~~--~~~-~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i~~  143 (265)
                      .|+|.|+|.+++..+.-+.+.|.|.||.|.|..-.++. .+  ... ...+..|+.|.|.|.+..- .+...|.+..+..
T Consensus       109 ~V~vaGrV~~~R~~Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~~GeleI~~~~i~l  188 (659)
T PTZ00385        109 TVRVAGRVTSVRDIGKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQRGELSVAASRMLI  188 (659)
T ss_pred             EEEEEEEEEeeeccCCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecCCceEEEEeeEEEE
Confidence            49999999999988877888999999999998865431 11  111 2358899999999988764 4666776666554


Q ss_pred             CC
Q 024592          144 II  145 (265)
Q Consensus       144 v~  145 (265)
                      ++
T Consensus       189 Ls  190 (659)
T PTZ00385        189 LS  190 (659)
T ss_pred             ec
Confidence            43

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=94.39  E-value=0.11  Score=34.93  Aligned_cols=52  Identities=13%  Similarity=0.271  Sum_probs=43.4

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +..+-.||.+|.+.      .|++..+|++.++++...+...++.|...|.|.. .|.+
T Consensus         2 t~~q~~iL~~l~~~------~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~   54 (59)
T PF01047_consen    2 TPSQFRILRILYEN------GGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPD   54 (59)
T ss_dssp             THHHHHHHHHHHHH------SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             CHHHHHHHHHHHHc------CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence            34566788888764      4799999999999999999999999999999998 6654

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

Probab=94.36  E-value=0.19  Score=34.59  Aligned_cols=55  Identities=20%  Similarity=0.260  Sum_probs=44.9

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC--Cceeec
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE--FHYKSA  262 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd--~hyk~t  262 (265)
                      ..+..|+.++...       +++..+|++.++++...++.+|+.|.+.|.|.. -+.  .+|..|
T Consensus         7 ~~~~~il~~l~~~-------~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~   64 (78)
T cd00090           7 PTRLRILRLLLEG-------PLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLT   64 (78)
T ss_pred             hHHHHHHHHHHHC-------CcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeC
Confidence            5677888887652       289999999999999999999999999999998 544  344444

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=94.30  E-value=0.1  Score=35.73  Aligned_cols=48  Identities=17%  Similarity=0.268  Sum_probs=41.1

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++....||..|..      ..++++.+|++.++++...+..-|..|.+.|.|=.
T Consensus         9 ~p~R~~Il~~L~~------~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~   56 (61)
T PF12840_consen    9 DPTRLRILRLLAS------NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV   56 (61)
T ss_dssp             SHHHHHHHHHHHH------CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHhc------CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence            3678889999933      35899999999999999999999999999999854

...

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=94.25  E-value=0.28  Score=33.56  Aligned_cols=44  Identities=20%  Similarity=0.299  Sum_probs=38.1

Q ss_pred             CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      ...++..+|++.++++...|..+|..|.++|.|......+|..+
T Consensus        23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~~~~~~l~   66 (67)
T cd00092          23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKYRVN   66 (67)
T ss_pred             cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence            45689999999999999999999999999999988445577654

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=94.23  E-value=0.28  Score=49.28  Aligned_cols=65  Identities=23%  Similarity=0.258  Sum_probs=48.5

Q ss_pred             eEEEEEEEEEEeee----CCCeEEEEEEc-CCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEE
Q 024592           68 NTITVVGIVCDMQD----KEPQFIFLIDD-GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~----~~t~~~y~LdD-gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i  136 (265)
                      ..|++.|.|.+...    ....+.+.+.| +||.|.+++|.. .   -....++.|+.|.|+|+++.++++.++
T Consensus        33 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~F~~-~---~~~~~~~~g~~~~~~Gk~~~~~~~~~~  102 (630)
T TIGR00643        33 ERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNR-A---FLKKKFKVGSKVVVYGKVKSSKFKAYL  102 (630)
T ss_pred             CEEEEEEEEEEeEeccCCCCceEEEEEEECCCCEEEEEEECC-H---HHHhhCCCCCEEEEEEEEEeeCCEEEE
Confidence            35777888776432    12468999999 999999998852 1   123578999999999999998876543

>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A

Probab=94.13  E-value=0.1  Score=37.67  Aligned_cols=55  Identities=24%  Similarity=0.323  Sum_probs=40.3

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV  263 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~  263 (265)
                      .+--+||++++       +.+.++.+|+..++++...+.+.|++|.+.|.| .-++..|..|.
T Consensus         6 ~Ii~~IL~~l~-------~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI-~~~~~~Y~lTe   60 (77)
T PF14947_consen    6 EIIFDILKILS-------KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLI-KKKDGKYRLTE   60 (77)
T ss_dssp             HHHHHHHHHH--------TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSE-EEETTEEEE-H
T ss_pred             HHHHHHHHHHH-------cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCe-eCCCCEEEECc
Confidence            34455666664       347889999999999999999999999999999 64677898885

>PTZ00425 asparagine-tRNA ligase; Provisional

Probab=93.95  E-value=0.17  Score=50.25  Aligned_cols=61  Identities=16%  Similarity=0.213  Sum_probs=44.7

Q ss_pred             eEEEEEEEEEEeeeCCC--eEEEEEEcCCC--eEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           68 NTITVVGIVCDMQDKEP--QFIFLIDDGTG--RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t--~~~y~LdDgTG--~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      ..|+|.|||.+++....  .+...|.||||  .|.|..- ...........+..|+-|+|.|.+..
T Consensus        82 ~~Vtl~GWv~~iR~~g~~~~~Fv~lrDgsg~~~iQiVv~-~~~~~~~~l~~l~~gs~v~v~G~v~~  146 (586)
T PTZ00425         82 QIITVCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVD-QSIENYEKLLKCGVGCCFRFTGKLII  146 (586)
T ss_pred             CEEEEEEEEeehhhcCCceEEEEEEECCCCCcceEEEEC-CchHHHHHHhcCCCccEEEEEEEEEc
Confidence            46999999999998663  67779999998  4777542 21111112346889999999999975

>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR

Probab=93.79  E-value=0.27  Score=35.69  Aligned_cols=64  Identities=25%  Similarity=0.215  Sum_probs=41.7

Q ss_pred             EEEEEEEeeeCCCeEEEEEEcCCCe-----EEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEE
Q 024592           72 VVGIVCDMQDKEPQFIFLIDDGTGR-----IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYS  140 (265)
Q Consensus        72 iVG~V~~v~~~~t~~~y~LdDgTG~-----I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~  140 (265)
                      +-|+|..+......--|-|.|.++-     -+.++-...    . ...+++|+.|+|.|++.+|++..+|....
T Consensus         2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~----~-~~~~~~Gd~V~vtG~v~ey~g~tql~~~~   70 (78)
T cd04486           2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTG----S-GADVAVGDLVRVTGTVTEYYGLTQLTAVS   70 (78)
T ss_pred             eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecC----C-CCCCCCCCEEEEEEEEEeeCCeEEEccCC
Confidence            4578887766543445668886432     112111111    1 46789999999999999999988877643

YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.

>TIGR00498 lexA SOS regulatory protein LexA

Probab=93.69  E-value=0.097  Score=44.50  Aligned_cols=55  Identities=18%  Similarity=0.146  Sum_probs=45.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCC-HHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLP-MDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~-~~~v~~al~~L~~eG~IYs  253 (265)
                      +|++.|.+||++|++... ......++.+|++.++++ ...|...|+.|...|.|-.
T Consensus         3 ~lt~~q~~iL~~l~~~~~-~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~   58 (199)
T TIGR00498         3 PLTARQQEVLDLIRAHIE-STGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIER   58 (199)
T ss_pred             ccCHHHHHHHHHHHHHHH-hcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEec
Confidence            478899999999985411 223457888999999998 9999999999999999977

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=93.69  E-value=0.18  Score=44.89  Aligned_cols=54  Identities=22%  Similarity=0.318  Sum_probs=46.3

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      -.||++|.+.     +.+++..||++.++++.+.+...|..|.++|.|.. -++..|..+
T Consensus        14 l~iL~~l~~~-----~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg   68 (263)
T PRK09834         14 LMVLRALNRL-----DGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFRLT   68 (263)
T ss_pred             HHHHHHHHhc-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEEEc
Confidence            3477888642     34699999999999999999999999999999999 778888765

>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70)

Probab=93.64  E-value=0.19  Score=38.33  Aligned_cols=62  Identities=18%  Similarity=0.176  Sum_probs=43.2

Q ss_pred             eEEEEEEEEEEeee---------CCCeEEEEEEcC-CCeEEEEEecccccccccccccCCCCEEEEEE-EeeeeC
Q 024592           68 NTITVVGIVCDMQD---------KEPQFIFLIDDG-TGRIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQ  131 (265)
Q Consensus        68 ~~V~iVG~V~~v~~---------~~t~~~y~LdDg-TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~  131 (265)
                      ..++|+|+|..+.+         ....+.+.|-|. +|.|.|.+|.+...  ...+.|++|+.+.+.+ +|+..+
T Consensus        10 ~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~--~f~~~l~eG~vy~i~~~~V~~a~   82 (104)
T cd04474          10 NKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVD--KFYDLLEVGKVYYISKGSVKVAN   82 (104)
T ss_pred             CcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHH--HhhcccccccEEEEeccEEeecc
Confidence            46788888876421         134578999999 89999999986432  2346789998777764 455443

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct

>PRK02983 lysS lysyl-tRNA synthetase; Provisional

Probab=93.57  E-value=0.55  Score=50.13  Aligned_cols=73  Identities=19%  Similarity=0.130  Sum_probs=52.8

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc---ccccccCCCCEEEEEEEeeee-CCccEEEEEEe
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF---NEVNQISKGMYVRVYGHLKAF-QDKRSLNAYSL  141 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i  141 (265)
                      .|+|.|+|.+++.......+.|.|+||.|.|..=.+...+.   .....+..|+.|.|.|.+..- .+...|.+..+
T Consensus       653 ~V~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~~ge~ei~~~~i  729 (1094)
T PRK02983        653 EVSVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSRNGTLSLLVTSW  729 (1094)
T ss_pred             EEEEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcCCCCEEEEEeEE
Confidence            59999999999998888888999999999997643321110   012357899999999998643 34455555444

>PRK12423 LexA repressor; Provisional

Probab=93.49  E-value=0.094  Score=44.95  Aligned_cols=52  Identities=17%  Similarity=0.211  Sum_probs=44.4

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCc--CHHHHHHhcC-CCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGV--HRNVISQQLN-LPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv--~~~~I~~~l~-~~~~~v~~al~~L~~eG~IYs  253 (265)
                      |++-|++||++|++.   -.+.|+  ++.||++.|+ .+...|+++|+.|...|+|-.
T Consensus         4 lt~~q~~il~~l~~~---i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~   58 (202)
T PRK12423          4 LTPKRAAILAFIRER---IAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEV   58 (202)
T ss_pred             CCHHHHHHHHHHHHH---HHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence            678899999999864   224455  9999999999 589999999999999999976

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=93.45  E-value=0.26  Score=31.34  Aligned_cols=41  Identities=17%  Similarity=0.186  Sum_probs=34.6

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceee
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKS  261 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~  261 (265)
                      ..++..+|++.++++...+.++|..|.++|.|.... .+|..
T Consensus         7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~-~~~~i   47 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG-GRIVI   47 (48)
T ss_pred             eccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC-CEEEE
Confidence            357899999999999999999999999999997632 45543

>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=93.33  E-value=0.98  Score=36.97  Aligned_cols=55  Identities=18%  Similarity=0.235  Sum_probs=43.6

Q ss_pred             eEEEEEEEEEE--eee-CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee
Q 024592           68 NTITVVGIVCD--MQD-KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK  128 (265)
Q Consensus        68 ~~V~iVG~V~~--v~~-~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~  128 (265)
                      ..|++-|.|..  +.. ....+.|.|.|+...|.|.+--.      .++.|++|.-|-|.|++.
T Consensus        52 ~~vrvgG~V~~gSi~~~~~~~~~F~ltD~~~~i~V~Y~G~------lPd~F~eg~~VVv~G~~~  109 (148)
T PRK13254         52 RRFRLGGLVEKGSVQRGDGLTVRFVVTDGNATVPVVYTGI------LPDLFREGQGVVAEGRLQ  109 (148)
T ss_pred             CeEEEeEEEecCcEEeCCCCEEEEEEEeCCeEEEEEECCC------CCccccCCCEEEEEEEEC
Confidence            57888888864  444 56789999999988888876432      367799999999999985

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=93.21  E-value=0.24  Score=44.32  Aligned_cols=54  Identities=20%  Similarity=0.348  Sum_probs=45.6

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      -.||++|...     +.++++.||++.++++.+.+...|..|++.|.|+. -+...|...
T Consensus        28 l~IL~~~~~~-----~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG   82 (271)
T PRK10163         28 IAILQYLEKS-----GGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIG   82 (271)
T ss_pred             HHHHHHHHhC-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEec
Confidence            3478888642     45799999999999999999999999999999998 667778643

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=93.18  E-value=0.29  Score=39.34  Aligned_cols=53  Identities=15%  Similarity=0.111  Sum_probs=46.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..|-.||..|..      +.|++..+|++.++++...|-.+|+.|+..|.|+. .|.
T Consensus        37 glt~~q~~vL~~l~~------~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~   90 (144)
T PRK11512         37 DITAAQFKVLCSIRC------AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP   90 (144)
T ss_pred             CCCHHHHHHHHHHHH------cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc
Confidence            577788889998854      34899999999999999999999999999999998 664

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=93.07  E-value=0.38  Score=41.15  Aligned_cols=63  Identities=16%  Similarity=0.151  Sum_probs=52.4

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-e-cCCceeeccCC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-I-DEFHYKSAVNA  265 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-i-Dd~hyk~t~~~  265 (265)
                      ..++..+..||.+|.+.      .++++.+|++.++++.+.+...|..|.+.|.|.. - ....|+.|.-|
T Consensus       139 ~~ls~~~~~IL~~l~~~------g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G  203 (203)
T TIGR01884       139 AGLSREELKVLEVLKAE------GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG  203 (203)
T ss_pred             cCCCHHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence            35677888999999753      3689999999999999999999999999999999 4 45567777543

Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.

>PRK08486 single-stranded DNA-binding protein; Provisional

Probab=92.86  E-value=0.74  Score=38.99  Aligned_cols=78  Identities=18%  Similarity=0.209  Sum_probs=48.2

Q ss_pred             EeEEEEEEEEEE-ee--e---CCCeEEEEEE--------c-----CCCeEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592           67 VNTITVVGIVCD-MQ--D---KEPQFIFLID--------D-----GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHL  127 (265)
Q Consensus        67 v~~V~iVG~V~~-v~--~---~~t~~~y~Ld--------D-----gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i  127 (265)
                      ++.|.|+|+|.. .+  .   ....+.|+|.        |     .|--|.|..|...++  .....|+.|+.|-|.|+|
T Consensus         2 ~N~V~LvGrL~~DPElr~t~sG~~va~fslAv~r~~~~~~Ge~~e~t~fi~v~~fg~~AE--~~~~~l~KG~~V~VeGrL   79 (182)
T PRK08486          2 FNKVILVGNLTRDVELRYLPSGSAIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAE--IANQYLSKGSKVLIEGRL   79 (182)
T ss_pred             eeEEEEEEEecCCCEEEECCCCCEEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHH--HHHHHcCCCCEEEEEEEE
Confidence            467888888854 11  1   2235566662        2     244588999975432  123568999999999999


Q ss_pred             ee--eCCc-------cEEEEEEeeeCCC
Q 024592          128 KA--FQDK-------RSLNAYSLRPIID  146 (265)
Q Consensus       128 ~~--f~~~-------~~i~~~~i~~v~d  146 (265)
                      +.  |.++       ..|.+..|..+..
T Consensus        80 ~~~~y~dkdG~~r~~~eI~a~~v~~L~~  107 (182)
T PRK08486         80 TFESWMDQNGQKRSKHTITAESMQMLDS  107 (182)
T ss_pred             EeCcEECCCCcEEEEEEEEEeEEEECCC
Confidence            74  6433       3455555655543

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=92.85  E-value=0.22  Score=31.76  Aligned_cols=41  Identities=15%  Similarity=0.310  Sum_probs=32.7

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      ..+..+|++.|+..      .-.+..+|++.+++++..|..-+..|.
T Consensus         2 D~~D~~Il~~Lq~d------~r~s~~~la~~lglS~~~v~~Ri~rL~   42 (42)
T PF13404_consen    2 DELDRKILRLLQED------GRRSYAELAEELGLSESTVRRRIRRLE   42 (42)
T ss_dssp             -HHHHHHHHHHHH-------TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHc------CCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence            46888999999874      357999999999999999999998873

...

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=92.85  E-value=0.32  Score=35.42  Aligned_cols=49  Identities=22%  Similarity=0.328  Sum_probs=37.5

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..-.+|-+|...   ..+.-++.++|+++++.++..+++.++.|...|.|-+
T Consensus         9 ~Al~~l~~la~~---~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s   57 (83)
T PF02082_consen    9 YALRILLYLARH---PDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIES   57 (83)
T ss_dssp             HHHHHHHHHHCT---TTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhC---CCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEe
Confidence            334556666553   2222399999999999999999999999999999977

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=92.81  E-value=0.28  Score=41.40  Aligned_cols=52  Identities=17%  Similarity=0.240  Sum_probs=45.7

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEF  257 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~  257 (265)
                      +...+|+++|+..     ..+++..+|+++|++.-.+|+..|-.|..+|.||.+|+.
T Consensus         4 ~~~~~i~~~l~~~-----~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~~~~   55 (183)
T PHA02701          4 DCASLILTLLSSS-----GDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCEDGC   55 (183)
T ss_pred             hHHHHHHHHHHhc-----CCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecCCCC
Confidence            4678899999974     335999999999999999999999999999999987664

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=92.73  E-value=0.28  Score=38.87  Aligned_cols=48  Identities=8%  Similarity=0.205  Sum_probs=43.8

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..|+.+|++++|+.+      =+++.++...++.+...++..+.+|+..|+||-
T Consensus        11 ~eLk~rIvElVRe~G------RiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~   58 (127)
T PF06163_consen   11 EELKARIVELVREHG------RITIKQLVAKTGASRNTVKRYLRELVARGDLYR   58 (127)
T ss_pred             HHHHHHHHHHHHHcC------CccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe
Confidence            468999999999853      479999999999999999999999999999996

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=92.70  E-value=0.24  Score=29.76  Aligned_cols=30  Identities=23%  Similarity=0.407  Sum_probs=26.0

Q ss_pred             cCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          222 VHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      ++.+||++.++.+.+.|-.+|..|..+|.|
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLERQGLI   32 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence            578999999999999999999999999987

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=92.64  E-value=0.25  Score=42.95  Aligned_cols=47  Identities=19%  Similarity=0.359  Sum_probs=41.5

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-++.|+.++++.      -+++.++|+++|+++...+|.-|+.|+.+|.|=.
T Consensus        11 ~tr~~il~lL~~~------g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~   57 (218)
T COG2345          11 STRERILELLKKS------GPVSADELAEELGISPMAVRRHLDDLEAEGLVEV   57 (218)
T ss_pred             cHHHHHHHHHhcc------CCccHHHHHHHhCCCHHHHHHHHHHHHhCcceee
Confidence            5678899999864      3889999999999999999999999999997654

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=92.62  E-value=0.38  Score=41.69  Aligned_cols=51  Identities=12%  Similarity=0.182  Sum_probs=37.9

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+.|.+-|.+.. .....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus        13 i~~~l~~~I~~g~-~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r   64 (238)
T TIGR02325        13 IADKIEQEIAAGH-LRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRA   64 (238)
T ss_pred             HHHHHHHHHHcCC-CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            4455555555421 1112223 7789999999999999999999999999997

All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=92.57  E-value=0.38  Score=41.72  Aligned_cols=51  Identities=14%  Similarity=0.186  Sum_probs=38.3

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+.|.+-|.+..- ....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus         5 i~~~l~~~I~~g~~-~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r   56 (233)
T TIGR02404         5 IYQDLEQKITHGQY-KEGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQK   56 (233)
T ss_pred             HHHHHHHHHHhCCC-CCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            45566666654321 111123 6899999999999999999999999999997

subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.

>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function

Probab=92.53  E-value=0.29  Score=36.77  Aligned_cols=52  Identities=25%  Similarity=0.487  Sum_probs=42.3

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecC
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDE  256 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd  256 (265)
                      ++++...||..|+..   ..|   +..-|++.++++.++|+.+|+.|.+.|.|=.++.
T Consensus         5 ~~~l~~~IL~hl~~~---~~D---y~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g   56 (92)
T PF10007_consen    5 LDPLDLKILQHLKKA---GPD---YAKSIARRLKIPLEEVREALEKLEEMGLLERVEG   56 (92)
T ss_pred             cChhHHHHHHHHHHH---CCC---cHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecC
Confidence            356788899999875   233   5677899999999999999999999999865443

>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family

Probab=92.40  E-value=0.38  Score=42.28  Aligned_cols=51  Identities=16%  Similarity=0.070  Sum_probs=43.1

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceee
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKS  261 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~  261 (265)
                      .||++|.+.     ..++++.||++.++++.+.+...|..|.+.|.+.. |+..|..
T Consensus        13 ~IL~~l~~~-----~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~-~~~~Y~l   63 (248)
T TIGR02431        13 AVIEAFGAE-----RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS-DGRLFWL   63 (248)
T ss_pred             HHHHHHhcC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe-CCCEEEe
Confidence            477777642     46899999999999999999999999999999986 4567764

Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=92.35  E-value=0.25  Score=34.03  Aligned_cols=35  Identities=26%  Similarity=0.318  Sum_probs=31.3

Q ss_pred             CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ...+...+|++.|+++++.+.+.|..|.++|.|-.
T Consensus        20 ~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~   54 (60)
T PF01325_consen   20 GGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEY   54 (60)
T ss_dssp             TSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             CCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEe
Confidence            46899999999999999999999999999999853

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PTZ00417 lysine-tRNA ligase; Provisional

Probab=92.33  E-value=0.69  Score=46.04  Aligned_cols=75  Identities=15%  Similarity=0.124  Sum_probs=51.9

Q ss_pred             EEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccc---cc-ccc-ccccCCCCEEEEEEEeeee-CCccEEEEEEe
Q 024592           69 TITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQ---ME-FNE-VNQISKGMYVRVYGHLKAF-QDKRSLNAYSL  141 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~---~~-~~~-~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i  141 (265)
                      .|+|.|||.+++... .-..+.|.|.+|.|.|..-.+..   .+ -.. ...+..|+.|.|.|.+..- .+...|.+..+
T Consensus       134 ~v~v~Grv~~~R~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~t~~gel~i~~~~i  213 (585)
T PTZ00417        134 ILNVTGRIMRVSASGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKSKKGELSIFPKET  213 (585)
T ss_pred             eEEEEEEEEeeecCCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcCCCCceEEEEEEEE
Confidence            389999999999887 45667887888898888753321   11 011 2468999999999996543 45566666555


Q ss_pred             ee
Q 024592          142 RP  143 (265)
Q Consensus       142 ~~  143 (265)
                      ..
T Consensus       214 ~l  215 (585)
T PTZ00417        214 II  215 (585)
T ss_pred             EE
Confidence            43

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=92.30  E-value=0.43  Score=41.36  Aligned_cols=51  Identities=20%  Similarity=0.251  Sum_probs=38.4

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+.|.+-|.+.. .....=+ +..+++++++.+...||+||+.|.+||.||.
T Consensus         6 i~~~l~~~I~~g~-~~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r   57 (230)
T TIGR02018         6 IKQDILERIRSGE-WPPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLER   57 (230)
T ss_pred             HHHHHHHHHHhCC-CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            4555666665421 1112224 7799999999999999999999999999997

This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=92.24  E-value=0.46  Score=41.56  Aligned_cols=51  Identities=18%  Similarity=0.299  Sum_probs=38.2

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+.|.+-|.+.. .....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus        10 i~~~L~~~I~~g~-~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r   61 (240)
T PRK09764         10 IADRIREQIARGE-LKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILES   61 (240)
T ss_pred             HHHHHHHHHHcCC-CCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            4555656555432 1112234 6799999999999999999999999999996

>PRK05813 single-stranded DNA-binding protein; Provisional

Probab=92.23  E-value=1.7  Score=37.91  Aligned_cols=79  Identities=16%  Similarity=0.193  Sum_probs=53.5

Q ss_pred             EeEEEEEEEEEEe-----e-eCCCeEEEEEE-----cCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC----
Q 024592           67 VNTITVVGIVCDM-----Q-DKEPQFIFLID-----DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ----  131 (265)
Q Consensus        67 v~~V~iVG~V~~v-----~-~~~t~~~y~Ld-----DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~----  131 (265)
                      -+.|.|+|.+.+=     + ....+.+|+|.     |.|-.|+|..|..-.+    ...+..|+.|.|.|+|++|+    
T Consensus         8 ~NkV~L~Grl~~d~e~~~~~~G~~~~~f~laV~R~s~~~D~i~v~v~~rlae----~~~l~kG~~v~VeGqlrsy~~~~~   83 (219)
T PRK05813          8 NNKVYLEGKVVSELEFSHEMYGEGFYNFKLEVPRLSDSKDILPVTVSERLLA----GMDLKVGTLVIVEGQLRSYNKFID   83 (219)
T ss_pred             cCEEEEEEEEcCCceEEEEeCCeEEEEEEEEeeccCCCccEEEEEEEhhhhh----hhcccCCCEEEEEEEEEEeccCCC
Confidence            4688889988551     1 12345556554     7788899999976542    22389999999999999884    


Q ss_pred             Ccc----EEEEEEeeeCCChhH
Q 024592          132 DKR----SLNAYSLRPIIDFNE  149 (265)
Q Consensus       132 ~~~----~i~~~~i~~v~d~Ne  149 (265)
                      +++    .|.|-.|+.+...++
T Consensus        84 G~~R~vl~V~a~~i~~l~~~~~  105 (219)
T PRK05813         84 GKNRLILTVFARNIEYCDERSD  105 (219)
T ss_pred             CcEEEEEEEEEEEEEEccCCCc
Confidence            332    345555666665433

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=92.23  E-value=0.48  Score=31.45  Aligned_cols=44  Identities=23%  Similarity=0.295  Sum_probs=37.0

Q ss_pred             HHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          206 VLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       206 Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      |+++|. .      ..++..+|++.++++...+.++|+.|.++|.|.. -+.
T Consensus         2 il~~l~-~------~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~   46 (66)
T smart00418        2 ILKLLA-E------GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREG   46 (66)
T ss_pred             HHHHhh-c------CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecC
Confidence            566664 2      3579999999999999999999999999999987 544

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=92.22  E-value=0.21  Score=44.39  Aligned_cols=46  Identities=17%  Similarity=0.311  Sum_probs=40.4

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      .=+++|+++|++.      .=++++++++.|+.++..||.-|.+|.++|.+=
T Consensus         5 eR~~~Il~~l~~~------g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~   50 (253)
T COG1349           5 ERHQKILELLKEK------GKVSVEELAELFGVSEMTIRRDLNELEEQGLLL   50 (253)
T ss_pred             HHHHHHHHHHHHc------CcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence            3567899999874      257999999999999999999999999999874

>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea

Probab=92.22  E-value=0.38  Score=33.76  Aligned_cols=49  Identities=10%  Similarity=0.014  Sum_probs=40.6

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .-.|+.+|.+.      ..+++.+|.+..+++..++.-||-.|..|+.|+- -.+.
T Consensus        10 AG~Vw~~L~~~------~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~~   59 (65)
T PF10771_consen   10 AGKVWQLLNEN------GEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEEKNG   59 (65)
T ss_dssp             HHHHHHHHCCS------SSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETT
T ss_pred             HHHHHHHHhhC------CCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeCC
Confidence            34688999763      3689999999999999999999999999999998 4443

The function is not known. ; PDB: 2L02_B 2L01_A.

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=92.20  E-value=0.22  Score=44.26  Aligned_cols=47  Identities=13%  Similarity=0.216  Sum_probs=40.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .=+++|+++|++.      .-+++.++++.|+.++..||.-|..|.++|.|.-
T Consensus         5 eR~~~Il~~L~~~------~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r   51 (256)
T PRK10434          5 QRQAAILEYLQKQ------GKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIR   51 (256)
T ss_pred             HHHHHHHHHHHHc------CCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            3567799999874      2489999999999999999999999999997643

>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]

Probab=92.16  E-value=0.96  Score=43.83  Aligned_cols=76  Identities=20%  Similarity=0.224  Sum_probs=57.2

Q ss_pred             EEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc---ccccccCCCCEEEEEEEeeeeC-CccEEEEEEeeeCC
Q 024592           70 ITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF---NEVNQISKGMYVRVYGHLKAFQ-DKRSLNAYSLRPII  145 (265)
Q Consensus        70 V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~g~yVrV~G~i~~f~-~~~~i~~~~i~~v~  145 (265)
                      |.+.|+|..++.......+.|.|.+|.|.+..-.+...+.   .....+..||+|-|.|.+-.-+ |..+|.+..++.++
T Consensus        64 v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~GelSv~v~~~~lLs  143 (502)
T COG1190          64 VSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTGELSVSVEELRLLS  143 (502)
T ss_pred             eEEecceeeecccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCCceEEEEEEEeeec
Confidence            9999999999988888888999999999988765532211   1234567899999999976544 77777776655443

>PRK14999 histidine utilization repressor; Provisional

Probab=92.07  E-value=0.49  Score=41.36  Aligned_cols=52  Identities=10%  Similarity=0.142  Sum_probs=39.2

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+...|.+-|.+.. .....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus        16 qi~~~i~~~I~~g~-~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r   68 (241)
T PRK14999         16 TVKQDICKKIAGGV-WQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVR   68 (241)
T ss_pred             HHHHHHHHHHHcCC-CCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            35555666665431 1222235 7899999999999999999999999999996

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=92.05  E-value=0.45  Score=42.10  Aligned_cols=52  Identities=13%  Similarity=0.167  Sum_probs=44.1

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      .||++|.+      ..++++.||+++++++.+.+...|..|.+.|.|+. -++..|...
T Consensus        18 ~IL~~l~~------~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG   70 (257)
T PRK15090         18 GILQALGE------EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLT   70 (257)
T ss_pred             HHHHHhhc------CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEec
Confidence            47777754      23689999999999999999999999999999998 677778653

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=92.01  E-value=0.27  Score=35.71  Aligned_cols=54  Identities=19%  Similarity=0.228  Sum_probs=41.6

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      |++-|+.||..|=+. .....+-|.-.+|++.++.++..||+.+..|.+.|.|.+
T Consensus         2 Lt~rq~~IL~alV~~-Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~   55 (78)
T PF03444_consen    2 LTERQREILKALVEL-YIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVES   55 (78)
T ss_pred             CCHHHHHHHHHHHHH-HHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence            456777777754322 113345677799999999999999999999999999985

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=91.99  E-value=0.17  Score=36.35  Aligned_cols=49  Identities=12%  Similarity=0.129  Sum_probs=41.6

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      ..+.+..+.++.+.+.      .+|++..||++.+++++..|+..+..+.++|.+
T Consensus        14 ~~l~~~~r~af~L~R~------~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~   62 (73)
T TIGR03879        14 TWVDSLAEAAAALARE------EAGKTASEIAEELGRTEQTVRNHLKGETKAGGL   62 (73)
T ss_pred             hcCCHHHHHHHHHHHH------HcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence            3567788888887754      259999999999999999999999999888865

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=91.94  E-value=0.61  Score=35.74  Aligned_cols=54  Identities=13%  Similarity=0.236  Sum_probs=45.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++..+-.||.+|....  ..+.+++..+|++.++++...|-..++.|...|.|.-
T Consensus        22 ~ls~~q~~vL~~l~~~~--~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r   75 (109)
T TIGR01889        22 NLSLEELLILYYLGKLE--NNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSK   75 (109)
T ss_pred             CCCHHHHHHHHHHHhhh--ccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEec
Confidence            46677888998887210  1245899999999999999999999999999999997

This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=91.93  E-value=0.28  Score=43.54  Aligned_cols=47  Identities=9%  Similarity=0.270  Sum_probs=41.1

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-++.|+++|++.      .-+++.+|+++|+.++..||.-|..|.++|.|.-
T Consensus         5 ~R~~~Il~~l~~~------~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r   51 (252)
T PRK10906          5 QRHDAIIELVKQQ------GYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILR   51 (252)
T ss_pred             HHHHHHHHHHHHc------CCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            4567899999764      2589999999999999999999999999999854

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=91.93  E-value=0.5  Score=41.30  Aligned_cols=31  Identities=16%  Similarity=0.247  Sum_probs=29.8

Q ss_pred             CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          223 HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       223 ~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +-.+++++++.+...||+||+.|++||.||.
T Consensus        37 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r   67 (241)
T PRK10079         37 AEQQLAARYEVNRHTLRRAIDQLVEKGWVQR   67 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            6799999999999999999999999999997

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=91.83  E-value=0.45  Score=42.04  Aligned_cols=54  Identities=22%  Similarity=0.353  Sum_probs=46.2

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      -.||++|.+.     +.++++.+|+++++++.+.+...|..|.+.|.+.. -++.+|..+
T Consensus         7 l~iL~~l~~~-----~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg   61 (246)
T COG1414           7 LAILDLLAEG-----PGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRLG   61 (246)
T ss_pred             HHHHHHHHhC-----CCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEeeh
Confidence            4588888763     45789999999999999999999999999999999 555688754

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=91.67  E-value=0.58  Score=40.86  Aligned_cols=31  Identities=16%  Similarity=0.254  Sum_probs=29.8

Q ss_pred             CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          223 HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       223 ~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +-.+++++++.+...||+||+.|.+||.|+.
T Consensus        35 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r   65 (241)
T PRK11402         35 TENELCTQYNVSRITIRKAISDLVADGVLIR   65 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            7799999999999999999999999999997

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=91.48  E-value=0.58  Score=41.01  Aligned_cols=52  Identities=17%  Similarity=0.277  Sum_probs=38.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+.+.|.+-|.+.. -....=+ +-.+++++++.+...||+||+.|.++|.|+.
T Consensus        11 qI~~~i~~~I~~G~-~~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r   63 (236)
T COG2188          11 QIAEDIRQRIESGE-LPPGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVR   63 (236)
T ss_pred             HHHHHHHHHHHhCC-CCCCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEE
Confidence            35566666665432 1111223 6789999999999999999999999999996

>PRK11569 transcriptional repressor IclR; Provisional

Probab=91.36  E-value=0.51  Score=42.26  Aligned_cols=52  Identities=19%  Similarity=0.296  Sum_probs=44.5

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceee
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKS  261 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~  261 (265)
                      .||++|.+.     +.++++.||++.++++.+.+...|..|+++|.+.. -+...|..
T Consensus        32 ~IL~~l~~~-----~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~~~Y~l   84 (274)
T PRK11569         32 KLLEWIAES-----NGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGELGHWAI   84 (274)
T ss_pred             HHHHHHHhC-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEec
Confidence            477777652     45799999999999999999999999999999988 66778864

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=91.35  E-value=0.64  Score=35.93  Aligned_cols=53  Identities=15%  Similarity=0.120  Sum_probs=46.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|.. -|.
T Consensus        25 ~lt~~q~~iL~~l~~~------~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~   78 (118)
T TIGR02337        25 GLTEQQWRILRILAEQ------GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKAS   78 (118)
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCC
Confidence            5677888899998753      4789999999999999999999999999999998 544

This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=91.27  E-value=0.67  Score=37.09  Aligned_cols=55  Identities=13%  Similarity=0.158  Sum_probs=46.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++.-|-.||..|...     +.|++..+|++.++++...|...++.|+..|.|.. .|+.
T Consensus        28 glt~~q~~vL~~l~~~-----~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~   83 (144)
T PRK03573         28 ELTQTHWVTLHNIHQL-----PPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCAS   83 (144)
T ss_pred             CCCHHHHHHHHHHHHc-----CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCC
Confidence            5667787888888642     34789999999999999999999999999999999 6653

>PRK07459 single-stranded DNA-binding protein; Provisional

Probab=91.26  E-value=0.82  Score=36.02  Aligned_cols=61  Identities=18%  Similarity=0.320  Sum_probs=42.5

Q ss_pred             EeEEEEEEEEEE---ee---eCCCeEEEEEE-------cCCCeEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           67 VNTITVVGIVCD---MQ---DKEPQFIFLID-------DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        67 v~~V~iVG~V~~---v~---~~~t~~~y~Ld-------DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      ++.|.|+|++..   ++   .....+.|.|-       +.|-=+.|..|...+.  .....++.|+.|.|.|+|+.
T Consensus         3 ~N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~l~~   76 (121)
T PRK07459          3 LNSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQ--VAADYVKKGSLIGITGSLKF   76 (121)
T ss_pred             ccEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHH--HHHHHcCCCCEEEEEEEEEe
Confidence            467888998865   22   12246677776       4465699999976432  22456899999999999985

>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN)

Probab=91.14  E-value=0.47  Score=32.74  Aligned_cols=57  Identities=21%  Similarity=0.364  Sum_probs=41.2

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHH-HHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDK-LMEALESLNENSLVYSIDEFHYKSAVNA  265 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~-v~~al~~L~~eG~IYsiDd~hyk~t~~~  265 (265)
                      +.+.|+.-|+-      ..|++.+++.++++.+..+ +.+.|+.|.++|.| .+++++++.|.-|
T Consensus         7 ~~e~i~~~LR~------~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll-~~~~~~l~lT~~G   64 (66)
T PF06969_consen    7 LREYIMLGLRC------NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLL-EIDGGRLRLTEKG   64 (66)
T ss_dssp             HHHHHHHHHHH------HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSE-EE-SSEEEE-TTT
T ss_pred             HHHHHHHHHHh------HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCE-EEeCCEEEECccc
Confidence            44555555654      3699999999999977555 58889999999998 5778899988754

This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.

>PRK06751 single-stranded DNA-binding protein; Provisional

Probab=91.12  E-value=0.9  Score=38.16  Aligned_cols=61  Identities=25%  Similarity=0.413  Sum_probs=40.3

Q ss_pred             EeEEEEEEEEEE-ee--e---CCCeEEEEEE------cCCC-----eEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           67 VNTITVVGIVCD-MQ--D---KEPQFIFLID------DGTG-----RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        67 v~~V~iVG~V~~-v~--~---~~t~~~y~Ld------DgTG-----~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      +..|.|+|+|.. .+  .   ....+.|.|-      +..|     -|.|..|...+.  .....++.|+.|.|.|+|+.
T Consensus         2 mN~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae--~~~~~l~KG~~V~VeGrL~~   79 (173)
T PRK06751          2 MNRVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQGEREADFINCVIWRKQAE--NVANYLKKGSLAGVDGRLQT   79 (173)
T ss_pred             ceEEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHH--HHHHHcCCCCEEEEEEEEEe
Confidence            367888888854 22  1   1245667662      2223     488899976432  23456899999999999986

>PRK07275 single-stranded DNA-binding protein; Provisional

Probab=91.02  E-value=1.4  Score=36.54  Aligned_cols=61  Identities=21%  Similarity=0.396  Sum_probs=40.1

Q ss_pred             EeEEEEEEEEEE-e--ee---CCCeEEEEEE------cC-----CCeEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           67 VNTITVVGIVCD-M--QD---KEPQFIFLID------DG-----TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        67 v~~V~iVG~V~~-v--~~---~~t~~~y~Ld------Dg-----TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      ++.|.|+|++.. .  +.   ....+.|+|-      +.     |--|.|..|...+.  ....-++.|+.|-|.|+|+.
T Consensus         2 ~N~v~LiGrL~~DPElr~t~sG~~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae--~~~~~l~KG~~V~VeGrl~~   79 (162)
T PRK07275          2 INNVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAE--NLANWAKKGALIGVTGRIQT   79 (162)
T ss_pred             eeEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHH--HHHHHcCCCCEEEEEEEEEe
Confidence            467888888854 2  21   2245566663      22     33489999976432  12456899999999999974

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=90.88  E-value=0.62  Score=36.76  Aligned_cols=47  Identities=21%  Similarity=0.251  Sum_probs=39.1

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-.+|..|...    .+..+++.+|+++++++..-+++.|+.|...|.|.+
T Consensus        11 al~~l~~la~~----~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~   57 (130)
T TIGR02944        11 ATLVLTTLAQN----DSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS   57 (130)
T ss_pred             HHHHHHHHHhC----CCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence            34466666542    245799999999999999999999999999999987

The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=90.80  E-value=0.64  Score=35.69  Aligned_cols=47  Identities=21%  Similarity=0.339  Sum_probs=40.6

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+..||++|.+.     +.-++.++|.+++     +++...|-.+|+.|.+.|.|-.
T Consensus         2 qR~~Il~~l~~~-----~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~   53 (116)
T cd07153           2 QRLAILEVLLES-----DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE   53 (116)
T ss_pred             HHHHHHHHHHhC-----CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence            356799999863     4568999999998     4899999999999999999988

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>PRK02801 primosomal replication protein N; Provisional

Probab=90.74  E-value=2.3  Score=32.28  Aligned_cols=33  Identities=15%  Similarity=0.170  Sum_probs=25.3

Q ss_pred             EEEEEecccccccccccccCCCCEEEEEEEeeeeC
Q 024592           97 IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ  131 (265)
Q Consensus        97 I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~  131 (265)
                      |+|..|-+.++  .....+..|+.|.|.|+|+.+.
T Consensus        50 i~~va~G~~Ae--~~~~~l~kGs~v~V~G~L~~~~   82 (101)
T PRK02801         50 MPVIVSGNQFQ--AITQSITVGSKITVQGFISCHQ   82 (101)
T ss_pred             EEEEEEcHHHH--HHHhhcCCCCEEEEEEEEEEeE
Confidence            89999976442  1233689999999999999854

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=90.67  E-value=0.79  Score=36.02  Aligned_cols=46  Identities=22%  Similarity=0.177  Sum_probs=38.8

Q ss_pred             CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-e-cCCceeeccC
Q 024592          219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-I-DEFHYKSAVN  264 (265)
Q Consensus       219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-i-Dd~hyk~t~~  264 (265)
                      +..++.++|++.++++...+++.|+.|...|.|-+ - .+..|+.+.+
T Consensus        23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~   70 (132)
T TIGR00738        23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLARP   70 (132)
T ss_pred             CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCCCC
Confidence            44899999999999999999999999999999987 3 3347776543

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

>PRK06863 single-stranded DNA-binding protein; Provisional

Probab=90.58  E-value=1.9  Score=36.00  Aligned_cols=80  Identities=23%  Similarity=0.287  Sum_probs=48.3

Q ss_pred             EeEEEEEEEEEE---eee---CCCeEEEEEE------c-CCC-------eEEEEEecccccccccccccCCCCEEEEEEE
Q 024592           67 VNTITVVGIVCD---MQD---KEPQFIFLID------D-GTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGH  126 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~  126 (265)
                      +++|.|+|+|..   ++.   ....+.|+|-      | .+|       -+.|..|.....  .....|+.|+.|.|.|+
T Consensus         4 ~N~V~LiGrLg~DPElR~t~nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE--~v~~~LkKGs~V~VeGr   81 (168)
T PRK06863          4 INKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAE--VAGEYLRKGSQVYVEGR   81 (168)
T ss_pred             ccEEEEEEEcCCCCEEEEcCCCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHH--HHHHHCCCCCEEEEEEE
Confidence            678889998865   222   1234555554      1 122       377778865322  23456899999999999


Q ss_pred             eee--eCCc-------cEEEEEEeeeCCChh
Q 024592          127 LKA--FQDK-------RSLNAYSLRPIIDFN  148 (265)
Q Consensus       127 i~~--f~~~-------~~i~~~~i~~v~d~N  148 (265)
                      |+.  |.++       ..|.+..|..+...+
T Consensus        82 L~~r~w~DkdG~~r~~~eI~a~~i~~L~~r~  112 (168)
T PRK06863         82 LKTRKWQDQNGQDRYTTEIQGDVLQMLGGRN  112 (168)
T ss_pred             EEeCCccCCCCCEEEEEEEEEeEEEECCCCC
Confidence            986  4332       345555565555443

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=90.57  E-value=0.6  Score=37.50  Aligned_cols=59  Identities=5%  Similarity=0.041  Sum_probs=45.0

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA  265 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~~  265 (265)
                      +.-+.|+.++..      ...+++.+|++.|+++...|...|..|...|.|.......|..|..|
T Consensus         8 dyL~~I~~l~~~------~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G   66 (142)
T PRK03902          8 DYIEQIYLLIEE------KGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKG   66 (142)
T ss_pred             HHHHHHHHHHhc------CCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEecCceEEECHHH
Confidence            344556666544      23569999999999999999999999999999975444567777654

>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []

Probab=90.41  E-value=1  Score=32.94  Aligned_cols=63  Identities=11%  Similarity=0.150  Sum_probs=47.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC--------CCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN--------LPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~--------~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      .+.+|-+.|..+|-+..  .+...++.+.|.+.|.        =+.+-|+++|..|+.|+.||...+-.|-.|
T Consensus         8 qfiPL~EvlC~~I~dln--~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfivt   78 (80)
T PF10264_consen    8 QFIPLPEVLCWVISDLN--AAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIYHTGEGYFIVT   78 (80)
T ss_pred             cceeHHHHHHHHHHHHh--ccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCceeeCCCceEeeC
Confidence            45678888888877652  4567788999988882        244559999999999999999777666554

This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.

>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3

Probab=90.35  E-value=0.53  Score=33.07  Aligned_cols=51  Identities=18%  Similarity=0.295  Sum_probs=39.4

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      .+++++|+++|++.+    ......-+++..|+.+..+|+..|-.|..+|.|+..
T Consensus         3 ~~~ee~Il~~L~~~g----~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~   53 (66)
T PF02295_consen    3 QDLEEKILDFLKELG----GSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKE   53 (66)
T ss_dssp             HHHHHHHHHHHHHHT----SSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             hhHHHHHHHHHHhcC----CccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeC
Confidence            368899999999852    345555555666778899999999999999999763

5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=90.32  E-value=0.53  Score=41.74  Aligned_cols=47  Identities=15%  Similarity=0.224  Sum_probs=41.1

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-+.+|+++|++.      .-+++.+|++.|+.++..||.-|..|.++|.|-.
T Consensus         5 ~R~~~Il~~l~~~------~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r   51 (251)
T PRK13509          5 QRHQILLELLAQL------GFVTVEKVIERLGISPATARRDINKLDESGKLKK   51 (251)
T ss_pred             HHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4567799999863      3689999999999999999999999999999853

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=90.30  E-value=0.29  Score=41.43  Aligned_cols=45  Identities=4%  Similarity=0.111  Sum_probs=39.2

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      .-++.|+++|++.      .=+++.++++.|+.++..||.-|..|.++|++
T Consensus         7 ~R~~~Il~~l~~~------~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~   51 (185)
T PRK04424          7 ERQKALQELIEEN------PFITDEELAEKFGVSIQTIRLDRMELGIPELR   51 (185)
T ss_pred             HHHHHHHHHHHHC------CCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence            3567799999874      24799999999999999999999999999976

>KOG0555 consensus Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=90.23  E-value=0.48  Score=44.63  Aligned_cols=67  Identities=22%  Similarity=0.368  Sum_probs=49.9

Q ss_pred             EEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee-CCc
Q 024592           66 DVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF-QDK  133 (265)
Q Consensus        66 ~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f-~~~  133 (265)
                      .=.+|++-|||-+++.+.+-+...|-||||.+.|.+-..-.. +.+.-.+..-.-|.|+|.|+.. .||
T Consensus       122 r~qrVkv~gWVhrlR~qk~l~FivLrdg~gflqCVl~~kl~~-~yd~~~Ls~essv~vYG~i~~~p~GK  189 (545)
T KOG0555|consen  122 RGQRVKVFGWVHRLRRQKSLIFIVLRDGTGFLQCVLSDKLCQ-SYDALTLSTESSVTVYGTIKKLPEGK  189 (545)
T ss_pred             cCceEEeehhhHhhhhcCceEEEEEecCCceEEEEEcchhhh-hhccccccccceEEEEEEEecCcCCC
Confidence            336899999999998888888889999999999997654221 1223345566788999998876 443

>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []

Probab=90.01  E-value=0.93  Score=31.81  Aligned_cols=49  Identities=10%  Similarity=0.150  Sum_probs=35.9

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEE
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IY  252 (265)
                      +++.|+++|+...  .+-.=.=+.++++.+ ...+.+|.+++..|++||.+-
T Consensus         2 ~K~~Ile~L~~k~--~~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~   51 (67)
T PF08679_consen    2 AKQKILEFLEAKK--KKKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKLE   51 (67)
T ss_dssp             HHHHHHHHHSSCC--CHSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHhcc--CCCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeEE
Confidence            6788999998432  112234578888866 699999999999999999874

The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.

>PRK09954 putative kinase; Provisional

Probab=89.99  E-value=0.56  Score=43.45  Aligned_cols=46  Identities=17%  Similarity=0.320  Sum_probs=40.7

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      +....+||++|++++      =++..+|+++|+++...|+..|..|.++|.|
T Consensus         2 ~~~~~~il~~l~~~~------~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i   47 (362)
T PRK09954          2 NNREKEILAILRRNP------LIQQNEIADILQISRSRVAAHIMDLMRKGRI   47 (362)
T ss_pred             ChHHHHHHHHHHHCC------CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            456778999999742      5899999999999999999999999999877

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=89.88  E-value=0.6  Score=41.15  Aligned_cols=45  Identities=18%  Similarity=0.372  Sum_probs=39.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      .-+.+|+++|++.      ..+++++|++.|++++..||.-|.+|.++|.|
T Consensus         4 ~R~~~Il~~l~~~------~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l   48 (240)
T PRK10411          4 ARQQAIVDLLLNH------TSLTTEALAEQLNVSKETIRRDLNELQTQGKI   48 (240)
T ss_pred             HHHHHHHHHHHHc------CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            3567799999863      37899999999999999999999999999876

>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=89.78  E-value=6.7  Score=32.32  Aligned_cols=84  Identities=13%  Similarity=0.082  Sum_probs=54.5

Q ss_pred             eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEE--EeeeC--CCeEEEEEEcCCCeEEEEEecccccccccccccCCC
Q 024592           43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVC--DMQDK--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKG  118 (265)
Q Consensus        43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~--~v~~~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g  118 (265)
                      =.|.+++.......+          ..+++=|.|.  ++...  ...+.|.|.|+...|.|.+---      -++-|++|
T Consensus        37 F~tpsEv~~~~~~~~----------~~~RlGG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEG  100 (155)
T PRK13159         37 LFTPSQVRAGAAAGY----------QQFRLGGMVKAGSIQRAADSLKVSFTVIDKNAATQVEYTGI------LPDLFRDN  100 (155)
T ss_pred             EECHHHHhcCCcccC----------CeEEEccEEecCcEEEcCCCcEEEEEEEcCCcEEEEEEccC------CCccccCC
Confidence            356666665422222          4555556665  45544  3479999999999998875421      35678999


Q ss_pred             CEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592          119 MYVRVYGHLKAFQDKRSLNAYSLRPIID  146 (265)
Q Consensus       119 ~yVrV~G~i~~f~~~~~i~~~~i~~v~d  146 (265)
                      .=|-+.|++.  +  -.+.+..|--=.|
T Consensus       101 qgVVaeG~~~--~--g~F~A~~vLAKHd  124 (155)
T PRK13159        101 QSVIANGRMQ--G--GRFVANEVLAKHD  124 (155)
T ss_pred             CeEEEEEEEc--C--CEEEEeEEEecCC
Confidence            9999999986  2  3555555543334

>PRK06752 single-stranded DNA-binding protein; Validated

Probab=89.73  E-value=3  Score=32.17  Aligned_cols=77  Identities=17%  Similarity=0.319  Sum_probs=45.8

Q ss_pred             eEEEEEEEEEE---ee---eCCCeEEEEEE------cC-----CCeEEEEEecccccccccccccCCCCEEEEEEEeee-
Q 024592           68 NTITVVGIVCD---MQ---DKEPQFIFLID------DG-----TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA-  129 (265)
Q Consensus        68 ~~V~iVG~V~~---v~---~~~t~~~y~Ld------Dg-----TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~-  129 (265)
                      +.|.|+|++..   +.   .....+.|+|-      |.     |--|.|..|...+.  .....+..|+.|.|.|+|+. 
T Consensus         3 N~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~l~~~   80 (112)
T PRK06752          3 NRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAE--NVTEYCTKGSLVGITGRIHTR   80 (112)
T ss_pred             eEEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHH--HHHHhcCCCCEEEEEEEEEeC
Confidence            56777777754   11   11234555554      22     23488888875332  12346899999999999986 


Q ss_pred             -eCC---c----cEEEEEEeeeCCC
Q 024592          130 -FQD---K----RSLNAYSLRPIID  146 (265)
Q Consensus       130 -f~~---~----~~i~~~~i~~v~d  146 (265)
                       |.+   +    ..|.+..|..++.
T Consensus        81 ~~~~~~G~~~~~~ei~a~~i~~l~~  105 (112)
T PRK06752         81 NYEDDQGKRIYITEVVIESITFLER  105 (112)
T ss_pred             ccCCCCCcEEEEEEEEEEEEEECCC
Confidence             443   2    2466666665543

>PRK08763 single-stranded DNA-binding protein; Provisional

Probab=89.72  E-value=1.8  Score=35.98  Aligned_cols=61  Identities=13%  Similarity=0.149  Sum_probs=40.5

Q ss_pred             EeEEEEEEEEEE---eee---CCCeEEEEEE------cCCC-------eEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592           67 VNTITVVGIVCD---MQD---KEPQFIFLID------DGTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGHL  127 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld------DgTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i  127 (265)
                      ++.|.|+|.|.+   ++.   ....+.|+|-      |..|       -+.|..|..-+.  .....++.|+.|.|.|+|
T Consensus         5 ~Nkv~LiGrLg~DPelr~t~~G~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae--~v~~~L~KGs~V~VeGrL   82 (164)
T PRK08763          5 INKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGE--IAGEYLRKGSQCYIEGSI   82 (164)
T ss_pred             ceEEEEEEEecCCCeEEEcCCCCeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHH--HHHHhcCCCCEEEEEEEE
Confidence            788999999966   221   2245666664      2222       388888864321  223558999999999999


Q ss_pred             ee
Q 024592          128 KA  129 (265)
Q Consensus       128 ~~  129 (265)
                      +.
T Consensus        83 ~~   84 (164)
T PRK08763         83 RY   84 (164)
T ss_pred             Ee
Confidence            86

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=89.71  E-value=0.55  Score=42.09  Aligned_cols=47  Identities=15%  Similarity=0.208  Sum_probs=40.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-+..|+++|++.+      -+++.+|++.|+.++..||.-|..|.++|.+.-
T Consensus        17 eR~~~Il~~L~~~~------~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r   63 (269)
T PRK09802         17 ERREQIIQRLRQQG------SVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVR   63 (269)
T ss_pred             HHHHHHHHHHHHcC------CEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEE
Confidence            45677899998742      399999999999999999999999999999854

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=89.70  E-value=1.4  Score=34.95  Aligned_cols=32  Identities=13%  Similarity=0.241  Sum_probs=31.0

Q ss_pred             cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          222 VHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      -|+.++|..++.++..|++|.++|..+|.||+
T Consensus        36 PSvRelA~~~~VNpnTv~raY~eLE~eG~i~t   67 (125)
T COG1725          36 PSVRELAKDLGVNPNTVQRAYQELEREGIVET   67 (125)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            48999999999999999999999999999998

>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]

Probab=89.65  E-value=1.4  Score=35.81  Aligned_cols=54  Identities=19%  Similarity=0.205  Sum_probs=45.2

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++-+..||++|.+..    + .++.++|.+.+     +++...|..+|+.|.+.|.|.. -.++
T Consensus        19 ~T~qR~~vl~~L~~~~----~-~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~   78 (145)
T COG0735          19 LTPQRLAVLELLLEAD----G-HLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG   78 (145)
T ss_pred             cCHHHHHHHHHHHhcC----C-CCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence            5678889999998742    3 49999999988     3999999999999999999988 4433

>PRK06293 single-stranded DNA-binding protein; Provisional

Probab=89.58  E-value=3  Score=34.61  Aligned_cols=61  Identities=18%  Similarity=0.214  Sum_probs=40.3

Q ss_pred             eEEEEEEEEEE-e--e---eCCCeEEEEEE--------cCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee
Q 024592           68 NTITVVGIVCD-M--Q---DKEPQFIFLID--------DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF  130 (265)
Q Consensus        68 ~~V~iVG~V~~-v--~---~~~t~~~y~Ld--------DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f  130 (265)
                      +.|.|+|++.. .  +   .....+.|+|-        +.|-=|.|..|...+.  .....++.|+.|-|.|+|+.-
T Consensus         2 N~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae--~v~~yL~KG~~V~VeGrL~~~   76 (161)
T PRK06293          2 MFGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYD--KMLPYLKKGSGVIVAGEMSPE   76 (161)
T ss_pred             eEEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHH--HHHHhCCCCCEEEEEEEEEeC
Confidence            56888888854 2  1   12245666665        2344588999975432  124558999999999999863

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=89.47  E-value=1.5  Score=36.73  Aligned_cols=56  Identities=14%  Similarity=0.179  Sum_probs=43.8

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhc--CCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQL--NLPMDKLMEALESLNENSLVYSIDEFHYKSAV  263 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l--~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~  263 (265)
                      ....|++++.-.      .|. ...+|+++|  +++.++|+++|++|..-|.|=-..+..|+.|.
T Consensus        25 ~~~~ir~l~~l~------~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~   83 (171)
T PF14394_consen   25 YHPAIRELLPLM------PFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTD   83 (171)
T ss_pred             HHHHHHHHhhcC------CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEec
Confidence            445566666543      233 899999999  89999999999999999999774446787765

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=89.41  E-value=1.8  Score=30.14  Aligned_cols=50  Identities=12%  Similarity=0.172  Sum_probs=40.5

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceee
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKS  261 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~  261 (265)
                      .+|++++++.       -++..+|+++++++...|+..+..|.++|.... . ...|..
T Consensus         3 ~~il~~L~~~-------~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~-~~g~~l   53 (69)
T TIGR00122         3 LRLLALLADN-------PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV-GKGYRL   53 (69)
T ss_pred             HHHHHHHHcC-------CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec-CCceEe
Confidence            4677777642       367999999999999999999999999999776 5 555543

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=89.37  E-value=1.2  Score=40.85  Aligned_cols=52  Identities=15%  Similarity=0.307  Sum_probs=43.4

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCe-EEeecCCcee
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSL-VYSIDEFHYK  260 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~-IYsiDd~hyk  260 (265)
                      ..+||++|++      +..++.++|+++|+++...|.++|..|.++|. |+++....|.
T Consensus         6 ~~~il~~L~~------~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~~~Gy~   58 (319)
T PRK11886          6 MLQLLSLLAD------GDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVKGKGYR   58 (319)
T ss_pred             HHHHHHHHHc------CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEecCCeEE
Confidence            4568888875      35789999999999999999999999999999 8775544564

>PHA02943 hypothetical protein; Provisional

Probab=89.30  E-value=1.1  Score=36.68  Aligned_cols=46  Identities=17%  Similarity=0.167  Sum_probs=38.3

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-..+||++|+.       -..+..+|++.|+++-.+++-+|.-|..||.|-+
T Consensus        11 ~R~~eILE~Lk~-------G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vkr   56 (165)
T PHA02943         11 TRMIKTLRLLAD-------GCKTTSRIANKLGVSHSMARNALYQLAKEGMVLK   56 (165)
T ss_pred             HHHHHHHHHHhc-------CCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEE
Confidence            345668888832       1457999999999999999999999999999865

>TIGR00617 rpa1 replication factor-a protein 1 (rpa1)

Probab=89.29  E-value=2.8  Score=42.06  Aligned_cols=65  Identities=20%  Similarity=0.419  Sum_probs=46.1

Q ss_pred             EEEEEEEEEEeee------C-----CCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEE-EeeeeCCccE
Q 024592           69 TITVVGIVCDMQD------K-----EPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQDKRS  135 (265)
Q Consensus        69 ~V~iVG~V~~v~~------~-----~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~~~~~  135 (265)
                      .|.|+|+|.++..      .     .....++|.|.|| +|++.+|.+.+..    ....++..|.+.| +++.|++ +.
T Consensus       312 ~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~~A~~----~~~~~~~Vva~kg~~V~~f~g-~s  386 (608)
T TIGR00617       312 LVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATK----FDVSVQPVIAIKGVRVSDFGG-KS  386 (608)
T ss_pred             CccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhh----cCCCCCCEEEEEeEEEEecCC-ce
Confidence            6788888887632      1     1357899999999 5999999876531    1256778877774 5788965 46


Q ss_pred             EEE
Q 024592          136 LNA  138 (265)
Q Consensus       136 i~~  138 (265)
                      |..
T Consensus       387 Ls~  389 (608)
T TIGR00617       387 LST  389 (608)
T ss_pred             Eec
Confidence            654

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=89.26  E-value=0.8  Score=35.53  Aligned_cols=49  Identities=16%  Similarity=0.339  Sum_probs=40.8

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +..+..||++|.+.     +.-++.++|.+.|     +++...|-.+|+.|.+.|.|-.
T Consensus         7 T~~R~~Il~~l~~~-----~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~   60 (120)
T PF01475_consen    7 TPQRLAILELLKES-----PEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRK   60 (120)
T ss_dssp             HHHHHHHHHHHHHH-----SSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHcC-----CCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEE
Confidence            56788899999975     2378999999988     3888999999999999999988

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

>PRK06958 single-stranded DNA-binding protein; Provisional

Probab=89.06  E-value=2.9  Score=35.37  Aligned_cols=61  Identities=16%  Similarity=0.159  Sum_probs=39.6

Q ss_pred             EeEEEEEEEEEEe---ee--C-CCeEEEEEE------c--------CCCeEEEEEecccccccccccccCCCCEEEEEEE
Q 024592           67 VNTITVVGIVCDM---QD--K-EPQFIFLID------D--------GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH  126 (265)
Q Consensus        67 v~~V~iVG~V~~v---~~--~-~t~~~y~Ld------D--------gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~  126 (265)
                      ++.|.|+|+|..-   ..  . ...+.|+|-      |        .|--+.|..|...+.  .....|+.|+.|.|.|+
T Consensus         4 ~N~V~LiGrLg~DPElr~t~nG~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE--~v~~~LkKGs~V~VeGr   81 (182)
T PRK06958          4 VNKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAE--IVGEYLKKGSSVYIEGR   81 (182)
T ss_pred             ccEEEEEEEecCCCeEEEcCCCCEEEEEEEEeccccccccCCcccccceEEEEEEehHHHH--HHHHHhCCCCEEEEEEE
Confidence            6788999998652   11  1 235667663      1        233477777764321  22456899999999999


Q ss_pred             eee
Q 024592          127 LKA  129 (265)
Q Consensus       127 i~~  129 (265)
                      |+.
T Consensus        82 L~~   84 (182)
T PRK06958         82 IRT   84 (182)
T ss_pred             EEe
Confidence            996

>PF14502 HTH_41: Helix-turn-helix domain

Probab=88.89  E-value=0.84  Score=30.01  Aligned_cols=32  Identities=19%  Similarity=0.212  Sum_probs=29.7

Q ss_pred             cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          222 VHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      -+++|.+++|+.+.-.|+.||.+|.++|.|.-
T Consensus         7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~L   38 (48)
T PF14502_consen    7 PTISEYSEKFGVSRGTIQNALKFLEENGAIKL   38 (48)
T ss_pred             CCHHHHHHHhCcchhHHHHHHHHHHHCCcEEe
Confidence            47899999999999999999999999999875

>TIGR03337 phnR transcriptional regulator protein

Probab=88.73  E-value=1.5  Score=37.74  Aligned_cols=51  Identities=18%  Similarity=0.295  Sum_probs=38.7

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+.+.+.|++..- ....=+ +..+++++|+.+...||+||+.|.++|.||.
T Consensus         6 i~~~l~~~I~~g~~-~~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~   57 (231)
T TIGR03337         6 IKDHLSYQIRAGAL-LPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYR   57 (231)
T ss_pred             HHHHHHHHHHcCCC-CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEE
Confidence            55666676765321 111123 6799999999999999999999999999997

This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.

>PRK00215 LexA repressor; Validated

Probab=88.57  E-value=0.66  Score=39.54  Aligned_cols=54  Identities=22%  Similarity=0.272  Sum_probs=44.6

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCC-CHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNL-PMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~-~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++..|..||++|++... ......+..+|++.+++ +...+...|..|.+.|.|-.
T Consensus         2 lt~~q~~il~~i~~~~~-~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~   56 (205)
T PRK00215          2 LTKRQQEILDFIRDHIE-ETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRR   56 (205)
T ss_pred             CCHHHHHHHHHHHHHHH-HhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence            46789999999975210 22456799999999999 99999999999999999966

>PRK09462 fur ferric uptake regulator; Provisional

Probab=88.23  E-value=1.9  Score=34.91  Aligned_cols=51  Identities=16%  Similarity=0.325  Sum_probs=43.3

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++.-+..||++|.+.    .+.-++.++|.++|     +++...|-.+|+.|.+.|.|-.
T Consensus        15 ~T~qR~~Il~~l~~~----~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~   70 (148)
T PRK09462         15 VTLPRLKILEVLQEP----DNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTR   70 (148)
T ss_pred             CCHHHHHHHHHHHhC----CCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence            567888999999863    23478999999988     3789999999999999999976

>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing

Probab=87.96  E-value=1.9  Score=34.76  Aligned_cols=62  Identities=21%  Similarity=0.357  Sum_probs=35.3

Q ss_pred             eEEEEEEcCCCeEEEEEecccccc-----c-----------cc----cccc-CCCCEEEEEEEeeeeCCc--cEEEEEEe
Q 024592           85 QFIFLIDDGTGRIECSRWAHEQME-----F-----------NE----VNQI-SKGMYVRVYGHLKAFQDK--RSLNAYSL  141 (265)
Q Consensus        85 ~~~y~LdDgTG~I~~~~w~~~~~~-----~-----------~~----~~~~-~~g~yVrV~G~i~~f~~~--~~i~~~~i  141 (265)
                      .+.+.|.|+||.+.+..|.+....     .           ..    ...+ -..-.++|.++...|+++  ..+++..|
T Consensus        55 ~l~~~i~D~tg~~~~~~F~~~a~~l~G~~a~el~~~~~~~~~~~~~~~~~~~~~~~~f~v~~~~~~y~~e~r~~~~v~~i  134 (146)
T PF08646_consen   55 RLSLKISDGTGSIWVTLFDEEAEQLLGMSADELKELKEEDPEEFPKIIKKLLGKEFVFRVRVKKESYNDESRVKYTVVRI  134 (146)
T ss_dssp             EEEEEEEETTEEEEEEEEHHHHHHHHCCHHCCCHHHCCC-HHHHHHHHHCTTT-EEEEEEEEEE--------EEEEEEEE
T ss_pred             EEEEEEEeCCCeEEEEEEhHHHHHHhCCCHHHHHHHHhhchhHHHHHHHHhhCcEEEEEEEEEEhhhCCceEEEEEEEEe
Confidence            367789999999999999764320     0           00    0111 222356888899999865  45788888


Q ss_pred             eeCCC
Q 024592          142 RPIID  146 (265)
Q Consensus       142 ~~v~d  146 (265)
                      .||+-
T Consensus       135 ~~vd~  139 (146)
T PF08646_consen  135 EPVDY  139 (146)
T ss_dssp             EE--H
T ss_pred             EeCCH
Confidence            88853

It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

Probab=87.93  E-value=1  Score=32.73  Aligned_cols=38  Identities=11%  Similarity=0.226  Sum_probs=35.3

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .=+++++|++.++++.+++...|..++.+|.|.- ||..
T Consensus        23 ~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~   61 (88)
T smart00088       23 SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV   61 (88)
T ss_pred             ceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence            4689999999999999999999999999999999 9864

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.

>smart00753 PAM PCI/PINT associated module

Probab=87.93  E-value=1  Score=32.73  Aligned_cols=38  Identities=11%  Similarity=0.226  Sum_probs=35.3

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .=+++++|++.++++.+++...|..++.+|.|.- ||..
T Consensus        23 ~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~   61 (88)
T smart00753       23 SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV   61 (88)
T ss_pred             ceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence            4689999999999999999999999999999999 9864

>PRK09010 single-stranded DNA-binding protein; Provisional

Probab=87.93  E-value=2.8  Score=35.35  Aligned_cols=66  Identities=20%  Similarity=0.230  Sum_probs=41.5

Q ss_pred             EEeEEEEEEEEEEe---ee---CCCeEEEEEE------c-CCC-------eEEEEEecccccccccccccCCCCEEEEEE
Q 024592           66 DVNTITVVGIVCDM---QD---KEPQFIFLID------D-GTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYG  125 (265)
Q Consensus        66 ~v~~V~iVG~V~~v---~~---~~t~~~y~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G  125 (265)
                      -++.|.|||+|..-   +.   ....+.|+|-      | .+|       -+.|..|...+.  .....|+.|+.|.|.|
T Consensus         5 ~~N~V~LiGrLg~DPelR~t~nG~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae--~~~~~L~KGs~V~VeG   82 (177)
T PRK09010          5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAE--VAGEYLRKGSQVYIEG   82 (177)
T ss_pred             CceEEEEEEEeCCCceEEEcCCCCEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHH--HHHHhcCCCCEEEEEE
Confidence            36888999988552   21   2234555554      2 133       367888865322  1245689999999999


Q ss_pred             Eeee--eCCc
Q 024592          126 HLKA--FQDK  133 (265)
Q Consensus       126 ~i~~--f~~~  133 (265)
                      +|+.  |.++
T Consensus        83 rL~~~~yedk   92 (177)
T PRK09010         83 QLRTRKWTDQ   92 (177)
T ss_pred             EEEeccccCC
Confidence            9975  5443

>PRK10870 transcriptional repressor MprA; Provisional

Probab=87.92  E-value=2.2  Score=35.68  Aligned_cols=57  Identities=12%  Similarity=0.072  Sum_probs=47.8

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .+++..|-.||..|...    .+.+++..+|++.++++...+...|+.|...|.|.- -|.+
T Consensus        51 ~gLt~~q~~iL~~L~~~----~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~  108 (176)
T PRK10870         51 QGINETLFMALITLESQ----ENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDN  108 (176)
T ss_pred             CCCCHHHHHHHHHHhcC----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence            35677788899888752    245799999999999999999999999999999998 5544

>TIGR00621 ssb single stranded DNA-binding protein (ssb)

Probab=87.86  E-value=2  Score=35.61  Aligned_cols=61  Identities=20%  Similarity=0.260  Sum_probs=38.6

Q ss_pred             EeEEEEEEEEEE---eeeC---CCeEEEEEE-------------cCCCeEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592           67 VNTITVVGIVCD---MQDK---EPQFIFLID-------------DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHL  127 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~~---~t~~~y~Ld-------------DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i  127 (265)
                      ++.|.|+|.|..   ++..   ...+.|+|.             |.|--|.|..|...+.  .....++.|+.|.|.|+|
T Consensus         4 ~N~V~L~G~l~~dPe~r~t~~G~~v~~fsvA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~L   81 (164)
T TIGR00621         4 VNKVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAE--VAAQYLKKGSLVYVEGRL   81 (164)
T ss_pred             ccEEEEEEEeCCCCEEEECCCCCEEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHH--HHHHhCCCCCEEEEEEEE
Confidence            466777777755   2211   123334432             2244688999976432  234578999999999999


Q ss_pred             ee
Q 024592          128 KA  129 (265)
Q Consensus       128 ~~  129 (265)
                      +.
T Consensus        82 ~~   83 (164)
T TIGR00621        82 RT   83 (164)
T ss_pred             Ee
Confidence            85

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A

Probab=87.64  E-value=0.72  Score=33.56  Aligned_cols=45  Identities=20%  Similarity=0.238  Sum_probs=37.1

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +-.|+.+|...      ..++..+|.+.++++...+...|..|.++|.|=.
T Consensus         2 Rl~Il~~L~~~------~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~   46 (80)
T PF13601_consen    2 RLAILALLYAN------EEATFSELKEELGLTDGNLSKHLKKLEEAGYVEV   46 (80)
T ss_dssp             HHHHHHHHHHH------SEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHhhc------CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEE
Confidence            45678887653      4799999999999999999999999999999865

>PRK11050 manganese transport regulator MntR; Provisional

Probab=87.56  E-value=2  Score=35.11  Aligned_cols=44  Identities=14%  Similarity=0.052  Sum_probs=36.9

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV  263 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~  263 (265)
                      .+++..+|++.|+++.+.|..+|..|...|.|.......+..|.
T Consensus        50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~~~v~LT~   93 (152)
T PRK11050         50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGVFLTP   93 (152)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCceEECc
Confidence            47899999999999999999999999999999873334555554

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=87.38  E-value=2.3  Score=31.82  Aligned_cols=36  Identities=19%  Similarity=0.403  Sum_probs=33.4

Q ss_pred             CCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          218 NNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       218 ~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ....++..+|++.++++.+.|..+|..|...|.|..
T Consensus        44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r   79 (95)
T TIGR01610        44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR   79 (95)
T ss_pred             cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            356899999999999999999999999999999985

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=87.28  E-value=1.2  Score=37.84  Aligned_cols=36  Identities=22%  Similarity=0.326  Sum_probs=31.9

Q ss_pred             CCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          218 NNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       218 ~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ...=++..+++++|+++..-||+||..|..+|.|-.
T Consensus        31 pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~   66 (212)
T TIGR03338        31 PGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRN   66 (212)
T ss_pred             CCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE
Confidence            344578899999999999999999999999999865

This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.

>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=87.15  E-value=4.6  Score=33.44  Aligned_cols=55  Identities=18%  Similarity=0.236  Sum_probs=43.0

Q ss_pred             eEEEEEEEEE--EeeeCC--CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee
Q 024592           68 NTITVVGIVC--DMQDKE--PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK  128 (265)
Q Consensus        68 ~~V~iVG~V~--~v~~~~--t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~  128 (265)
                      ..|++=|.|.  ++....  ..+.|+|.|+...|.|.+--.      -++.|++|.=|-|.|++.
T Consensus        58 ~~iRvgG~V~~GSi~r~~~~l~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEG~gVVveG~~~  116 (160)
T PRK13165         58 QRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTYEGI------LPDLFREGQGIVAQGVLE  116 (160)
T ss_pred             CEEEEeeEEeCCcEEECCCCeEEEEEEEcCCeEEEEEEccc------CCccccCCCeEEEEEEEC
Confidence            5677888887  565543  379999999999998876422      356789999999999985

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=87.05  E-value=1.4  Score=37.22  Aligned_cols=47  Identities=19%  Similarity=0.176  Sum_probs=40.0

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .....||+.|...+      -++.++|+..|+++..+||+.|..|.++|.|-.
T Consensus        22 ~~~~~Vl~~L~~~g------~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~   68 (178)
T PRK06266         22 EEGFEVLKALIKKG------EVTDEEIAEQTGIKLNTVRKILYKLYDARLADY   68 (178)
T ss_pred             ccHhHHHHHHHHcC------CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence            45567888887531      379999999999999999999999999999974

>PF15072 DUF4539: Domain of unknown function (DUF4539)

Probab=86.97  E-value=1.9  Score=31.91  Aligned_cols=49  Identities=16%  Similarity=0.197  Sum_probs=37.5

Q ss_pred             EEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEE
Q 024592           71 TVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYV  121 (265)
Q Consensus        71 ~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yV  121 (265)
                      ++++.|+++..........|.|.||+|.|..-.+--.  +....+..|..+
T Consensus         6 ~l~v~Iks~~~~~~D~~v~l~DpTG~i~~tiH~~v~~--~y~~~l~~GavL   54 (86)
T PF15072_consen    6 CLVVIIKSIVPSSEDAFVVLKDPTGEIRGTIHRKVLE--EYGDELSPGAVL   54 (86)
T ss_pred             EEEEEEEEeeccCCCeEEEEECCCCcEEEEEeHHHHh--hcCCccccCEEE
Confidence            5789999998877789999999999999998754322  234567777644

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=86.89  E-value=2.1  Score=37.16  Aligned_cols=51  Identities=10%  Similarity=0.190  Sum_probs=37.8

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +...|.+.|.+. ......=+ +..+|+++|+.+..-||+||..|..+|.|..
T Consensus        12 ~~~~l~~~I~~g-~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~   63 (239)
T PRK04984         12 AEEYIIESIWNN-RFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI   63 (239)
T ss_pred             HHHHHHHHHHcC-CCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            334444444432 12333456 5889999999999999999999999999986

>PRK05733 single-stranded DNA-binding protein; Provisional

Probab=86.89  E-value=2.7  Score=35.24  Aligned_cols=62  Identities=19%  Similarity=0.191  Sum_probs=40.2

Q ss_pred             EeEEEEEEEEEEe---ee---CCCeEEEEEE------c-CCC-------eEEEEEecccccccccccccCCCCEEEEEEE
Q 024592           67 VNTITVVGIVCDM---QD---KEPQFIFLID------D-GTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGH  126 (265)
Q Consensus        67 v~~V~iVG~V~~v---~~---~~t~~~y~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~  126 (265)
                      ++.|.|+|+|..-   +.   ....+.|.|-      | .+|       =+.|..|...+.  .....++.|+.|.|.|+
T Consensus         5 mNkV~LiGrlg~DPElr~t~nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae--~v~~~l~KGs~V~VeGr   82 (172)
T PRK05733          5 VNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAE--IAGEYLRKGSQVYIEGK   82 (172)
T ss_pred             ceEEEEEEEecCCCEEEECCCCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHH--HHHHHhCCCCEEEEEEE
Confidence            6788999998652   11   2234555543      1 233       288888865332  23456899999999999


Q ss_pred             eeee
Q 024592          127 LKAF  130 (265)
Q Consensus       127 i~~f  130 (265)
                      |+.-
T Consensus        83 Lr~~   86 (172)
T PRK05733         83 LQTR   86 (172)
T ss_pred             EEeC
Confidence            9863

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=86.64  E-value=1.2  Score=35.83  Aligned_cols=33  Identities=6%  Similarity=0.185  Sum_probs=31.5

Q ss_pred             CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          221 GVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      =++.++|+++++++..-|+++|..|..+|.|.+
T Consensus        25 ~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s   57 (141)
T PRK11014         25 MTSISEVTEVYGVSRNHMVKIINQLSRAGYVTA   57 (141)
T ss_pred             ccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEE
Confidence            478999999999999999999999999999987

>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks

Probab=86.63  E-value=1.8  Score=30.97  Aligned_cols=49  Identities=20%  Similarity=0.379  Sum_probs=44.1

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++-.||+.|...    .+.|+...++.+.++.+...+--.+..|.+.|.|.-
T Consensus         2 ~~~~~~Le~I~rs----R~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k   50 (75)
T PF04182_consen    2 DIQYCLLERIARS----RYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVK   50 (75)
T ss_pred             chHHHHHHHHHhc----CCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEE
Confidence            5678899999764    478999999999999999999999999999999976

This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=86.62  E-value=1.4  Score=38.40  Aligned_cols=41  Identities=10%  Similarity=0.118  Sum_probs=36.3

Q ss_pred             CCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          217 ANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       217 ~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      ....+++..+|++.++++...+...|..|.++|.|.- .+..
T Consensus        17 ~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r   58 (217)
T PRK14165         17 NNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPR   58 (217)
T ss_pred             CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCC
Confidence            3356899999999999999999999999999999988 6543

>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional

Probab=86.39  E-value=1.4  Score=39.07  Aligned_cols=47  Identities=13%  Similarity=0.153  Sum_probs=40.1

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-+.+|+++|++.      .-+++.++++.|+.++..||.-|.+|...+.+|=
T Consensus         7 eR~~~I~~~l~~~------~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~~~~g   53 (252)
T PRK10681          7 ERIGQLLQALKRS------DKLHLKDAAALLGVSEMTIRRDLNAHSAPVVLLG   53 (252)
T ss_pred             HHHHHHHHHHHHc------CCCcHHHHHHHhCCCHHHHHHHHHHhhcCeEEEC
Confidence            3567799999874      3589999999999999999999999998887553

>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase

Probab=86.35  E-value=0.87  Score=42.11  Aligned_cols=54  Identities=22%  Similarity=0.387  Sum_probs=45.6

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      .++++-...||.+|++.    .+.||-..+|..+.+++...|.++|..|++.++|=++
T Consensus        80 ~~l~~~e~lvy~~I~~a----g~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~v  133 (327)
T PF05158_consen   80 KGLSDEERLVYQLIEEA----GNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSV  133 (327)
T ss_dssp             -SSSCCHHHHHHHHHHH----TTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCHHHHHHHHHHHHh----CCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEe
Confidence            56788889999999985    4689999999999999999999999999999999873

The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=86.35  E-value=2.3  Score=35.42  Aligned_cols=57  Identities=16%  Similarity=0.092  Sum_probs=46.2

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe-ecCCcee
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS-IDEFHYK  260 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs-iDd~hyk  260 (265)
                      .+..+..||++|.+.     +.-++.++|.++|     +++...|...|+.|.+.|.|-. -..+.|.
T Consensus        24 ~T~qR~~IL~~l~~~-----~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~~~~~~   86 (169)
T PRK11639         24 LTPQRLEVLRLMSLQ-----PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNSYV   86 (169)
T ss_pred             CCHHHHHHHHHHHhc-----CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEecCCcEE
Confidence            457888899999863     3578999999988     3789999999999999999987 3444453

>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=86.29  E-value=5.5  Score=32.96  Aligned_cols=65  Identities=20%  Similarity=0.222  Sum_probs=47.4

Q ss_pred             eEEEEEEEEE--EeeeC--CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEe
Q 024592           68 NTITVVGIVC--DMQDK--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSL  141 (265)
Q Consensus        68 ~~V~iVG~V~--~v~~~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i  141 (265)
                      ..+++=|.|.  ++...  ...+.|.|.|+...|.|.+--.      -++.|++|.=|-|.|++..   .-.+.|..|
T Consensus        58 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEG~gVVveG~~~~---~g~F~A~ev  126 (159)
T PRK13150         58 QRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGI------LPDLFREGQGVVVQGTLEK---GNHVLAHEV  126 (159)
T ss_pred             CEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEecc------CCccccCCCeEEEEEEECC---CCEEEEeEE
Confidence            6778888887  56553  3579999999999998875432      3567899999999999853   234555444

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=86.15  E-value=2.4  Score=35.95  Aligned_cols=54  Identities=11%  Similarity=0.028  Sum_probs=46.7

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      -+++.-|-.||.+|...      .|++..+|++.+.++.+.|...|+.|...|.|.- .|.
T Consensus        41 ~gLt~~q~~iL~~L~~~------~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~   95 (185)
T PRK13777         41 YDLNINEHHILWIAYHL------KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKE   95 (185)
T ss_pred             CCCCHHHHHHHHHHHhC------CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCC
Confidence            35777888899998753      4899999999999999999999999999999997 554

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=86.14  E-value=1.9  Score=38.02  Aligned_cols=45  Identities=13%  Similarity=0.245  Sum_probs=38.1

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..||+.|+..     +.-++..+|+++++++..-|++++..|...|.|.+
T Consensus       186 ~~IL~~L~~~-----egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~  230 (251)
T TIGR02787       186 EHIFEELDGN-----EGLLVASKIADRVGITRSVIVNALRKLESAGVIES  230 (251)
T ss_pred             HHHHHHhccc-----cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4477777542     34579999999999999999999999999999987

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

>PRK07274 single-stranded DNA-binding protein; Provisional

Probab=85.87  E-value=3.4  Score=32.89  Aligned_cols=61  Identities=16%  Similarity=0.288  Sum_probs=39.0

Q ss_pred             EeEEEEEEEEEEe---ee---CCCeEEEEEE------cCCC-----eEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           67 VNTITVVGIVCDM---QD---KEPQFIFLID------DGTG-----RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        67 v~~V~iVG~V~~v---~~---~~t~~~y~Ld------DgTG-----~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      ++.|.|+|++..-   ..   ....+.|+|-      |..|     -+.|..|...+.  .-...++.|+.|.|.|+|+.
T Consensus         2 mN~v~LiGrL~~dPelr~t~~g~~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae--~v~~~l~KG~~V~V~Grl~~   79 (131)
T PRK07274          2 YNKVILIGRLTATPELVKTANDKSVARVTLAVNRRFKNQNGEREADFINVVLWGKLAE--TLASYASKGSLISIDGELRT   79 (131)
T ss_pred             eeEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHH--HHHHHcCCCCEEEEEEEEEe
Confidence            4678888888652   11   1235666665      3233     377888864321  12455899999999999886

>PHA03103 double-strand RNA-binding protein; Provisional

Probab=85.78  E-value=2.4  Score=35.94  Aligned_cols=50  Identities=22%  Similarity=0.296  Sum_probs=41.2

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCC
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEF  257 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~  257 (265)
                      |=.++++.|..      .++++..+|+++|+++-.+|+..|-.|..+|.||..|+.
T Consensus        14 lv~~~~~~l~~------~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~~~~   63 (183)
T PHA03103         14 LVKKEVKNLGL------GEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMSDSN   63 (183)
T ss_pred             HHHHHHHHhcc------CCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecCCCC
Confidence            44444555543      469999999999999999999999999999999987764

>PRK07217 replication factor A; Reviewed

Probab=85.68  E-value=2.2  Score=39.01  Aligned_cols=57  Identities=28%  Similarity=0.290  Sum_probs=41.0

Q ss_pred             eEEEEEEcCCCeEEEEEeccccc--------cc--------------ccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592           85 QFIFLIDDGTGRIECSRWAHEQM--------EF--------------NEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus        85 ~~~y~LdDgTG~I~~~~w~~~~~--------~~--------------~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~  142 (265)
                      ++.+.||||||.++|++..+...        +.              ......-.|.|++|+|.+  |  -+++.+..+.
T Consensus       218 rik~vlDDGt~~~~~~~~~e~te~l~G~~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~~--~--g~~l~~~~~~  293 (311)
T PRK07217        218 RIKGVLDDGEEVQEVIFNREATEELTGITLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGPT--L--GRYLLADSVE  293 (311)
T ss_pred             EEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEecc--C--CcEEEeeEee
Confidence            89999999999999998864221        00              011124689999999976  3  3688888887


Q ss_pred             eCC
Q 024592          143 PII  145 (265)
Q Consensus       143 ~v~  145 (265)
                      +.+
T Consensus       294 ~~~  296 (311)
T PRK07217        294 PLT  296 (311)
T ss_pred             ccc
Confidence            774

>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors

Probab=85.65  E-value=0.71  Score=35.10  Aligned_cols=45  Identities=24%  Similarity=0.300  Sum_probs=33.9

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      +-.-.|+++|-..      ..++-++|++.++++..++|++|..|.++|.|
T Consensus        13 ~~~~~Il~~L~~~------~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv   57 (105)
T PF02002_consen   13 EEAVRILDALLRK------GELTDEDLAKKLGLKPKEVRKILYKLYEDGLV   57 (105)
T ss_dssp             STTHHHHHHHHHH--------B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-
T ss_pred             chHHHHHHHHHHc------CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence            3456788888653      25788999999999999999999999999999

Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=85.61  E-value=3.1  Score=26.79  Aligned_cols=41  Identities=17%  Similarity=0.300  Sum_probs=32.3

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE  247 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~  247 (265)
                      +++.+..|+..+.        .|++..+|++.++++...|+..+..+..
T Consensus         4 l~~~e~~i~~~~~--------~g~s~~eia~~l~is~~tv~~~~~~~~~   44 (58)
T smart00421        4 LTPREREVLRLLA--------EGLTNKEIAERLGISEKTVKTHLSNIMR   44 (58)
T ss_pred             CCHHHHHHHHHHH--------cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5566666776652        3789999999999999999998887643

lux regulon (activates the bioluminescence operon

>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain

Probab=85.61  E-value=2.3  Score=31.21  Aligned_cols=65  Identities=18%  Similarity=0.065  Sum_probs=46.9

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe--ecCCceeeccCC
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS--IDEFHYKSAVNA  265 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs--iDd~hyk~t~~~  265 (265)
                      +++..=+||..|...-  ..-+=|+.+.|.+..+++..++...|..|...+.|..  ..-+-|+.|..|
T Consensus         4 L~~~d~rvL~aiE~gm--k~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~G   70 (82)
T PF09202_consen    4 LSKEDFRVLRAIEMGM--KNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLG   70 (82)
T ss_dssp             --HHHHHHHHHHHTTT--TT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHH
T ss_pred             CCHHHHHHHHHHHHcc--cCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccCCCcceEEEeecc
Confidence            4556667888886642  4457899999999999999999999999999999988  333578877643

It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=85.58  E-value=2.5  Score=30.83  Aligned_cols=56  Identities=18%  Similarity=0.217  Sum_probs=41.6

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceee
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKS  261 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~  261 (265)
                      ....++.++...    ++.-++=++|++.|+++...|-+.++.|-++|.=.. +-..-|+.
T Consensus         4 ~~~~~~~ll~~~----~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L   60 (79)
T COG1654           4 TSQMLLLLLLLL----TGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKGYLL   60 (79)
T ss_pred             hHHHHHHHHHHc----CCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCceec
Confidence            445566665543    345789999999999999999999999999996444 44445543

>PRK08182 single-stranded DNA-binding protein; Provisional

Probab=85.58  E-value=3.8  Score=33.44  Aligned_cols=60  Identities=15%  Similarity=0.188  Sum_probs=38.9

Q ss_pred             eEEEEEEEEEE---ee--eCCC-----eEEEEEE------cCCC--------eEEEEEecccccccccccccCCCCEEEE
Q 024592           68 NTITVVGIVCD---MQ--DKEP-----QFIFLID------DGTG--------RIECSRWAHEQMEFNEVNQISKGMYVRV  123 (265)
Q Consensus        68 ~~V~iVG~V~~---v~--~~~t-----~~~y~Ld------DgTG--------~I~~~~w~~~~~~~~~~~~~~~g~yVrV  123 (265)
                      +.|.|+|.+..   +.  ...+     .+.|.|-      +.+|        -|.|..|...+.  .....|+.|+.|-|
T Consensus         3 N~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae--~v~~~l~KG~~V~V   80 (148)
T PRK08182          3 THFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAE--HWARLYQKGMRVLV   80 (148)
T ss_pred             cEEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHH--HHHHhcCCCCEEEE
Confidence            57888888855   11  1222     5677772      2233        378889975332  12456899999999


Q ss_pred             EEEeee
Q 024592          124 YGHLKA  129 (265)
Q Consensus       124 ~G~i~~  129 (265)
                      .|+|+.
T Consensus        81 ~GrL~~   86 (148)
T PRK08182         81 EGRMER   86 (148)
T ss_pred             EEEEEe
Confidence            999975

>COG3888 Predicted transcriptional regulator [Transcription]

Probab=85.13  E-value=1.9  Score=38.63  Aligned_cols=49  Identities=22%  Similarity=0.414  Sum_probs=43.8

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .++++|+..|+..    .++|+..-||-+..+++.+.+-++|..|.++|.|--
T Consensus         4 ~~reklir~Lk~a----~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~R   52 (321)
T COG3888           4 SLREKLIRELKRA----GPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKR   52 (321)
T ss_pred             cHHHHHHHHHHhc----CCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeee
Confidence            4788899999984    478999999999999999999999999999998754

>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids

Probab=85.13  E-value=1.9  Score=32.12  Aligned_cols=62  Identities=26%  Similarity=0.397  Sum_probs=35.1

Q ss_pred             EeEEEEEEEEEE---eeeC--C-CeEEEEEE--c------C-----CCeEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592           67 VNTITVVGIVCD---MQDK--E-PQFIFLID--D------G-----TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHL  127 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~~--~-t~~~y~Ld--D------g-----TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i  127 (265)
                      ++.|.|+|.|..   +...  . ..+.|.|.  +      +     |--+.|..|.+.+.  .-...++.|+.|.|.|++
T Consensus         1 mN~v~l~G~l~~~p~~~~~~~g~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~--~~~~~l~kG~~V~V~G~l   78 (104)
T PF00436_consen    1 MNKVTLIGRLGKDPELRYTKNGTPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAE--NVAEYLKKGDRVYVEGRL   78 (104)
T ss_dssp             EEEEEEEEEESSSEEEEEETTSEEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHH--HHHHH--TT-EEEEEEEE
T ss_pred             CcEEEEEEEECCCcEEEECCCCCEEEEEEEEEecEEeeeeccCccceEEEEEEeeeeccc--ccceEEcCCCEEEEEEEE
Confidence            467888998844   2221  1 23444432  2      1     12377888865332  223458999999999999


Q ss_pred             eee
Q 024592          128 KAF  130 (265)
Q Consensus       128 ~~f  130 (265)
                      +..
T Consensus        79 ~~~   81 (104)
T PF00436_consen   79 RTR   81 (104)
T ss_dssp             EEE
T ss_pred             Eee
Confidence            875

It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....

>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70)

Probab=85.03  E-value=3.7  Score=33.77  Aligned_cols=72  Identities=13%  Similarity=0.238  Sum_probs=43.4

Q ss_pred             eEEEEEEcCCCeEEEEEecccccc-------------ccc-------ccccCCCC--EEEEEEEeeeeCC--ccEEEEEE
Q 024592           85 QFIFLIDDGTGRIECSRWAHEQME-------------FNE-------VNQISKGM--YVRVYGHLKAFQD--KRSLNAYS  140 (265)
Q Consensus        85 ~~~y~LdDgTG~I~~~~w~~~~~~-------------~~~-------~~~~~~g~--yVrV~G~i~~f~~--~~~i~~~~  140 (265)
                      .+.+.|.|+||.+.+..|.+....             ...       ... ..|.  .++|..+...|++  +...++..
T Consensus        69 ~l~~~i~D~Tg~~~~~~F~~~ae~l~G~sa~el~~~~~~~~~~~~~~i~~-~~gk~~~f~v~~~~~~y~~e~~~~~~v~~  147 (166)
T cd04476          69 ILSLNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQD-LVGKTFLFRVSVKEETYNDEGRIRYTVVK  147 (166)
T ss_pred             EEEEEEEeCCCCEEEEEehHHHHHHhCCCHHHHHHHhhcCHHHHHHHHHH-hhCceEEEEEEEEehhcCCcceEEEEEEE
Confidence            477899999999999999753320             000       111 1233  4555566667887  55666666


Q ss_pred             eeeCCChhHHHHHHHHHH
Q 024592          141 LRPIIDFNEITSHFVECI  158 (265)
Q Consensus       141 i~~v~d~Nei~~H~Levi  158 (265)
                      +.|+. +.....++|+-+
T Consensus       148 i~~~~-~~~~~~~l~~~i  164 (166)
T cd04476         148 VAPVD-YKKESKRLIQSI  164 (166)
T ss_pred             cccCC-HHHHHHHHHHHh
Confidence            66664 334566666544

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun

>PRK13732 single-stranded DNA-binding protein; Provisional

Probab=85.01  E-value=3.5  Score=34.70  Aligned_cols=61  Identities=16%  Similarity=0.201  Sum_probs=40.8

Q ss_pred             EeEEEEEEEEEE---eee---CCCeEEEEEEc-------CCC-------eEEEEEecccccccccccccCCCCEEEEEEE
Q 024592           67 VNTITVVGIVCD---MQD---KEPQFIFLIDD-------GTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGH  126 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~---~~t~~~y~LdD-------gTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~  126 (265)
                      ++.|.|+|+|..   +..   ....+.|+|--       .+|       -+.|..|..-+.  .....++.|+.|.|.|+
T Consensus         6 mN~V~LiGrLg~DPElR~t~nG~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae--~v~~~L~KG~~V~VeGr   83 (175)
T PRK13732          6 INKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAE--VAGEYLRKGAQVYIEGQ   83 (175)
T ss_pred             ceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHH--HHHHhcCCCCEEEEEEE
Confidence            688999999965   221   22456666642       234       367888865322  22355899999999999


Q ss_pred             eee
Q 024592          127 LKA  129 (265)
Q Consensus       127 i~~  129 (265)
                      |+.
T Consensus        84 L~~   86 (175)
T PRK13732         84 LRT   86 (175)
T ss_pred             EEe
Confidence            986

>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=85.00  E-value=2.2  Score=41.94  Aligned_cols=63  Identities=17%  Similarity=0.271  Sum_probs=48.7

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-ccccccccCCCCEEEEEEEeeee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-EFNEVNQISKGMYVRVYGHLKAF  130 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~~~~~~~~~~g~yVrV~G~i~~f  130 (265)
                      ..|+|.|||-.+++...-+...|-|.+|.+.+..-.++.. --+....++.-..|+|.|.++.=
T Consensus        16 ~~V~L~GWV~r~Rd~GgliFiDLRDr~GivQvv~~~~~~~~~~~~a~~lr~E~vi~V~G~V~~R   79 (585)
T COG0173          16 QTVTLSGWVHRRRDHGGLIFIDLRDREGIVQVVFDPEDSPEAFEVASRLRNEFVIQVTGTVRAR   79 (585)
T ss_pred             CEEEEEeeeeeccccCCeEEEEcccCCCeEEEEECCccCHHHHHHHHhcCceEEEEEEEEEEec
Confidence            5799999999999888888889999999877775543211 11345678888899999988764

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=84.89  E-value=1.7  Score=30.50  Aligned_cols=33  Identities=12%  Similarity=0.275  Sum_probs=30.3

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      ..++.++|+..++.+...|...|..|.++|.|=
T Consensus        27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~   59 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSRETVSRILKRLKDEGIIE   59 (76)
T ss_dssp             EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            457899999999999999999999999999773

...

>PRK07772 single-stranded DNA-binding protein; Provisional

Probab=84.71  E-value=3.3  Score=35.20  Aligned_cols=32  Identities=38%  Similarity=0.629  Sum_probs=24.6

Q ss_pred             eEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           96 RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        96 ~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      -|+|..|...+.  .....|+.|+.|.|.|+|+.
T Consensus        54 fi~V~~Wg~~Ae--~va~~L~KGd~V~V~GrL~~   85 (186)
T PRK07772         54 FLRCSIWRQAAE--NVAESLTKGMRVIVTGRLKQ   85 (186)
T ss_pred             EEEEEEecHHHH--HHHHhcCCCCEEEEEEEEEc
Confidence            478999976432  23456899999999999985

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=84.59  E-value=1.9  Score=41.96  Aligned_cols=61  Identities=26%  Similarity=0.294  Sum_probs=50.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec--CCceeeccC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSID--EFHYKSAVN  264 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD--d~hyk~t~~  264 (265)
                      +++..+..||..|...      .+++..+|++.++++.+.|..+++.|...|.|-..|  ...|..|..
T Consensus         3 ~Lt~~e~~vL~~L~~~------~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~~~~~i~LTee   65 (489)
T PRK04172          3 ELHPNEKKVLKALKEL------KEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEE   65 (489)
T ss_pred             CCCHHHHHHHHHHHhC------CCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEeeeEEEEEECHH
Confidence            4678899999999642      378999999999999999999999999999988733  346666654

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=84.45  E-value=1.8  Score=38.65  Aligned_cols=50  Identities=18%  Similarity=0.337  Sum_probs=44.4

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCC-cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNG-VHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~G-v~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      ..|++..+.|+++|++.+      | +...||.+.+++|...|-.+|..|+..|.|=
T Consensus       191 ~~L~~~e~~il~~i~~~G------Gri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe  241 (258)
T COG2512         191 YDLNEDEKEILDLIRERG------GRITQAELRRALGLSKTTVSRILRRLEKRGLIE  241 (258)
T ss_pred             CCCCHHHHHHHHHHHHhC------CEEeHHHHHHhhCCChHHHHHHHHHHHhCCceE
Confidence            357888899999999853      5 7889999999999999999999999999873

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=84.13  E-value=2.8  Score=35.85  Aligned_cols=45  Identities=16%  Similarity=0.234  Sum_probs=39.4

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++|+.++.+.     ..|.+..||+++|++++..|+.-+.+|...|.+-.
T Consensus       165 r~Vl~~~~~g-----~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~  209 (225)
T PRK10046        165 NAVRKLFKEP-----GVQHTAETVAQALTISRTTARRYLEYCASRHLIIA  209 (225)
T ss_pred             HHHHHHHHcC-----CCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEE
Confidence            4788888642     34899999999999999999999999999999866

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=84.03  E-value=2.3  Score=28.54  Aligned_cols=42  Identities=14%  Similarity=0.226  Sum_probs=34.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE  247 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~  247 (265)
                      .|++.+..|+.++..        |.+..+|++.+++++..|+.-+..+..
T Consensus         3 ~LT~~E~~vl~~l~~--------G~~~~eIA~~l~is~~tV~~~~~~i~~   44 (58)
T PF00196_consen    3 SLTERELEVLRLLAQ--------GMSNKEIAEELGISEKTVKSHRRRIMK   44 (58)
T ss_dssp             SS-HHHHHHHHHHHT--------TS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHh--------cCCcchhHHhcCcchhhHHHHHHHHHH
Confidence            477888889999864        899999999999999999988877653

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=83.87  E-value=2.1  Score=31.46  Aligned_cols=39  Identities=18%  Similarity=0.165  Sum_probs=33.1

Q ss_pred             HHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeecc
Q 024592          224 RNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAV  263 (265)
Q Consensus       224 ~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t~  263 (265)
                      +.+|++.++++...|..+|+.|.+.|.|.. -+ --|..|.
T Consensus         2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~-~~~~lT~   41 (96)
T smart00529        2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY-RGITLTE   41 (96)
T ss_pred             HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC-CceEech
Confidence            468999999999999999999999999999 54 3565554

iron dependent repressor

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=83.86  E-value=4.5  Score=26.14  Aligned_cols=41  Identities=12%  Similarity=0.179  Sum_probs=31.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHH
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESL  245 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L  245 (265)
                      .|++-++.|+...-       -+|.+..+|++.++++...|+.....-
T Consensus         4 ~L~~~er~vi~~~y-------~~~~t~~eIa~~lg~s~~~V~~~~~~a   44 (50)
T PF04545_consen    4 QLPPREREVIRLRY-------FEGLTLEEIAERLGISRSTVRRILKRA   44 (50)
T ss_dssp             TS-HHHHHHHHHHH-------TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHh-------cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence            57788888887653       248899999999999999998876654

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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=83.51  E-value=4.6  Score=32.11  Aligned_cols=43  Identities=21%  Similarity=0.194  Sum_probs=35.9

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec-CCceeec
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID-EFHYKSA  262 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD-d~hyk~t  262 (265)
                      .-++.++|++++++|..-++++|+.|...|.|-+ -- ..-|..+
T Consensus        24 ~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~   68 (135)
T TIGR02010        24 GPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLG   68 (135)
T ss_pred             CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEecc
Confidence            4689999999999999999999999999999977 22 2356544

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

>PRK07135 dnaE DNA polymerase III DnaE; Validated

Probab=83.17  E-value=3.6  Score=43.47  Aligned_cols=58  Identities=9%  Similarity=0.013  Sum_probs=43.7

Q ss_pred             EEEEEEEEEEeee----CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           69 TITVVGIVCDMQD----KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        69 ~V~iVG~V~~v~~----~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      .|+++|.|.+++.    ......++|+|.||.|+|..|.+.-.   ....+.+++++.|.|+.+.
T Consensus       899 ~~~v~g~i~~~~~~~K~g~~maf~~~eD~~~~~e~~~F~~~~~---~~~~l~~~~~~~~~~~~~~  960 (973)
T PRK07135        899 EYRLAIEVKNVKRLRKANKEYKKVILSDDSVEITIFVNDNDYL---LFETLKKGDIYEFLISKSK  960 (973)
T ss_pred             eEEEEEEEEEEEEEeeCCCeEEEEEEEECCCcEEEEEcHHHHH---HHHHhhcCCEEEEEEEEcC
Confidence            4678888877542    34677889999999999999975321   2234888899999998766

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=83.16  E-value=3  Score=27.30  Aligned_cols=40  Identities=10%  Similarity=0.094  Sum_probs=28.3

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES  244 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~  244 (265)
                      .|++.++.|+....-       .|.+..+|++.++++++.|+..+..
T Consensus        10 ~L~~~~r~i~~l~~~-------~g~s~~eIa~~l~~s~~~v~~~l~r   49 (54)
T PF08281_consen   10 QLPERQREIFLLRYF-------QGMSYAEIAEILGISESTVKRRLRR   49 (54)
T ss_dssp             CS-HHHHHHHHHHHT-------S---HHHHHHHCTS-HHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH-------HCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            467788888877543       4999999999999999999887753

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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=83.07  E-value=2.4  Score=34.93  Aligned_cols=42  Identities=24%  Similarity=0.277  Sum_probs=35.3

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      -.|++.|-..      .-++.++|++.|+++..+||++|..|.++|.|
T Consensus        17 v~Vl~aL~~~------~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv   58 (158)
T TIGR00373        17 GLVLFSLGIK------GEFTDEEISLELGIKLNEVRKALYALYDAGLA   58 (158)
T ss_pred             HHHHHHHhcc------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            4577765432      24899999999999999999999999999998

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.

>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function

Probab=83.02  E-value=6  Score=32.71  Aligned_cols=43  Identities=19%  Similarity=0.310  Sum_probs=27.2

Q ss_pred             EEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE
Q 024592           77 CDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY  124 (265)
Q Consensus        77 ~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~  124 (265)
                      ........++.|.|.|.||.++|..+-.-.     .-..++||-+|.+
T Consensus       123 ~KK~v~~~~~~YeI~DnTG~MeVvv~G~~~-----ni~CEeGDKLrL~  165 (170)
T PF02760_consen  123 HKKTVNKKNTIYEIQDNTGKMEVVVYGKWH-----NIKCEEGDKLRLF  165 (170)
T ss_dssp             EEEEEESSEEEEEEEETTEEEEEEEEGGGC-----GCC--TT-EEEEE
T ss_pred             EEEEEcCCeEEEEEecCCCcEEEEEeccCc-----ccccCCCCeEEEE
Confidence            334455678999999999999999764321     1345677755543

It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.

>PRK04036 DNA polymerase II small subunit; Validated

Probab=82.98  E-value=4.5  Score=39.62  Aligned_cols=61  Identities=16%  Similarity=0.276  Sum_probs=42.4

Q ss_pred             eEEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee
Q 024592           68 NTITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK  128 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~  128 (265)
                      ..|.|||.|.++.... ....+.|+|.||+|.+..-.+...-......+-.|..|-|.|++.
T Consensus       154 ~~~~viG~v~~~~~~~~g~~~~~LED~sgrv~l~~~~~~~~~~~~~~~lvtg~vv~v~G~~~  215 (504)
T PRK04036        154 EEVSIIGMVSDIRSTKNGHKIVELEDTTGTFPVLIMKDREDLAELADELLLDEVIGVEGTLS  215 (504)
T ss_pred             ceEEEEEEEEEeecccCCceEEEEECCCCeEEEEeecchhhhhhhhhcccCceEEEEEEEEc
Confidence            4689999999886443 344789999999999876322100001134688899999999875

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=82.96  E-value=3.4  Score=35.43  Aligned_cols=37  Identities=16%  Similarity=0.174  Sum_probs=33.0

Q ss_pred             CCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          217 ANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       217 ~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ....=++..+|+++|+++..-||+||..|..+|.|..
T Consensus        30 ~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~   66 (221)
T PRK11414         30 KPGARLITKNLAEQLGMSITPVREALLRLVSVNALSV   66 (221)
T ss_pred             CCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEe
Confidence            3345678899999999999999999999999999976

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=82.86  E-value=2.5  Score=27.05  Aligned_cols=33  Identities=12%  Similarity=0.232  Sum_probs=24.0

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE  243 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~  243 (265)
                      ...|+++++        .|+++.+|++.++++...|...|.
T Consensus        11 ~~~i~~l~~--------~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   11 IEEIKELYA--------EGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHHH--------TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHHH--------CCCCHHHHHHHHCcCHHHHHHHHh
Confidence            456777764        389999999999999999987763

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=82.77  E-value=4.4  Score=36.51  Aligned_cols=43  Identities=14%  Similarity=0.204  Sum_probs=36.0

Q ss_pred             Cc-CHHHHHHhcC--CCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592          221 GV-HRNVISQQLN--LPMDKLMEALESLNENSLVYSIDEFHYKSAV  263 (265)
Q Consensus       221 Gv-~~~~I~~~l~--~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~  263 (265)
                      |- ...+|+++|+  ++.++|+++|++|..-|.|=-..|..|+.|.
T Consensus       136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y~~t~  181 (271)
T TIGR02147       136 FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFYKQTD  181 (271)
T ss_pred             CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcEEeec
Confidence            44 6889999997  9999999999999999999764445677764

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB)

Probab=82.69  E-value=3.6  Score=30.23  Aligned_cols=36  Identities=25%  Similarity=0.270  Sum_probs=26.6

Q ss_pred             CCCeEEEEEecccccccccccccCCCCEEEEEEEeeee
Q 024592           93 GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF  130 (265)
Q Consensus        93 gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f  130 (265)
                      .+--+.|..|.+.+.  .-...++.|++|.|.|+++..
T Consensus        42 ~~~~~~v~~~g~~a~--~~~~~~~kG~~V~v~G~l~~~   77 (100)
T cd04496          42 ETDWIRVVAFGKLAE--NAAKYLKKGDLVYVEGRLRTR   77 (100)
T ss_pred             ccEEEEEEEEhHHHH--HHHHHhCCCCEEEEEEEEEec
Confidence            344589999976332  223468999999999999875

SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart

>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis

Probab=82.62  E-value=3.4  Score=32.27  Aligned_cols=49  Identities=20%  Similarity=0.287  Sum_probs=43.8

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .++..-++.|+++.+.        -.++.||+..+++|..-++--+..|.+.|+|--
T Consensus        39 ~~l~pE~~~Il~lC~~--------~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v   87 (114)
T PF05331_consen   39 AGLGPEHRAILELCRR--------PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRV   87 (114)
T ss_pred             CCCCHHHHHHHHHHCC--------CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEE
Confidence            4678899999998764        569999999999999999999999999999864

The function of these proteins is unknown.

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=82.41  E-value=2.2  Score=37.53  Aligned_cols=47  Identities=21%  Similarity=0.429  Sum_probs=41.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..+-+||++|+..      .++++.||++.+++|-+.+..-+..|.+.|.|-+
T Consensus        23 ~vRv~Il~lL~~k------~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT   69 (308)
T COG4189          23 KVRVAILQLLHRK------GPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRT   69 (308)
T ss_pred             HHHHHHHHHHHHh------CCCCHHHHHHHhCCchhhhhhhHHHHHhcCceee
Confidence            4667789999874      3699999999999999999999999999999876

>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences

Probab=82.40  E-value=2.5  Score=35.01  Aligned_cols=46  Identities=20%  Similarity=0.352  Sum_probs=39.7

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcC--CCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLN--LPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~--~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ...|+++|+..     +.-.++.+|..-|+  ++-..|.++|+.|.++|.|-.
T Consensus         3 e~~Il~y~~~q-----NRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~   50 (169)
T PF07106_consen    3 EDAILEYMKEQ-----NRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVE   50 (169)
T ss_pred             HHHHHHHHHHc-----CCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeee
Confidence            46799999874     46789999999994  999999999999999998744

TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=82.37  E-value=3  Score=43.62  Aligned_cols=42  Identities=12%  Similarity=0.086  Sum_probs=36.2

Q ss_pred             CCCcCHHHHHHhc------------CCCHHHHHHHHHHHhhCCeEEeecCCcee
Q 024592          219 NNGVHRNVISQQL------------NLPMDKLMEALESLNENSLVYSIDEFHYK  260 (265)
Q Consensus       219 ~~Gv~~~~I~~~l------------~~~~~~v~~al~~L~~eG~IYsiDd~hyk  260 (265)
                      ..++++++|.+.+            ++++++++++|+.|..+|.||.....+||
T Consensus       857 ~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~~~l~~L~~~g~i~~~~~g~y~  910 (915)
T PTZ00111        857 NKSLDLNEVLSLCHKTFKDNRDHKDGEIYKLISEVLNKMVQEGTAVRENNSYYL  910 (915)
T ss_pred             CCceeHHHHHHHHHhhccccchhccCCCHHHHHHHHHHHHhCCeEeeeCCCchh
Confidence            3589999998654            59999999999999999999996666787

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=82.21  E-value=3.7  Score=32.19  Aligned_cols=47  Identities=17%  Similarity=0.198  Sum_probs=41.1

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +...+||.+|...      ..+++.+|++.++++.+.|-.-|..|.+.|.|-+
T Consensus        16 ptRl~IL~~L~~~------~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~   62 (117)
T PRK10141         16 ETRLGIVLLLRES------GELCVCDLCTALDQSQPKISRHLALLRESGLLLD   62 (117)
T ss_pred             HHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence            5777899998642      2589999999999999999999999999999955

>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length

Probab=82.02  E-value=5  Score=30.03  Aligned_cols=61  Identities=18%  Similarity=0.183  Sum_probs=47.1

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH----------HHhhCCeE-Ee-ecC--CceeeccC
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE----------SLNENSLV-YS-IDE--FHYKSAVN  264 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~----------~L~~eG~I-Ys-iDd--~hyk~t~~  264 (265)
                      +.+..+||.+|.+.    -.+.....+|++..+.+.++|.-||.          .|+.-|.+ .. .+.  ..|+.|.-
T Consensus         8 S~~R~~vl~~L~~~----yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~lT~~   82 (90)
T PF07381_consen    8 SKVRKKVLEYLCSI----YPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRLTEK   82 (90)
T ss_pred             HHHHHHHHHHHHHc----CCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEeChh
Confidence            46889999999875    24688999999999999999999995          58888998 44 322  25555543

The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.

>PRK05813 single-stranded DNA-binding protein; Provisional

Probab=81.67  E-value=5.7  Score=34.64  Aligned_cols=81  Identities=17%  Similarity=0.350  Sum_probs=54.0

Q ss_pred             eEEeEEEEEEEEEEe---ee---CCCeEEEEEEc-----CCCeEEEEEecccccccccccccCCCCEEEEEEEeee--eC
Q 024592           65 ADVNTITVVGIVCDM---QD---KEPQFIFLIDD-----GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQ  131 (265)
Q Consensus        65 ~~v~~V~iVG~V~~v---~~---~~t~~~y~LdD-----gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~  131 (265)
                      ...+.|.|+|.+..-   +.   ....+.|+|-=     .|--|+|..|...+.   ....++.|+.|.|.|+|+.  |.
T Consensus       107 ~~~N~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~~td~i~~v~wg~~Ae---~~~~l~KG~~V~V~GrL~sr~y~  183 (219)
T PRK05813        107 KNPNEIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYNKSDYIPCIAWGRNAR---FCKTLEVGDNIRVWGRVQSREYQ  183 (219)
T ss_pred             CCccEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCCCceEEEEEEEhHHhH---HHhhCCCCCEEEEEEEEEecceE
Confidence            447899999999652   21   22456666652     244699999976442   2345999999999999986  43


Q ss_pred             Cc-----------cEEEEEEeeeCCChh
Q 024592          132 DK-----------RSLNAYSLRPIIDFN  148 (265)
Q Consensus       132 ~~-----------~~i~~~~i~~v~d~N  148 (265)
                      ++           -.|.+..+..++...
T Consensus       184 ~k~g~~~g~kr~~~eV~v~~i~~l~~~~  211 (219)
T PRK05813        184 KKLSEGEVVTKVAYEVSISKMEKVEKEE  211 (219)
T ss_pred             cCCCCccceEEEEEEEEEEEEEEcCChh
Confidence            21           246666776665533

>PRK03837 transcriptional regulator NanR; Provisional

Probab=81.65  E-value=4.9  Score=34.74  Aligned_cols=35  Identities=17%  Similarity=0.227  Sum_probs=31.6

Q ss_pred             CCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          219 NNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       219 ~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+=+ +..+|+++|+.+..-||+||..|..+|.|..
T Consensus        34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~   69 (241)
T PRK03837         34 GDQLPSERELMAFFGVGRPAVREALQALKRKGLVQI   69 (241)
T ss_pred             CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            3446 7899999999999999999999999999976

>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins

Probab=81.60  E-value=2.1  Score=31.57  Aligned_cols=39  Identities=23%  Similarity=0.343  Sum_probs=35.7

Q ss_pred             CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      ..-+++++|++.|++++++++..|..|+.+|.|-- ||..
T Consensus        58 y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~   97 (105)
T PF01399_consen   58 YSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQV   97 (105)
T ss_dssp             -SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETT
T ss_pred             hcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECC
Confidence            45799999999999999999999999999999998 8864

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=81.58  E-value=3.8  Score=36.21  Aligned_cols=59  Identities=14%  Similarity=0.211  Sum_probs=45.4

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA  265 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~~  265 (265)
                      ..-+||..|...     ..-++..||++.++++.+-|-+-+.+|.+||+|=+----+|..|.-|
T Consensus        11 t~fqIL~ei~~~-----qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~gR~~Y~iTkkG   69 (260)
T COG1497          11 TRFQILSEIAVR-----QPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEGRGEYEITKKG   69 (260)
T ss_pred             hHHHHHHHHHHh-----CCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecCCeeEEEehhH
Confidence            445577666432     23578999999999999999999999999999988333478877543

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=81.52  E-value=5.3  Score=35.90  Aligned_cols=62  Identities=15%  Similarity=0.113  Sum_probs=48.9

Q ss_pred             CCChhHHHHHHHhcCcCCCC-CCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCcee
Q 024592          198 EGKSIDQMVLDFLRRPEFLA-NNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYK  260 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~-~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk  260 (265)
                      .+....++||..|++...-+ =..=-+.++|-+.|+++-.+.++||-.|..+|.||. |-+.|+
T Consensus       222 ~l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q-~g~~t~  284 (287)
T COG2996         222 MLDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQ-DGDGTE  284 (287)
T ss_pred             hhhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEE-cCceEE
Confidence            46678899999998764211 122347899999999999999999999999999998 555554

>PRK06642 single-stranded DNA-binding protein; Provisional

Probab=81.52  E-value=6.1  Score=32.39  Aligned_cols=61  Identities=15%  Similarity=0.198  Sum_probs=41.1

Q ss_pred             EeEEEEEEEEEE---eee---CCCeEEEEEE------cC-CC-------eEEEEEecc-cccccccccccCCCCEEEEEE
Q 024592           67 VNTITVVGIVCD---MQD---KEPQFIFLID------DG-TG-------RIECSRWAH-EQMEFNEVNQISKGMYVRVYG  125 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld------Dg-TG-------~I~~~~w~~-~~~~~~~~~~~~~g~yVrV~G  125 (265)
                      ++.|.|+|+|..   ++.   ....+.|+|-      |. +|       =+.|..|.. .+.  .....++.|+.|.|.|
T Consensus         5 ~N~V~LiGrLg~DPElr~t~~G~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae--~~~~~l~KG~~V~V~G   82 (152)
T PRK06642          5 LNKVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVS--VVERYVTKGSKLYIEG   82 (152)
T ss_pred             ceEEEEEEEccCCceEEECCCCCEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHH--HHHHhCCCCCEEEEEE
Confidence            688999999965   222   2246777776      21 22       377888874 221  1234589999999999


Q ss_pred             Eeee
Q 024592          126 HLKA  129 (265)
Q Consensus       126 ~i~~  129 (265)
                      +|+.
T Consensus        83 rL~~   86 (152)
T PRK06642         83 SLQT   86 (152)
T ss_pred             EEEe
Confidence            9986

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=81.45  E-value=5.2  Score=25.78  Aligned_cols=40  Identities=18%  Similarity=0.282  Sum_probs=31.1

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE  247 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~  247 (265)
                      +..+..|+.++.        .|++..+|++.++++...|+..+..+..
T Consensus         2 ~~~e~~i~~~~~--------~~~s~~eia~~l~~s~~tv~~~~~~~~~   41 (57)
T cd06170           2 TPREREVLRLLA--------EGKTNKEIADILGISEKTVKTHLRNIMR   41 (57)
T ss_pred             CHHHHHHHHHHH--------cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            345666776653        3789999999999999999998887654

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2

Probab=81.39  E-value=3.5  Score=28.41  Aligned_cols=47  Identities=21%  Similarity=0.160  Sum_probs=36.8

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++-.+|.++|-..      -..+..+|.+..+++.++|+++|--|+..+.++-
T Consensus        13 ~~~~~V~~~Ll~~------G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y   59 (62)
T PF08221_consen   13 EIVAKVGEVLLSR------GRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQY   59 (62)
T ss_dssp             HHHHHHHHHHHHC-------SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred             hHHHHHHHHHHHc------CCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeee
Confidence            4667788877553      2468999999999999999999999999988763

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. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.

>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO

Probab=81.20  E-value=6.3  Score=30.01  Aligned_cols=57  Identities=14%  Similarity=0.216  Sum_probs=42.9

Q ss_pred             CCCChhHHHHHH-HhcCcC-CCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          197 DEGKSIDQMVLD-FLRRPE-FLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       197 ~~l~~~~~~Vl~-~i~~~~-~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+++.-+-+|+. ++|.+- ..+...-|+..+|++..+++.+.|.+++.+|++.|.|..
T Consensus        28 ~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~   86 (100)
T PF04492_consen   28 ADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIR   86 (100)
T ss_pred             ccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            356655556554 455432 224456899999999999999999999999999999954

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=81.06  E-value=4  Score=35.81  Aligned_cols=35  Identities=23%  Similarity=0.303  Sum_probs=31.4

Q ss_pred             CCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          219 NNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       219 ~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus        23 G~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~   58 (253)
T PRK10421         23 GMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLS   58 (253)
T ss_pred             CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            3457 5789999999999999999999999999976

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=81.04  E-value=4.5  Score=35.33  Aligned_cols=37  Identities=14%  Similarity=0.261  Sum_probs=32.5

Q ss_pred             CCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          217 ANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       217 ~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ....-+ +..+|+++|+.+..-||+||..|..+|.|-.
T Consensus        26 ~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~   63 (251)
T PRK09990         26 KVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIET   63 (251)
T ss_pred             CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            344567 6889999999999999999999999999965

>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed

Probab=80.91  E-value=3.3  Score=39.43  Aligned_cols=57  Identities=18%  Similarity=0.152  Sum_probs=44.2

Q ss_pred             HHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccC
Q 024592          206 VLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVN  264 (265)
Q Consensus       206 Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~  264 (265)
                      |+..+.+..  ..+++++.++|+++++.+++.+++.++.|.+.|.|-..+++.|..+.|
T Consensus       297 iL~~l~~~~--~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~~~g~~~l~rd  353 (412)
T PRK04214        297 LLGRLDQAR--KHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRGERGQWVLARD  353 (412)
T ss_pred             HHHHHHHHH--hcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEecCCCceEecCC
Confidence            555553211  234699999999999999999999999999999997666567876544

>PHA00738 putative HTH transcription regulator

Probab=80.62  E-value=4.7  Score=31.13  Aligned_cols=48  Identities=21%  Similarity=0.324  Sum_probs=42.4

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+.+++||++|...      +.+.+.+|++.++++-+.|-.-|.-|.+.|.|-+
T Consensus        11 dptRr~IL~lL~~~------e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~s   58 (108)
T PHA00738         11 KILRRKILELIAEN------YILSASLISHTLLLSYTTVLRHLKILNEQGYIEL   58 (108)
T ss_pred             CHHHHHHHHHHHHc------CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEE
Confidence            47899999999752      2589999999999999999999999999998855

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=80.57  E-value=3  Score=26.59  Aligned_cols=38  Identities=13%  Similarity=0.174  Sum_probs=20.3

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE  243 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~  243 (265)
                      |+.-++..+..+.+       .|.++.+||+.|+.+.+.|...|.
T Consensus         5 Lt~~eR~~I~~l~~-------~G~s~~~IA~~lg~s~sTV~relk   42 (44)
T PF13936_consen    5 LTPEERNQIEALLE-------QGMSIREIAKRLGRSRSTVSRELK   42 (44)
T ss_dssp             -------HHHHHHC-------S---HHHHHHHTT--HHHHHHHHH
T ss_pred             hhhhHHHHHHHHHH-------cCCCHHHHHHHHCcCcHHHHHHHh
Confidence            44445555555443       599999999999999999988775

>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []

Probab=80.29  E-value=2.1  Score=29.10  Aligned_cols=36  Identities=19%  Similarity=0.264  Sum_probs=30.8

Q ss_pred             CCCCcCHHHHHHhc---CCCHHHHHHHHHHHhhCCeEEe
Q 024592          218 NNNGVHRNVISQQL---NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       218 ~~~Gv~~~~I~~~l---~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      -..|++.+++.+++   +++...+...|+.|+.+|.|-.
T Consensus        14 lr~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~   52 (59)
T PF09106_consen   14 LRPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKV   52 (59)
T ss_dssp             TSS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEE
T ss_pred             CccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeee
Confidence            46899999999988   6899999999999999999875

Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	265
4gop_B	136	Structure And Conformational Change Of A Replicatio		1e-16
2pi2_A	270	Full-Length Replication Protein A Subunits Rpa14 An		5e-15
2pqa_A	131	Crystal Structure Of Full-Length Human Rpa 1432 HET		5e-11
1l1o_B	128	Structure Of The Human Replication Protein A (Rpa)		6e-11
1quq_A	129	Complex Of Replication Protein A Subunits Rpa14 And		6e-11
3kdf_D	132	X-Ray Crystal Structure Of The Human Replication Pr		1e-10

>pdb|4GOP|B Chain B, Structure And Conformational Change Of A Replication Protein A Heterotrimer Bound To Ssdna Length = 136

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 42/129 (32%), Positives = 75/129 (58%), Gaps = 2/129 (1%)
Query: 40  TLLPMTVKQXXXXXXXXXXXXXI-DGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIE 98
           TL P+T++Q             I DGA++  +T V +V ++        + ++DGTG+IE
Sbjct: 8   TLRPVTIRQILNAEQPHPDAEFILDGAELGQLTFVAVVRNISRNATNVAYSVEDGTGQIE 67
Query: 99  CSRW-AHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVEC 157
             +W      + ++ ++I   +YVRV G LK+FQ++RS+++  +RP+ID+NE+  H +E 
Sbjct: 68  VRQWLDSSSDDSSKASEIRNNVYVRVLGTLKSFQNRRSISSGHMRPVIDYNEVMFHRLEA 127
Query: 158 IYVQLYNTR 166
           ++  L  TR
Sbjct: 128 VHAHLQVTR 136

>pdb|2PI2|A Chain A, Full-Length Replication Protein A Subunits Rpa14 And Rpa32 Length = 270

Iteration: 1
 Score = 78.2 bits (191), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 117/243 (48%), Gaps = 13/243 (5%)
Query: 26  PDPSSSFSKNR-NVRTLLPMTVKQXXXXXXXXXXXXXIDGADVNTITVVGIVCDMQDKEP 84
           P PS +  K+R   + ++P T+ Q             I   +++ +T+VGI+   +    
Sbjct: 30  PAPSQAEKKSRARAQHIVPCTISQLLSATLVDEVFR-IGNVEISQVTIVGIIRHAEKAPT 88
Query: 85  QFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRP 143
             ++ IDD T   ++  +W       +E   +    YV+V GHL++FQ+K+SL A+ + P
Sbjct: 89  NIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMP 148
Query: 144 IIDFNEITSHFVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSID 203
           + D NE T+H +E I   +  ++     S      ++  + E      N +    G ++ 
Sbjct: 149 LEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAGNFGGNSFMPANGLTVA 208
Query: 204 Q-MVLDFLR---RPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFH 258
           Q  VL+ ++   RPE L       +++ +Q  ++ +  + +A++ L+    +YS +D+ H
Sbjct: 209 QNQVLNLIKACPRPEGLN-----FQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDH 263
Query: 259 YKS 261
           +KS
Sbjct: 264 FKS 266

>pdb|2PQA|A Chain A, Crystal Structure Of Full-Length Human Rpa 1432 HETERODIMER Length = 131

Iteration: 1
 Score = 64.7 bits (156), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 55/98 (56%), Gaps = 1/98 (1%)
Query: 62  IDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMY 120
           I   +++ +T+VGI+   +      ++ IDD T   ++  +W       +E   +    Y
Sbjct: 25  IGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETY 84
Query: 121 VRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECI 158
           V+V GHL++FQ+K+SL A+ + P+ D NE T+H +E I
Sbjct: 85  VKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVI 122

>pdb|1L1O|B Chain B, Structure Of The Human Replication Protein A (Rpa) Trimerization Core Length = 128

Iteration: 1
 Score = 64.7 bits (156), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 55/98 (56%), Gaps = 1/98 (1%)
Query: 62  IDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMY 120
           I   +++ +T+VGI+   +      ++ IDD T   ++  +W       +E   +    Y
Sbjct: 23  IGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETY 82
Query: 121 VRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECI 158
           V+V GHL++FQ+K+SL A+ + P+ D NE T+H +E I
Sbjct: 83  VKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVI 120

>pdb|1QUQ|A Chain A, Complex Of Replication Protein A Subunits Rpa14 And Rpa32 Length = 129

Iteration: 1
 Score = 64.3 bits (155), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 55/98 (56%), Gaps = 1/98 (1%)
Query: 62  IDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMY 120
           I   +++ +T+VGI+   +      ++ IDD T   ++  +W       +E   +    Y
Sbjct: 24  IGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETY 83
Query: 121 VRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECI 158
           V+V GHL++FQ+K+SL A+ + P+ D NE T+H +E I
Sbjct: 84  VKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVI 121

>pdb|3KDF|D Chain D, X-Ray Crystal Structure Of The Human Replication Protein A C From Wheat Germ Cell Free Expression Length = 132

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 54/98 (55%), Gaps = 1/98 (1%)
Query: 62  IDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMY 120
           I   +++ +T+VGI+   +      ++ IDD T    +  +W       +E   +    Y
Sbjct: 26  IGNVEISQVTIVGIIRHAEKAPTNIVYKIDDXTAAPXDVRQWVDTDDTSSENTVVPPETY 85
Query: 121 VRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECI 158
           V+V GHL++FQ+K+SL A+ + P+ D NE T+H +E I
Sbjct: 86  VKVAGHLRSFQNKKSLVAFKIXPLEDXNEFTTHILEVI 123

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	265
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	1e-56
3kdf_D	132	Replication protein A 32 kDa subunit; wheat GERM c	2e-41
3kf6_A	159	Protein STN1; OB fold, chromosomal protein, DNA-bi	4e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-06

>2pi2_A Replication protein A 32 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2z6k_A 1dpu_A 1z1d_A Length = 270

 Score =  181 bits (461), Expect = 1e-56
 Identities = 62/269 (23%), Positives = 122/269 (45%), Gaps = 11/269 (4%)

Query: 1   MYSGEFDG---AAAFAGGGFMPSQATTVPDPSSSFSKNRNVR--TLLPMTVKQLSELSSN 55
           M++  F+    ++    GG+  S         S   K    R   ++P T+ QL   +  
Sbjct: 1   MWNSGFESYGSSSYGGAGGYTQSPGGFGSPAPSQAEKKSRARAQHIVPCTISQLLSATLV 60

Query: 56  DESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGR-IECSRWAHEQMEFNEVNQ 114
           DE    I   +++ +T+VGI+   +      ++ IDD T   ++  +W       +E   
Sbjct: 61  DEV-FRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTV 119

Query: 115 ISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTRLRGGSSNQ 174
           +    YV+V GHL++FQ+K+SL A+ + P+ D NE T+H +E I   +  ++     S  
Sbjct: 120 VPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSAG 179

Query: 175 PQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NL 233
               ++  + E      N +    G ++ Q  +  L +        G++   +  QL ++
Sbjct: 180 RAPISNPGMSEAGNFGGNSFMPANGLTVAQNQVLNLIKAC--PRPEGLNFQDLKNQLKHM 237

Query: 234 PMDKLMEALESLNENSLVYS-IDEFHYKS 261
            +  + +A++ L+    +YS +D+ H+KS
Sbjct: 238 SVSSIKQAVDFLSNEGHIYSTVDDDHFKS 266

>3kdf_D Replication protein A 32 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} PDB: 2pqa_A 1quq_A 1l1o_B Length = 132

 Score =  137 bits (347), Expect = 2e-41
 Identities = 37/131 (28%), Positives = 69/131 (52%), Gaps = 2/131 (1%)

Query: 37  NVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGR 96
             + ++P T+ QL   +  DE    I   +++ +T+VGI+   +      ++ IDD T  
Sbjct: 2   RAQHIVPCTISQLLSATLVDEV-FRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAA 60

Query: 97  -IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFV 155
            ++  +W       +E   +    YV+V GHL++FQ+K+SL A+ + P+ D NE T+H +
Sbjct: 61  PMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHIL 120

Query: 156 ECIYVQLYNTR 166
           E I   +  ++
Sbjct: 121 EVINAHMVLSK 131

>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe} Length = 159

 Score = 56.5 bits (136), Expect = 4e-10
 Identities = 23/121 (19%), Positives = 51/121 (42%), Gaps = 5/121 (4%)

Query: 43  PMTVKQLSELSSNDESSASI---DGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGR-IE 98
           PM +  + ++S +      I    G  +  I +VG +  +   E + +  +DD +G  + 
Sbjct: 20  PMFISDVHKISFHPHLQRYIGFWMGFPIRWIQIVGYIAAIDIYEGKHVLTVDDCSGMVLR 79

Query: 99  CSRWAHEQMEFNEV-NQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVEC 157
                 +    ++    +S G  V V+G + +F+ +  L A S   + D N+    + + 
Sbjct: 80  VVFIIQDDFSMSKRAISMSPGNVVCVFGKINSFRSEVELIAQSFEELRDPNDEWKAWQKR 139

Query: 158 I 158
           +
Sbjct: 140 M 140

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.4 bits (109), Expect = 6e-06
 Identities = 38/295 (12%), Positives = 87/295 (29%), Gaps = 92/295 (31%)

Query: 18  MPSQATTV-PDPSSSFS------KNR--NVRTLLPMTVKQLSELSSNDESSA-------- 60
           +P +  T  P   S  +           N + +    +  + E S N    A        
Sbjct: 318 LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377

Query: 61  -SIDGADVN-TITVVGIV-CDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISK 117
            S+     +    ++ ++  D+   +   +                ++  +++ V +  K
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVMVV---------------VNKLHKYSLVEKQPK 422

Query: 118 GMYVRVYG---HLKAFQD------KRSLNAYSLR----------PIID---FNEITSHFV 155
              + +      LK   +      +  ++ Y++           P +D   ++ I  H  
Sbjct: 423 ESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLK 482

Query: 156 ECIYVQLYNT---------------RLRGGSSNQPQMTNS--NHLKEYNA-ISSNHYSFD 197
              + +                   R    + N      +    LK Y   I  N   ++
Sbjct: 483 NIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYE 542

Query: 198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY 252
               +   +LDFL + E           + S+  +L    L  AL  + E+  ++
Sbjct: 543 R---LVNAILDFLPKIE--------ENLICSKYTDL----LRIAL--MAEDEAIF 580

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 8e-06
 Identities = 31/160 (19%), Positives = 49/160 (30%), Gaps = 22/160 (13%)

Query: 104 HEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSLNAY----SLRPII---DFNEI--TSH 153
           H  M+F E  +     Y  +      AF    + +        + I+   + + I  +  
Sbjct: 4   HHHMDF-ETGEHQYQ-YKDILSVFEDAF--VDNFDCKDVQDMPKSILSKEEIDHIIMSKD 59

Query: 154 FVECIYVQLYNTRLRGGSSNQPQMTNSNHLKEYNAISSNHYSFDEGKSIDQMVLDFLRRP 213
            V      L+ T L        +         Y  + S   +     S+   +    R  
Sbjct: 60  AVSGTLR-LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDR 118

Query: 214 EFLANNNGVH--RNVISQQLNLPMDKLMEALESLNENSLV 251
             L N+N V    NV   Q   P  KL +AL  L     V
Sbjct: 119 --LYNDNQVFAKYNVSRLQ---PYLKLRQALLELRPAKNV 153

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	265
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	100.0
3kdf_D	132	Replication protein A 32 kDa subunit; wheat GERM c	100.0
4gop_B	136	Putative uncharacterized protein; OB fold, ssDNA b	100.0
3kf6_A	159	Protein STN1; OB fold, chromosomal protein, DNA-bi	99.9
3kf8_A	220	Protein STN1; OB fold; 2.40A {Candida tropicalis m	99.24
2k50_A	115	Replication factor A related protein; uncharacteri	98.62
3mxn_B	150	RECQ-mediated genome instability protein 2; bloom	98.58
2kbn_A	109	Conserved protein; nucleic acid binding protein, b	98.57
2k75_A	106	Uncharacterized protein TA0387; closed beta barrel	98.53
1o7i_A	119	SSB, SSO2364, single stranded DNA binding protein;	98.5
3e0e_A	97	Replication protein A; structural genomics, PSI-2,	98.25
3dm3_A	105	Replication factor A; probably plays AN essential	97.92
1nnx_A	109	Protein YGIW; structural genomics, hypothetical pr	97.45
1wjj_A	145	Hypothetical protein F20O9.120; DNA-binding protei	97.27
3au7_A	402	TIAS, putative uncharacterized protein; ATP hydrol	97.27
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.13
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.03
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	96.95
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	96.78
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.77
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.7
3f2b_A	1041	DNA-directed DNA polymerase III alpha chain; DNA p	96.69
1wyd_A	429	Hypothetical aspartyl-tRNA synthetase; archaea, LI	96.56
3m4p_A	456	Ehasnrs, asparaginyl-tRNA synthetase, putative; am	96.52
1l0w_A	580	Aspartyl-tRNA synthetase; space-grown crystal, dim	96.5
2xgt_A	435	Asparaginyl-tRNA synthetase, cytoplasmic; ligase,	96.46
1c0a_A	585	Aspartyl tRNA synthetase; protein-RNA complex, lig	96.46
3nem_A	438	Aspartyl-tRNA synthetase; rossmann fold, OB fold,	96.4
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	96.4
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	96.36
1eov_A	487	ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy	96.36
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.31
1e1o_A	504	Lysyl-tRNA synthetase, heat inducible; ligase, ami	96.27
1n9w_A	422	Aspartyl-tRNA synthetase 2; biosynthetic protein;	96.15
4ex5_A	529	Lysine--tRNA ligase; structural genomics, niaid, n	96.14
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.12
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	96.11
1x54_A	434	Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthe	96.1
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	96.1
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	95.97
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	95.91
3a74_A	493	Lysyl-tRNA synthetase; aminoacyl tRNA synthetase,	95.76
3i7f_A	548	Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-bi	95.69
1qzg_A	187	Protection of telomeres protein 1; protrein-DNA co	95.65
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	95.46
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	95.42
3bju_A	521	Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase,	95.4
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	95.4
1y0u_A	96	Arsenical resistance operon repressor, putative; s	95.39
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	95.35
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	95.12
4dka_C	105	RNA-editing complex protein MP81; krepa1, VHH, sin	95.08
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	95.06
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	95.0
3r0a_A	123	Putative transcriptional regulator; structural gen	94.94
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	94.91
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	94.89
2w25_A	150	Probable transcriptional regulatory protein; trans	94.88
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	94.83
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	94.81
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	94.8
1sfx_A	109	Conserved hypothetical protein AF2008; structural	94.68
2hpi_A	1220	DNA polymerase III alpha subunit; POL-beta-like nu	94.57
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	94.38
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	94.37
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	94.31
2dk8_A	81	DNA-directed RNA polymerase III 39 kDa polypeptide	94.3
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	94.28
1p6r_A	82	Penicillinase repressor; transcription regulation,	94.26
3kdf_A	121	Replication protein A 14 kDa subunit; wheat GERM c	94.21
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	94.1
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	93.98
4gs3_A	107	Single-stranded DNA-binding protein; primosome, ol	93.9
2nnn_A	140	Probable transcriptional regulator; structural gen	93.78
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	93.76
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	93.65
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	93.56
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	93.47
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	93.42
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	93.37
2kko_A	108	Possible transcriptional regulatory protein (possi	93.34
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	93.31
1l1o_C	181	Replication protein A 70 kDa DNA-binding subunit;	93.3
1xjv_A	294	Protection of telomeres 1; protein-DNA complex, si	93.22
2pex_A	153	Transcriptional regulator OHRR; transcription regu	93.21
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	93.13
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	93.12
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	93.12
4ah6_A	617	Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo	93.07
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	93.0
1sr3_A	136	APO-CCME; OB fold, beta barrel, flexible C-termina	92.97
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	92.85
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	92.77
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	92.77
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	92.74
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	92.74
4gop_A	114	Putative uncharacterized protein; OB fold, ssDNA b	92.73
2gxg_A	146	146AA long hypothetical transcriptional regulator;	92.72
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	92.72
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	92.71
3by6_A	126	Predicted transcriptional regulator; structural ge	92.7
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	92.68
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	92.66
1ynx_A	114	Replication factor-A protein 1; canonical OB fold,	92.64
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	92.57
1j6q_A	136	Cytochrome C maturation protein E; all-beta protei	92.56
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	92.49
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	92.42
2pi2_E	142	Replication protein A 14 kDa subunit; FULL-length	92.34
2vn2_A	128	DNAD, chromosome replication initiation protein; D	92.33
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	92.31
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	92.29
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	92.29
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	92.24
3jth_A	98	Transcription activator HLYU; transcription factor	92.22
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	92.2
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	92.2
1ku9_A	152	Hypothetical protein MJ223; putative transcription	92.13
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	92.11
3f3x_A	144	Transcriptional regulator, MARR family, putative;	92.08
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	92.05
3s2w_A	159	Transcriptional regulator, MARR family; structural	91.95
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	91.94
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	91.94
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	91.92
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	91.91
1txy_A	104	Primosomal replication protein N; OB fold, dimer,	91.9
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	91.89
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	91.85
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	91.83
1jmc_A	246	Protein (replication protein A (RPA)); human ssDNA	91.81
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	91.78
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	91.71
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	91.63
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	91.58
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	91.57
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	91.55
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	91.53
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	91.48
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	91.37
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	91.35
3bja_A	139	Transcriptional regulator, MARR family, putative;	91.32
3tqy_A	158	Single-stranded DNA-binding protein; DNA replicati	91.22
2eth_A	154	Transcriptional regulator, putative, MAR family; M	91.2
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	91.12
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	91.11
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	91.05
1ucr_A	78	Protein DSVD; dissimilatory sulfite reductase D, D	91.05
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	90.99
3nqo_A	189	MARR-family transcriptional regulator; structural	90.93
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	90.89
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	90.79
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	90.77
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	90.56
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	90.47
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	90.47
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	90.47
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	90.35
3eet_A	272	Putative GNTR-family transcriptional regulator; st	90.28
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	90.25
3koj_A	108	Uncharacterized protein YCF41; single-strand bindi	90.23
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	90.17
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	90.09
2w57_A	150	Ferric uptake regulation protein; gene regulation,	90.07
1mkm_A	249	ICLR transcriptional regulator; structural genomic	90.07
2g7u_A	257	Transcriptional regulator; ICLR family, structural	90.06
1okr_A	123	MECI, methicillin resistance regulatory protein ME	90.06
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	89.97
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	89.94
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	89.82
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	89.78
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	89.74
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	89.57
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	89.51
2h09_A	155	Transcriptional regulator MNTR; transcription regu	89.43
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	89.4
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	89.29
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	89.28
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	89.16
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	89.12
1bia_A	321	BIRA bifunctional protein; transcription regulatio	89.07
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	89.01
2pg4_A	95	Uncharacterized protein; structural genomics, join	88.85
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	88.77
1z91_A	147	Organic hydroperoxide resistance transcriptional;	88.77
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	88.64
3k8a_A	103	Putative primosomal replication protein; beta-barr	88.63
1z05_A	429	Transcriptional regulator, ROK family; structural	88.53
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	88.52
2l02_A	82	Uncharacterized protein; structural genomics, nort	88.5
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	88.44
1qvc_A	145	Single stranded DNA binding protein monomer; beta-	88.42
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	88.38
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	88.36
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	88.25
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	88.24
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	88.23
3stb_C	148	RNA-editing complex protein MP42; editosome, nanob	88.08
4fx0_A	148	Probable transcriptional repressor protein; helix-	88.07
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	87.97
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	87.92
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	87.88
1jmc_A	246	Protein (replication protein A (RPA)); human ssDNA	87.87
2kct_A	94	Cytochrome C-type biogenesis protein CCME; solutio	87.79
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	87.78
3fhw_A	115	Primosomal replication protein N; PRIB BPR162 X-RA	87.76
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	87.67
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	87.6
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	87.51
2vw9_A	134	Single-stranded DNA binding protein; DNA replicati	87.49
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	87.41
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	87.27
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	86.76
2fxa_A	207	Protease production regulatory protein HPR; protea	86.73
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	86.72
3vdy_A	116	SSB, single-stranded DNA-binding protein SSBB; OB	86.61
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	86.6
2l01_A	77	Uncharacterized protein; structural genomics, nort	86.59
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	86.56
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	86.5
3rn5_A	208	Interferon-inducible protein AIM2; OB fold, DNA bi	86.44
1jb7_A	495	Telomere-binding protein alpha subunit; DNA-protei	86.43
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	86.14
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	86.11
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	86.11
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	86.03
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	85.83
1v1q_A	134	Primosomal replication protein N; primosome, DNA r	85.81
3en2_A	101	Probable primosomal replication protein N; PRIB RS	85.71
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	85.58
3eiv_A	199	Single-stranded DNA-binding protein 2; DNA damage,	85.51
1se8_A	301	Single-strand binding protein; DNA binding protein	85.49
2obp_A	96	Putative DNA-binding protein; structural genomics,	85.44
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	85.26
3afp_A	168	Single-stranded DNA-binding protein; OB-fold, quat	85.12
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	85.07
4ets_A	162	Ferric uptake regulation protein; metal binding pr	85.07
1lva_A	258	Selenocysteine-specific elongation factor; winged-	84.71
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	84.65
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	84.37
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	84.23
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	84.02
1z9f_A	153	Single-strand binding protein; TM0604, single stra	83.96
3df8_A	111	Possible HXLR family transcriptional factor; APC89	83.6
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	83.6
3c57_A	95	Two component transcriptional regulatory protein;	83.02
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	82.96
1ylf_A	149	RRF2 family protein; structural genomics, transcri	82.95
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	82.77
1yyv_A	131	Putative transcriptional regulator; reductive meth	82.57
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	82.37
1hsj_A	487	Fusion protein consisting of staphylococcus access	82.31
1se8_A	301	Single-strand binding protein; DNA binding protein	82.24
2fxq_A	264	Single-strand binding protein; strand beta-sheet e	82.07
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	82.03
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	81.92
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	81.53
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	81.49
3c7j_A	237	Transcriptional regulator, GNTR family; structural	81.37
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	81.25
3ulp_A	124	Single-strand binding protein; OB-fold, DNA bindin	81.23
2o0m_A	345	Transcriptional regulator, SORC family; structural	81.18
4dam_A	128	Single-stranded DNA-binding protein 1; OB-fold; 1.	81.09
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	80.85
4hik_A	143	Protection of telomeres protein 1; specificity, pl	80.56
3rlo_A	204	Gamma-interferon-inducible protein 16; HIN200/OB f	80.51
1bja_A	95	Transcription regulatory protein MOTA; activation	80.41
3k69_A	162	Putative transcription regulator; putative transcr	80.24
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	80.14
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	80.12

>2pi2_A Replication protein A 32 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2z6k_A 1dpu_A 1z1d_A

Probab=100.00  E-value=3.2e-60  Score=423.09  Aligned_cols=256  Identities=22%  Similarity=0.396  Sum_probs=119.7

Q ss_pred             CCCCCCccCCcccCCCCCCC-CCCCCCC-cCcCCcccceeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeC
Q 024592            5 EFDGAAAFAGGGFMPSQATT-VPDPSSS-FSKNRNVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDK   82 (265)
Q Consensus         5 ~~~~~~~~~gGGf~~~~~~~-~~~~~~~-~~k~~~~~~~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~   82 (265)
                      .|.+.+.++|||||+|+++. +++.+++ +++.++.++|+|||||||++++.. ++.|+|+|++|++|+|||+|++++..
T Consensus         8 ~~~~~~~~~~ggf~~~~~~~~~~~~~~~~~~~~~~~~~l~PvtIkqil~a~~~-d~~f~i~g~~i~~V~ivG~V~~i~~~   86 (270)
T 2pi2_A            8 SYGSSSYGGAGGYTQSPGGFGSPAPSQAEKKSRARAQHIVPCTISQLLSATLV-DEVFRIGNVEISQVTIVGIIRHAEKA   86 (270)
T ss_dssp             ---------------------------------CCCCCCEECCHHHHHHCEEE-TTEEEETTEEESEEEEEEEEEEEEEC
T ss_pred             CcCCcCCCCCCCcccCCCCCCCCCCCCCccccCCCCCceEEEEHHHHhcCccC-CCcEEECCEEEEEEEEEEEEEEEEec
Confidence            46666777889999876532 1222222 333568899999999999999432 56899999999999999999999999


Q ss_pred             CCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHH
Q 024592           83 EPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQ  161 (265)
Q Consensus        83 ~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~  161 (265)
                      .+++.|+|+|+|| +|+|++|.+.+.+......+++|+||||+|+|+.|+++++|.++.||||+|+||+++|+|||+++|
T Consensus        87 ~~~~~~~L~D~TG~~I~~k~W~~~~~~~~~~~~~~~G~yVrV~G~v~~f~g~~qi~i~~ir~v~d~nEi~~H~Le~i~~h  166 (270)
T 2pi2_A           87 PTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAH  166 (270)
T ss_dssp             SSEEEEEEECSSSSCEEEEEECC-------CCCCCTTCEEEEEEEEEEETTEEEEEEEEEEECSCTHHHHHHHHHHHHHH
T ss_pred             cceEEEEEECCCCCEEEEEEEcCcCcccchhhcCCCCCEEEEEEEEEecCCeeEEEEEEEEecCCHhHHHHHHHHHHHHH
Confidence            9999999999999 899999987543223457899999999999999999999999999999999999999999999999


Q ss_pred             HHhccCCCCCCCCCCCCCCCCcccccc--ccCCCCCCCCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHH
Q 024592          162 LYNTRLRGGSSNQPQMTNSNHLKEYNA--ISSNHYSFDEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKL  238 (265)
Q Consensus       162 l~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~n~~~~~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v  238 (265)
                      |+++++.+...+. .......++....  .+.+.++.+++++++++||++||++.   +++|+|+++|+++| ++++++|
T Consensus       167 l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Vl~~i~~~~---~~~Gi~~~~I~~~l~~~~~~~v  242 (270)
T 2pi2_A          167 MVLSKANSQPSAG-RAPISNPGMSEAGNFGGNSFMPANGLTVAQNQVLNLIKACP---RPEGLNFQDLKNQLKHMSVSSI  242 (270)
T ss_dssp             HHHHHHTCCC----------------------------------------------------------------------
T ss_pred             HHHccCCcccccc-CCCcCCCCcccccccCcccccCCCCCCHHHHHHHHHHHhCC---CccCCCHHHHHHHhcCCCHHHH
Confidence            9999886532110 0000000000000  01122222467889999999999863   47899999999999 6999999


Q ss_pred             HHHHHHHhhCCeEEe-ecCCceeeccCC
Q 024592          239 MEALESLNENSLVYS-IDEFHYKSAVNA  265 (265)
Q Consensus       239 ~~al~~L~~eG~IYs-iDd~hyk~t~~~  265 (265)
                      +++|++|++|||||+ +||+|||+|+++
T Consensus       243 ~~al~~L~~eG~IYsTiDd~h~k~t~~~  270 (270)
T 2pi2_A          243 KQAVDFLSNEGHIYSTVDDDHFKSTDAE  270 (270)
T ss_dssp             ----------------------------
T ss_pred             HHHHHHHHhCCEEeccccccceeeccCC
Confidence            999999999999999 999999999763

>3kdf_D Replication protein A 32 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 2pqa_A 1quq_A 1l1o_B

Probab=100.00  E-value=4.3e-40  Score=263.69  Aligned_cols=129  Identities=27%  Similarity=0.531  Sum_probs=112.5

Q ss_pred             cccceeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCC-eEEEEEeccccccccccccc
Q 024592           37 NVRTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQI  115 (265)
Q Consensus        37 ~~~~~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~  115 (265)
                      +.++++|||||||++|... ++.|.++|+++++|+|||+|+++++.++++.|+|+|+|| .|+|++|.+++.+......+
T Consensus         2 r~~~l~PvtIkqil~a~~~-~~~f~i~g~~i~~V~iVG~V~~~~~~~~~~~~~ldD~TG~~I~~~~W~~~~~~~~~~~~~   80 (132)
T 3kdf_D            2 RAQHIVPCTISQLLSATLV-DEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVV   80 (132)
T ss_dssp             ---CCEECCHHHHHTCEES-SSCEEETTEECCEEEEEEEEEEEEECSSEEEEEEECSSSSCEEEEEEC---------CCC
T ss_pred             CCCceeeEEHHHHhhCccC-CCcEEECCEEEEEEEEEEEEEEEEEcCCeEEEEEECCCCCEEEEEEEccCCCcccccccc
Confidence            5789999999999999432 568999999999999999999999999999999999999 99999998765443446789


Q ss_pred             CCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHHHHhcc
Q 024592          116 SKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTR  166 (265)
Q Consensus       116 ~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~~~  166 (265)
                      ++|+||||+|+++.|+++++|.++.|||++|+||+++|+|||+++||+++|
T Consensus        81 ~~g~yVrV~G~l~~f~g~~qi~~~~ir~v~d~Nei~~H~Le~i~~hl~~~k  131 (132)
T 3kdf_D           81 PPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSK  131 (132)
T ss_dssp             CTTCEEEEEEEEEEETTEEEEEEEEEEECSSTHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCEEEEEEEEEeECCEEEEEEEEEEEcCCccHHHHHHHHHHHHHHeecC
Confidence            999999999999999999999999999999999999999999999999987

>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=100.00  E-value=8.4e-40  Score=263.30  Aligned_cols=132  Identities=31%  Similarity=0.611  Sum_probs=115.9

Q ss_pred             CCcccceeeeeHHHHhcC-CCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-ccccc
Q 024592           35 NRNVRTLLPMTVKQLSEL-SSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-EFNEV  112 (265)
Q Consensus        35 ~~~~~~~~PvtIkqi~~a-~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~~~~~  112 (265)
                      .+..++|+|||||||++| +..+++.|+++|+++++|+|||+|+++++.++++.|+|+|+||.|+|++|.+.+. +....
T Consensus         3 ~~~~~~l~PvtIkqil~a~~~~~~~~f~i~g~~i~~V~iVG~V~~~~~~~~~~~~~ldD~TG~I~~~~W~~~~~~~~~~~   82 (136)
T 4gop_B            3 KAGNNTLRPVTIRQILNAEQPHPDAEFILDGAELGQLTFVAVVRNISRNATNVAYSVEDGTGQIEVRQWLDSSSDDSSKA   82 (136)
T ss_dssp             ----CCEEECCHHHHHHCBCCSSSCCCBSSSSBCCEEEEEEEEEEEEECSSEEEEEEECSSCEEEEEEECC--------C
T ss_pred             CCCCCcEEeEEHHHHhhccccCCCCcEEECCEEEEEEEEEEEEEEEEecCCeEEEEEECCCCCEEEEEecccCCcccccc
Confidence            457899999999999999 4545679999999999999999999999999999999999999999999986543 22346


Q ss_pred             cccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHHHHhcc
Q 024592          113 NQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTR  166 (265)
Q Consensus       113 ~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~~~  166 (265)
                      +.+++|+||+|+|+++.|+++++|+++.|||++|+||+++|+|||+++||+++|
T Consensus        83 ~~~~~g~yVrV~G~v~~f~g~~qi~~~~ir~v~d~Nei~~H~Le~i~~hl~~t~  136 (136)
T 4gop_B           83 SEIRNNVYVRVLGTLKSFQNRRSISSGHMRPVIDYNEVMFHRLEAVHAHLQVTR  136 (136)
T ss_dssp             CSCCTTCEEEEEEEEEEETTEEEEEESEEEECSSHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccCCCCEEEEEEEEEEeCCEEEEEEEEEEECCCccHHHHHHHHHHHHHHhhcC
Confidence            789999999999999999999999999999999999999999999999999986

>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe}

Probab=99.90  E-value=1.3e-22  Score=166.42  Aligned_cols=128  Identities=17%  Similarity=0.253  Sum_probs=108.1

Q ss_pred             cccceeeeeHHHHhcCCCC---CCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCC-eEEEEEeccccccc-cc
Q 024592           37 NVRTLLPMTVKQLSELSSN---DESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTG-RIECSRWAHEQMEF-NE  111 (265)
Q Consensus        37 ~~~~~~PvtIkqi~~a~~~---~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG-~I~~~~w~~~~~~~-~~  111 (265)
                      .....+|+.|++|++....   ++..+.+.|+||++|+|||.|+++++.++++.|+|||+|| .|+|++|.+...+. ..
T Consensus        14 t~~~~v~L~i~DI~~l~~~~~~~~~~~f~~n~PI~~V~IvGiVv~~~~~~~~~~ytIDD~TG~~I~cv~w~~~~~~~~~~   93 (159)
T 3kf6_A           14 TLSRWNPMFISDVHKISFHPHLQRYIGFWMGFPIRWIQIVGYIAAIDIYEGKHVLTVDDCSGMVLRVVFIIQDDFSMSKR   93 (159)
T ss_dssp             --CCCCBCCHHHHTTCBCCCC---CCEEETTEEECEEEEEEEEEEEEEETTEEEEEEECSSSCEEEEEEEGGGCHHHHHH
T ss_pred             chhheecchHHHHHhchhcCCCCCcceeECCeEEEEEEEEEEEEEEEEeCCEEEEEEecCCCCeEEEEEEccCCCCcccc
Confidence            3567899999999998321   2334468999999999999999999999999999999999 59999998863221 12


Q ss_pred             ccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHHHHh
Q 024592          112 VNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYN  164 (265)
Q Consensus       112 ~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~  164 (265)
                      ...+.+|+||||.|+|+.|+++++|.++.++++.|+|+...||.+++.....+
T Consensus        94 ~~~l~~G~~VrV~G~v~~fr~~rqI~~~~i~~v~d~n~Ev~~W~~~~r~~~~l  146 (159)
T 3kf6_A           94 AISMSPGNVVCVFGKINSFRSEVELIAQSFEELRDPNDEWKAWQKRMRYKKNL  146 (159)
T ss_dssp             HTTCCTTCEEEEEEEEECSSSSCEEEEEEEEEECSTHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCEEEEEEEEEeeCCEEEEEEEEEEECCCcHHHHHHHHHHHHHHHhC
Confidence            34589999999999999999999999999999999999999999999887654

>3kf8_A Protein STN1; OB fold; 2.40A {Candida tropicalis mya-3404}

Probab=99.24  E-value=3.4e-10  Score=96.38  Aligned_cols=124  Identities=16%  Similarity=0.222  Sum_probs=94.5

Q ss_pred             cceeeeeHHHHhcCCC----------CCCCCeEECCeEEeEEEEEEEEEEeeeCC--------CeEEEEEEcCCCe---E
Q 024592           39 RTLLPMTVKQLSELSS----------NDESSASIDGADVNTITVVGIVCDMQDKE--------PQFIFLIDDGTGR---I   97 (265)
Q Consensus        39 ~~~~PvtIkqi~~a~~----------~~~~~f~i~g~~v~~V~iVG~V~~v~~~~--------t~~~y~LdDgTG~---I   97 (265)
                      ...+|+.|++|+....          ...+.|.+.++||..|+|+|+|+.++...        .++.|+|||+||.   |
T Consensus        47 ~~~vpL~I~DI~~l~~~~~~yg~~~~~~~~i~f~~NhPI~~V~IvG~VVg~~~k~~r~~~~~~~~~~l~IDDsSG~~s~i  126 (220)
T 3kf8_A           47 DKTIPLFISDINNSPNLYGIYNYIADHLRHVVLVNNYPVNQINIFGKIVYEQYKEKEFNGVEESYVILVISDFIGIDSKI  126 (220)
T ss_dssp             TSEEECCHHHHHTCCCTHHHHGGGGGGCTTCEEETTEEECEEEEEEEEEEEEEECCBCSSCBCCEEEEEEECCCSSSCEE
T ss_pred             CcccceEhHHhhhchhhhcccccccccCccEEEECCcccEEEEEEEEEEEEEEEeccccccccceEEEEEeCCCCCCceE
Confidence            4699999999998731          11246889999999999999999997655        4699999999996   7


Q ss_pred             EEEEecccccccc-cccccCCCCEEEEEEEeeeeCC--------ccEEEEEEeeeC----CChhHHHHHHHHHHHHHH
Q 024592           98 ECSRWAHEQMEFN-EVNQISKGMYVRVYGHLKAFQD--------KRSLNAYSLRPI----IDFNEITSHFVECIYVQL  162 (265)
Q Consensus        98 ~~~~w~~~~~~~~-~~~~~~~g~yVrV~G~i~~f~~--------~~~i~~~~i~~v----~d~Nei~~H~Levi~~~l  162 (265)
                      .|+.-........ .......|..|+|.|.++.|++        .++|.+.++..+    .|+....-||-+++.-+-
T Consensus       127 ~~k~~~~~~~~~gl~l~~~~~G~iV~VkG~i~~~r~~~~~~~~~~rei~ve~i~vl~~~~~dl~~Ei~~W~~~~~fR~  204 (220)
T 3kf8_A          127 RVRLSQEQFKEVGLTLDKKNYGKIVELEGEIYNWYDSINVSKKPDRELKVSKITVLSHRPDGLHFEFEQWKKRMEFRK  204 (220)
T ss_dssp             EEEEEHHHHHTTTCCTTSCCTTCEEEEEEEEEECCCSTTTTSCCCEEEEEEEEEEEESSSCCHHHHHHHHHHHHHHHH
T ss_pred             EEEecHHHhhccCccccccCCCeEEEEEEEEEeeccccccccccceEEEEEEEEEeccCCCcHHHHHHHHHHHHHHHH
Confidence            7765432111100 1122457999999999999998        899999999999    566777788888777654

>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=98.62  E-value=3.8e-08  Score=75.76  Aligned_cols=83  Identities=16%  Similarity=0.271  Sum_probs=63.5

Q ss_pred             eEEEEEEEEEEe-ee------C---CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEe--eeeCCccE
Q 024592           68 NTITVVGIVCDM-QD------K---EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHL--KAFQDKRS  135 (265)
Q Consensus        68 ~~V~iVG~V~~v-~~------~---~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i--~~f~~~~~  135 (265)
                      ..|.++|+|.++ ..      .   ..+..++|.|.||.|++++|.+...   ....+++|++|.|.|.+  ..|+++.+
T Consensus        17 ~~v~i~~~V~~~~~~~~~~~k~G~~~~~~~~~l~D~TG~I~~t~w~~~~~---~~~~l~~G~vv~i~g~~v~~~f~g~~q   93 (115)
T 2k50_A           17 AETPVTGRVMKISSPRTFTTRKGREGKLANVIIADDTGELRAVFWTENIK---LLKKFREGDVIRIKDVNIRGGFGGRKE   93 (115)
T ss_dssp             CEEEEEEEEEEECCCEECCCTTSSCCEEEEEEEEETTEEEEEEEETTGGG---GGGTCCTTSEEEEEEEEECCCSSSSCE
T ss_pred             CEeEEEEEEEECCCceEEEcCCCCEEEEEEEEEEeCCCeEEEEEeCchhh---hhhcCCCCCEEEEEeeEEccccCCeEE
Confidence            457888999887 21      1   3578899999999999999976532   23578999999999998  56999999


Q ss_pred             EEEEEeeeCCChhHHHHH
Q 024592          136 LNAYSLRPIIDFNEITSH  153 (265)
Q Consensus       136 i~~~~i~~v~d~Nei~~H  153 (265)
                      |.+...+.|.-..++.+|
T Consensus        94 L~~~~~~~i~~~~~~~~~  111 (115)
T 2k50_A           94 AHLMPRSTVEVLDPLEHH  111 (115)
T ss_dssp             EEECTTCCEEEESSCCC-
T ss_pred             EEECCCceEEECCccccc
Confidence            999877766544444433

>3mxn_B RECQ-mediated genome instability protein 2; bloom syndrome, helicase, RMI, topoisomerase, replication PR replication; 1.55A {Homo sapiens} PDB: 4day_B 3nbh_B

Probab=98.58  E-value=1.9e-06  Score=68.19  Aligned_cols=117  Identities=16%  Similarity=0.131  Sum_probs=89.6

Q ss_pred             ccceeeeeHHHHhcCCCCCCCCeEEC-------CeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccc
Q 024592           38 VRTLLPMTVKQLSELSSNDESSASID-------GADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFN  110 (265)
Q Consensus        38 ~~~~~PvtIkqi~~a~~~~~~~f~i~-------g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~  110 (265)
                      ....+-|-.+||.++.......+++.       ..+++.|.+=|.|+.. +.   -.+.|+|+||.+.+.--.+-.   .
T Consensus        22 ~~PpvK~l~~QLr~~~~~~~~~w~l~r~~~g~~~l~~s~VWmQG~VV~~-~~---g~~~LdDgTG~~~v~g~~~vp---~   94 (150)
T 3mxn_B           22 RSPPLKVLAEQLRRDAEGGPGAWRLSRAAAGRGPLDLAAVWMQGRVVMA-DR---GEARLRDPSGDFSVRGLERVP---R   94 (150)
T ss_dssp             SSCCEECCHHHHHHHEESCTTCCEECCTTTTCCCEECSEEEEEEEEEEE-ET---TEEEEEETTEEEEEECGGGSC---C
T ss_pred             CCCcHHHHHHHHHHHhhCCCceEEEEecccCCccceeEEEEEEeEEEEe-CC---CeEEEECCCceEEEeeccccC---C
Confidence            34456788999998843334456554       2589999999999996 22   238999999999876543321   1


Q ss_pred             cccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC-hhHHHHHHHHHHHHH
Q 024592          111 EVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID-FNEITSHFVECIYVQ  161 (265)
Q Consensus       111 ~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d-~Nei~~H~Levi~~~  161 (265)
                      -...++.|+||-|+|.+..-.....|.+.+|.-+++ ++-...+.|||+.+|
T Consensus        95 g~p~l~~G~YVMV~G~v~~~s~eP~i~AvKm~DLS~~p~~E~mW~lEV~el~  146 (150)
T 3mxn_B           95 GRPCLVPGKYVMVMGVVQACSPEPCLQAVKMTDLSDNPIHESMWELEVEDLH  146 (150)
T ss_dssp             CSCCCSTTCEEEEEEEEEECSSSCEEEEEEEEECCSCHHHHHHHHHHHHHHH
T ss_pred             CCcccCCCCEEEEEEEEEecCCCceEEEEEeeeCCCCcchHHHHHHHHHHHH
Confidence            134589999999999999988889999999988886 567789999999987

>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Methanosarcina mazei} PDB: 2ken_A

Probab=98.57  E-value=4.3e-07  Score=69.46  Aligned_cols=73  Identities=14%  Similarity=0.192  Sum_probs=60.4

Q ss_pred             eEEEEEEEEEEeeeC---CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeeeCCccEEEEEEeee
Q 024592           68 NTITVVGIVCDMQDK---EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAFQDKRSLNAYSLRP  143 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~---~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f~~~~~i~~~~i~~  143 (265)
                      ..|.++|+|.++...   ..+....|.|.||+|.++.|.++.     .+.+++|+.|+|. |.++.|+|+.+|++.....
T Consensus        16 ~~v~v~~~V~~~~~~~~~~~~~~~~l~DeTG~I~~t~W~~~~-----~~~~~~G~~V~i~n~~v~~~~G~~~L~v~~~~~   90 (109)
T 2kbn_A           16 QWANLKAKVIQLWENTHESISQVGLLGDETGIIKFTIWKNAE-----LPLLEQGESYLLRSVVVGEYNDRFQVQVNKNSS   90 (109)
T ss_dssp             CEEEEEEEEEEEEECCCSSEEEEEEEECTTCCEEEEEEGGGC-----CCCCCTTCEEEEEEEEEEEETTEEEEEECSSSE
T ss_pred             CcEEEEEEEEEeEcCCCCeEEEEEEEECCCCeEEEEEECccc-----ccccCCCCEEEEEEEEEEEECCEEEEEECCceE
Confidence            568999999988653   346678999999999999998542     4689999999999 8999999999999976554


Q ss_pred             CC
Q 024592          144 II  145 (265)
Q Consensus       144 v~  145 (265)
                      |+
T Consensus        91 I~   92 (109)
T 2kbn_A           91 IE   92 (109)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum}

Probab=98.53  E-value=2.3e-07  Score=70.68  Aligned_cols=76  Identities=18%  Similarity=0.301  Sum_probs=61.2

Q ss_pred             EEEEEEEEEEeee-----CC---CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeeeCCccEEEEE
Q 024592           69 TITVVGIVCDMQD-----KE---PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAFQDKRSLNAY  139 (265)
Q Consensus        69 ~V~iVG~V~~v~~-----~~---t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f~~~~~i~~~  139 (265)
                      .|.++++|.++.+     ..   ......|.|.||+|.++.|.+.         +++|+.|+|. |.++.|+++.+|.+.
T Consensus        15 ~v~v~~~V~~~~~~~~~k~G~~~~v~~~~l~DeTG~I~~tlW~~~---------l~~Gdvv~i~ng~v~~~~g~~~L~v~   85 (106)
T 2k75_A           15 YVSVIGKITGIHKKEYESDGTTKSVYQGYIEDDTARIRISSFGKQ---------LQDSDVVRIDNARVAQFNGYLSLSVG   85 (106)
T ss_dssp             EEEEEEEEEEEEEEEEEETTEEEEEEEEEEECSSCEEEEEEESSC---------CCTTEEEEEEEEEEEEETTEEEEEEC
T ss_pred             eEEEEEEEEEccccccccCCCeeEEEEEEEEcCCCeEEEEEEcCc---------cCCCCEEEEEeeEEeEECCEEEEEEC
Confidence            4667777766532     22   2778999999999999999762         8999999999 999999999999984


Q ss_pred             ---EeeeCCChhHHHHH
Q 024592          140 ---SLRPIIDFNEITSH  153 (265)
Q Consensus       140 ---~i~~v~d~Nei~~H  153 (265)
                         .|.++.++.++.+|
T Consensus        86 ~~~~I~~~~~~~~~~~~  102 (106)
T 2k75_A           86 DSSRIESVNVNIPLEHH  102 (106)
T ss_dssp             TTSEEEECCSCCCCSCC
T ss_pred             CcEEEEECCCCCccccc
Confidence               57788888777554

>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3

Probab=98.50  E-value=5.7e-07  Score=69.72  Aligned_cols=74  Identities=22%  Similarity=0.329  Sum_probs=59.5

Q ss_pred             EEEEEEEEEEeee--------C-CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeeeCCccEEEE
Q 024592           69 TITVVGIVCDMQD--------K-EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAFQDKRSLNA  138 (265)
Q Consensus        69 ~V~iVG~V~~v~~--------~-~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f~~~~~i~~  138 (265)
                      .|.++++|.++..        . ..+..+.|.|.||+|.++.|.+.+      +.+++|++|+|. |+++.|+|+.+|.+
T Consensus        14 ~v~~~~~V~~~~~~~~~~~k~G~~~~~~~~l~D~TG~I~~tlW~~~~------~~~~~G~vv~i~~g~v~~~~g~~qL~i   87 (119)
T 1o7i_A           14 SVNVTVRVLEASEARQIQTKNGVRTISEAIVGDETGRVKLTLWGKHA------GSIKEGQVVKIENAWTTAFKGQVQLNA   87 (119)
T ss_dssp             SEEEEEEEEEECCCEEECCTTCCEEEEEEEEEETTEEEEEEEEGGGT------TCCCTTCEEEEEEEEEEEETTEEEEEE
T ss_pred             cEEEEEEEEECCCCeeEEecCCCEEEEEEEEEeCCCEEEEEEECChh------hcCCCCCEEEEEeEEEEEeCCEEEEEE
Confidence            4777788877631        1 258899999999999999997653      358999999999 99999999999999


Q ss_pred             EE---eeeCCChh
Q 024592          139 YS---LRPIIDFN  148 (265)
Q Consensus       139 ~~---i~~v~d~N  148 (265)
                      ..   |.++.+++
T Consensus        88 ~~~~~i~~~~~~~  100 (119)
T 1o7i_A           88 GSKTKIAEASEDG  100 (119)
T ss_dssp             CTTCEEEECCCTT
T ss_pred             CCCEEEEEcCCcC
Confidence            76   66666533

>3e0e_A Replication protein A; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.60A {Methanococcus maripaludis} PDB: 2k5v_A

Probab=98.25  E-value=5.8e-06  Score=61.75  Aligned_cols=72  Identities=18%  Similarity=0.184  Sum_probs=55.8

Q ss_pred             eEEEEEEEEEEeee-----C-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEE
Q 024592           68 NTITVVGIVCDMQD-----K-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLN  137 (265)
Q Consensus        68 ~~V~iVG~V~~v~~-----~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~  137 (265)
                      ..|.++|+|.++..     .     .....+.|.|.||+|.+..|.+...    . .+++|++|+|.|.++.+.+..+|+
T Consensus        12 ~~v~i~~~V~~~~~~r~~~~~~G~~~~v~~~~l~DeTG~I~~tlW~~~~~----~-~i~~Gdvv~i~g~v~~~~~~~el~   86 (97)
T 3e0e_A           12 LSGTINAEVVTAYPKKEFSRKDGTKGQLKSLFLKDDTGSIRGTLWNELAD----F-EVKKGDIAEVSGYVKQGYSGLEIS   86 (97)
T ss_dssp             EEEEEEEEEEEECCCEEEC----CCEEEEEEEEEETTEEEEEEEEGGGGG----C-CCCTTCEEEEEEEEEEC--CEEEE
T ss_pred             CcEEEEEEEEECCCceEEEcCCCCeeEEEEEEEECCCCcEEEEEECCccc----c-ccCCCCEEEEEEEEEEcCCeEEEE
Confidence            57889999988741     1     1367799999999999999987542    1 799999999999999999988888


Q ss_pred             EEEeeeC
Q 024592          138 AYSLRPI  144 (265)
Q Consensus       138 ~~~i~~v  144 (265)
                      +-.--.|
T Consensus        87 ~g~~~~i   93 (97)
T 3e0e_A           87 VDNIGII   93 (97)
T ss_dssp             EEEEEEE
T ss_pred             ECCCcEE
Confidence            7655443

>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii}

Probab=97.92  E-value=7.1e-05  Score=56.63  Aligned_cols=73  Identities=23%  Similarity=0.306  Sum_probs=57.1

Q ss_pred             eEEEEEEEEEEeee-----C-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee-CCccEE
Q 024592           68 NTITVVGIVCDMQD-----K-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF-QDKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~-----~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f-~~~~~i  136 (265)
                      ..|.|+|+|.++.+     .     .....++|.|.||+|.+..|.+...    . .+++|+.|++.|.++.+ ++...|
T Consensus        15 ~~v~v~g~V~~~~~~r~~~~~~G~~~~v~~~~l~D~TG~IrvtlW~~~a~----~-~l~~Gdvv~i~g~vk~~~~g~~eL   89 (105)
T 3dm3_A           15 MTATFEGEVISALPIKEFKRADGSIGKLKSFIVRDETGSIRVTLWDNLTD----I-DVGRGDYVRVRGYIREGYYGGLEC   89 (105)
T ss_dssp             EEEEEEEEEEEEEEEEEEECTTSCEEEEEEEEEEETTEEEEEEEEGGGGG----S-CCCTTCEEEEEEEEEECTTSSEEE
T ss_pred             CeEEEEEEEEECCCceEEEcCCCCeeEEEEEEEECCCCcEEEEEECcccc----c-ccCCCCEEEEEEEEEEccCCCEEE
Confidence            57888898888752     1     1256799999999999999987653    2 79999999999999998 458888


Q ss_pred             EEEEeeeCC
Q 024592          137 NAYSLRPII  145 (265)
Q Consensus       137 ~~~~i~~v~  145 (265)
                      .+-.--.|+
T Consensus        90 ~~g~~~~i~   98 (105)
T 3dm3_A           90 TANYVEILK   98 (105)
T ss_dssp             EEEEEEEEE
T ss_pred             EeCCceEEE
Confidence            886554443

>1nnx_A Protein YGIW; structural genomics, hypothetical protein, OB-fold, structure 2 function project, S2F, unknown function; 1.45A {Escherichia coli} SCOP: b.40.10.1

Probab=97.45  E-value=0.0025  Score=48.32  Aligned_cols=83  Identities=13%  Similarity=0.226  Sum_probs=61.2

Q ss_pred             eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEE
Q 024592           43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVR  122 (265)
Q Consensus        43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVr  122 (265)
                      ..|++|++++..  +          ..|.|-|.|+..-...   .|...|+||+|.+..=.+.    -.-..+.+++.|+
T Consensus        25 ~~TV~~a~~~~D--d----------~~V~L~G~Iv~~~~~d---~Y~F~D~TG~I~VeId~~~----w~g~~v~p~~~Vr   85 (109)
T 1nnx_A           25 VTTVESAKSLRD--D----------TWVTLRGNIVERISDD---LYVFKDASGTINVDIDHKR----WNGVTVTPKDTVE   85 (109)
T ss_dssp             CCCHHHHTTSCS--S----------EEEEEEEEEEEEEETT---EEEEEETTEEEEEECCGGG----STTCCCCTTSCEE
T ss_pred             eEeHHHHhhCcC--C----------CeEEEEEEEEEEeCCC---eEEEECCCccEEEEEChhh----cCCcccCCCCEEE
Confidence            478999987632  3          7899999998876443   4799999999998752111    0123578899999


Q ss_pred             EEEEeeeeCCccEEEEEEeeeC
Q 024592          123 VYGHLKAFQDKRSLNAYSLRPI  144 (265)
Q Consensus       123 V~G~i~~f~~~~~i~~~~i~~v  144 (265)
                      |+|.+..--....|-+.+|+.+
T Consensus        86 i~GevDkd~~~~eIdV~~i~~~  107 (109)
T 1nnx_A           86 IQGEVDKDWNSVEIDVKQIRKV  107 (109)
T ss_dssp             EEEEEEEETTEEEEEEEEEEEC
T ss_pred             EEEEECCCCCceEEEEEEEEEc
Confidence            9999997545678888888765

>1wjj_A Hypothetical protein F20O9.120; DNA-binding protein-related, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.40.4.3

Probab=97.27  E-value=0.0021  Score=51.31  Aligned_cols=71  Identities=20%  Similarity=0.170  Sum_probs=53.7

Q ss_pred             eEEEEEEEEEEeee-------------------CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEE-Ee
Q 024592           68 NTITVVGIVCDMQD-------------------KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG-HL  127 (265)
Q Consensus        68 ~~V~iVG~V~~v~~-------------------~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i  127 (265)
                      ..|.|+++|.++..                   ...-....|-|.||+|....|.+.      .+.+++|+.|++.+ .+
T Consensus        27 ~~v~l~~kVl~~~~v~~~~~~~R~dG~~~~~~r~~~V~~~lVgDeTG~I~ftlW~e~------~~~l~~Gd~v~i~na~v  100 (145)
T 1wjj_A           27 TGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETGCILFTARNDQ------VDLMKPGATVILRNSRI  100 (145)
T ss_dssp             CCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSCEEEEEECTTH------HHHTCTTCEEEEEEEEE
T ss_pred             CceEEEEEEEEcccccccccccccCCccccccCCceEEEEEEEcCCcEEEEEEecCC------cCcCCCCCEEEEeccEE
Confidence            34777777777542                   123567899999999999999763      34588999999987 59


Q ss_pred             eeeCCccEEEEEEeeeC
Q 024592          128 KAFQDKRSLNAYSLRPI  144 (265)
Q Consensus       128 ~~f~~~~~i~~~~i~~v  144 (265)
                      +.|++...|.+-.--.|
T Consensus       101 ~~~~G~~~L~vgk~g~I  117 (145)
T 1wjj_A          101 DMFKGTMRLGVDKWGRI  117 (145)
T ss_dssp             EEETTEEEEEECTTCCB
T ss_pred             EeECCEEEEEECCCEEE
Confidence            99999999888643333

>3au7_A TIAS, putative uncharacterized protein; ATP hydrolysis, RNA binding protein; 2.60A {Archaeoglobus fulgidus} PDB: 3amt_A* 3amu_A*

Probab=97.27  E-value=0.00097  Score=61.62  Aligned_cols=78  Identities=22%  Similarity=0.312  Sum_probs=63.0

Q ss_pred             eEEeEEEEEEEEEEe-e-eCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592           65 ADVNTITVVGIVCDM-Q-DKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus        65 ~~v~~V~iVG~V~~v-~-~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~  142 (265)
                      .+.+.+.+.|.|.+. . .....+.|+|+|+++.|+|..|.....-......+..||.|.|.|.++.  +  +|++.+++
T Consensus       282 ~~~~~~~v~G~V~~~P~~~~GGHV~f~l~d~~~~i~c~ayeptk~fr~~vr~L~~GD~V~v~G~v~~--g--tLnvEk~~  357 (402)
T 3au7_A          282 ENYRSYRLRGRVTLEPYDIEGGHVFFEIDTKFGSVKCAAFEPTKQFRNVIRLLRKGDVVEVYGSMKK--D--TINLEKIQ  357 (402)
T ss_dssp             CTTCEEEEEEEEEEEEEEETTTEEEEEEEETTEEEEEEECGGGTTHHHHHTTCCTTCEEEEEEEEET--T--EEEEEEEE
T ss_pred             ccCceEEEEEEEecCcEeccCceEEEEEEcCCCEEEEEEEccchHHHHHHhcCCCCCEEEEEEeecC--C--EEEEEEEE
Confidence            356789999999988 4 4557899999999999999999864321233567899999999999887  3  99999988


Q ss_pred             eCCC
Q 024592          143 PIID  146 (265)
Q Consensus       143 ~v~d  146 (265)
                      ++.-
T Consensus       358 v~~l  361 (402)
T 3au7_A          358 IVEL  361 (402)
T ss_dssp             EEEC
T ss_pred             Eccc
Confidence            8754

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=97.13  E-value=0.0009  Score=46.14  Aligned_cols=59  Identities=19%  Similarity=0.233  Sum_probs=47.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceee
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKS  261 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~  261 (265)
                      .+++.+.+||++|++.     ...++..+|+++|+++.+.|.+.|..|.++|.|-+-..-+|..
T Consensus         7 ~m~~~~~~IL~~L~~~-----~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~~~~G~y~l   65 (67)
T 2heo_A            7 TGDNLEQKILQVLSDD-----GGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSSPSPKYWSI   65 (67)
T ss_dssp             --CHHHHHHHHHHHHH-----CSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEEEETTEEEE
T ss_pred             cccHHHHHHHHHHHHc-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEecCCCceEee
Confidence            3556788999999753     2469999999999999999999999999999997733346654

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=97.03  E-value=0.0011  Score=47.75  Aligned_cols=53  Identities=19%  Similarity=0.268  Sum_probs=45.8

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSID  255 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD  255 (265)
                      ..++++||++|++.+   ....++..+|+++|+++...|+..|..|.++|.|..++
T Consensus         9 ~~~~~~IL~~L~~~~---pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g   61 (81)
T 1qbj_A            9 QDQEQRILKFLEELG---EGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA   61 (81)
T ss_dssp             HHHHHHHHHHHHHHC---TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEES
T ss_pred             hHHHHHHHHHHHHcC---CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecC
Confidence            357888999999752   24579999999999999999999999999999998743

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=96.95  E-value=0.00074  Score=48.01  Aligned_cols=52  Identities=19%  Similarity=0.264  Sum_probs=45.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSID  255 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD  255 (265)
                      +.+.+||++|++.+   .+.+++..+|+++|+++...|+..|..|.++|.|+.+.
T Consensus        14 ~~~~~IL~~L~~~~---~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~g   65 (77)
T 1qgp_A           14 DQEQRILKFLEELG---EGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA   65 (77)
T ss_dssp             HHHHHHHHHHHHHC---SSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHHHHcC---CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecC
Confidence            46788999999863   24589999999999999999999999999999998843

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=96.78  E-value=0.0015  Score=46.19  Aligned_cols=60  Identities=13%  Similarity=0.165  Sum_probs=49.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      .+.++.++||++|++.     ..-+.-.+|++.++++..+|.++|..|-.||.|+|----.|..+
T Consensus        16 ~~~d~eekVLe~Lkea-----G~PlkageIae~~GvdKKeVdKaik~LKkEgkI~SPkRCyw~~~   75 (80)
T 2lnb_A           16 REGHLEQRILQVLTEA-----GSPVKLAQLVKECQAPKRELNQVLYRMKKELKVSLTSPATWCLG   75 (80)
T ss_dssp             HHHHHHHHHHHHHHHH-----TSCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEETTEEEES
T ss_pred             ccchHHHHHHHHHHHc-----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCccCCCCceeeCC
Confidence            3567899999999985     34688899999999999999999999999999998323355443

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=96.77  E-value=0.0015  Score=47.05  Aligned_cols=51  Identities=24%  Similarity=0.348  Sum_probs=44.7

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecC
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDE  256 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd  256 (265)
                      ..+...+||++|++.       |++..+|+++|+++...|+..|..|..+|.|...+.
T Consensus        15 ~~~~~~~IL~lL~~~-------g~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~~~   65 (82)
T 1oyi_A           15 NAEIVCEAIKTIGIE-------GATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDD   65 (82)
T ss_dssp             SHHHHHHHHHHHSSS-------TEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECSS
T ss_pred             hHHHHHHHHHHHHHc-------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCC
Confidence            347889999999852       499999999999999999999999999999987433

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=96.70  E-value=0.00078  Score=48.23  Aligned_cols=49  Identities=14%  Similarity=0.224  Sum_probs=44.1

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHH-HHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMD-KLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~-~v~~al~~L~~eG~IYs  253 (265)
                      +.+.+++||.+|+..      .+.+..+|++.|+++.. .||..|..|..+|.|..
T Consensus         9 ~~~~~~~IL~~Lk~~------g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~   58 (79)
T 1xmk_A            9 MAEIKEKICDYLFNV------SDSSALNLAKNIGLTKARDINAVLIDMERQGDVYR   58 (79)
T ss_dssp             HHHHHHHHHHHHHHT------CCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEE
T ss_pred             chhHHHHHHHHHHHc------CCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEe
Confidence            347899999999974      26899999999999999 99999999999999985

>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C, DNA polymerase III; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB: 3f2c_A* 3f2d_A*

Probab=96.69  E-value=0.0059  Score=62.73  Aligned_cols=79  Identities=23%  Similarity=0.332  Sum_probs=60.7

Q ss_pred             EeEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee--eCCccEEEEE
Q 024592           67 VNTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQDKRSLNAY  139 (265)
Q Consensus        67 v~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~~~~~i~~~  139 (265)
                      ...|.|-|.|-+++..     ..-++|.|.|.|++|.|+.|.+...+.+....+++|++|+|.|++..  |.....+.+.
T Consensus        17 ~~~~~~~g~v~~~~~~~~~~~~~~~~~~~td~~~~~~~k~f~~~~~~~~~~~~~~~g~~~~~~g~~~~d~~~~~~~~~~~   96 (1041)
T 3f2b_A           17 ERRVVVQGYVFDAEVSELKSGRTLLTMKITDYTNSILVKMFSRDKEDAELMSGVKKGMWVKVRGSVQNDTFVRDLVIIAN   96 (1041)
T ss_dssp             EEEEEEEEEEEEEEEEECTTSCEEEEEEEECSSCEEEEEEECSSHHHHHHHHTCCTTCEEEEEEEEEEETTTTEEEEEEE
T ss_pred             cceEEEEEEEEEEEEEEccCCCEEEEEEEEeCCCCEEEEEeecccchHHHHhcCCCCCEEEEEEEEEeccCCcceEEEee
Confidence            4689999999877542     24679999999999999999775543334567999999999999874  5566677777


Q ss_pred             EeeeCC
Q 024592          140 SLRPII  145 (265)
Q Consensus       140 ~i~~v~  145 (265)
                      .|.+++
T Consensus        97 ~~~~~~  102 (1041)
T 3f2b_A           97 DLNEIA  102 (1041)
T ss_dssp             EEEEEC
T ss_pred             eeEEec
Confidence            776654

>1wyd_A Hypothetical aspartyl-tRNA synthetase; archaea, LIGA; HET: EPE; 2.30A {Sulfolobus tokodaii}

Probab=96.56  E-value=0.013  Score=54.65  Aligned_cols=74  Identities=18%  Similarity=0.191  Sum_probs=56.5

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCC---ccEEEEEEee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQD---KRSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~---~~~i~~~~i~  142 (265)
                      ..|+|.|||.+++....-+.+.|.|+||.|.|..-.+.+ ..+....+..|+.|.|.|.+..-..   ...|.+..+.
T Consensus        17 ~~V~v~Gwv~~~R~~g~~~F~~lrD~~g~iQ~v~~~~~~-~~~~~~~l~~~~~v~v~G~v~~~~~~~~~~el~~~~~~   93 (429)
T 1wyd_A           17 KEVIWAGWVHLLRDLGGKKFIILRDKTGLGQVVVDKNSS-AFGISQELTQESVIQVRGIVKADKRAPRGIELHAEEIT   93 (429)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEECTTST-THHHHTTCCTTCEEEEEEEEEECSSSGGGEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEeCChH-HHHHHHhCCCCCEEEEEEEEEecCCCCccEEEEEeEEE
Confidence            369999999999988888888999999999998754321 1122357899999999999987643   4566665553

>3m4p_A Ehasnrs, asparaginyl-tRNA synthetase, putative; aminoacyl-tRNA synthetase, tRNA ligase, AARS, translation, ATP-binding, nucleotide-binding; HET: 4AD; 2.83A {Entamoeba histolytica} PDB: 3m4q_A

Probab=96.52  E-value=0.016  Score=54.50  Aligned_cols=77  Identities=17%  Similarity=0.333  Sum_probs=55.8

Q ss_pred             eEEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC-----------CccE
Q 024592           68 NTITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ-----------DKRS  135 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~-----------~~~~  135 (265)
                      ..|+|.|||.+++..+ .-+.+.|.|+||.|.|..-.++..+......+..|+.|.|.|.|..-.           +...
T Consensus        31 ~~V~v~Gwv~~~R~~Gk~~~Fi~LrD~sg~iQvv~~~~~~~~~~~~~~l~~g~~V~V~G~v~~~~~~~~~~~~~t~g~~E  110 (456)
T 3m4p_A           31 KLVTFKGWAYHIRKARKTLIFVELRDGSGYCQCVIFGKELCEPEKVKLLTRECSLEITGRLNAYAGKNHPPEIADILNLE  110 (456)
T ss_dssp             SEEEEEEEEEEEECCSSSEEEEEEECSSCEEEEEEESTTTTCHHHHTTCCTTCEEEEEEEEECCCSSSCCCSCTTBCSSE
T ss_pred             CEEEEEEEEEEEecCCCceEEEEEEeCCccEEEEEecccchhhHHhhcCCCccEEEEEeEEEecCCcccCcccCCCCcEE
Confidence            4799999999998885 466679999999999876542211111234689999999999997422           4567


Q ss_pred             EEEEEeeeC
Q 024592          136 LNAYSLRPI  144 (265)
Q Consensus       136 i~~~~i~~v  144 (265)
                      |.+..+..+
T Consensus       111 l~~~~i~vl  119 (456)
T 3m4p_A          111 MQVTEWKVI  119 (456)
T ss_dssp             EEEEEEEEE
T ss_pred             EEEeEEEEE
Confidence            777776544

>1l0w_A Aspartyl-tRNA synthetase; space-grown crystal, dimeric enzyme, flexible domains, ligase; 2.01A {Thermus thermophilus} SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1efw_A* 1g51_A

Probab=96.50  E-value=0.014  Score=56.60  Aligned_cols=75  Identities=12%  Similarity=0.184  Sum_probs=57.3

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee--------CCccEEEEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF--------QDKRSLNAY  139 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f--------~~~~~i~~~  139 (265)
                      ..|+|.|||.+++....-+.+.|.|+||.|.|..-.+.. .-+....+..|+.|.|.|.|+.-        .+...|.+.
T Consensus        17 ~~V~l~GwV~~~R~~G~~~Fi~LrD~~g~iQvv~~~~~~-~~~~~~~l~~e~~V~V~G~v~~~~~~~~~~~~ge~Ei~~~   95 (580)
T 1l0w_A           17 EEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASP-AYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELS   95 (580)
T ss_dssp             CEEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECTTST-THHHHTTCCTTCEEEEEEEEEECSSCCTTSTTTTEEEEEE
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEeCChh-HHHHHhcCCCCcEEEEEEEEEcCCCcCccCCCccEEEEEe
Confidence            369999999999988888888999999999998754321 11224568999999999999864        355677776


Q ss_pred             Eeee
Q 024592          140 SLRP  143 (265)
Q Consensus       140 ~i~~  143 (265)
                      .+..
T Consensus        96 ~i~v   99 (580)
T 1l0w_A           96 ALEV   99 (580)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6543

>2xgt_A Asparaginyl-tRNA synthetase, cytoplasmic; ligase, ATP-binding, protein biosynthesis; HET: NSS; 1.90A {Brugia malayi} PDB: 2xti_A*

Probab=96.46  E-value=0.021  Score=53.38  Aligned_cols=77  Identities=18%  Similarity=0.287  Sum_probs=55.7

Q ss_pred             eEEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC------CccEEEEEE
Q 024592           68 NTITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ------DKRSLNAYS  140 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~------~~~~i~~~~  140 (265)
                      ..|+|.|||.+++..+ .-+.+.|.|+||.|.|..-.+.. +......+..|+.|.|.|.|+.-.      +...|.+..
T Consensus        12 ~~V~v~Gwv~~~R~~Gk~~~Fi~LrD~~g~iQvv~~~~~~-~~~~~~~l~~~~~v~v~G~v~~~~~~~~~~g~~El~~~~   90 (435)
T 2xgt_A           12 ERVCIKGWIHRMRRQGKSLMFFILRDGTGFLQVLLMDKLC-QTYDALTVNTECTVEIYGAIKEVPEGKEAPNGHELIADF   90 (435)
T ss_dssp             SEEEEEEEEEEEEECTTSEEEEEEECSSCEEEEEEEGGGG-SSHHHHHCCTTCEEEEEEEEEECC------TTEEEEEEE
T ss_pred             CEEEEEEEEEEecccCCCcEEEEEEECCceEEEEECCcch-hHHHHhcCCCCCEEEEEEEEEecCCCcCCCCcEEEEEEE
Confidence            3699999999999885 56778999999999988742211 111112589999999999998632      446777766


Q ss_pred             eeeCC
Q 024592          141 LRPII  145 (265)
Q Consensus       141 i~~v~  145 (265)
                      +..+.
T Consensus        91 ~~vl~   95 (435)
T 2xgt_A           91 WKIIG   95 (435)
T ss_dssp             EEEEE
T ss_pred             EEEee
Confidence            66554

>1c0a_A Aspartyl tRNA synthetase; protein-RNA complex, ligase/RNA complex; HET: 4SU H2U QUO G7M 5MU PSU AMP AMO; 2.40A {Escherichia coli} SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1il2_A* 1eqr_A*

Probab=96.46  E-value=0.013  Score=56.96  Aligned_cols=78  Identities=17%  Similarity=0.175  Sum_probs=58.2

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee----------CCccEEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF----------QDKRSLN  137 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f----------~~~~~i~  137 (265)
                      ..|+|.|||.+++....-+.+.|.|+||.|.|..-.+....-+....+..|+.|.|.|.|+.-          .+...|.
T Consensus        16 ~~V~l~GwV~~~R~~G~~~Fi~LrD~~g~iQvv~~~~~~~~~~~~~~l~~e~~V~V~G~v~~~~~~~~n~~~~~geiEl~   95 (585)
T 1c0a_A           16 QQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNEFCIQVTGTVRARDEKNINRDMATGEIEVL   95 (585)
T ss_dssp             CEEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECGGGHHHHHHHTTCCTTCEEEEEEEEEECCTTTCCTTSTTTTEEEE
T ss_pred             CEEEEEEEEEEEecCCCcEEEEEEECCeeEEEEEeCCchHHHHHHhcCCCCCEEEEEeEEEccCcccccccCCCccEEEE
Confidence            369999999999988888889999999999988743221101223568999999999999864          3556777


Q ss_pred             EEEeeeCC
Q 024592          138 AYSLRPII  145 (265)
Q Consensus       138 ~~~i~~v~  145 (265)
                      +..+..+.
T Consensus        96 ~~~i~vl~  103 (585)
T 1c0a_A           96 ASSLTIIN  103 (585)
T ss_dssp             EEEEEEEE
T ss_pred             EeEEEEEe
Confidence            76665443

>3nem_A Aspartyl-tRNA synthetase; rossmann fold, OB fold, ligase; HET: AMO ATP; 1.89A {Thermococcus kodakarensis} PDB: 3nel_A* 3nen_A 1b8a_A*

Probab=96.40  E-value=0.016  Score=54.22  Aligned_cols=76  Identities=14%  Similarity=0.117  Sum_probs=56.9

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccccCCCCEEEEEEEeeeeC---CccEEEEEEee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQISKGMYVRVYGHLKAFQ---DKRSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~g~yVrV~G~i~~f~---~~~~i~~~~i~  142 (265)
                      ..|+|.|||.+++....-+.+.|.|+||.|.|..-.+...+  -+....+..|+.|.|.|.++.-.   +...|.+..+.
T Consensus        17 ~~V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~~~~V~V~G~v~~~~~~~~~~el~~~~i~   96 (438)
T 3nem_A           17 QKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIV   96 (438)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSCHHHHHHGGGCCTTCEEEEEEEEEECTTSTTSEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEEEEEeCCCCCCcEEEEEEEEE
Confidence            46999999999998887777799999999998875432110  12245689999999999998754   45667776655


Q ss_pred             e
Q 024592          143 P  143 (265)
Q Consensus       143 ~  143 (265)
                      .
T Consensus        97 v   97 (438)
T 3nem_A           97 V   97 (438)
T ss_dssp             E
T ss_pred             E
Confidence            4

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=96.40  E-value=0.0034  Score=44.73  Aligned_cols=46  Identities=26%  Similarity=0.255  Sum_probs=40.2

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSID  255 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD  255 (265)
                      .+|+++|++.      .-+++++|+++|+.++..||.-|+.|.+.|.|.-++
T Consensus         5 ~~Il~~L~~~------g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~~   50 (78)
T 1xn7_A            5 IQVRDLLALR------GRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ   50 (78)
T ss_dssp             HHHHHHHHHS------CSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHc------CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            4588999764      368999999999999999999999999999986653

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=96.36  E-value=0.0059  Score=44.73  Aligned_cols=53  Identities=17%  Similarity=0.413  Sum_probs=48.4

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+++.-|..||.+|.+.    .+.|+...+|+++++++...|..+|+.|+..|+|..
T Consensus        16 ~~Lt~~q~~Vl~~I~~~----g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr   68 (91)
T 2dk5_A           16 KGSDNQEKLVYQIIEDA----GNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKA   68 (91)
T ss_dssp             CCSCSSHHHHHHHHHHH----CTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCCHHHHHHHHHHHHc----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            57888999999999874    256999999999999999999999999999999995

>1eov_A ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA synthetase, tRNA ligase, APO-enzyme, OB-fold,; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.1 d.104.1.1 PDB: 1asy_A* 1asz_A*

Probab=96.36  E-value=0.015  Score=55.16  Aligned_cols=77  Identities=10%  Similarity=0.104  Sum_probs=57.3

Q ss_pred             eEEEEEEEEEEeeeCCCe-EEEEEEcCCCeEEEEEecccc---c-c-cccccccCCCCEEEEEEEeeeeC--------Cc
Q 024592           68 NTITVVGIVCDMQDKEPQ-FIFLIDDGTGRIECSRWAHEQ---M-E-FNEVNQISKGMYVRVYGHLKAFQ--------DK  133 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~-~~y~LdDgTG~I~~~~w~~~~---~-~-~~~~~~~~~g~yVrV~G~i~~f~--------~~  133 (265)
                      ..|+|.|||.+++..... +.+.|.|++|.|.|..-.+.+   . + .+....+..|+.|.|.|.+..-.        +.
T Consensus        37 ~~V~v~GwV~~~R~~g~~l~Fi~LrD~~g~iQvv~~~~~~~~~~~~~~~~~~~l~~e~~V~V~G~v~~~~~~~~~~~~g~  116 (487)
T 1eov_A           37 KEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQN  116 (487)
T ss_dssp             CEEEEEEEEEEEEECSSSEEEEEEEETTEEEEEEEECCSSSSSCHHHHHHHTTCCTTCEEEEEEEEEECSSCCTTSSEEE
T ss_pred             CEEEEEEEEEEeeccCCccEEEEEEECCccEEEEEeccccccccHHHHHHHhcCCCCCEEEEEEEEEeCCCCCcCCCCCc
Confidence            469999999999988877 788999999999998754311   1 1 11235689999999999998764        34


Q ss_pred             cEEEEEEeeeC
Q 024592          134 RSLNAYSLRPI  144 (265)
Q Consensus       134 ~~i~~~~i~~v  144 (265)
                      ..|.+..+..+
T Consensus       117 ~El~~~~i~vl  127 (487)
T 1eov_A          117 LEIHITKIYTI  127 (487)
T ss_dssp             EEEEEEEEEEE
T ss_pred             EEEEEEEEEEe
Confidence            66666665443

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=96.31  E-value=0.0043  Score=44.05  Aligned_cols=53  Identities=15%  Similarity=0.226  Sum_probs=41.9

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..+++||++|++.-......-+++.||++.|++++..|+.-|..|.++|.|-.
T Consensus         4 ~r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R   56 (77)
T 2jt1_A            4 SIVTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEK   56 (77)
T ss_dssp             THHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            46788999998741000012478999999999999999999999999999954

>1e1o_A Lysyl-tRNA synthetase, heat inducible; ligase, aminoacyl-tRNA synthetase, protein biosynthesis; HET: LYS; 2.12A {Escherichia coli} SCOP: b.40.4.1 d.104.1.1 PDB: 1e1t_A* 1e22_A* 1e24_A* 1lyl_A 1bbu_A* 1bbw_A 1krs_A 1krt_A

Probab=96.27  E-value=0.031  Score=53.24  Aligned_cols=76  Identities=18%  Similarity=0.200  Sum_probs=57.8

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cc-cccccCCCCEEEEEEEeeee-CCccEEEEEEeeeC
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FN-EVNQISKGMYVRVYGHLKAF-QDKRSLNAYSLRPI  144 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~-~~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i~~v  144 (265)
                      .|+|.|||.+++.....+.+.|.|+||.|.|..-.+...+  -. ....+..|+.|.|.|.|..- .+...|.+..+..+
T Consensus        66 ~V~v~Gwv~~~R~~gk~~F~~LrD~sg~iQvv~~~~~~~~~~~~~~~~~l~~g~~V~V~G~v~~~~~ge~ei~~~~i~vl  145 (504)
T 1e1o_A           66 EVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLL  145 (504)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSSTTHHHHTGGGCCTTCEEEEEEEEEECTTCCEEEEEEEEEEE
T ss_pred             EEEEEEEEEEEecCCCcEEEEEEECCeeEEEEEECCcCCHHHHHHHHhcCCCCCEEEEEEEEEecCCceEEEEEEEEEEe
Confidence            6999999999998888888899999999999875442111  11 34568999999999998763 45667777666443

>1n9w_A Aspartyl-tRNA synthetase 2; biosynthetic protein; 2.30A {Thermus thermophilus} SCOP: b.40.4.1 d.104.1.1 PDB: 3kfu_A*

Probab=96.15  E-value=0.041  Score=51.21  Aligned_cols=69  Identities=13%  Similarity=0.165  Sum_probs=55.1

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccC-CCCEEEEEEEeeeeCC---ccEEEEEEeee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQIS-KGMYVRVYGHLKAFQD---KRSLNAYSLRP  143 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~-~g~yVrV~G~i~~f~~---~~~i~~~~i~~  143 (265)
                      ..|+|.|+|.+++....-+.+.|.|++|.|.|..-.         ..+. .|+.|.|.|.+..-..   ...|.+..+..
T Consensus        14 ~~V~v~Gwv~~~R~~g~~~F~~lrD~~g~iQ~v~~~---------~~l~~~~~~v~v~G~v~~~~~~~~~~el~~~~~~v   84 (422)
T 1n9w_A           14 QEVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGG---------LKLPLPESALRVRGLVVENAKAPGGLEVQAKEVEV   84 (422)
T ss_dssp             SEEEEEEEEEEEEECSSEEEEEEEETTEEEEEEEES---------CCCCCTTCEEEEEEEEEECTTSTTSEEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCEEEEEEEEc---------cccCCCCCEEEEEEEEEecCCCCccEEEEEeEEEE
Confidence            369999999999988887888999999999988532         4578 8999999999987643   46677666654


Q ss_pred             CC
Q 024592          144 II  145 (265)
Q Consensus       144 v~  145 (265)
                      +.
T Consensus        85 l~   86 (422)
T 1n9w_A           85 LS   86 (422)
T ss_dssp             EE
T ss_pred             ec
Confidence            43

>4ex5_A Lysine--tRNA ligase; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: LYS; 2.40A {Burkholderia thailandensis}

Probab=96.14  E-value=0.018  Score=55.17  Aligned_cols=77  Identities=16%  Similarity=0.168  Sum_probs=57.2

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccccCCCCEEEEEEEeeee-CCccEEEEEEeeeC
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQISKGMYVRVYGHLKAF-QDKRSLNAYSLRPI  144 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i~~v  144 (265)
                      ..|+|.|||.+++....-+.+.|.|+||.|.|..-.+...+  -+....+..|+.|.|.|.+..- .+...|.+..++.+
T Consensus        87 ~~V~v~GwV~~~R~~Gk~~Fi~LrD~sg~iQvv~~~~~~~~~~~~~~~~l~~gd~V~V~G~v~~t~~gelel~~~~i~vL  166 (529)
T 4ex5_A           87 LEVAIAGRMMLKRVMGKASFATVQDGSGQIQFFVTPADVGAETYDAFKKWDLGDIVAARGVLFRTNKGELSVKCTQLRLL  166 (529)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEECSSCEEEEEECHHHHCHHHHHHHHTCCTTCEEEEEEEEEECTTSCEEEEEEEEEEE
T ss_pred             cEEEEEEEEEeeecCCCeEEEEEEeCCeeEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEEcCCCcEEEEEEEEEEE
Confidence            46999999999988887778899999999998765432110  1123468999999999998764 36677777666543

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=96.12  E-value=0.0053  Score=43.44  Aligned_cols=45  Identities=24%  Similarity=0.290  Sum_probs=39.9

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+||++|.+.      ..+++.+|++.++++...|+..|+.|.++|.|..
T Consensus         2 r~~Il~~L~~~------~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~   46 (81)
T 2htj_A            2 KNEILEFLNRH------NGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQR   46 (81)
T ss_dssp             HHHHHHHHHHS------CCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            56799999753      2589999999999999999999999999999974

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=96.11  E-value=0.0048  Score=44.90  Aligned_cols=45  Identities=22%  Similarity=0.235  Sum_probs=39.9

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      .+|+++|++.      .-+++.+|++.|+.++..||.-|+.|.+.|.|.-+
T Consensus         5 ~~Il~~L~~~------g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~   49 (87)
T 2k02_A            5 MEVRDMLALQ------GRMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRI   49 (87)
T ss_dssp             HHHHHHHHHS------CSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEE
T ss_pred             HHHHHHHHHc------CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4588999763      36899999999999999999999999999999873

>1x54_A Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthetase, riken structural genomics/proteom initiative, RSGI, structural genomics, ligase; HET: 4AD; 1.45A {Pyrococcus horikoshii} PDB: 1x55_A* 1x56_A

Probab=96.10  E-value=0.019  Score=53.74  Aligned_cols=77  Identities=19%  Similarity=0.230  Sum_probs=57.7

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-c-cccccccCCCCEEEEEEEeeeeCC---ccEEEEEEee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-E-FNEVNQISKGMYVRVYGHLKAFQD---KRSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~-~~~~~~~~~g~yVrV~G~i~~f~~---~~~i~~~~i~  142 (265)
                      ..|+|.|||.+++....-+.+.|.|+||.|.|..-.+... + -+....+..|+.|.|.|.+..-..   ...|.+..+.
T Consensus        17 ~~V~v~G~v~~~R~~g~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~~~~v~v~G~v~~~~~~~~~~el~~~~~~   96 (434)
T 1x54_A           17 KKVRLAGWVYTNMRVGKKIFLWIRDSTGIVQAVVAKNVVGEETFEKAKKLGRESSVIVEGIVKADERAPGGAEVHVEKLE   96 (434)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEECHHHHCHHHHHHHHTCCTTCEEEEEEEEEECTTSGGGEEEEEEEEE
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCEEEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEecCCCCccEEEEEeEEE
Confidence            3699999999999888888889999999999987532210 0 122356899999999999987653   4667776665


Q ss_pred             eC
Q 024592          143 PI  144 (265)
Q Consensus       143 ~v  144 (265)
                      .+
T Consensus        97 vl   98 (434)
T 1x54_A           97 VI   98 (434)
T ss_dssp             EE
T ss_pred             Ee
Confidence            43

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.10  E-value=0.0075  Score=44.56  Aligned_cols=58  Identities=16%  Similarity=0.398  Sum_probs=51.4

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCc
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFH  258 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~h  258 (265)
                      .+|++.+..||.+|++.    .+.||...+|..+++++...|..+|..|+..|+|.++-.-+
T Consensus        33 ~~Lt~~E~lVy~~I~~a----Gn~GIw~kdL~~~tnL~~~~vtkiLK~LE~k~lIK~Vksv~   90 (95)
T 2yu3_A           33 KGSDNQEKLVYQIIEDA----GNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVS   90 (95)
T ss_dssp             CSCSHHHHHHHHHHHHH----TTSCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEECCSC
T ss_pred             cCCCHHHHHHHHHHHHh----CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEecCcc
Confidence            57889999999999985    36799999999999999999999999999999999943333

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=95.97  E-value=0.01  Score=39.31  Aligned_cols=44  Identities=18%  Similarity=0.407  Sum_probs=39.3

Q ss_pred             hHHHHHHHhcCcCCCCCCCC-cCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          202 IDQMVLDFLRRPEFLANNNG-VHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~G-v~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      ...+||+.||+.+      | +.++.+++.++.+.++|.++|..|.+.|+|
T Consensus        11 ~e~~lL~yIr~sG------GildI~~~a~kygV~kdeV~~~LrrLe~KGLI   55 (59)
T 2xvc_A           11 TERELLDYIVNNG------GFLDIEHFSKVYGVEKQEVVKLLEALKNKGLI   55 (59)
T ss_dssp             CHHHHHHHHHHTT------SEEEHHHHHHHHCCCHHHHHHHHHHHHHTTSE
T ss_pred             cHHHHHHHHHHcC------CEEeHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence            4578999999742      5 499999999999999999999999999998

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=95.91  E-value=0.025  Score=39.80  Aligned_cols=54  Identities=17%  Similarity=0.135  Sum_probs=46.4

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEF  257 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~  257 (265)
                      ++...|+++|...+   .++..+..+|+++|+++-.+|+.+|-.|...|.|+.++..
T Consensus        12 ~~~~~v~~~i~~L~---~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~~~~   65 (75)
T 1sfu_A           12 EIFSLVKKEVLSLN---TNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSN   65 (75)
T ss_dssp             HHHHHHHHHHHTSC---TTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             HHHHHHHHHHHhCC---CCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecCCCC
Confidence            68888999988753   3445999999999999999999999999999999985543

>3a74_A Lysyl-tRNA synthetase; aminoacyl tRNA synthetase, ligase, protein biosynthesis, AMI tRNA synthetase, ATP-binding, magnesium; HET: B4P LYN; 1.80A {Geobacillus stearothermophilus} PDB: 3e9h_A* 3e9i_A*

Probab=95.76  E-value=0.029  Score=53.26  Aligned_cols=76  Identities=17%  Similarity=0.134  Sum_probs=57.1

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-c-cccccccCCCCEEEEEEEeeee-CCccEEEEEEeeeC
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-E-FNEVNQISKGMYVRVYGHLKAF-QDKRSLNAYSLRPI  144 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~-~~~~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i~~v  144 (265)
                      .|+|.|||.+++.....+.+.|.|+||.|.|..-.+... + .+....+..|+.|.|.|.+..- .+...|.+..+..+
T Consensus        58 ~V~v~Gwv~~~R~~gk~~F~~LrD~sg~iQvv~~~~~~~~~~~~~~~~l~~g~~v~V~G~v~~~~~ge~ei~~~~i~vl  136 (493)
T 3a74_A           58 EVAVAGRIMTKRGMGKAGFAHIQDVTGQIQIYVRQDDVGEQQYELFKISDLGDIVGVRGTMFKTKVGELSIKVSSYEFL  136 (493)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEEHHHHHHHHHHHHHHCCTTCEEEEEEEEEECTTCCEEEEEEEEEEE
T ss_pred             EEEEEEEEEEEecCCCcEEEEEEECCEeEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEeCCCCcEEEEEEEEEEc
Confidence            699999999999888888889999999999987543211 0 1123568999999999998764 45567777666443

>3i7f_A Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-binding, aminoacyl-tRNA synthetase, LI nucleotide-binding, protein biosynthesis; 2.80A {Entamoeba histolytica}

Probab=95.69  E-value=0.061  Score=51.67  Aligned_cols=77  Identities=16%  Similarity=0.210  Sum_probs=57.7

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc---cccccccCCCCEEEEEEEeeeeC--------CccEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME---FNEVNQISKGMYVRVYGHLKAFQ--------DKRSL  136 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~---~~~~~~~~~g~yVrV~G~i~~f~--------~~~~i  136 (265)
                      ..|+|.|||.+++....-+.+.|.|++|.|.|..-.++..+   .+....+..|+.|.|.|.|+.-.        +...|
T Consensus        63 ~~V~v~Gwv~~~R~~gkl~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~El  142 (548)
T 3i7f_A           63 KTVTIRARVQAVRGKGNMVFLFLRKGIYTCQALVMKSETISKEFVQFCQKISAESICDITGIVKAVEKPIEKATQQDVEI  142 (548)
T ss_dssp             CEEEEEEEEEEEEECSSEEEEEEEETTEEEEEEEECSSSSCHHHHHHHHTCCTTEEEEEEEEEEECSSCCTTSSSCSEEE
T ss_pred             CEEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEECCCccCHHHHHHHhCCCCCCEEEEEEEEEeCCcccccCCCCcEEE
Confidence            47999999999998887777789999999999886532111   11245689999999999998753        45667


Q ss_pred             EEEEeeeC
Q 024592          137 NAYSLRPI  144 (265)
Q Consensus       137 ~~~~i~~v  144 (265)
                      .+..|..+
T Consensus       143 ~~~~i~vl  150 (548)
T 3i7f_A          143 HVTSIAVV  150 (548)
T ss_dssp             EEEEEEEE
T ss_pred             EEeEEEEE
Confidence            77666543

>1qzg_A Protection of telomeres protein 1; protrein-DNA complex, single-stranded telomeric DNA, DNA binding protein/DNA complex; HET: TMP; 1.90A {Schizosaccharomyces pombe} SCOP: b.40.4.3 PDB: 1qzh_A

Probab=95.65  E-value=0.34  Score=39.99  Aligned_cols=86  Identities=15%  Similarity=0.230  Sum_probs=61.6

Q ss_pred             eeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEee---e--CCC---eEEEEEEcCC----C-eEEEEEeccccc
Q 024592           41 LLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQ---D--KEP---QFIFLIDDGT----G-RIECSRWAHEQM  107 (265)
Q Consensus        41 ~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~---~--~~t---~~~y~LdDgT----G-~I~~~~w~~~~~  107 (265)
                      ..=.+|+++++.... .          ..|.++|+|++..   .  +.+   .++|+|-|.+    + .|.|.+|.....
T Consensus        27 ~~~~~~r~~l~~~~~-g----------~~VNviGVVvd~~~P~~S~rGtkD~~~TltI~D~S~~~~~~gL~v~iF~~~~e   95 (187)
T 1qzg_A           27 LTFQSIRSSQELQKK-N----------TIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGN   95 (187)
T ss_dssp             EEEECHHHHTSCCSS-C----------EEEEEEEEEEEEEEEEECSSTTCCEEEEEEEECTTSCTTSCCEEEEEEESSSS
T ss_pred             eeEEEHHHHHhhccC-C----------CEEEEEEEEEEccCceecCCCCccEEEEEEEEeCCCCCCCCceEEEEECCChh
Confidence            444567777643211 1          5789999998864   2  233   5899999977    3 499999976542


Q ss_pred             cccccccc-CCCCEEEEEE-EeeeeCCccEEEEEE
Q 024592          108 EFNEVNQI-SKGMYVRVYG-HLKAFQDKRSLNAYS  140 (265)
Q Consensus       108 ~~~~~~~~-~~g~yVrV~G-~i~~f~~~~~i~~~~  140 (265)
                         ..+.+ .+||.|++.. +|+.|+++.++....
T Consensus        96 ---~LP~V~~~GDIIlL~rvkiq~~~g~~~~v~~~  127 (187)
T 1qzg_A           96 ---DLPVIKQVGQPLLLHQITLRSYRDRTQGLSKD  127 (187)
T ss_dssp             ---CSCCCCSTTCEEEEEEEEEEEETTEEEEEEEE
T ss_pred             ---hCCCCCCCCCEEEEEEEEEEEECCeEEEEEcC
Confidence               46776 8999999986 589999998876543

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=95.46  E-value=0.022  Score=45.65  Aligned_cols=48  Identities=10%  Similarity=0.281  Sum_probs=42.6

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      +..+..+||+.|++.      .-++..+|++++++++..|+..|+.|.++|.|-
T Consensus         1 lD~~d~~il~~L~~~------~~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i~   48 (162)
T 3i4p_A            1 MDRLDRKILRILQED------STLAVADLAKKVGLSTTPCWRRIQKMEEDGVIR   48 (162)
T ss_dssp             CCHHHHHHHHHHTTC------SCSCHHHHHHHHTCCHHHHHHHHHHHHHTTSSC
T ss_pred             CCHHHHHHHHHHHHC------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            356889999999874      357999999999999999999999999999984

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=95.42  E-value=0.021  Score=44.72  Aligned_cols=48  Identities=13%  Similarity=0.257  Sum_probs=43.3

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      +++++.+||++|++.      ..++..+|+++++++...|+..|..|.++|.|-
T Consensus         3 ld~~d~~il~~L~~~------~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   50 (144)
T 2cfx_A            3 LDQIDLNIIEELKKD------SRLSMRELGRKIKLSPPSVTERVRQLESFGIIK   50 (144)
T ss_dssp             CCHHHHHHHHHHHHC------SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            567889999999763      358999999999999999999999999999994

>3bju_A Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP- binding, cytoplasm, ligase, nucleotide-binding, phosphoprotein, polymorphism; HET: LYS ATP; 2.31A {Homo sapiens}

Probab=95.40  E-value=0.07  Score=50.98  Aligned_cols=100  Identities=11%  Similarity=0.160  Sum_probs=66.1

Q ss_pred             eeeeeHHHHhcC-CCCCCCCeEECCeEEeEEEEEEEEEEeeeCC-CeEEEEEEcCCCeEEEEEecccc-c-cc-cc-ccc
Q 024592           41 LLPMTVKQLSEL-SSNDESSASIDGADVNTITVVGIVCDMQDKE-PQFIFLIDDGTGRIECSRWAHEQ-M-EF-NE-VNQ  114 (265)
Q Consensus        41 ~~PvtIkqi~~a-~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~-t~~~y~LdDgTG~I~~~~w~~~~-~-~~-~~-~~~  114 (265)
                      -+..+++++... .....+. ...|   ..|+|.|||.+++... .-..+.|.|++|.|.|..-.+.. . +. .. ...
T Consensus        32 ~~~~~~~~~~~~~~~~~~~~-~~~~---~~V~v~Grv~~~R~~gkk~~F~~LrD~sg~iQvv~~~~~~~~~~~~~~~~~~  107 (521)
T 3bju_A           32 HVDISLTDFIQKYSHLQPGD-HLTD---ITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNK  107 (521)
T ss_dssp             CCCSCHHHHHHHHTTCCTTC-BCSS---CCEEEEEEEEEEEESSSSEEEEEEEETTEEEEEEEEGGGSSCHHHHHHHHHH
T ss_pred             cCccchHHHHHHhhhhcccc-ccCC---cEEEEEEEEEEEecCCCCcEEEEEEECCEEEEEEEECCccCCHHHHHHHHhc
Confidence            344678888764 1100000 0112   4699999999999887 67778999999999998765432 1 10 11 235


Q ss_pred             cCCCCEEEEEEEeeee-CCccEEEEEEeeeC
Q 024592          115 ISKGMYVRVYGHLKAF-QDKRSLNAYSLRPI  144 (265)
Q Consensus       115 ~~~g~yVrV~G~i~~f-~~~~~i~~~~i~~v  144 (265)
                      +..|+.|.|.|.+..- .+...|.+..+..+
T Consensus       108 l~~gd~V~V~G~v~~t~~ge~ei~~~~i~~l  138 (521)
T 3bju_A          108 LRRGDIIGVQGNPGKTKKGELSIIPYEITLL  138 (521)
T ss_dssp             CCTTCEEEEEEEEEECTTCCEEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEecCCCCEEEEEeEEEEe
Confidence            8999999999998754 45567777665544

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=95.40  E-value=0.026  Score=39.74  Aligned_cols=51  Identities=16%  Similarity=0.325  Sum_probs=44.2

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++.-+..||++|.+.    ....+++++|++.+     +++...|...|+.|.+.|.|-.
T Consensus        15 ~t~~r~~IL~~l~~~----~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~   70 (83)
T 2fu4_A           15 VTLPRLKILEVLQEP----DNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTR   70 (83)
T ss_dssp             CCHHHHHHHHHHTSG----GGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEE
T ss_pred             cCHHHHHHHHHHHhC----CCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEE
Confidence            567788899999763    11468999999999     8999999999999999999988

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=95.39  E-value=0.042  Score=39.84  Aligned_cols=56  Identities=18%  Similarity=0.224  Sum_probs=46.7

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA  265 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~~  265 (265)
                      ..+..||.+| .       ..+++.+|++.++++...|...|..|.+.|.|.... .+|..+..|
T Consensus        31 ~~r~~Il~~L-~-------~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~-g~y~l~~~g   86 (96)
T 1y0u_A           31 PVRRKILRML-D-------KGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG-ERWVVTDAG   86 (96)
T ss_dssp             HHHHHHHHHH-H-------TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET-TEEEECTTT
T ss_pred             HHHHHHHHHH-c-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC-CEEEECCCc
Confidence            5677899988 3       148999999999999999999999999999998832 488777553

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=95.35  E-value=0.016  Score=43.93  Aligned_cols=59  Identities=10%  Similarity=0.159  Sum_probs=50.0

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc--CCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL--NLPMDKLMEALESLNENSLVYSIDEFHYKSAV  263 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l--~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~  263 (265)
                      +...+++||++|++.      .-+++.+|++.+  +++...|++.|..|.+.|.|-....-.|..|.
T Consensus        11 md~~d~~IL~~L~~~------g~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~~rg~Y~LT~   71 (111)
T 3b73_A           11 MTIWDDRILEIIHEE------GNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPLANGVYVITE   71 (111)
T ss_dssp             CCHHHHHHHHHHHHH------SCBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEECSTTCEEECH
T ss_pred             cCHHHHHHHHHHHHc------CCCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEecCCceEEECc
Confidence            678899999999864      257999999999  99999999999999999999873333777764

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=95.12  E-value=0.033  Score=43.66  Aligned_cols=48  Identities=17%  Similarity=0.311  Sum_probs=42.6

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      +++.+.+||.+|+..      ..++..+|++.++++...+...|+.|.+.|.|-
T Consensus         1 ld~~~~~il~~L~~~------~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~   48 (150)
T 2pn6_A            1 MDEIDLRILKILQYN------AKYSLDEIAREIRIPKATLSYRIKKLEKDGVIK   48 (150)
T ss_dssp             CCHHHHHHHHHHTTC------TTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSC
T ss_pred             CChHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence            356788999999763      368999999999999999999999999999984

>4dka_C RNA-editing complex protein MP81; krepa1, VHH, single domain antibody, protein binding, RNA BI protein-immune system complex; 1.97A {Trypanosoma brucei} PDB: 4dk3_C 4dk6_C

Probab=95.08  E-value=0.14  Score=37.97  Aligned_cols=64  Identities=19%  Similarity=0.212  Sum_probs=40.1

Q ss_pred             eEEEEEEEEEEeee----CCCeEEEEEE-cCCC-----eEEEEEecccccccccccccCCCCEEEEEEEeeeeC
Q 024592           68 NTITVVGIVCDMQD----KEPQFIFLID-DGTG-----RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ  131 (265)
Q Consensus        68 ~~V~iVG~V~~v~~----~~t~~~y~Ld-DgTG-----~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~  131 (265)
                      +++.+||.|.+|.+    ...-..|+|. |+.+     .+.++.+-+....+.-...+++|..|+|.|+||...
T Consensus         4 sn~vlvG~V~DVQ~Gfl~~~~V~Qftl~~d~e~~~eke~~tVRC~Gd~~~~~~lk~~lk~g~~v~V~GrLRm~p   77 (105)
T 4dka_C            4 SNALMIGRIADVQHGFLGAMTVTQYVLEVDGGASGEKEFIVIRCMGDNFPASLLKDQVKLGSRVLVQGTLRMNR   77 (105)
T ss_dssp             CEEEEEEEEEEEEEEEETTEEEEEEEEEECC----CCEEEEEEEECC---------CCCTTCEEEEEEEEECCC
T ss_pred             cceEEEEEEEEeeecccccceEEEEEEEEeCCCCCcccEEEEEEcCccchHHHHHHHHhCCCEEEEEeEEEeee
Confidence            57899999999987    3344555543 4443     366666655432122346799999999999999863

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=95.06  E-value=0.025  Score=44.54  Aligned_cols=48  Identities=10%  Similarity=0.241  Sum_probs=43.6

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      ++.++.+||++|++.      ..++..+|++.+++++..|+..|..|.++|.|-
T Consensus         7 ld~~d~~il~~L~~~------~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   54 (151)
T 2dbb_A            7 LDRVDMQLVKILSEN------SRLTYRELADILNTTRQRIARRIDKLKKLGIIR   54 (151)
T ss_dssp             CCHHHHHHHHHHHHC------TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            678899999999863      368999999999999999999999999999994

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=95.00  E-value=0.058  Score=38.73  Aligned_cols=56  Identities=16%  Similarity=0.226  Sum_probs=46.2

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeec
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF--HYKSA  262 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t  262 (265)
                      +.+..||.+|.+      ..++++.+|++.++++...|...|..|.+.|.|.. -|..  .|..|
T Consensus        24 ~~~~~il~~l~~------~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~~r~~~y~l~   82 (99)
T 3cuo_A           24 PKRLLILCMLSG------SPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRDAQRILYSIK   82 (99)
T ss_dssp             HHHHHHHHHHTT------CCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSSCEEEEEC
T ss_pred             hHHHHHHHHHHh------CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEC
Confidence            577889999864      24789999999999999999999999999999987 5543  34444

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=94.94  E-value=0.031  Score=42.73  Aligned_cols=51  Identities=14%  Similarity=0.270  Sum_probs=45.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCC-cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNG-VHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~G-v~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++..+..||.+|.+.     +.. +++.+|++.++++...|...|+.|.+.|.|..
T Consensus        23 gLt~~e~~il~~L~~~-----~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r   74 (123)
T 3r0a_A           23 NLTKADLNVMKSFLNE-----PDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQR   74 (123)
T ss_dssp             TCCHHHHHHHHHHHHS-----TTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHHC-----CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            5788999999999753     223 99999999999999999999999999999976

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=94.91  E-value=0.037  Score=44.90  Aligned_cols=49  Identities=18%  Similarity=0.333  Sum_probs=44.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      .+++++.+||++|+..      ..++..+|++++++++..|+..|+.|.++|.|-
T Consensus        14 ~ld~~d~~IL~~L~~~------~~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~   62 (171)
T 2ia0_A           14 HLDDLDRNILRLLKKD------ARLTISELSEQLKKPESTIHFRIKKLQERGVIE   62 (171)
T ss_dssp             CCCHHHHHHHHHHHHC------TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            4778999999999863      358999999999999999999999999999993

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=94.89  E-value=0.03  Score=44.17  Aligned_cols=49  Identities=10%  Similarity=0.195  Sum_probs=44.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      .++..+.+||++|++.      ..++..+|++++++++..++..|..|.++|.|-
T Consensus         5 ~ld~~d~~il~~L~~~------~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   53 (152)
T 2cg4_A            5 LIDNLDRGILEALMGN------ARTAYAELAKQFGVSPETIHVRVEKMKQAGIIT   53 (152)
T ss_dssp             CCCHHHHHHHHHHHHC------TTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             ccCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcc
Confidence            3678899999999863      368999999999999999999999999999995

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=94.88  E-value=0.037  Score=43.48  Aligned_cols=49  Identities=12%  Similarity=0.200  Sum_probs=43.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      .++..+.+||.+|+..      ..++..+|++.++++...+...|+.|.+.|.|-
T Consensus         4 ~ld~~~~~iL~~L~~~------~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   52 (150)
T 2w25_A            4 ALDDIDRILVRELAAD------GRATLSELATRAGLSVSAVQSRVRRLESRGVVQ   52 (150)
T ss_dssp             CCCHHHHHHHHHHHHC------TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             ccCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            3678899999999753      368999999999999999999999999999994

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=94.83  E-value=0.014  Score=48.36  Aligned_cols=55  Identities=13%  Similarity=0.083  Sum_probs=45.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .|+..|.+||++|++.-. ......++.||++.|+++...+...|..|.+.|.|..
T Consensus         2 ~lt~~q~~il~~I~~~~~-~~g~~~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~   56 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIE-KNGYPPSVREIARRFRITPRGALLHLIALEKKGYIER   56 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHH-HHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEC
T ss_pred             CcCHHHHHHHHHHHHHHH-HhCCCCCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEe
Confidence            477899999999876311 1123479999999999999999999999999999965

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=94.81  E-value=0.024  Score=43.87  Aligned_cols=48  Identities=15%  Similarity=0.305  Sum_probs=42.4

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      +++.+..|+..|+..      ..++..+|++.++++...++..|+.|.++|.|-
T Consensus         2 ld~~~~~il~~L~~~------~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~   49 (141)
T 1i1g_A            2 IDERDKIILEILEKD------ARTPFTEIAKKLGISETAVRKRVKALEEKGIIE   49 (141)
T ss_dssp             CCSHHHHHHHHHHHC------TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEe
Confidence            456888999999753      357999999999999999999999999999995

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=94.80  E-value=0.046  Score=43.56  Aligned_cols=49  Identities=16%  Similarity=0.255  Sum_probs=43.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      .++..+.+||++|+..      ..++..+|++.++++...++..|..|.++|.|-
T Consensus         7 ~ld~~~~~il~~L~~~------~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   55 (162)
T 2p5v_A            7 TLDKTDIKILQVLQEN------GRLTNVELSERVALSPSPCLRRLKQLEDAGIVR   55 (162)
T ss_dssp             CCCHHHHHHHHHHHHC------TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEe
Confidence            4678899999999863      258999999999999999999999999999994

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=94.68  E-value=0.053  Score=39.30  Aligned_cols=52  Identities=21%  Similarity=0.257  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++..+..||.+|...      .+++..+|++.++++...|...|..|.+.|.|.. .+
T Consensus        17 ~l~~~~~~il~~l~~~------~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~~~   69 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLER------GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIV   69 (109)
T ss_dssp             CCCHHHHHHHHHHHHH------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEee
Confidence            4678888999999653      3689999999999999999999999999999988 55

>2hpi_A DNA polymerase III alpha subunit; POL-beta-like nucleotidyltransferase fold, transferase; HET: DNA; 3.00A {Thermus aquaticus} PDB: 2hpm_A* 3e0d_A*

Probab=94.57  E-value=0.042  Score=57.34  Aligned_cols=75  Identities=13%  Similarity=0.173  Sum_probs=43.7

Q ss_pred             eEEEEEEEEEEeeeC-----CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEee
Q 024592           68 NTITVVGIVCDMQDK-----EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~-----~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~  142 (265)
                      ..|++.|.|.+++..     .....++|+|.||.++|.+|.+.-.  .....+.++..|.|.|++..-. ..+|.+..+.
T Consensus      1043 ~~v~v~G~v~~~~~~~Tk~G~~maf~tleD~tg~~evvvf~~~~~--~~~~~l~~~~~~~v~G~v~~~~-~~~l~~~~i~ 1119 (1220)
T 2hpi_A         1043 PKVLLSGMVEEVVRKPTRSGGMMARFTLSDETGALEVVVFGRAYE--GVSPKLKEDIPLLVLAEVEKGE-ELRVLAQAVW 1119 (1220)
T ss_dssp             CEEEEEEEECCC------------CEEEEETTEEEEEC---------------CTTCEEEEEEEEC------CEEEEEEE
T ss_pred             CeEEEEEEEEEEEEeecCCCCeEEEEEEEECCCCEEEEEcHHHHH--HHHHHhccCCEEEEEEEEEECC-CcEEEEeeee
Confidence            457899999887633     2357789999999999999976432  2345689999999999997543 5678888877


Q ss_pred             eCC
Q 024592          143 PII  145 (265)
Q Consensus       143 ~v~  145 (265)
                      +++
T Consensus      1120 ~l~ 1122 (1220)
T 2hpi_A         1120 TLE 1122 (1220)
T ss_dssp             EHH
T ss_pred             cHH
Confidence            553

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=94.37  E-value=0.038  Score=43.54  Aligned_cols=49  Identities=18%  Similarity=0.268  Sum_probs=43.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      .++..+.+||++|++.      ..++..+|++.++++...|+..|..|.++|.|-
T Consensus         4 ~ld~~~~~il~~L~~~------~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   52 (151)
T 2cyy_A            4 PLDEIDKKIIKILQND------GKAPLREISKITGLAESTIHERIRKLRESGVIK   52 (151)
T ss_dssp             CCCHHHHHHHHHHHHC------TTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             CcCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            4678899999999863      368999999999999999999999999999984

>2b0l_A GTP-sensing transcriptional pleiotropic repressor; CODY, DNA-binding, nucleotide-binding, transcript regulation, winged HTH motif.; 2.90A {Bacillus subtilis} SCOP: a.4.5.66

Probab=94.31  E-value=0.044  Score=40.75  Aligned_cols=33  Identities=18%  Similarity=0.370  Sum_probs=31.2

Q ss_pred             Cc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          221 GV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       221 Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      -+ +..+|++.|+++...|+++|..|.++|.|+.
T Consensus        42 ~lps~~eLa~~lgVSr~tVr~al~~L~~~GlI~~   75 (102)
T 2b0l_A           42 GLLVASKIADRVGITRSVIVNALRKLESAGVIES   75 (102)
T ss_dssp             EEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            35 9999999999999999999999999999987

>2dk8_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, RNA_POL_RPC34 domain, RNA polymerase III C39 subunit, NPPSFA; NMR {Mus musculus} SCOP: a.4.5.85

Probab=94.30  E-value=0.045  Score=39.13  Aligned_cols=48  Identities=13%  Similarity=0.263  Sum_probs=42.5

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEE
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IY  252 (265)
                      ..+..+||++++..     .+||+-++|...+ +++.++.-++|..|..+|.|=
T Consensus        13 ~~ie~~IL~l~~~~-----P~GItd~~L~~~~p~~~~~~r~~aIN~LL~~gkie   61 (81)
T 2dk8_A           13 VEIENRIIELCHQF-----PHGITDQVIQNEMPHIEAQQRAVAINRLLSMGQLD   61 (81)
T ss_dssp             HHHHHHHHHHHHHC-----SSCEEHHHHHHHCTTSCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHHhC-----CCCCCHHHHHHHCCCCCHHHHHHHHHHHHHcCCeE
Confidence            46888999999874     4799999999999 589999999999999988763

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=94.28  E-value=0.1  Score=39.59  Aligned_cols=55  Identities=15%  Similarity=0.327  Sum_probs=47.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...    ...+++..+|++.++++...|..+|+.|.+.|.|.. -|.
T Consensus        31 ~lt~~~~~iL~~l~~~----~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~   86 (141)
T 3bro_A           31 DLTGTQMTIIDYLSRN----KNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSG   86 (141)
T ss_dssp             TCCHHHHHHHHHHHHT----TTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHC----CCCCcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEeeCCC
Confidence            4677888899999763    234899999999999999999999999999999998 553

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=94.26  E-value=0.11  Score=36.33  Aligned_cols=55  Identities=9%  Similarity=0.128  Sum_probs=47.1

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC----CCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN----LPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~----~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .+++..+..||.+|...      .++++.+|++.++    ++...|...|+.|.+.|.|-. -|..
T Consensus         5 ~~lt~~e~~vL~~L~~~------~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~gr   64 (82)
T 1p6r_A            5 PQISDAELEVMKVIWKH------SSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKEGR   64 (82)
T ss_dssp             CCCCHHHHHHHHHHHTS------SSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             CCCCHHHHHHHHHHHcC------CCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEecCC
Confidence            35788999999999762      3799999999995    789999999999999999987 5554

>3kdf_A Replication protein A 14 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 1quq_B 1l1o_A

Probab=94.21  E-value=0.81  Score=35.00  Aligned_cols=80  Identities=19%  Similarity=0.259  Sum_probs=51.2

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID  146 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d  146 (265)
                      +.|+|||+|.++.....  +++|.++-| .|.|+.-..-+      +  ..+.||.|+|++..   +..|.+.......+
T Consensus        23 k~VrivGkV~~~~~~g~--~~~l~s~Dg~~Vtv~l~~p~~------~--~l~~~vEViG~V~~---~~tI~~~~~~~fg~   89 (121)
T 3kdf_A           23 KPVCFVGRLEKIHPTGK--MFILSDGEGKNGTIELMEPLD------E--EISGIVEVVGRVTA---KATILCTSYVQFKE   89 (121)
T ss_dssp             CEEEEEEEEEEECTTSS--EEEEECTTSCEEEEECSSCCS------S--CCCSEEEEEEEECT---TSCEEEEEEEECCC
T ss_pred             CeEEEEEEEEEEcCCCC--EEEEEeCCCCEEEEEeCCCCC------c--ccCcEEEEEEEECC---CCeEEEEEEEecCC
Confidence            78999999998865444  456766654 68777542111      1  22569999999974   56777777776654


Q ss_pred             ----hh-HHHHHHHHHHHH
Q 024592          147 ----FN-EITSHFVECIYV  160 (265)
Q Consensus       147 ----~N-ei~~H~Levi~~  160 (265)
                          ++ +..-++.+.++.
T Consensus        90 ~~~~fD~~~yn~lv~l~~~  108 (121)
T 3kdf_A           90 DSHPFDLGLYNEAVKIIHD  108 (121)
T ss_dssp             SSSCCCHHHHHHHHHHHHH
T ss_pred             CCcccCHHHHHHHHHHHhc
Confidence                44 333444555444

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=94.10  E-value=0.1  Score=39.70  Aligned_cols=55  Identities=20%  Similarity=0.352  Sum_probs=48.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...    .+.+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        28 ~lt~~~~~vL~~l~~~----~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~   83 (139)
T 3eco_A           28 DITNEQGHTLGYLYAH----QQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDA   83 (139)
T ss_dssp             TCCHHHHHHHHHHHHS----TTTCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHhc----CCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCC
Confidence            5678888999999763    246999999999999999999999999999999998 553

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=93.98  E-value=0.059  Score=41.39  Aligned_cols=62  Identities=18%  Similarity=0.176  Sum_probs=46.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      +++..+..+|.+|....  ....++++.+|++.++++...|..+|+.|.++|.|.... ..|..|
T Consensus        10 ~lt~~~~~~L~~l~~l~--~~~~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~~-~~~~Lt   71 (139)
T 2x4h_A           10 NLSRREFSYLLTIKRYN--DSGEGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKKE-DGVWIT   71 (139)
T ss_dssp             -CCHHHHHHHHHHHHHH--TTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET-TEEEEC
T ss_pred             hcCHHHHHHHHHHHHHH--hcCCCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEecC-CeEEEC
Confidence            45666777777664321  123579999999999999999999999999999998722 455554

>4gs3_A Single-stranded DNA-binding protein; primosome, oligonucleotide/oligosaccharide binding domain, D binding protein; 1.09A {Thermoanaerobacter tengcongensis}

Probab=93.90  E-value=0.45  Score=35.65  Aligned_cols=59  Identities=22%  Similarity=0.325  Sum_probs=39.8

Q ss_pred             eEEEEEEEEEE-----eee-CCCeEEEEEE-----cCCCeEEEEEecccccccccccccCCCCEEEEEEEeeee
Q 024592           68 NTITVVGIVCD-----MQD-KEPQFIFLID-----DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF  130 (265)
Q Consensus        68 ~~V~iVG~V~~-----v~~-~~t~~~y~Ld-----DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f  130 (265)
                      ++|.|+|++..     .+. .....+|+|.     |.+--|.|..|..-+.    ...+..|+.|.|.|++++|
T Consensus        12 N~V~LiGrl~~dpelr~t~~G~~v~~f~lAV~R~~~~~Dfi~ivvw~klAe----~~~~~kG~~v~v~G~lrsy   81 (107)
T 4gs3_A           12 NTVTLVGKVFTPLEFSHELYGEKFFNFILEVPRLSETKDYLPITISNRLFE----GMNLEVGTRVKIEGQLRSY   81 (107)
T ss_dssp             SCEEEEEEECSCCEEEEEETTEEEEEEEEEEECTTSCEEEEEEEEEGGGST----TCCCCTTCEEEEEEEEEEE
T ss_pred             CEEEEEEEECCCceEEEecCCcEEEEEEEEeCCCCCCCcEEEEEEEhHHhh----HHhhcCCCEEEEEEEEEec
Confidence            67888888844     112 2245555554     4455699999976543    2335689999999999875

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=93.78  E-value=0.094  Score=39.75  Aligned_cols=53  Identities=13%  Similarity=0.131  Sum_probs=46.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        35 ~l~~~~~~iL~~l~~~------~~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~~~~   88 (140)
T 2nnn_A           35 GLTPTQWAALVRLGET------GPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSADP   88 (140)
T ss_dssp             CCCHHHHHHHHHHHHH------SSBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEEEET
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCC
Confidence            4667888899999753      2899999999999999999999999999999998 654

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=93.76  E-value=0.16  Score=38.68  Aligned_cols=53  Identities=19%  Similarity=0.197  Sum_probs=45.8

Q ss_pred             CCChhHHHHHHHh-cCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFL-RRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i-~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+| ..      ..+++..+|++.++++...|..+|+.|.+.|.|.. .|.
T Consensus        34 ~l~~~~~~iL~~l~~~------~~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~~~~   88 (146)
T 2fbh_A           34 GLSQARWLVLLHLARH------RDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVA   88 (146)
T ss_dssp             CCTTTHHHHHHHHHHC------SSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCB
T ss_pred             CCCHHHHHHHHHHHHc------CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeecCCC
Confidence            4667788899998 54      24799999999999999999999999999999988 553

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=93.65  E-value=0.18  Score=36.34  Aligned_cols=53  Identities=13%  Similarity=0.196  Sum_probs=46.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHH----HHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVI----SQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I----~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|    ++.++++...|...|+.|++.|.|.. .|.
T Consensus         5 ~lt~~q~~iL~~l~~~------~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~~   62 (99)
T 1tbx_A            5 PFFYPEAIVLAYLYDN------EGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQER   62 (99)
T ss_dssp             SSBCHHHHHHHHHTTC------TTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEecC
Confidence            5677888999999652      47899999    88889999999999999999999998 665

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=93.56  E-value=0.077  Score=40.35  Aligned_cols=52  Identities=13%  Similarity=0.188  Sum_probs=45.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .+
T Consensus        28 ~l~~~~~~iL~~l~~~------~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~~~   80 (142)
T 3bdd_A           28 GISLTRYSILQTLLKD------APLHQLALQERLQIDRAAVTRHLKLLEESGYIIRKRN   80 (142)
T ss_dssp             SSCHHHHHHHHHHHHH------CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCHHHHHHHHHHHhC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence            4567788899999753      3799999999999999999999999999999988 55

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=93.47  E-value=0.21  Score=38.19  Aligned_cols=34  Identities=12%  Similarity=0.286  Sum_probs=31.3

Q ss_pred             CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .=+ +..+|+++|+++...|++||..|.++|.|+.
T Consensus        35 ~~Lps~~~La~~~~vSr~tvr~Al~~L~~~G~i~~   69 (125)
T 3neu_A           35 DKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYA   69 (125)
T ss_dssp             CBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEE
Confidence            345 5999999999999999999999999999987

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=93.42  E-value=0.16  Score=38.33  Aligned_cols=53  Identities=13%  Similarity=0.232  Sum_probs=46.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        26 ~l~~~~~~iL~~l~~~------~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~~~   79 (138)
T 3bpv_A           26 NLTDAQVACLLRIHRE------PGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDP   79 (138)
T ss_dssp             TCCHHHHHHHHHHHHS------TTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCC
Confidence            5677888899999752      4799999999999999999999999999999998 654

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=93.37  E-value=0.13  Score=37.14  Aligned_cols=53  Identities=17%  Similarity=0.139  Sum_probs=42.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++..+..++..+...     +.+++..+|++.++++...|...|+.|.+.|.|.. -+
T Consensus        18 ~l~~~~~~~l~~l~~~-----~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~~   71 (109)
T 2d1h_A           18 KITDTDVAVLLKMVEI-----EKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKT   71 (109)
T ss_dssp             TCCHHHHHHHHHHHHH-----CSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             cCCHHHHHHHHHHHHc-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecc
Confidence            4556666666554321     24799999999999999999999999999999998 54

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=93.34  E-value=0.1  Score=38.75  Aligned_cols=56  Identities=18%  Similarity=0.221  Sum_probs=45.3

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeecc
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF--HYKSAV  263 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t~  263 (265)
                      +.+..||.+|.+       .++++.+|++.++++...|...|..|.+.|.|.. -+..  .|+.+.
T Consensus        25 ~~r~~IL~~L~~-------~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~~gr~~~y~l~~   83 (108)
T 2kko_A           25 GRRLQILDLLAQ-------GERAVEAIATATGMNLTTASANLQALKSGGLVEARREGTRQYYRIAG   83 (108)
T ss_dssp             STTHHHHHHHTT-------CCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEETTEEEEEESC
T ss_pred             HHHHHHHHHHHc-------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECh
Confidence            355678888853       3689999999999999999999999999999987 6554  455543

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=93.31  E-value=0.082  Score=45.48  Aligned_cols=60  Identities=10%  Similarity=0.140  Sum_probs=51.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeecc
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAV  263 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t~  263 (265)
                      +++..+..||.+|.+.      .++++.+|++.++++.+.+...|..|.+.|.|-. -....|..|.
T Consensus       149 ~L~~~~~~IL~~L~~~------~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~~r~~~~~LT~  209 (244)
T 2wte_A          149 DYSREEMKLLNVLYET------KGTGITELAKMLDKSEKTLINKIAELKKFGILTQKGKDRKVELNE  209 (244)
T ss_dssp             CCCHHHHHHHHHHHHH------TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTTEEEECH
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCccEEEECH
Confidence            6788899999998653      3799999999999999999999999999999987 4556677664

>1l1o_C Replication protein A 70 kDa DNA-binding subunit; eukaryotic SSB, ssDNA binding protein, OB-fold; 2.80A {Homo sapiens} SCOP: b.40.4.3

Probab=93.30  E-value=0.27  Score=40.24  Aligned_cols=76  Identities=13%  Similarity=0.152  Sum_probs=49.4

Q ss_pred             eEEEEEEcCCCeEEEEEecccccc-----c--------ccccc----c--CCCC--EEEEEEEeeeeCCc--cEEEEEEe
Q 024592           85 QFIFLIDDGTGRIECSRWAHEQME-----F--------NEVNQ----I--SKGM--YVRVYGHLKAFQDK--RSLNAYSL  141 (265)
Q Consensus        85 ~~~y~LdDgTG~I~~~~w~~~~~~-----~--------~~~~~----~--~~g~--yVrV~G~i~~f~~~--~~i~~~~i  141 (265)
                      .+.+.|.|.||.+.|..|.+.+..     .        .....    +  ..+.  .+++..+...|+++  ...++..+
T Consensus        80 ~l~~~i~D~Tg~~~~t~F~~~ae~ilG~sA~el~~l~e~~~~~~~~~~~~~~~~~~~f~l~vk~e~yn~e~r~~~~v~~~  159 (181)
T 1l1o_C           80 ILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELKDKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDV  159 (181)
T ss_dssp             EEEEEEECSSCEEEEEEEHHHHHHHHSSCHHHHHHHTTSCHHHHHHHHHHTTTCEEEEEEEEECCCC-----CEEEEEEE
T ss_pred             EEEEEEEeCCCCEEEEEEhHHHHHHhCCCHHHHHHHHhhChHHHHHHHHHhcCceEEEEEEEEEeecCCEEEEEEEEEEe
Confidence            467899999999999999764321     0        00000    1  1233  35555566678766  56888889


Q ss_pred             eeCCChhHHHHHHHHHHHHH
Q 024592          142 RPIIDFNEITSHFVECIYVQ  161 (265)
Q Consensus       142 ~~v~d~Nei~~H~Levi~~~  161 (265)
                      .|| |+.+..-|+|+.|...
T Consensus       160 ~~v-d~~~e~~~L~~~i~~~  178 (181)
T 1l1o_C          160 KPV-DYREYGRRLVMSIRRS  178 (181)
T ss_dssp             EEC-CHHHHHHHHHHHHHHH
T ss_pred             eeC-CHHHHHHHHHHHHHHh
Confidence            998 6788899999998643

>1xjv_A Protection of telomeres 1; protein-DNA complex, single-stranded DNA, transcription/DNA complex; 1.73A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 3kjo_A 3kjp_A

Probab=93.22  E-value=0.9  Score=39.84  Aligned_cols=68  Identities=18%  Similarity=0.258  Sum_probs=51.3

Q ss_pred             eEEEEEEEEEEeee----C--CCeEEEEEEcCCC-eEEEEEeccccccccccccc-CCCCEEEEE-EEeeeeCCccEEEE
Q 024592           68 NTITVVGIVCDMQD----K--EPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQI-SKGMYVRVY-GHLKAFQDKRSLNA  138 (265)
Q Consensus        68 ~~V~iVG~V~~v~~----~--~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~-~~g~yVrV~-G~i~~f~~~~~i~~  138 (265)
                      ..|.++|+|+++..    +  .-.++|+|-|.+- .|.|.+|....   +..+.+ .+|+.|++. -+|+.|+++.++..
T Consensus        16 ~~vnvigVV~~~~~p~~s~G~d~~~tl~I~D~S~~gl~v~iF~~~~---~~LP~v~~~GDII~l~~vki~~~~g~~~~v~   92 (294)
T 1xjv_A           16 TIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNY---EALPIIYKNGDIVRFHRLKIQVYKKETQGIT   92 (294)
T ss_dssp             EEEEEEEEEEEEEEEEECSSSSEEEEEEEECTTCCEEEEEEEESSG---GGSCCCCSTTCEEEEEEEEEEEETTEEEEEE
T ss_pred             CeeEEEEEEEEcCCCccCCCCeEEEEEEEEcCCCCCEEEEEECCCh---HHCCCCCCCCCEEEEEEEEEEEECCeEEEEc
Confidence            56889999988753    2  2368999999652 39999997643   246666 999999998 45889999877644

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=93.21  E-value=0.1  Score=40.52  Aligned_cols=53  Identities=19%  Similarity=0.149  Sum_probs=45.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        44 ~l~~~~~~iL~~l~~~------~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   97 (153)
T 2pex_A           44 DLTYPQYLVMLVLWET------DERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRTRAA   97 (153)
T ss_dssp             TCCHHHHHHHHHHHHS------CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCCHHHHHHHHHHHhC------CCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCc
Confidence            5677888899998752      3799999999999999999999999999999998 553

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=93.13  E-value=0.11  Score=39.62  Aligned_cols=53  Identities=9%  Similarity=0.036  Sum_probs=46.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        30 ~l~~~~~~iL~~l~~~------~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~~~~   83 (145)
T 2a61_A           30 GITPAQFDILQKIYFE------GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDP   83 (145)
T ss_dssp             TCCHHHHHHHHHHHHH------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCC
Confidence            4677888899999753      3799999999999999999999999999999998 653

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=93.12  E-value=0.17  Score=37.91  Aligned_cols=35  Identities=14%  Similarity=0.136  Sum_probs=31.8

Q ss_pred             Cc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeec
Q 024592          221 GV-HRNVISQQLNLPMDKLMEALESLNENSLVYSID  255 (265)
Q Consensus       221 Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiD  255 (265)
                      -+ +..+|+++|+++...|++||..|.++|.|+...
T Consensus        32 ~lPs~~~La~~~~vSr~tvr~al~~L~~~Gli~~~~   67 (113)
T 3tqn_A           32 MIPSIRKISTEYQINPLTVSKAYQSLLDDNVIEKRR   67 (113)
T ss_dssp             EECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            45 899999999999999999999999999998743

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=93.12  E-value=0.25  Score=38.20  Aligned_cols=53  Identities=11%  Similarity=0.147  Sum_probs=45.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        40 ~lt~~~~~iL~~l~~~------~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~~~~   93 (155)
T 3cdh_A           40 GLRVPEWRVLACLVDN------DAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRVADA   93 (155)
T ss_dssp             TCCHHHHHHHHHHSSC------SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC--
T ss_pred             CCCHHHHHHHHHHHHC------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            5677888999999753      3799999999999999999999999999999987 553

>4ah6_A Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo sapiens}

Probab=93.07  E-value=0.14  Score=49.94  Aligned_cols=73  Identities=11%  Similarity=0.097  Sum_probs=51.7

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccc-c-cccccccCCCCEEEEEEEeeee----------CCccE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQM-E-FNEVNQISKGMYVRVYGHLKAF----------QDKRS  135 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~-~-~~~~~~~~~g~yVrV~G~i~~f----------~~~~~  135 (265)
                      ..|+|.|||.+++..   +.+.|.|++|.|.|..-.+... + .+....+..|+.|.|.|.|+.-          .+...
T Consensus        25 ~~V~l~GwV~~~R~~---~Fi~LrD~~g~iQvv~~~~~~~~~~~~~~~~l~~e~~V~V~G~v~~~~~~~~n~~~~tgeiE  101 (617)
T 4ah6_A           25 QEVTLCGWIQYRRQN---TFLVLRDFDGLVQVIIPQDESAASVKKILCEAPVESVVQVSGTVISRPAGQENPKMPTGEIE  101 (617)
T ss_dssp             CEEEEEEEECCCCTT---TEEEEECSSCEEEEECCCSSSSHHHHHHHHHCCSSCEEEEEEEEEECSTTCCCTTSTTTTEE
T ss_pred             CEEEEEEEeeeecCe---EEEEEEeCCcCEEEEEeCCcCcHHHHHHHhcCCCCCEEEEEEEEEeCCccccCccCCCCcEE
Confidence            479999999988643   4678999999999886433211 0 0124568999999999999752          24567


Q ss_pred             EEEEEeee
Q 024592          136 LNAYSLRP  143 (265)
Q Consensus       136 i~~~~i~~  143 (265)
                      |.+..+..
T Consensus       102 l~~~~i~v  109 (617)
T 4ah6_A          102 IKVKTAEL  109 (617)
T ss_dssp             EEEEEEEE
T ss_pred             EEEeEEEE
Confidence            77766654

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=93.00  E-value=0.19  Score=38.48  Aligned_cols=53  Identities=15%  Similarity=0.183  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        33 glt~~q~~vL~~l~~~------~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~   86 (140)
T 3hsr_A           33 DLTYTGYIVLMAIEND------EKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREE   86 (140)
T ss_dssp             TCCHHHHHHHHHSCTT------CEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEecCCC
Confidence            5778888999999752      4899999999999999999999999999999998 554

>1sr3_A APO-CCME; OB fold, beta barrel, flexible C-terminal domain, chaperone; NMR {Escherichia coli} SCOP: b.40.9.1

Probab=92.97  E-value=0.46  Score=37.14  Aligned_cols=56  Identities=25%  Similarity=0.303  Sum_probs=44.0

Q ss_pred             eEEEEEEEEEE--eeeC--CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           68 NTITVVGIVCD--MQDK--EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        68 ~~V~iVG~V~~--v~~~--~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      ..|+|-|.|..  +...  ...+.|.|.|+...|.|.+--.      .++.|++|.-|-|.|++..
T Consensus        29 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEGqgVVa~G~l~~   88 (136)
T 1sr3_A           29 QRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVSYEGI------LPDLFREGQGVVVQGELEK   88 (136)
T ss_dssp             SEEEEEEEECTTTCEECSSSSEEEEEEECSSCEEEEEEESC------CCTTCCTTSEEEEEEEECS
T ss_pred             CEEEEeeEEeCCcEEEcCCCCEEEEEEEeCCcEEEEEECCC------CCccccCCCeEEEEEEECC
Confidence            57889999973  5443  5689999999988898885432      3577899999999999853

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=92.85  E-value=0.091  Score=38.89  Aligned_cols=48  Identities=23%  Similarity=0.250  Sum_probs=40.4

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +...+|+..+..+     ...++..+|++.++++...|+++|..|.++|.|..
T Consensus        18 ~~~l~Il~~l~~~-----g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~   65 (110)
T 1q1h_A           18 DDVIDVLRILLDK-----GTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSY   65 (110)
T ss_dssp             STTHHHHHHHHHH-----CSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEE
T ss_pred             hHHHHHHHHHHHc-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4666788877543     22489999999999999999999999999999977

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=92.77  E-value=0.2  Score=38.22  Aligned_cols=53  Identities=15%  Similarity=0.214  Sum_probs=46.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        26 ~lt~~~~~iL~~l~~~------~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~~~~   79 (144)
T 1lj9_A           26 SLTRGQYLYLVRVCEN------PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDA   79 (144)
T ss_dssp             TCTTTHHHHHHHHHHS------TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHC------cCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCC
Confidence            4667788899988752      3899999999999999999999999999999998 654

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=92.77  E-value=0.19  Score=36.92  Aligned_cols=55  Identities=22%  Similarity=0.207  Sum_probs=45.4

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeec
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF--HYKSA  262 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t  262 (265)
                      +.+..||.+|..       .++++.+|++.++++.+.|...|..|.+.|.|.. -+..  +|..+
T Consensus        26 ~~r~~IL~~L~~-------~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~~gr~~~y~l~   83 (106)
T 1r1u_A           26 YNRIRIMELLSV-------SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLD   83 (106)
T ss_dssp             HHHHHHHHHHHH-------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEES
T ss_pred             HHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEC
Confidence            567789988862       2589999999999999999999999999999988 6544  45544

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=92.74  E-value=0.2  Score=38.71  Aligned_cols=53  Identities=8%  Similarity=0.248  Sum_probs=39.2

Q ss_pred             hhHHHHHHHhcCc---CCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRP---EFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~---~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++-.+|++.|+..   +.....+=+ +..++++.|+.+...||+|+..|..+|.|+.
T Consensus        14 PlY~QI~~~i~~~I~~G~l~pG~~LPser~La~~~gVSr~tVReAl~~L~~eGlv~~   70 (134)
T 4ham_A           14 PIYEQIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQELERQEVIIT   70 (134)
T ss_dssp             CHHHHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHHHHcCCCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            4555565555431   111223346 6889999999999999999999999999987

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=92.74  E-value=0.13  Score=40.09  Aligned_cols=52  Identities=13%  Similarity=0.091  Sum_probs=44.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|
T Consensus        46 ~lt~~~~~iL~~l~~~------~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~~~   98 (162)
T 2fa5_A           46 GMAIPEWRVITILALY------PGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRETH   98 (162)
T ss_dssp             CCCHHHHHHHHHHHHS------TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---
T ss_pred             CCCHHHHHHHHHHHhC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeecC
Confidence            5677888899998752      3799999999999999999999999999999987 54

>4gop_A Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=92.73  E-value=0.29  Score=37.08  Aligned_cols=66  Identities=15%  Similarity=0.253  Sum_probs=45.5

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeCCc---cEEEEEEeee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDK---RSLNAYSLRP  143 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~---~~i~~~~i~~  143 (265)
                      ..|+|||+|.++..    -+++|..++| .|.|+.-.+        ..++.+.||.|+|++..-.+.   ..|.+....+
T Consensus        19 ~~VrivGkV~~~~g----~~~~l~s~d~~~Vtv~l~~~--------~~~~~~~~vEViG~V~~~~~~~~~~~I~~~~~~~   86 (114)
T 4gop_A           19 QTVRIVGKVHKVTG----NTLLMQTSDLGNVEIAMTPD--------SDVSSSTFVEVTGKVSDAGSSFQANQIREFTTVD   86 (114)
T ss_dssp             SEEEEEEEEEEEET----TEEEEECTTSCEEEEECCSS--------CCGGGCSEEEEEEEECTTSSEEEEEEEEECSCCC
T ss_pred             CeEEEEEEEeeeCC----CEEEEEeCCCCEEEEEeCCC--------CCcccCcEEEEEEEEcCCCCcccCCeEEEEEEEe
Confidence            68999999999874    4678887764 687775322        234578999999999854332   6666655544


Q ss_pred             CC
Q 024592          144 II  145 (265)
Q Consensus       144 v~  145 (265)
                      .-
T Consensus        87 ~g   88 (114)
T 4gop_A           87 CG   88 (114)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=92.72  E-value=0.37  Score=36.66  Aligned_cols=51  Identities=16%  Similarity=0.170  Sum_probs=45.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++..+-.||.+|. .      .+++..+|++.++++...|...|+.|.+.|.|.. .|
T Consensus        34 ~l~~~~~~iL~~l~-~------~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~   85 (146)
T 2gxg_A           34 NLSYLDFLVLRATS-D------GPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRD   85 (146)
T ss_dssp             TCCHHHHHHHHHHT-T------SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCHHHHHHHHHHh-c------CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeecC
Confidence            46778888999986 3      3799999999999999999999999999999988 55

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=92.72  E-value=0.19  Score=36.96  Aligned_cols=55  Identities=16%  Similarity=0.169  Sum_probs=44.9

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeec
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF--HYKSA  262 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t  262 (265)
                      +.+..||.+|. .      .++++.+|++.++++...|...|..|.+.|.|.. -+..  .|..|
T Consensus        21 ~~r~~IL~~L~-~------~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~gr~~~y~l~   78 (114)
T 2oqg_A           21 ETRWEILTELG-R------ADQSASSLATRLPVSRQAIAKHLNALQACGLVESVKVGREIRYRAL   78 (114)
T ss_dssp             HHHHHHHHHHH-H------SCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEC
T ss_pred             hHHHHHHHHHH-c------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEecCCEEEEEec
Confidence            57788999983 2      2589999999999999999999999999999987 5543  25544

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=92.71  E-value=0.14  Score=39.27  Aligned_cols=52  Identities=13%  Similarity=0.118  Sum_probs=45.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|
T Consensus        37 ~l~~~~~~iL~~l~~~------~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~   89 (148)
T 3nrv_A           37 GIGMTEWRIISVLSSA------SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGH   89 (148)
T ss_dssp             TCCHHHHHHHHHHHHS------SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---
T ss_pred             CCCHHHHHHHHHHHcC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecC
Confidence            5778888999999753      2899999999999999999999999999999987 55

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=92.70  E-value=0.27  Score=37.64  Aligned_cols=35  Identities=11%  Similarity=0.202  Sum_probs=32.0

Q ss_pred             CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      .=+ +..+|+++|+++...|++||..|..+|.|+..
T Consensus        33 ~~lPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~   68 (126)
T 3by6_A           33 DQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTI   68 (126)
T ss_dssp             CEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            346 89999999999999999999999999999873

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=92.68  E-value=0.11  Score=38.02  Aligned_cols=43  Identities=14%  Similarity=0.125  Sum_probs=37.3

Q ss_pred             CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccC
Q 024592          221 GVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVN  264 (265)
Q Consensus       221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~  264 (265)
                      |+...+|+..+++++..++..+++|.+.|.|-..+. .|..|.-
T Consensus        20 ~~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~~~-~~~LT~k   62 (95)
T 1r7j_A           20 GSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGK-QYMLTKK   62 (95)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT-EEEECHH
T ss_pred             CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEECC-eeEEChh
Confidence            389999999999999999999999999999987433 4887754

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=92.66  E-value=0.28  Score=37.41  Aligned_cols=52  Identities=15%  Similarity=0.270  Sum_probs=45.4

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      -+++..+-.||.+|...       |++..+|++.++++...|...|+.|.+.|.|.. .|
T Consensus        34 ~~lt~~~~~iL~~l~~~-------~~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~~   86 (146)
T 3tgn_A           34 VALTNTQEHILMLLSEE-------SLTNSELARRLNVSQAAVTKAIKSLVKEGMLETSKD   86 (146)
T ss_dssp             SCCCHHHHHHHHHHTTC-------CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---
T ss_pred             cCCCHHHHHHHHHHHhC-------CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeccC
Confidence            46788999999999752       299999999999999999999999999999988 64

>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=92.64  E-value=0.074  Score=40.21  Aligned_cols=44  Identities=16%  Similarity=0.145  Sum_probs=33.2

Q ss_pred             CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEE-Eeee
Q 024592           84 PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKA  129 (265)
Q Consensus        84 t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~  129 (265)
                      ..+.+.|-|.||.|.|..|.+...  .-.+.|++|+.+.|.+ +|+.
T Consensus        40 ~~~~~~L~De~G~I~at~~~~~~~--~f~~~l~eG~vy~Is~~~V~~   84 (114)
T 1ynx_A           40 KLFNVNFLDTSGEIRATAFNDFAT--KFNEILQEGKVYYVSKAKLQP   84 (114)
T ss_dssp             EEEEEEEEETTEEEEEEECHHHHH--HHHHHSCSSSEEEEESCEEEE
T ss_pred             eEEEEEEECCCCeEEEEECHHHHH--HHHhhcccCcEEEECCcEEEE
Confidence            468889999999999999986432  2245689999888875 3444

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=92.57  E-value=0.22  Score=39.53  Aligned_cols=55  Identities=11%  Similarity=0.151  Sum_probs=46.3

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      .+++..+-.||.+|...     ..++++.+|++.++++...|...|+.|++.|.|.. .|.
T Consensus        49 ~glt~~q~~vL~~L~~~-----~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~~~  104 (166)
T 3deu_A           49 LELTQTHWVTLHNIHQL-----PPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCA  104 (166)
T ss_dssp             TTCCHHHHHHHHHHHHS-----CSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             cCCCHHHHHHHHHHHHc-----CCCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEeeCCC
Confidence            46788888999998652     34799999999999999999999999999999998 654

>1j6q_A Cytochrome C maturation protein E; all-beta protein, heme delivery,cytochrome C maturation, OB- (oligonucleotide binding)fold; NMR {Shewanella putrefaciens} SCOP: b.40.9.1 PDB: 1lm0_A

Probab=92.56  E-value=0.63  Score=36.40  Aligned_cols=65  Identities=22%  Similarity=0.182  Sum_probs=47.9

Q ss_pred             eEEEEEEEEEE--eeeC--CCeEEEEEEc-CCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEe
Q 024592           68 NTITVVGIVCD--MQDK--EPQFIFLIDD-GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSL  141 (265)
Q Consensus        68 ~~V~iVG~V~~--v~~~--~t~~~y~LdD-gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i  141 (265)
                      ..|+|.|.|..  +...  ...+.|.|.| +...|.|.+--.      .++.|++|.-|-|.|++..   .-.+.|..|
T Consensus        33 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~~v~V~Y~Gi------lPDlFrEGqgVVa~G~l~~---~g~F~A~eV  102 (136)
T 1j6q_A           33 QRIRVGGMVTVGSMVRDPNSLHVQFAVHDSLGGEILVTYDDL------LPDLFREGQGIVAQGVLGE---DGKLAATEV  102 (136)
T ss_dssp             CEEEEEEEECTTCCEECTTSSCEEEEEECTTCCCEEEEECSC------CTTSCCSSSEEEEEEEECS---TTSEEEEEE
T ss_pred             CEEEEeEEEeCCcEEecCCCCEEEEEEEcCCCCEEEEEECCC------CCccccCCCeEEEEEEECC---CCeEEEEEE
Confidence            57899999963  5543  5689999999 777898885432      3577999999999999853   234555554

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=92.49  E-value=0.18  Score=45.09  Aligned_cols=58  Identities=16%  Similarity=0.192  Sum_probs=47.2

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceee
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKS  261 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~  261 (265)
                      ++.+++||++|++.    ...-++-++|+++|+++...|.+.|..|.++|..-. +...-|+.
T Consensus         2 ~~~~~~iL~~L~~~----~g~~~Sg~eLa~~lgvSr~aV~k~i~~L~~~G~~i~~~~~~GY~L   60 (323)
T 3rkx_A            2 SKYSQDVLQLLYKN----KPNYISGQSIAESLNISRTAVKKVIDQLKLEGCKIDSVNHKGHLL   60 (323)
T ss_dssp             -CHHHHHHHHHHHH----TTSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEEETTTEEEE
T ss_pred             chHHHHHHHHHHhC----CCCccCHHHHHHHHCCCHHHHHHHHHHHHhcCCeEEEeCCCeEEE
Confidence            45788999999752    234689999999999999999999999999999555 66666664

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=92.42  E-value=0.11  Score=39.49  Aligned_cols=55  Identities=15%  Similarity=0.163  Sum_probs=47.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...    .+.+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        34 ~lt~~q~~vL~~l~~~----~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   89 (127)
T 2frh_A           34 SISFEEFAVLTYISEN----KEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNE   89 (127)
T ss_dssp             CCCHHHHHHHHHHHHT----CCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCS
T ss_pred             CCCHHHHHHHHHHHhc----cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence            5677888899998753    245899999999999999999999999999999987 554

>2pi2_E Replication protein A 14 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2pqa_B 2z6k_C

Probab=92.34  E-value=1.4  Score=34.64  Aligned_cols=66  Identities=18%  Similarity=0.227  Sum_probs=45.1

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeCCC
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIID  146 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v~d  146 (265)
                      ..|+|||+|.++....  -.++|..+.| .|.|+.-..        -....+.||.|+|++..   +..|.+..+.+..|
T Consensus        44 k~VriVGkV~~~~~~G--~~~~l~s~Dg~~VtV~l~~p--------L~~~~~~~VEViG~V~~---~~tI~~~~~~~fGd  110 (142)
T 2pi2_E           44 KPVCFVGRLEKIHPTG--KMFILSDGEGKNGTIELMEP--------LDEEISGIVEVVGRVTA---KATILCTSYVQFKE  110 (142)
T ss_dssp             CEEEEEEEEEEECTTS--SEEEEECTTSCEEEEECSSC--------CSSCCCSEEEEEEEECT---TSCEEEEEEEECCC
T ss_pred             CEEEEEEEEeEEcCCC--CEEEEEeCCCcEEEEEeCCC--------CCccCCCEEEEEEEECC---CCcEEEEEEEecCC
Confidence            6899999999985433  4456776654 688775211        01134789999999955   56777777777665

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=92.33  E-value=0.18  Score=38.75  Aligned_cols=57  Identities=7%  Similarity=-0.020  Sum_probs=43.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++.-+-.||-.|.... .....+.+..+|++++++++.+|..+|+.|++.|.|-- .+
T Consensus        29 gLt~~e~~vll~L~~~~-~~~~~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~~   86 (128)
T 2vn2_A           29 GLGEGELVLLLHMQSFF-EEGVLFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEEH   86 (128)
T ss_dssp             TCCHHHHHHHHHHHHHH-TTTCSSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEECC-
T ss_pred             CCCHHHHHHHHHHHHHH-hcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeE
Confidence            46666666776665421 12345689999999999999999999999999999977 44

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=92.31  E-value=0.22  Score=42.33  Aligned_cols=53  Identities=19%  Similarity=0.257  Sum_probs=45.2

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      .||++|.+.     +.++++.||++.++++...+...|..|.+.|.|.. -++..|..+
T Consensus        10 ~iL~~l~~~-----~~~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~~~~~Y~lg   63 (241)
T 2xrn_A           10 SIMRALGSH-----PHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGFRLG   63 (241)
T ss_dssp             HHHHHHHTC-----TTCEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEECGGGCEEEEC
T ss_pred             HHHHHHHhC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCeEEEC
Confidence            478887652     34799999999999999999999999999999998 666788764

>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: a.4.5.47

Probab=92.29  E-value=0.1  Score=37.48  Aligned_cols=39  Identities=15%  Similarity=0.239  Sum_probs=36.4

Q ss_pred             CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      -.=++++.|++.|+++++++.+.|..|+.+|.|+- ||.-
T Consensus        28 Y~~Isl~~La~ll~ls~~~vE~~ls~mI~~~~l~akIDq~   67 (84)
T 1ufm_A           28 YNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQI   67 (84)
T ss_dssp             CSEEEHHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETT
T ss_pred             cCeeeHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEEEeCC
Confidence            45789999999999999999999999999999999 9974

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=92.29  E-value=0.24  Score=38.08  Aligned_cols=53  Identities=11%  Similarity=0.147  Sum_probs=46.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        37 ~lt~~~~~iL~~l~~~------~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~~~   90 (152)
T 3bj6_A           37 GVTVGQRAILEGLSLT------PGATAPQLGAALQMKRQYISRILQEVQRAGLIERRTNP   90 (152)
T ss_dssp             TCCHHHHHHHHHHHHS------TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             CCCHHHHHHHHHHHhC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence            5677888999999753      3799999999999999999999999999999998 553

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=92.24  E-value=0.2  Score=38.68  Aligned_cols=54  Identities=19%  Similarity=0.277  Sum_probs=45.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++.-+-.||.+|...     +.+++..+|++.++++...|...|+.|++.|.|.. .|.
T Consensus        36 glt~~q~~vL~~l~~~-----~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~~~~   90 (150)
T 3fm5_A           36 GLRVRSYSVLVLACEQ-----AEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDP   90 (150)
T ss_dssp             TCCHHHHHHHHHHHHS-----TTCCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC----
T ss_pred             CCCHHHHHHHHHHHhC-----CCCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeeCCc
Confidence            5677888899988642     34689999999999999999999999999999988 554

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=92.22  E-value=0.26  Score=35.50  Aligned_cols=49  Identities=18%  Similarity=0.238  Sum_probs=42.1

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +.+..|+.+|.+       .++++.+|++.++++...|...|..|.+.|.|-. -+.
T Consensus        23 ~~r~~Il~~L~~-------~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g   72 (98)
T 3jth_A           23 ERRLQILCMLHN-------QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKEA   72 (98)
T ss_dssp             HHHHHHHHHTTT-------SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             HHHHHHHHHHhc-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            567788888864       3689999999999999999999999999999976 443

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=92.20  E-value=0.27  Score=37.58  Aligned_cols=53  Identities=17%  Similarity=0.109  Sum_probs=46.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        28 ~lt~~q~~iL~~l~~~------~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   81 (145)
T 3g3z_A           28 DLNYNLFAVLYTLATE------GSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQEGE   81 (145)
T ss_dssp             TCCHHHHHHHHHHHHH------CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCCS
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeccCC
Confidence            5778888999999753      2699999999999999999999999999999998 554

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=92.20  E-value=0.4  Score=36.91  Aligned_cols=35  Identities=17%  Similarity=0.189  Sum_probs=31.8

Q ss_pred             CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      .=+ +..+|+++|+++...||+||..|..+|.|+..
T Consensus        26 ~~LPse~~La~~~gvSr~tVr~Al~~L~~~Gli~~~   61 (129)
T 2ek5_A           26 QRVPSTNELAAFHRINPATARNGLTLLVEAGILYKK   61 (129)
T ss_dssp             SCBCCHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEE
T ss_pred             CcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence            345 78999999999999999999999999999873

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=92.13  E-value=0.34  Score=36.86  Aligned_cols=54  Identities=15%  Similarity=0.100  Sum_probs=45.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+..||.+|...     +.+++..+|++.++++.+.|...|+.|.+.|.|.. .|.
T Consensus        23 gl~~~~~~il~~L~~~-----~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~~~~   77 (152)
T 1ku9_A           23 GLNKSVGAVYAILYLS-----DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIK   77 (152)
T ss_dssp             TCCHHHHHHHHHHHHC-----SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             CCChhHHHHHHHHHHc-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecC
Confidence            4667788899888421     24799999999999999999999999999999988 543

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=92.11  E-value=0.24  Score=37.68  Aligned_cols=58  Identities=19%  Similarity=0.101  Sum_probs=43.1

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec-CCceeecc
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID-EFHYKSAV  263 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD-d~hyk~t~  263 (265)
                      .-.||.+|...   ..+..++..+|+++++++...++++|..|...|.|.+ -. .-.|..+.
T Consensus        11 al~iL~~la~~---~~~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~~g~~ggy~L~~   70 (129)
T 2y75_A           11 GLTIMIELAKK---HGEGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIRGAYGGYVLGS   70 (129)
T ss_dssp             HHHHHHHHHHT---TTSCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC----CCEEESS
T ss_pred             HHHHHHHHHhC---CCCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEecCCCCCceEeCC
Confidence            34566666542   1245689999999999999999999999999999988 33 34576543

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=92.08  E-value=0.18  Score=38.59  Aligned_cols=53  Identities=13%  Similarity=0.120  Sum_probs=46.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++..+-.||.+|...      .+ +..+|++.++++...|...|+.|.+.|.|.. .|..
T Consensus        34 ~lt~~~~~iL~~l~~~------~~-~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~   87 (144)
T 3f3x_A           34 NLSYLDFSILKATSEE------PR-SMVYLANRYFVTQSAITAAVDKLEAKGLVRRIRDSK   87 (144)
T ss_dssp             SCCHHHHHHHHHHHHS------CE-EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHC------CC-CHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence            5677888899999753      24 9999999999999999999999999999998 6654

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=92.05  E-value=0.16  Score=38.76  Aligned_cols=53  Identities=15%  Similarity=0.212  Sum_probs=42.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        34 ~lt~~~~~vL~~l~~~------~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~   87 (142)
T 3ech_A           34 DLTPPDVHVLKLIDEQ------RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNP   87 (142)
T ss_dssp             CCCHHHHHHHHHHHHT------TTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC----
T ss_pred             CCCHHHHHHHHHHHhC------CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeeccCC
Confidence            5778888999999763      3899999999999999999999999999999998 654

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=91.95  E-value=0.23  Score=38.71  Aligned_cols=53  Identities=23%  Similarity=0.261  Sum_probs=46.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.- .|.
T Consensus        47 ~lt~~q~~vL~~l~~~------~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~  100 (159)
T 3s2w_A           47 GIGSGQFPFLMRLYRE------DGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQRDE  100 (159)
T ss_dssp             TCCTTTHHHHHHHHHS------CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            4667778899998652      4899999999999999999999999999999998 654

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=91.94  E-value=0.21  Score=38.11  Aligned_cols=53  Identities=11%  Similarity=0.095  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        34 ~lt~~~~~iL~~l~~~------~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~   87 (143)
T 3oop_A           34 DVTPEQWSVLEGIEAN------EPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREIST   87 (143)
T ss_dssp             SSCHHHHHHHHHHHHH------SSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeeccCCC
Confidence            5678888999999753      4899999999999999999999999999999998 553

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=91.94  E-value=0.23  Score=37.57  Aligned_cols=53  Identities=13%  Similarity=0.141  Sum_probs=46.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        33 ~lt~~~~~iL~~l~~~------~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~~~   86 (142)
T 2fbi_A           33 GLTEQQWRVIRILRQQ------GEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAP   86 (142)
T ss_dssp             TCCHHHHHHHHHHHHH------CSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCC
Confidence            4677888899998753      3799999999999999999999999999999988 554

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=91.92  E-value=0.15  Score=36.51  Aligned_cols=47  Identities=21%  Similarity=0.239  Sum_probs=41.5

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+..||.+|...      .+++..+|++.++++...|...|..|.+.|.|..
T Consensus        16 ~~~~~iL~~L~~~------~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~   62 (100)
T 1ub9_A           16 PVRLGIMIFLLPR------RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKT   62 (100)
T ss_dssp             HHHHHHHHHHHHH------SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             hHHHHHHHHHHhc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5677899888642      3689999999999999999999999999999986

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=91.91  E-value=0.26  Score=38.43  Aligned_cols=53  Identities=19%  Similarity=0.239  Sum_probs=46.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        49 ~lt~~~~~iL~~l~~~------~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~  102 (162)
T 3cjn_A           49 GLSTAKMRALAILSAK------DGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRREVDS  102 (162)
T ss_dssp             TCCHHHHHHHHHHHHS------CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecCCC
Confidence            5677888999999752      3799999999999999999999999999999988 553

>1txy_A Primosomal replication protein N; OB fold, dimer, DNA binding protein; 2.00A {Escherichia coli} SCOP: b.40.4.3 PDB: 1woc_A 2pnh_A 4apv_A

Probab=91.90  E-value=1.8  Score=31.79  Aligned_cols=76  Identities=21%  Similarity=0.356  Sum_probs=47.4

Q ss_pred             EeEEEEEEEEEEe---eeC---CCeEEEEEE-----cCCCe-------EEEEEecccccccccccccCCCCEEEEEEEee
Q 024592           67 VNTITVVGIVCDM---QDK---EPQFIFLID-----DGTGR-------IECSRWAHEQMEFNEVNQISKGMYVRVYGHLK  128 (265)
Q Consensus        67 v~~V~iVG~V~~v---~~~---~t~~~y~Ld-----DgTG~-------I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~  128 (265)
                      ++.|.|+|.+..-   +..   ...+.|.|.     +.|+-       |.|..|-..+.  ....-+..|+.|.|.|+|+
T Consensus         2 ~N~v~L~G~l~~dpelR~t~~G~~v~~f~lA~~~~~~~~~~~r~~~~~~~vv~~g~~Ae--~~~~~l~KG~~V~V~G~L~   79 (104)
T 1txy_A            2 TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQ--AITHSITVGSRITVQGFIS   79 (104)
T ss_dssp             CEEEEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESSTTH--HHHTTCCTTCEEEEEEEEE
T ss_pred             cEEEEEEEEECCCceEEECCCCCEEEEEEEEEeCccccCCceeceeEEEEEEEEhHHHH--HHHhhCCCCCEEEEEEEEE
Confidence            3678888888653   211   234555552     34677       99999976442  1234589999999999998


Q ss_pred             eeC---Cc--cEEEEEEeeeC
Q 024592          129 AFQ---DK--RSLNAYSLRPI  144 (265)
Q Consensus       129 ~f~---~~--~~i~~~~i~~v  144 (265)
                      .-.   |.  ..|.+..|..+
T Consensus        80 ~~~~~~G~~r~~v~~~~i~~l  100 (104)
T 1txy_A           80 CHKAKNGLSKMVLHAEQIELI  100 (104)
T ss_dssp             C--------CCEEEEEEEEEC
T ss_pred             eccCCCCCEEEEEEEEEEEEC
Confidence            742   21  23566666555

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=91.89  E-value=0.27  Score=37.66  Aligned_cols=53  Identities=17%  Similarity=0.236  Sum_probs=46.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        39 ~l~~~~~~iL~~l~~~------~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   92 (150)
T 2rdp_A           39 PITPPQFVALQWLLEE------GDLTVGELSNKMYLACSTTTDLVDRMERNGLVARVRDE   92 (150)
T ss_dssp             SSCHHHHHHHHHHHHH------CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCC
Confidence            5677888899998753      3799999999999999999999999999999988 553

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=91.85  E-value=0.33  Score=36.65  Aligned_cols=53  Identities=15%  Similarity=0.115  Sum_probs=46.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        31 ~lt~~~~~iL~~l~~~------~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~   84 (138)
T 1jgs_A           31 DITAAQFKVLCSIRCA------ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP   84 (138)
T ss_dssp             TSCHHHHHHHHHHHHH------SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             CCCHHHHHHHHHHHhc------CCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCc
Confidence            4677888899998653      3789999999999999999999999999999998 554

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=91.83  E-value=0.46  Score=35.96  Aligned_cols=52  Identities=10%  Similarity=0.050  Sum_probs=42.3

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCcee
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYK  260 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk  260 (265)
                      +..+|++.++.       .+..+.++++.++++++.+++.|..|..+|.|..++++.|-
T Consensus         8 l~~~i~~~~~~-------~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~~~~~~   59 (121)
T 2pjp_A            8 IWQKAEPLFGD-------EPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYY   59 (121)
T ss_dssp             HHHHHGGGCSS-------SCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEETTEEE
T ss_pred             HHHHHHHHHHh-------CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCceE
Confidence            44555655532       46799999999999999999999999999999996666654

>1jmc_A Protein (replication protein A (RPA)); human ssDNA binding replication protein A(RPA), single stranded DNA-binding protein, protein-ssDNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 1fgu_A

Probab=91.81  E-value=0.36  Score=40.94  Aligned_cols=66  Identities=18%  Similarity=0.402  Sum_probs=46.4

Q ss_pred             eEEEEEEEEEEeee------C--C---CeEEEEEEcCCCe-EEEEEecccccccccccccCCCCEEEEEE-EeeeeCCcc
Q 024592           68 NTITVVGIVCDMQD------K--E---PQFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQDKR  134 (265)
Q Consensus        68 ~~V~iVG~V~~v~~------~--~---t~~~y~LdDgTG~-I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~~~~  134 (265)
                      ..|.|+|+|.++..      .  .   ....+.|.|.||. |.|.+|.+.+..    .....|..|.+.| +++.|++ +
T Consensus       139 ~~vDViG~V~~v~~~~~~~~k~~g~~~~~r~~~l~D~sg~~i~~tLWg~~a~~----~~~~~~~vv~i~~~~v~~f~g-~  213 (246)
T 1jmc_A          139 SLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADK----FDGSRQPVLAIKGARVSDFGG-R  213 (246)
T ss_dssp             CEEEEEEEEEEECCCEEEEETTTTEEEEEEEEEEECTTCCEEEEEEEHHHHHH----CCCTTCCEEEEEEEEEECTTS-S
T ss_pred             CceeEEEEEEEecCeEEEEEecCCCccEEEEEEEECCCCCEEEEEEEchhhhh----cccCCCCEEEEEEEEEEecCC-e
Confidence            45788898887643      1  1   3678899999995 999999875431    1246677777665 4778854 6


Q ss_pred             EEEE
Q 024592          135 SLNA  138 (265)
Q Consensus       135 ~i~~  138 (265)
                      .|++
T Consensus       214 ~ls~  217 (246)
T 1jmc_A          214 SLSV  217 (246)
T ss_dssp             EEEC
T ss_pred             EEEe
Confidence            7765

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=91.78  E-value=0.51  Score=34.16  Aligned_cols=56  Identities=18%  Similarity=0.210  Sum_probs=45.5

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeecc
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF--HYKSAV  263 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t~  263 (265)
                      +.+..||..|.+       ..+++.+|++.++++...|...|..|.+.|.|-. -+..  +|..|.
T Consensus        23 ~~r~~Il~~L~~-------~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~   81 (102)
T 3pqk_A           23 PVRLMLVCTLVE-------GEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTE   81 (102)
T ss_dssp             HHHHHHHHHHHT-------CCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECSSSCCEEEECS
T ss_pred             HHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECc
Confidence            567789998864       1489999999999999999999999999999987 5443  455554

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=91.71  E-value=0.26  Score=38.68  Aligned_cols=53  Identities=13%  Similarity=0.072  Sum_probs=47.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|.. .|.
T Consensus        43 glt~~q~~iL~~l~~~------~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   96 (162)
T 3k0l_A           43 EISLPQFTALSVLAAK------PNLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDP   96 (162)
T ss_dssp             TCCHHHHHHHHHHHHC------TTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCC
Confidence            5778888999999753      3899999999999999999999999999999998 654

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=91.63  E-value=0.22  Score=38.46  Aligned_cols=53  Identities=11%  Similarity=0.204  Sum_probs=46.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        34 ~l~~~~~~iL~~l~~~------~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   87 (155)
T 1s3j_A           34 GVTPAQLFVLASLKKH------GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNT   87 (155)
T ss_dssp             TCCHHHHHHHHHHHHH------SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCC
Confidence            4677888899999753      3799999999999999999999999999999998 553

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=91.58  E-value=0.25  Score=39.14  Aligned_cols=53  Identities=9%  Similarity=0.014  Sum_probs=46.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        42 ~lt~~~~~iL~~L~~~------~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~   95 (168)
T 2nyx_A           42 NITIPQFRTLVILSNH------GPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHP   95 (168)
T ss_dssp             SCCHHHHHHHHHHHHH------CSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            5778888999999753      3799999999999999999999999999999988 654

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=91.57  E-value=0.24  Score=38.29  Aligned_cols=50  Identities=10%  Similarity=0.117  Sum_probs=44.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|++.|.|..
T Consensus        38 ~lt~~~~~iL~~l~~~------~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           38 GLTIQQLAMINVIYST------PGISVADLTKRLIITGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             TCCHHHHHHHHHHHHS------TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4677888899999753      3799999999999999999999999999999975

>3edp_A LIN2111 protein; APC88337, listeria innocua CLIP11262, structural GE PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.09A {Listeria innocua}

Probab=91.55  E-value=0.41  Score=40.60  Aligned_cols=51  Identities=18%  Similarity=0.219  Sum_probs=37.5

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+.|.+.|.+.. .....-+ +..+++++++.+...||+||+.|.++|.|+.
T Consensus        14 i~~~l~~~I~~g~-~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~   65 (236)
T 3edp_A           14 IASKIKDSINRDE-YKTGMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVR   65 (236)
T ss_dssp             HHHHHHHHHHTTS-SCCCC--CCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhCC-CCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4444555554421 1223456 7899999999999999999999999999987

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=91.53  E-value=0.23  Score=37.60  Aligned_cols=56  Identities=13%  Similarity=0.071  Sum_probs=43.5

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeec
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF--HYKSA  262 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t  262 (265)
                      +.+..||.+|...      .++++.+|++.++++.+.|...|..|.+.|.|-. -+..  .|..+
T Consensus        42 ~~rl~IL~~L~~~------~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~~gr~~~y~l~  100 (122)
T 1u2w_A           42 ENRAKITYALCQD------EELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLG  100 (122)
T ss_dssp             HHHHHHHHHHHHS------SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC----CCEEEES
T ss_pred             HHHHHHHHHHHHC------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEECCEEEEEEC
Confidence            4566788888642      3689999999999999999999999999999987 5433  45554

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=91.48  E-value=0.11  Score=40.00  Aligned_cols=44  Identities=7%  Similarity=0.024  Sum_probs=37.3

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV  263 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~  263 (265)
                      .++++.+|++.++++...|..+|+.|...|.|...-+-.|..|.
T Consensus        21 ~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~~~~~~~LT~   64 (142)
T 1on2_A           21 GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTS   64 (142)
T ss_dssp             SSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTTEEEECH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeeCceEEEch
Confidence            37999999999999999999999999999999873334566553

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=91.37  E-value=0.24  Score=42.66  Aligned_cols=53  Identities=9%  Similarity=0.182  Sum_probs=44.1

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      .||++|.+     .+.++++.||++.++++.+.+...|..|.+.|.|.. -+...|...
T Consensus        10 ~IL~~l~~-----~~~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~~~~~~~Y~lG   63 (260)
T 3r4k_A           10 TLLTYFNH-----GRLEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQVEGARSYRLG   63 (260)
T ss_dssp             HHHTTCBT-----TBSEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEECSSSSEEEEC
T ss_pred             HHHHHHhh-----CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEcC
Confidence            35666654     246899999999999999999999999999999998 555788754

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=91.35  E-value=0.77  Score=33.71  Aligned_cols=58  Identities=12%  Similarity=0.256  Sum_probs=45.8

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEe-ecCC-----ceeeccCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDEF-----HYKSAVNA  265 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYs-iDd~-----hyk~t~~~  265 (265)
                      ...-.||..|..       ..+++.+|++.+ +++...+...|+.|.+.|.|.. .|..     .|..|..|
T Consensus        14 ~~~~~IL~~L~~-------~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~~G   78 (107)
T 2hzt_A           14 KWKXVILXHLTH-------GKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYG   78 (107)
T ss_dssp             TTHHHHHHHHTT-------CCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTG
T ss_pred             ccHHHHHHHHHh-------CCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECccH
Confidence            345567777742       258999999999 9999999999999999999998 6542     46666543

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=91.32  E-value=0.21  Score=37.64  Aligned_cols=53  Identities=8%  Similarity=0.171  Sum_probs=46.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        30 ~l~~~~~~iL~~l~~~------~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~   83 (139)
T 3bja_A           30 DISYVQFGVIQVLAKS------GKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNP   83 (139)
T ss_dssp             TCCHHHHHHHHHHHHS------CSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeeccCC
Confidence            5677888899999652      3799999999999999999999999999999988 553

>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase; 2.60A {Coxiella burnetii}

Probab=91.22  E-value=1.2  Score=35.52  Aligned_cols=79  Identities=15%  Similarity=0.188  Sum_probs=49.0

Q ss_pred             EEeEEEEEEEEEE---eeeC---CCeEEEEEE------cC-CC-------eEEEEEecccccccccccccCCCCEEEEEE
Q 024592           66 DVNTITVVGIVCD---MQDK---EPQFIFLID------DG-TG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYG  125 (265)
Q Consensus        66 ~v~~V~iVG~V~~---v~~~---~t~~~y~Ld------Dg-TG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G  125 (265)
                      .++.|.|+|+|..   ++..   ...+.|+|.      |. +|       -|.|..|...+.  .....|+.|+.|.|.|
T Consensus         7 ~mN~V~LiGrL~~dPelr~t~~G~~v~~f~lA~~~~~~d~~~Ge~~e~t~~i~vv~wg~~Ae--~~~~~l~KG~~V~VeG   84 (158)
T 3tqy_A            7 GVNKVILIGNLGQDPEVRYTPNGNAVANVTLATSTTWRDKQTGELQERTEWHRIAFFNRLAE--IVGEYLRKGSKIYIEG   84 (158)
T ss_dssp             CEEEEEEEEEESSSCEEEECTTCCEEEEEEEEEEEEEECTTTCCEEEEEEEEEEEEETHHHH--HHHHHCCTTCEEEEEE
T ss_pred             ccCEEEEEEEECCCCEEEECCCCCEEEEEEEEEcCceeccCCCCEeeeeEEEEEEEEhHHHH--HHHhhcCCCCEEEEEE
Confidence            4788999999965   2222   235556552      22 44       378888865332  1223489999999999


Q ss_pred             Eeee--eC---Cc----cEEEEEEeeeCCC
Q 024592          126 HLKA--FQ---DK----RSLNAYSLRPIID  146 (265)
Q Consensus       126 ~i~~--f~---~~----~~i~~~~i~~v~d  146 (265)
                      +|+.  |.   |+    ..|.+..|..+..
T Consensus        85 ~L~~~~~~dkdG~~r~~~eV~a~~i~~L~~  114 (158)
T 3tqy_A           85 SLRTRKWQDKNGVDRYTTEIIANEMHMLDN  114 (158)
T ss_dssp             EEEEEEEECSSSCEEEEEEEEEEEEEECC-
T ss_pred             EEEeeeEECCCCCEEEEEEEEEeEEEEccC
Confidence            9985  53   32    3566666666654

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=91.20  E-value=0.27  Score=38.13  Aligned_cols=53  Identities=15%  Similarity=0.214  Sum_probs=46.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|++.|.|.. .|.
T Consensus        41 ~lt~~~~~iL~~l~~~------~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~   94 (154)
T 2eth_A           41 DMKTTELYAFLYVALF------GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDP   94 (154)
T ss_dssp             HSBHHHHHHHHHHHHH------CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCC
Confidence            4677888999999753      2799999999999999999999999999999988 553

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=91.11  E-value=0.45  Score=37.19  Aligned_cols=50  Identities=18%  Similarity=0.260  Sum_probs=43.9

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++.+..||++|.+.     +.-++.++|.+.+     +++...|-..|+.|.+.|.|-.
T Consensus        20 ~T~qR~~Il~~L~~~-----~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   74 (145)
T 2fe3_A           20 ITPQRHAILEYLVNS-----MAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKE   74 (145)
T ss_dssp             CCHHHHHHHHHHHHC-----SSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHhC-----CCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEE
Confidence            567888999999753     3468999999999     5999999999999999999988

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=91.05  E-value=0.34  Score=41.63  Aligned_cols=51  Identities=14%  Similarity=0.262  Sum_probs=41.7

Q ss_pred             HHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          206 VLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       206 Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      ||++|..     .+.++++.||++.++++...+...|..|.+.|.|.. -+. .|..+
T Consensus        28 iL~~l~~-----~~~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~~~~-~Y~lg   79 (260)
T 2o0y_A           28 LLELFDA-----AHPTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSRADG-SYSLG   79 (260)
T ss_dssp             HHTTCBT-----TBSSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEECTTS-CEEEC
T ss_pred             HHHHHhh-----CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCC-eEEec
Confidence            5555543     235899999999999999999999999999999988 444 78753

>1ucr_A Protein DSVD; dissimilatory sulfite reductase D, DNA binding motif, sulfate-reducing bacteria, winged-helix motif, unknown function; 1.20A {Desulfovibrio vulgaris} SCOP: a.4.5.45 PDB: 1wq2_A

Probab=91.05  E-value=0.25  Score=34.70  Aligned_cols=51  Identities=16%  Similarity=0.202  Sum_probs=40.4

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEE
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IY  252 (265)
                      .++++.|+++|+..+...  .=.=+.++++.+ ...+.+|.+++..|++||.+-
T Consensus         2 ee~K~~Ile~l~~k~~~K--skfYf~D~~k~~P~~k~r~vKK~~~~LV~Eg~le   53 (78)
T 1ucr_A            2 EEAKQKVVDFLNSKSGSK--SKFYFNDFTDLFPDMKQREVKKILTALVNDEVLE   53 (78)
T ss_dssp             CHHHHHHHHHHSSHHHHS--SCEEHHHHHHHCTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             hHHHHHHHHHHHhccccc--ccchHHHHHHHccccCHHHHHHHHHHHHhcCceE
Confidence            468999999998742111  124468999999 899999999999999999874

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=90.99  E-value=0.46  Score=31.52  Aligned_cols=44  Identities=20%  Similarity=0.346  Sum_probs=37.9

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+|..|.+.     ..|++.-|++.+++.+.++-|.+|+.|..+|.+--
T Consensus         7 aLLall~s~-----~QGMTaGEVAA~f~w~Le~ar~aLeqLf~~G~LRK   50 (68)
T 3i71_A            7 ELLALLTSV-----RQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRK   50 (68)
T ss_dssp             HHHHHHHHC-----TTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHH-----hccccHHHHHHHhCCcHHHHHHHHHHHHhcchhhh
Confidence            566677653     35999999999999999999999999999998754

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=90.93  E-value=0.38  Score=38.96  Aligned_cols=55  Identities=13%  Similarity=0.068  Sum_probs=47.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...    .+.+++..+|++.++++...|...|..|...|.|.. .|.
T Consensus        38 ~lt~~q~~vL~~L~~~----~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~   93 (189)
T 3nqo_A           38 ILTSRQYMTILSILHL----PEEETTLNNIARKMGTSKQNINRLVANLEKNGYVDVIPSP   93 (189)
T ss_dssp             SSCHHHHHHHHHHHHS----CGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             cCCHHHHHHHHHHHhc----cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            4778899999998753    235899999999999999999999999999999998 654

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=90.89  E-value=0.25  Score=38.18  Aligned_cols=53  Identities=21%  Similarity=0.195  Sum_probs=45.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|.. .|.
T Consensus        38 ~lt~~q~~iL~~l~~~------~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~   91 (149)
T 4hbl_A           38 GITYSQYLVMLTLWEE------NPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRERQQ   91 (149)
T ss_dssp             TCCHHHHHHHHHHHHS------SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC----
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeCCCC
Confidence            5778888999999652      4899999999999999999999999999999998 553

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=90.79  E-value=0.26  Score=45.83  Aligned_cols=70  Identities=16%  Similarity=0.274  Sum_probs=47.3

Q ss_pred             eEEEEEEEEEEeee------C-----CCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEE-EeeeeCCcc
Q 024592           68 NTITVVGIVCDMQD------K-----EPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQDKR  134 (265)
Q Consensus        68 ~~V~iVG~V~~v~~------~-----~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~~~~  134 (265)
                      ..|.|+|.|.++..      .     .....++|.|.|| +|.|.+|.+.+..-........|..|.+.| +|+.|+|+ 
T Consensus       134 ~~vDViG~V~~v~~~~~i~~k~~g~~~~kr~i~L~D~sg~~i~~tLWg~~A~~f~~~~~~~~~~VV~i~~~kV~~f~G~-  212 (444)
T 4gop_C          134 QQCDVIGILDSYGELSEIVSKASQRPVQKRELTLVDQGNRSVKLTLWGKTAETFPTNAGVDEKPVLAFKGVKVGDFGGR-  212 (444)
T ss_dssp             CCCBEEEEEEEECCCEEECCTTTCSCEEEEEEEEECTTCBEEEEEEEHHHHHTSTTSTTSSSCCEEEEESCEEECTTSS-
T ss_pred             CceEEEEEEEEcCCcEEEEEccCCceeeEEEEEEEeCCCCEEEEEEEhhhhhhhhhhhccCCCCEEEEEeEEEeecCCe-
Confidence            35677888877642      1     1367899999999 799999987543211111256778777665 58889985 


Q ss_pred             EEEE
Q 024592          135 SLNA  138 (265)
Q Consensus       135 ~i~~  138 (265)
                      .|++
T Consensus       213 ~ls~  216 (444)
T 4gop_C          213 SLSM  216 (444)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            6665

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=90.77  E-value=0.14  Score=39.55  Aligned_cols=55  Identities=13%  Similarity=0.216  Sum_probs=40.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...    .+.+++..+|++.++++...|...|+.|...|.|.. .|.
T Consensus        38 glt~~q~~vL~~l~~~----~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~   93 (148)
T 3jw4_A           38 GLNSQQGRMIGYIYEN----QESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPE   93 (148)
T ss_dssp             TCCHHHHHHHHHHHHH----TTTCCCHHHHHHC------CHHHHHHHHHHTTSBCCC---
T ss_pred             CCCHHHHHHHHHHHhC----CCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeeCCC
Confidence            5778888999999763    236899999999999999999999999999999987 553

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=90.56  E-value=0.58  Score=36.10  Aligned_cols=51  Identities=12%  Similarity=0.188  Sum_probs=43.8

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++.+..||++|.+.    .+.-++.++|.+.+     +++...|-..|+.|.+.|.|-.
T Consensus        16 ~T~qR~~Il~~L~~~----~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   71 (136)
T 1mzb_A           16 VTLPRVKILQMLDSA----EQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVR   71 (136)
T ss_dssp             CCHHHHHHHHHHHCC-----CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHHHHHhC----CCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEE
Confidence            567888999999863    11468999999998     5999999999999999999987

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=90.47  E-value=0.42  Score=36.68  Aligned_cols=49  Identities=14%  Similarity=0.237  Sum_probs=42.6

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++.+..||++|.+.     +.-++.++|.+.+     +++...|-..|+.|.+.|.|-.
T Consensus        10 T~qR~~Il~~l~~~-----~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~   63 (131)
T 2o03_A           10 TRQRAAISTLLETL-----DDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDT   63 (131)
T ss_dssp             HHHHHHHHHHHHHC-----CSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEE
T ss_pred             CHHHHHHHHHHHhC-----CCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEE
Confidence            56778899999752     3468999999998     6999999999999999999988

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=90.47  E-value=0.33  Score=37.96  Aligned_cols=53  Identities=9%  Similarity=0.060  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        50 glt~~q~~vL~~l~~~------~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~  103 (161)
T 3e6m_A           50 KLPTPKLRLLSSLSAY------GELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISD  103 (161)
T ss_dssp             TCCHHHHHHHHHHHHH------SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC--
T ss_pred             CCCHHHHHHHHHHHhC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCc
Confidence            5777888899999763      3899999999999999999999999999999998 553

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=90.47  E-value=0.23  Score=39.15  Aligned_cols=55  Identities=18%  Similarity=0.230  Sum_probs=45.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...    .+.+++..+|++.++++...|...|+.|+..|+|.. .|.
T Consensus        43 glt~~q~~vL~~l~~~----~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   98 (168)
T 3u2r_A           43 ELSAQQYNTLRLLRSV----HPEGMATLQIADRLISRAPDITRLIDRLDDRGLVLRTRKP   98 (168)
T ss_dssp             TCCHHHHHHHHHHHHH----TTSCEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHhc----CCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeecCCC
Confidence            5778888899999763    135899999999999999999999999999999998 664

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=90.35  E-value=0.29  Score=37.23  Aligned_cols=52  Identities=15%  Similarity=0.162  Sum_probs=45.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|..+|+.|.+.|.|.. .|
T Consensus        34 ~l~~~~~~iL~~l~~~------~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~   86 (142)
T 2bv6_A           34 NLTYPQFLVLTILWDE------SPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERS   86 (142)
T ss_dssp             TCCHHHHHHHHHHHHS------SEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecC
Confidence            4667888899998753      3699999999999999999999999999999988 55

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=90.28  E-value=0.46  Score=41.23  Aligned_cols=34  Identities=18%  Similarity=0.190  Sum_probs=31.6

Q ss_pred             CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-+ +..+++++++.+...||+||+.|.++|.|+.
T Consensus        51 ~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~   85 (272)
T 3eet_A           51 TRLPSQARIREEYGVSDTVALEARKVLMAEGLVEG   85 (272)
T ss_dssp             SBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            456 7899999999999999999999999999987

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=90.25  E-value=0.67  Score=36.16  Aligned_cols=54  Identities=15%  Similarity=0.199  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++.-|-.||.+|...     +.+++..+|++.++++...|...|+.|+..|.|.- .|.
T Consensus        28 gLt~~q~~vL~~L~~~-----~~~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~~~~   82 (151)
T 4aik_A           28 ELTQTHWVTLYNINRL-----PPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHTSA   82 (151)
T ss_dssp             CCCHHHHHHHHHHHHS-----CTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHc-----CCCCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEeecCC
Confidence            5777888899888642     34788899999999999999999999999999997 554

>3koj_A Uncharacterized protein YCF41; single-strand binding protein family, PF00436, SNR59A, NESG, structural genomics, PSI-2; 1.90A {Synechococcus elongatus pcc 6301}

Probab=90.23  E-value=1.5  Score=32.85  Aligned_cols=76  Identities=13%  Similarity=0.254  Sum_probs=47.0

Q ss_pred             EEeEEEEEEEEEEe---e--eCC--CeEEEEEE-------cCCCeEEEEEecccccccccccccCCCCEEEEEEEeee--
Q 024592           66 DVNTITVVGIVCDM---Q--DKE--PQFIFLID-------DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--  129 (265)
Q Consensus        66 ~v~~V~iVG~V~~v---~--~~~--t~~~y~Ld-------DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--  129 (265)
                      ..+.|.|+|.+..=   +  ...  ....|+|.       |.|--|.|..|..-++  ....-++.|+.|.|.|+|+.  
T Consensus        10 ~~~~v~LiGrL~~DPelR~t~~g~~~va~f~lAv~~~~~~~~t~fi~vv~wgk~AE--~~~~yl~KG~~V~VeGrL~~r~   87 (108)
T 3koj_A           10 HMNSCILQATVVEAPQLRYAQDNQTPVAEMVVQFPGLSSKDAPARLKVVGWGAVAQ--ELQDRCRLNDEVVLEGRLRINS   87 (108)
T ss_dssp             SCEEEEEEEEEEEEEEEEECTTSSSEEEEEEEEECC-----CCEEEEEEEETHHHH--HHHHHCCTTCEEEEEEEEEEEC
T ss_pred             ccceEEEEEEECCCCEEEEeCCCCEEEEEEEEEECCcccCCCcEEEEEEEEhHHHH--HHHHhCCCCCEEEEEEEEEeee
Confidence            45789999999652   2  122  34555553       3455699999976442  12345899999999999986  


Q ss_pred             eCC---c----cEEEEEEeee
Q 024592          130 FQD---K----RSLNAYSLRP  143 (265)
Q Consensus       130 f~~---~----~~i~~~~i~~  143 (265)
                      |.+   +    ..|.+..|.|
T Consensus        88 y~~kdG~kr~~tEVva~~i~P  108 (108)
T 3koj_A           88 LLKPDGNREKQTELTVTRVHH  108 (108)
T ss_dssp             --------CCEEEEEEEEEEC
T ss_pred             EECCCCCEEEEEEEEEEEEEC
Confidence            432   2    2456666554

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=90.17  E-value=0.53  Score=38.75  Aligned_cols=47  Identities=21%  Similarity=0.317  Sum_probs=41.8

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++.+.+||.+|+.       ..+++.+|++.++++...|...|+.|.+.|.|..
T Consensus        19 d~~~~~IL~~L~~-------~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~~   65 (192)
T 1uly_A           19 EDTRRKILKLLRN-------KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEV   65 (192)
T ss_dssp             SHHHHHHHHHHTT-------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHc-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4678889999972       2589999999999999999999999999999965

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=90.09  E-value=0.48  Score=36.76  Aligned_cols=55  Identities=13%  Similarity=0.085  Sum_probs=46.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++.-|-.||.+|...    .+.+++..+|++.++++...|...|+.|+..|+|.- .|.
T Consensus        32 gLt~~q~~vL~~L~~~----~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~~~   87 (147)
T 4b8x_A           32 GLTFARYEALVLLTFS----KSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNP   87 (147)
T ss_dssp             TCCHHHHHHHHHHHTS----GGGEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHHC----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEeecC
Confidence            5777788899888653    134699999999999999999999999999999998 664

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=90.07  E-value=0.48  Score=37.32  Aligned_cols=51  Identities=12%  Similarity=0.288  Sum_probs=43.7

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++..+..||++|.+.    .+.-++.++|.+.+     +++...|-..|+.|.+.|.|-.
T Consensus        15 ~T~qR~~Il~~L~~~----~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   70 (150)
T 2w57_A           15 VTLPRLKILEVLQQP----ECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTR   70 (150)
T ss_dssp             CCHHHHHHHHHHTSG----GGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHhC----CCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEE
Confidence            567888999999763    11468999999988     5899999999999999999987

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=90.07  E-value=0.53  Score=40.04  Aligned_cols=54  Identities=19%  Similarity=0.338  Sum_probs=44.2

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      -.||++|.+.     ..++++.||++.++++.+.+...|..|.+.|.|...++..|..+
T Consensus        11 l~iL~~l~~~-----~~~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~~~~Y~lg   64 (249)
T 1mkm_A           11 FEILDFIVKN-----PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPG   64 (249)
T ss_dssp             HHHHHHHHHC-----SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECTTSCEEEC
T ss_pred             HHHHHHHHhC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEECCCCcEEEC
Confidence            3578888642     34799999999999999999999999999999987545577654

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=90.06  E-value=0.57  Score=40.11  Aligned_cols=52  Identities=12%  Similarity=0.033  Sum_probs=42.4

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      +||++|.+     .+.++++.||++.++++.+.+...|..|.+.|.|... +..|..+
T Consensus        18 ~iL~~l~~-----~~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~~~-~~~Y~Lg   69 (257)
T 2g7u_A           18 AVLLAFDA-----QRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGS-GGRWSLT   69 (257)
T ss_dssp             HHHHTCSS-----SCSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE-TTEEEEC
T ss_pred             HHHHHHHh-----CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC-CCEEEEc
Confidence            35666643     2458999999999999999999999999999999774 4677754

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=90.06  E-value=0.29  Score=36.53  Aligned_cols=57  Identities=12%  Similarity=0.127  Sum_probs=48.6

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC----CCHHHHHHHHHHHhhCCeEEe-ecCCce
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN----LPMDKLMEALESLNENSLVYS-IDEFHY  259 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~----~~~~~v~~al~~L~~eG~IYs-iDd~hy  259 (265)
                      .+++..+..||.+|...      .+++..+|++.++    ++...|...|+.|.+.|.|.. -|+-.+
T Consensus         6 ~~lt~~~~~vL~~l~~~------~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~~rr~   67 (123)
T 1okr_A            6 YEISSAEWEVMNIIWMK------KYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIF   67 (123)
T ss_dssp             CCCCHHHHHHHHHHHHH------SSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEETTEE
T ss_pred             ccCCHHHHHHHHHHHhC------CCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEecCCeE
Confidence            36788899999999752      3799999999997    889999999999999999998 765433

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=89.97  E-value=0.56  Score=40.04  Aligned_cols=34  Identities=18%  Similarity=0.220  Sum_probs=31.4

Q ss_pred             CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .=+ +..+++++++.+...||+||+.|.++|.|+.
T Consensus        34 ~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~   68 (248)
T 3f8m_A           34 DPFPAEREIAEQFEVARETVRQALRELLIDGRVER   68 (248)
T ss_dssp             CBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            346 7899999999999999999999999999986

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=89.94  E-value=0.66  Score=35.69  Aligned_cols=55  Identities=20%  Similarity=0.303  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC----CCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN----LPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~----~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++..+-.||.+|-..     +.+++..+|++.++    ++...|...|+.|.+.|.|-. -|..
T Consensus         6 ~lt~~e~~vL~~L~~~-----~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~~r   65 (138)
T 2g9w_A            6 RLGDLERAVMDHLWSR-----TEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDDR   65 (138)
T ss_dssp             GCCHHHHHHHHHHHTC-----SSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC---
T ss_pred             cCCHHHHHHHHHHHhc-----CCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEecCC
Confidence            5778899999999762     24799999999997    799999999999999999998 6554

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=89.82  E-value=0.26  Score=36.36  Aligned_cols=55  Identities=9%  Similarity=0.099  Sum_probs=46.5

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC----CCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN----LPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~----~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .+++..+..||++|.+.      .+++..+|++.++    ++...|...|+.|++.|.|-. -|..
T Consensus        31 ~~LT~~e~~VL~~L~~~------~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~~gR   90 (99)
T 2k4b_A           31 FNVSNAELIVMRVIWSL------GEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKEGR   90 (99)
T ss_dssp             CCCCCSCSHHHHHHHHH------SCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEEETT
T ss_pred             CCCCHHHHHHHHHHHhC------CCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEeCCC
Confidence            35778888999999753      3799999999996    578999999999999999988 6554

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=89.78  E-value=0.3  Score=37.70  Aligned_cols=49  Identities=14%  Similarity=0.137  Sum_probs=43.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++..+-.||.+| ..      .+++..+|++.++++...|...|+.|.+.|.|..
T Consensus        35 ~lt~~q~~iL~~l-~~------~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r   83 (151)
T 3kp7_A           35 GISAEQSHVLNML-SI------EALTVGQITEKQGVNKAAVSRRVKKLLNAELVKL   83 (151)
T ss_dssp             TCCHHHHHHHHHH-HH------SCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC
T ss_pred             CCCHHHHHHHHHH-Hc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4677888999999 42      4899999999999999999999999999999984

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A

Probab=89.74  E-value=0.41  Score=43.59  Aligned_cols=45  Identities=18%  Similarity=0.192  Sum_probs=40.7

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +..||++|++.      ..++..+|++.++++...|.+.+++|+++|.|..
T Consensus        18 ~~~il~~l~~~------~~~sr~~la~~~~ls~~tv~~~v~~L~~~g~i~~   62 (406)
T 1z6r_A           18 AGAVYRLIDQL------GPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQE   62 (406)
T ss_dssp             HHHHHHHHHSS------CSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            35699999874      3689999999999999999999999999999988

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=89.57  E-value=0.6  Score=39.70  Aligned_cols=34  Identities=18%  Similarity=0.287  Sum_probs=31.4

Q ss_pred             CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .=+ +..+++++++.+...||+||..|.++|.|+.
T Consensus        32 ~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~   66 (243)
T 2wv0_A           32 MPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYR   66 (243)
T ss_dssp             CBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence            345 7899999999999999999999999999987

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=89.51  E-value=0.56  Score=35.09  Aligned_cols=55  Identities=11%  Similarity=0.204  Sum_probs=45.4

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeec
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF--HYKSA  262 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t  262 (265)
                      +.+..||.+|..       ..+++.+|++.++++...|...|..|.+.|.|-. -+..  +|..+
T Consensus        18 ~~R~~Il~~L~~-------~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l~   75 (118)
T 3f6o_A           18 PTRRAVLGRLSR-------GPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQGRVRTCAIE   75 (118)
T ss_dssp             HHHHHHHHHHHT-------CCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEC
T ss_pred             HHHHHHHHHHHh-------CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEecCCEEEEEEC
Confidence            577889999873       2579999999999999999999999999999988 5542  44443

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=89.43  E-value=0.39  Score=37.47  Aligned_cols=43  Identities=12%  Similarity=0.053  Sum_probs=35.9

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      .+++..+|++.++++...|+.+|..|.++|.|....+..+..|
T Consensus        53 ~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~~~~~~~lT   95 (155)
T 2h09_A           53 GEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMIPWRGVFLT   95 (155)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEETTTEEEEC
T ss_pred             CCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEecCCceEEC
Confidence            3689999999999999999999999999999877433445444

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=89.40  E-value=0.34  Score=42.14  Aligned_cols=53  Identities=15%  Similarity=0.215  Sum_probs=42.5

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      .||++|.+.     ..++++.||+++++++.+.+...|..|.+.|.|....+..|...
T Consensus        34 ~IL~~l~~~-----~~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~~~~~Y~LG   86 (275)
T 3mq0_A           34 RILDLVAGS-----PRDLTAAELTRFLDLPKSSAHGLLAVMTELDLLARSADGTLRIG   86 (275)
T ss_dssp             HHHHHHHHC-----SSCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEECTTSEEEEC
T ss_pred             HHHHHHhhC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCcEEeh
Confidence            478887653     35899999999999999999999999999999998434678754

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=89.29  E-value=0.37  Score=36.78  Aligned_cols=54  Identities=17%  Similarity=0.193  Sum_probs=44.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...     ..+++..+|++.++++...|...|+.|.+.|.|.. .|.
T Consensus        32 ~l~~~~~~iL~~l~~~-----~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~~~~   86 (147)
T 2hr3_A           32 PVQFSQLVVLGAIDRL-----GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP   86 (147)
T ss_dssp             HHHHHHHHHHHHHHHT-----TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCCHHHHHHHHHHHHc-----CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeCCCC
Confidence            4566778899888751     24799999999999999999999999999999988 553

>1fx7_A Iron-dependent repressor IDER; DTXR, iron-dependent regulator, signaling protein; 2.00A {Mycobacterium tuberculosis} SCOP: a.4.5.24 a.76.1.1 b.34.1.2 PDB: 1u8r_A

Probab=89.28  E-value=0.19  Score=42.42  Aligned_cols=61  Identities=18%  Similarity=0.211  Sum_probs=49.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCH--HHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeecc
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHR--NVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAV  263 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~--~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t~  263 (265)
                      +++..+..+|.+|....    +.|++.  .+|++.++++...|..+|+.|...|+|.. -| ..+..|.
T Consensus         3 ~lt~~~e~~L~~L~~l~----~~~~~~~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r~~~-~~v~LT~   66 (230)
T 1fx7_A            3 ELVDTTEMYLRTIYDLE----EEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGD-RHLELTE   66 (230)
T ss_dssp             TTSSHHHHHHHHHHHHH----HHTSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT-SCEEECH
T ss_pred             CCCHHHHHHHHHHHHHh----hcCCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC-ccEEECH
Confidence            46778888888876532    237777  99999999999999999999999999988 54 4555553

>3bwg_A Uncharacterized HTH-type transcriptional regulato; APC85486, YYDK, transcriptional regulator, structural genomi 2; 2.09A {Bacillus subtilis subsp} SCOP: a.4.5.6 d.190.1.2

Probab=89.16  E-value=0.69  Score=39.19  Aligned_cols=52  Identities=12%  Similarity=0.317  Sum_probs=38.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+.+.|.+.|.... .....=+ +..+++++++.+...||+||..|.++|.|+.
T Consensus         9 ~i~~~l~~~I~~g~-~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~g~i~~   61 (239)
T 3bwg_A            9 QIATEIETYIEEHQ-LQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQ   61 (239)
T ss_dssp             HHHHHHHHHHHHTT-CCTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHhCC-CCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            34455555444321 1223346 7899999999999999999999999999986

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=89.12  E-value=0.69  Score=36.39  Aligned_cols=50  Identities=14%  Similarity=0.265  Sum_probs=43.4

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++.+..||++|.+.     +.-++.++|.+.+     +++...|-..|+.|.+.|.|-.
T Consensus        25 ~T~qR~~IL~~l~~~-----~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   79 (150)
T 2xig_A           25 NSKQREEVVSVLYRS-----GTHLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISV   79 (150)
T ss_dssp             CHHHHHHHHHHHHHC-----SSCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHhC-----CCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEE
Confidence            457888899999753     3468999999988     5999999999999999999988

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=89.07  E-value=0.85  Score=40.48  Aligned_cols=55  Identities=7%  Similarity=0.134  Sum_probs=44.8

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceee
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKS  261 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~  261 (265)
                      ..+.+|+++|++      ..-++.++|+++|++++..|++.|+.|.+.|.+-. .....|..
T Consensus         5 ~r~~~Il~~L~~------~~~~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~i~~~~g~GY~l   60 (321)
T 1bia_A            5 TVPLKLIALLAN------GEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSL   60 (321)
T ss_dssp             HHHHHHHHHHTT------SSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEEETTTEEEC
T ss_pred             hHHHHHHHHHHc------CCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCcEEEecCCCcEE
Confidence            567789999964      24689999999999999999999999999998854 54445554

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=89.01  E-value=0.32  Score=35.45  Aligned_cols=35  Identities=23%  Similarity=0.249  Sum_probs=31.9

Q ss_pred             CCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          220 NGV-HRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       220 ~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      .-+ ++.+|++.|+++...|+++|..|.++|.|...
T Consensus        33 ~~lps~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~   68 (102)
T 1v4r_A           33 DTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSR   68 (102)
T ss_dssp             SBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEE
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            345 89999999999999999999999999999873

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=88.85  E-value=0.53  Score=33.64  Aligned_cols=34  Identities=15%  Similarity=0.068  Sum_probs=32.3

Q ss_pred             CCcCHHHHHHhcCCCHHH-HHHHHHHHhhCCeEEe
Q 024592          220 NGVHRNVISQQLNLPMDK-LMEALESLNENSLVYS  253 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~-v~~al~~L~~eG~IYs  253 (265)
                      .+++..+|++.++++... |...|+.|.+.|.|..
T Consensus        29 ~~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~   63 (95)
T 2pg4_A           29 YEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKE   63 (95)
T ss_dssp             CCCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHCCCchHHHHHHHHHHHHCCCeec
Confidence            379999999999999999 9999999999999986

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=88.77  E-value=0.31  Score=37.87  Aligned_cols=53  Identities=13%  Similarity=0.164  Sum_probs=44.6

Q ss_pred             CCChhHHHHHHHh-cCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFL-RRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i-~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+| ..      ..+++..+|++.++++...|...|+.|++.|.|.. .|.
T Consensus        44 ~l~~~~~~iL~~L~~~------~~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~~~~   98 (160)
T 3boq_A           44 GLSLAKFDAMAQLARN------PDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSA   98 (160)
T ss_dssp             SCCHHHHHHHHHHHHC------TTCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC---
T ss_pred             CCCHHHHHHHHHHHHc------CCCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCC
Confidence            5677888999999 44      24899999999999999999999999999999988 554

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=88.77  E-value=0.42  Score=36.41  Aligned_cols=52  Identities=15%  Similarity=0.162  Sum_probs=46.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|.. .|
T Consensus        37 ~l~~~~~~iL~~l~~~------~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~~~   89 (147)
T 1z91_A           37 NITYPQYLALLLLWEH------ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRS   89 (147)
T ss_dssp             CCCHHHHHHHHHHHHH------SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBC
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEeccC
Confidence            5777888899999753      2799999999999999999999999999999988 55

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=88.64  E-value=0.36  Score=37.59  Aligned_cols=55  Identities=5%  Similarity=0.119  Sum_probs=40.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++++-+-.|+=.|... ......+.+.++|++++++++.+|...|+.|++.|.|--
T Consensus        29 gLs~~E~~lLl~L~~~-~~~g~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i   83 (135)
T 2v79_A           29 GLNETELILLLKIKMH-LEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFI   83 (135)
T ss_dssp             TCCHHHHHHHHHHHHH-HTTTCCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEE
T ss_pred             CCCHHHHHHHHHHHHH-HhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            3555555544333321 113356899999999999999999999999999998865

>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold, DNA binding protein; 2.70A {Neisseria gonorrhoeae fa 1090}

Probab=88.63  E-value=4.7  Score=29.67  Aligned_cols=73  Identities=14%  Similarity=0.175  Sum_probs=43.2

Q ss_pred             eEEEEEEEEEEe---ee--C-CCeEEEEEEc-----CCC------e-EEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           68 NTITVVGIVCDM---QD--K-EPQFIFLIDD-----GTG------R-IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        68 ~~V~iVG~V~~v---~~--~-~t~~~y~LdD-----gTG------~-I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      +.|.|+|.+..-   +.  . .....|+|.=     ..|      . |.|..|-.-++    ...+..|+.|.|.|+|+.
T Consensus         8 Nkv~LiG~L~~dPelRytp~G~~v~~f~lA~~~~~~~~g~~~~~~~~i~vv~~gk~Ae----~~~l~KG~~v~veGrL~~   83 (103)
T 3k8a_A            8 NLVSLAALIEKAFPIRYTPAGIPVLDIILKHESWQEENGQQCLVQLEIPARILGRQAE----EWQYRQGDCATVEGFLAQ   83 (103)
T ss_dssp             EEEEEEEEEEEECCCEECTTSCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEHHHHH----HSTTCTTCEEEEEEEEEE
T ss_pred             cEEEEEEEECCCCceEECCCCCEEEEEEEEEcccCccCCCEEEeeEEEEEEEEhHHhh----hhccCCCCEEEEEEEEEE
Confidence            677888887652   11  1 1234444431     122      2 77788865442    345999999999999985


Q ss_pred             --eCCc-cEEEEEEeeeC
Q 024592          130 --FQDK-RSLNAYSLRPI  144 (265)
Q Consensus       130 --f~~~-~~i~~~~i~~v  144 (265)
                        |+++ ..+-+..|..+
T Consensus        84 rs~~~~~lvlhi~~i~~i  101 (103)
T 3k8a_A           84 KSRRSLMPMLRIQNIKEY  101 (103)
T ss_dssp             SSSSCCCEEEEEEEEEEC
T ss_pred             CccCCccEEEEEEEEEEc
Confidence              6554 22444555444

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=88.53  E-value=0.47  Score=43.63  Aligned_cols=45  Identities=13%  Similarity=0.195  Sum_probs=40.3

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +..||++|++.      ..++..+|++.++++...|.+.+++|+++|.|..
T Consensus        41 ~~~il~~l~~~------~~~sr~ela~~~gls~~tv~~~v~~L~~~gli~~   85 (429)
T 1z05_A           41 AGRVYKLIDQK------GPISRIDLSKESELAPASITKITRELIDAHLIHE   85 (429)
T ss_dssp             HHHHHHHHHHH------CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            34699999874      3689999999999999999999999999999976

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=88.52  E-value=0.44  Score=38.82  Aligned_cols=46  Identities=11%  Similarity=0.232  Sum_probs=38.9

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCe-EE
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSL-VY  252 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~-IY  252 (265)
                      -...|+++|++.     ...++..+|+++|+++...|+.-|..|.+.|. |.
T Consensus        22 R~~~Il~~L~~~-----~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~~I~   68 (187)
T 1j5y_A           22 RLKSIVRILERS-----KEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIV   68 (187)
T ss_dssp             HHHHHHHHHHHC-----SSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCE
T ss_pred             HHHHHHHHHHHc-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            456688888752     23599999999999999999999999999998 63

>2l02_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=88.50  E-value=0.75  Score=32.71  Aligned_cols=48  Identities=17%  Similarity=0.207  Sum_probs=41.2

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      .-.|+.+|.+.      ...++.+|.+..+++.+++.-||-.|..|+.|.- -++
T Consensus        10 AG~VW~~L~~~------~~~s~~el~k~t~l~d~el~lAIGWLaREdKI~~~~~~   58 (82)
T 2l02_A           10 AGKVWHALNEA------DGISIPELARKVNLSVESTALAVGWLARENKVVIERKN   58 (82)
T ss_dssp             HHHHHHHHHHC------CSBCHHHHHHHHTCCHHHHHHHHHHHHTTTSEEEEEET
T ss_pred             HHHHHHHHhcc------CCCCHHHHHHHhCCCHHHHHHHHHHHhccCceeEEeeC
Confidence            34688888763      3789999999999999999999999999999987 443

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=88.44  E-value=0.77  Score=34.24  Aligned_cols=56  Identities=13%  Similarity=0.124  Sum_probs=48.2

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC----CCHHHHHHHHHHHhhCCeEEe-ecCCc
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN----LPMDKLMEALESLNENSLVYS-IDEFH  258 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~----~~~~~v~~al~~L~~eG~IYs-iDd~h  258 (265)
                      .+++..+-.||.+|-+.      .+++..+|++.++    ++...|...|+.|.+.|.|.. -|...
T Consensus         6 ~~Lt~~q~~vL~~L~~~------~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~~r~   66 (126)
T 1sd4_A            6 VEISMAEWDVMNIIWDK------KSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSENI   66 (126)
T ss_dssp             CCCCHHHHHHHHHHHHS------SSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             CCCCHHHHHHHHHHHhc------CCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeCCCe
Confidence            36888999999999763      3799999999996    589999999999999999998 76553

>1qvc_A Single stranded DNA binding protein monomer; beta-barrel; 2.20A {Escherichia coli} SCOP: b.40.4.3 PDB: 1kaw_A 1eyg_A 1sru_A

Probab=88.42  E-value=1.4  Score=34.56  Aligned_cols=64  Identities=19%  Similarity=0.226  Sum_probs=43.4

Q ss_pred             EeEEEEEEEEEE---eee---CCCeEEEEEE------c--------CCCeEEEEEecccccccccccccCCCCEEEEEEE
Q 024592           67 VNTITVVGIVCD---MQD---KEPQFIFLID------D--------GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH  126 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld------D--------gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~  126 (265)
                      ++.|.|+|+|..   ++.   ....+.|+|.      |        .|--|.|..|...+.  .....++.|+.|.|.|+
T Consensus         5 mN~v~L~GrL~~dPelr~t~~G~~v~~f~lA~~~~~~~~~~Ge~~~~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~   82 (145)
T 1qvc_A            5 VNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAE--VASEYLRKGSQVYIEGQ   82 (145)
T ss_dssp             EEEEEEEEEESSCCEEECCSSSCCEEEEEEEECCCCSCCSSSSCCCCCEEEEEEEETHHHH--HHHHHCCTTCEEEEEEE
T ss_pred             eEEEEEEEEeCCCCEEEECCCCCEEEEEEEEEcCCcccccCCcEecccEEEEEEEehHHHH--HHHHhcCCCCEEEEEEE
Confidence            688999999955   221   2356778773      1        133489999976432  12234899999999999


Q ss_pred             eee--eCC
Q 024592          127 LKA--FQD  132 (265)
Q Consensus       127 i~~--f~~  132 (265)
                      |+.  |.+
T Consensus        83 L~~~~~~d   90 (145)
T 1qvc_A           83 LRTRKWTD   90 (145)
T ss_dssp             EEEEEECS
T ss_pred             EEeeEEEC
Confidence            986  543

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=88.38  E-value=0.84  Score=35.62  Aligned_cols=49  Identities=16%  Similarity=0.152  Sum_probs=39.7

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..-.+|-+|...   ..+.-++.++|+++++++..-++++|..|...|.|-+
T Consensus        12 yAl~~L~~La~~---~~~~~~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s   60 (143)
T 3t8r_A           12 YGLTLMISLAKK---EGQGCISLKSIAEENNLSDLYLEQLVGPLRNAGLIRS   60 (143)
T ss_dssp             HHHHHHHHHHTT---TTSCCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhC---CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEe
Confidence            444566666553   2234589999999999999999999999999999988

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=88.36  E-value=0.67  Score=38.65  Aligned_cols=45  Identities=16%  Similarity=0.189  Sum_probs=38.2

Q ss_pred             CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592          219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV  263 (265)
Q Consensus       219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~  263 (265)
                      ..+++..+|++.|+++...|..+|+.|.++|.|....+..+..|.
T Consensus        18 ~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~~~~i~LT~   62 (214)
T 3hrs_A           18 HNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDKKAGYLLTD   62 (214)
T ss_dssp             CSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTEEEECH
T ss_pred             CCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEecCCCeEECH
Confidence            458999999999999999999999999999999874445565554

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=88.25  E-value=0.34  Score=34.78  Aligned_cols=63  Identities=14%  Similarity=0.097  Sum_probs=43.8

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeecc
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF--HYKSAV  263 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t~  263 (265)
                      ++.-+-.||..|-...  .....++..+|++.++++...|...|+.|...|.|-. -|--  .+..|.
T Consensus        10 l~~~~~~iL~~l~~~~--~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~~~~d~R~~~v~LT~   75 (95)
T 2qvo_A           10 FKEKALEILMTIYYES--LGGNDVYIQYIASKVNSPHSYVWLIIKKFEEAKMVECELEGRTKIIRLTD   75 (95)
T ss_dssp             SCHHHHHHHHHHHHHH--HTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECH
T ss_pred             CchhHHHHHHHHHHcc--CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCccCCCCCCeEEEEECh
Confidence            4555566666553321  1122399999999999999999999999999999944 4432  344443

>1hw1_A FADR, fatty acid metabolism regulator protein; helix-turn-helix, helix bundle, transcription; 1.50A {Escherichia coli} SCOP: a.4.5.6 a.78.1.1 PDB: 1hw2_A 1e2x_A 1h9g_A* 1h9t_A

Probab=88.24  E-value=1.1  Score=37.46  Aligned_cols=36  Identities=14%  Similarity=0.183  Sum_probs=32.3

Q ss_pred             CCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          218 NNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       218 ~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ...=+ +..+++++|+.+...||+||..|..+|.|..
T Consensus        27 pG~~LPsE~eLa~~~gVSR~tVReAL~~L~~eGlv~~   63 (239)
T 1hw1_A           27 PGTILPAERELSELIGVTRTTLREVLQRLARDGWLTI   63 (239)
T ss_dssp             TTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            34457 6899999999999999999999999999986

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=88.23  E-value=0.86  Score=35.58  Aligned_cols=56  Identities=14%  Similarity=0.133  Sum_probs=44.5

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC----ceeecc
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF----HYKSAV  263 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~----hyk~t~  263 (265)
                      .....||..|..       ..+++.+|++.++++...+...|+.|.+.|.|-. .+..    .|..|.
T Consensus        24 ~w~l~IL~~L~~-------g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~~~~~d~~~~y~LT~   84 (146)
T 2f2e_A           24 GWSMLIVRDAFE-------GLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTD   84 (146)
T ss_dssp             SSHHHHHHHHHT-------TCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECH
T ss_pred             chHHHHHHHHHh-------CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEECc
Confidence            345567777742       2579999999999999999999999999999998 6643    565554

>3stb_C RNA-editing complex protein MP42; editosome, nanobody, single domain antibody, VH krepa3, krepa6, RNA binding protein-immune system complex; 2.50A {Trypanosoma brucei}

Probab=88.08  E-value=0.76  Score=36.41  Aligned_cols=73  Identities=19%  Similarity=0.255  Sum_probs=45.9

Q ss_pred             CCCeEECCeEEeEEEEEEEEEEeeeC----CCeEEEE--EEcCC---C-----eEEEEEecccccccccccccCCCCEEE
Q 024592           57 ESSASIDGADVNTITVVGIVCDMQDK----EPQFIFL--IDDGT---G-----RIECSRWAHEQMEFNEVNQISKGMYVR  122 (265)
Q Consensus        57 ~~~f~i~g~~v~~V~iVG~V~~v~~~----~t~~~y~--LdDgT---G-----~I~~~~w~~~~~~~~~~~~~~~g~yVr  122 (265)
                      +..+...-+.++.|.|+|+|.+...+    ..-..|+  ++...   |     -+.++.|- ......-...++.|+.|.
T Consensus        34 ~~~~~~h~r~vN~VvLmGRvtdpq~ry~~~~~Va~FtLAV~~~~~r~ge~~tdf~~V~vfG-g~lAE~i~~ylkkG~rVl  112 (148)
T 3stb_C           34 EGEVAAHWRCVNHCVMLGVVQNIQEGFVFEDKVLQFTLITDFEGPSPGDPDKDFHTVRVFD-SDYSSRVKEQLRDGEWFL  112 (148)
T ss_dssp             ----CCCCSCSEEEEEEEEEEEEEEEEETTEEEEEEEEEEECSSCCTTSCSEEEEEEEECS-HHHHHHHHHHCCTTCEEE
T ss_pred             chhhhhhheecceEEEEEEecCccccccCCCcEEEEEEEEecCCCCCCCCccceEEEEEEC-ChHHHHHHHHhcCCCEEE
Confidence            34566677889999999999887654    1234444  33221   2     27788885 111112245689999999


Q ss_pred             EEEEeeee
Q 024592          123 VYGHLKAF  130 (265)
Q Consensus       123 V~G~i~~f  130 (265)
                      |.|+|+.-
T Consensus       113 VeGRLrmn  120 (148)
T 3stb_C          113 VTGRLRMV  120 (148)
T ss_dssp             EEEEEEEE
T ss_pred             EEEEEEcc
Confidence            99999974

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=88.07  E-value=0.79  Score=35.63  Aligned_cols=58  Identities=12%  Similarity=0.133  Sum_probs=41.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd  256 (265)
                      +++.-|-.||.+|..... ....+++..+|++.++++...|...|+.|+..|.|-..|+
T Consensus        30 gLt~~q~~vL~~l~~~~~-~~~~~~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr~~~~   87 (148)
T 4fx0_A           30 GLTNTQFSTLAVISLSEG-SAGIDLTMSELAARIGVERTTLTRNLEVMRRDGLVRVMAG   87 (148)
T ss_dssp             TCCHHHHHHHHHHHC----------CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC----
T ss_pred             CCCHHHHHHHHHHHHhcC-CCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCC
Confidence            577788889998876421 2234699999999999999999999999999999933443

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=87.97  E-value=0.68  Score=39.84  Aligned_cols=52  Identities=13%  Similarity=0.053  Sum_probs=42.3

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      .||++|..     ...++++.||++.++++.+.+...|..|.+.|.|... +..|...
T Consensus        25 ~iL~~l~~-----~~~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~~~-~~~Y~Lg   76 (265)
T 2ia2_A           25 AVIRCFDH-----RNQRRTLSDVARATDLTRATARRFLLTLVELGYVATD-GSAFWLT   76 (265)
T ss_dssp             HHHHTCCS-----SCSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEES-SSEEEEC
T ss_pred             HHHHHHHh-----CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec-CCEEEEc
Confidence            36666653     2458999999999999999999999999999999773 4677653

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=87.92  E-value=0.61  Score=34.60  Aligned_cols=49  Identities=14%  Similarity=0.170  Sum_probs=41.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      ..+-.||..|..       .+++..+|++.+ +++...|...|+.|.+.|.|-. .|.
T Consensus        22 ~~~~~IL~~L~~-------~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~~~   72 (112)
T 1z7u_A           22 KWKLSLMDELFQ-------GTKRNGELMRALDGITQRVLTDRLREMEKDGLVHRESFN   72 (112)
T ss_dssp             TTHHHHHHHHHH-------SCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEEEC
T ss_pred             ccHHHHHHHHHh-------CCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEeecC
Confidence            455678877752       268999999999 9999999999999999999998 654

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=87.88  E-value=0.89  Score=35.27  Aligned_cols=50  Identities=14%  Similarity=0.108  Sum_probs=42.8

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++..+..||++|.+.     ..-++.++|.+.+     +++...|-..|+.|.+.|.|-.
T Consensus        12 ~T~qR~~Il~~L~~~-----~~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   66 (139)
T 3mwm_A           12 ATRQRAAVSAALQEV-----EEFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDV   66 (139)
T ss_dssp             HHHHHHHHHHHHTTC-----SSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEE
T ss_pred             cCHHHHHHHHHHHhC-----CCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence            356778899999863     2368999999988     4899999999999999999977

>1jmc_A Protein (replication protein A (RPA)); human ssDNA binding replication protein A(RPA), single stranded DNA-binding protein, protein-ssDNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 1fgu_A

Probab=87.87  E-value=0.46  Score=40.27  Aligned_cols=59  Identities=15%  Similarity=0.135  Sum_probs=41.3

Q ss_pred             EEEEEEEEEEeee---------CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEE-Eeee
Q 024592           69 TITVVGIVCDMQD---------KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKA  129 (265)
Q Consensus        69 ~V~iVG~V~~v~~---------~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~  129 (265)
                      .++|.|+|.++.+         ....+.+.|-|.+|.|.|..|.+...  .-.+.|++|+.+.+.+ +++.
T Consensus        20 ~w~I~~rV~~k~~~r~~~~~~~~g~~~~~~L~De~G~I~at~~~~~~~--~~~~~l~~G~vy~i~~~~v~~   88 (246)
T 1jmc_A           20 KWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRATAFNEQVD--KFFPLIEVNKVYYFSKGTLKI   88 (246)
T ss_dssp             CCEEEEEEEEECCCEEEECSSCEEEEEEEEEECSSCEEEEEEEHHHHH--HHGGGCCTTCEEEEECCEEEE
T ss_pred             ceEEEEEEEEecccceeeCCCCCceEEEEEEECCCCeEEEEEChHHHH--HhhhhcccCCEEEECCCEEEE
Confidence            4567777776521         12357889999999999999976432  2245689999888876 3444

>2kct_A Cytochrome C-type biogenesis protein CCME; solution structure, heme chaperone, cytochrome C biogenesis, OB-fold domain, NESG, PSI-2; NMR {Desulfovibrio vulgaris str}

Probab=87.79  E-value=6.3  Score=28.63  Aligned_cols=66  Identities=18%  Similarity=0.236  Sum_probs=47.8

Q ss_pred             eEEEEEEEEEE--eeeC--CCeEEEEEEcC---CCeEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEE
Q 024592           68 NTITVVGIVCD--MQDK--EPQFIFLIDDG---TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYS  140 (265)
Q Consensus        68 ~~V~iVG~V~~--v~~~--~t~~~y~LdDg---TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~  140 (265)
                      ..++|-|.|..  +...  +..+.|.|.|+   ...|.|.+---      .++.|++|.-|-+.|++..-  .-.+.|..
T Consensus         9 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~~~~v~V~Y~Gi------lPDlFrEGqgVV~~G~l~~~--~g~F~A~e   80 (94)
T 2kct_A            9 HTVRLFGTVAADGLTMLDGAPGVRFRLEDKDNTSKTVWVLYKGA------VPDTFKPGVEVIIEGGLAPG--EDTFKART   80 (94)
T ss_dssp             CCEEEEEEECSTTCEECTTSSEEEEEEECSSCTTCEEEEEEESC------CCTTCCTTCEEEEEEEECTT--CSEEEEEE
T ss_pred             CeEEEeeEEeCCeEEecCCCCEEEEEEEcCCCCCcEEEEEECCC------CCccccCCCeEEEEEEEeCC--CCEEEEeE
Confidence            46888899864  4443  57899999998   67788885432      35779999999999998531  23456655


Q ss_pred             e
Q 024592          141 L  141 (265)
Q Consensus       141 i  141 (265)
                      |
T Consensus        81 v   81 (94)
T 2kct_A           81 L   81 (94)
T ss_dssp             E
T ss_pred             E
Confidence            4

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=87.78  E-value=1.8  Score=32.69  Aligned_cols=49  Identities=18%  Similarity=0.187  Sum_probs=41.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      ..+..||.+|.+       .++++.+|++.++++...|...|..|.+.|.|-. -+.
T Consensus        46 ~~rl~IL~~L~~-------~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~~~g   95 (122)
T 1r1t_A           46 PNRLRLLSLLAR-------SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQG   95 (122)
T ss_dssp             HHHHHHHHHHTT-------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHHHHHHc-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            456678888853       2579999999999999999999999999999987 554

>3fhw_A Primosomal replication protein N; PRIB BPR162 X-RAY NESG, structural genomics, PSI-2, protein initiative; 1.90A {Bordetella parapertussis} PDB: 3dm4_A 3klw_A

Probab=87.76  E-value=5.1  Score=30.20  Aligned_cols=46  Identities=17%  Similarity=0.166  Sum_probs=34.3

Q ss_pred             EEEEEecccccccccccccCCCCEEEEEEEeeee--CCc-cEEEEEEeeeCC
Q 024592           97 IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAF--QDK-RSLNAYSLRPII  145 (265)
Q Consensus        97 I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f--~~~-~~i~~~~i~~v~  145 (265)
                      |.|..|-..++   ....+..|+.|.|.|+|+.-  +++ ..|.|..|..+.
T Consensus        49 i~vv~~Gk~AE---~~~~l~kGs~V~VeGrL~trs~~G~kl~l~a~~Ie~l~   97 (115)
T 3fhw_A           49 ISAVALGDLAL---LLADTPLGTEMQVQGFLAPARKDSVKVKLHLQQARRIA   97 (115)
T ss_dssp             EEEEEETHHHH---HHTTCCTTCEEEEEEEEEESSTTCSSEEEEEEEEEECC
T ss_pred             EEEEEEhHHHH---hhhccCCCCEEEEEEEEEECCCCCCEEEEEEEEEEEcC
Confidence            88899976442   23568999999999999973  333 468888888775

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=87.67  E-value=0.22  Score=39.99  Aligned_cols=56  Identities=18%  Similarity=0.108  Sum_probs=47.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...+   ...|++..+|++.++++...|...|+.|...|.|.. .|.
T Consensus        66 glt~~~~~iL~~L~~~~---~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~  122 (181)
T 2fbk_A           66 GLNAAGWDLLLTLYRSA---PPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDE  122 (181)
T ss_dssp             TCCHHHHHHHHHHHHHC---CSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC--
T ss_pred             CCCHHHHHHHHHHHHcC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEecCCC
Confidence            57788899999997642   224799999999999999999999999999999988 553

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=87.60  E-value=1.4  Score=29.41  Aligned_cols=42  Identities=10%  Similarity=0.098  Sum_probs=35.4

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      ..+++.+..|+.++.        +|.+..+|++.++++...|+..+..+.
T Consensus        10 ~~L~~~e~~il~~~~--------~g~s~~eIA~~l~is~~tV~~~~~~~~   51 (74)
T 1fse_A           10 PLLTKREREVFELLV--------QDKTTKEIASELFISEKTVRNHISNAM   51 (74)
T ss_dssp             CCCCHHHHHHHHHHT--------TTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH--------cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            458889999998872        378999999999999999988887654

>1stz_A Heat-inducible transcription repressor HRCA homol; circe element, structural genomics, BSGC structure FUN NIH, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.51 d.110.2.3

Probab=87.51  E-value=0.78  Score=41.21  Aligned_cols=49  Identities=10%  Similarity=0.190  Sum_probs=42.2

Q ss_pred             CChhHHHHHH-----HhcCcCCCCCCCCcCHHHHHHhc--CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLD-----FLRRPEFLANNNGVHRNVISQQL--NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~-----~i~~~~~~~~~~Gv~~~~I~~~l--~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++.-++.||+     ++++      ..-|...+|++++  +.++..||..|..|.++|.|..
T Consensus        15 l~eR~~~IL~~i~~~yl~~------~~pV~s~~La~~~~l~VS~aTIRrDL~~LE~~GlL~r   70 (338)
T 1stz_A           15 LNDRQRKVLYCIVREYIEN------KKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQ   70 (338)
T ss_dssp             CCHHHHHHHHHHHHHHHHH------CSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHHHHHHHHHHHc------CCCccHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence            4577888999     6654      3468999999999  8999999999999999999975

>2vw9_A Single-stranded DNA binding protein; DNA replication, single-stranded DNA, single-stranded DNA binding protein, oligonucleotide/oligosaccharide binding fold, OB-fold; 2.30A {Helicobacter pylori}

Probab=87.49  E-value=1.4  Score=34.03  Aligned_cols=49  Identities=24%  Similarity=0.266  Sum_probs=32.8

Q ss_pred             eEEEEEecccccccccccccCCCCEEEEEEEeee--eCC---c----cEEEEEEeeeCCC
Q 024592           96 RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQD---K----RSLNAYSLRPIID  146 (265)
Q Consensus        96 ~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~~---~----~~i~~~~i~~v~d  146 (265)
                      -|.|..|...+.  .....++.|+.|.|.|+|+.  |.+   +    ..|.+..|..+..
T Consensus        50 ~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~L~~~~~~dkdG~~r~~~ev~a~~i~~l~~  107 (134)
T 2vw9_A           50 FIDARLFGRTAE--IANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMDK  107 (134)
T ss_dssp             EEEEEEEHHHHH--HHHHHCCTTCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEEECCC
T ss_pred             EEEEEEEcHHHH--HHHHhCCCCCEEEEEEEEEeeeEECCCCCEEEEEEEEEEEEEEccC
Confidence            488888865332  12234899999999999986  532   2    2366777766654

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=87.41  E-value=1.2  Score=41.41  Aligned_cols=75  Identities=15%  Similarity=0.255  Sum_probs=52.0

Q ss_pred             eEEEEEEcCCCeEEEEEecccccc-------------ccc-------ccccCCCC--EEEEEEEeeeeCCc--cEEEEEE
Q 024592           85 QFIFLIDDGTGRIECSRWAHEQME-------------FNE-------VNQISKGM--YVRVYGHLKAFQDK--RSLNAYS  140 (265)
Q Consensus        85 ~~~y~LdDgTG~I~~~~w~~~~~~-------------~~~-------~~~~~~g~--yVrV~G~i~~f~~~--~~i~~~~  140 (265)
                      .+.+.|.|+||.+.|..|.+.+..             ..+       ... ..+.  .+||..+...|++.  ...++..
T Consensus       345 ~l~~~v~D~Tg~~~~~~F~~~a~~llG~sa~el~~~~~~d~~~~~~~~~~-~~~k~~~f~~~~k~~~y~~~~r~~~~v~~  423 (444)
T 4gop_C          345 ILSTNVADATGQMWLSGFNEDATQLIGMSAGELHKLREESESEFSAALHR-AANRMYMFNCRAKMDTFNDTARVRYTISR  423 (444)
T ss_dssp             CEEEEEEETTEEEEEEECHHHHHHHTTSCHHHHHHHHTTCHHHHHHHHHT-TSSCEEEEEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEEeCCCCEEEEEehHHHHHHcCCCHHHHHHHHhcChHHHHHHHHH-hhCcEEEEEEEEEeeeeCCeeEEEEEEEE
Confidence            467899999999999999753320             000       011 2233  45666666689887  5577788


Q ss_pred             eeeCCChhHHHHHHHHHHHHH
Q 024592          141 LRPIIDFNEITSHFVECIYVQ  161 (265)
Q Consensus       141 i~~v~d~Nei~~H~Levi~~~  161 (265)
                      +.|+ |+.+...++|+.|..+
T Consensus       424 ~~~~-d~~~~~~~l~~~i~~~  443 (444)
T 4gop_C          424 AAPV-DFAKAGMELVDAIRAY  443 (444)
T ss_dssp             EEEC-CHHHHHHHHHHHHHHH
T ss_pred             eeeC-CHHHHHHHHHHHHHhh
Confidence            8888 6888899999988654

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=87.27  E-value=0.22  Score=38.13  Aligned_cols=53  Identities=11%  Similarity=0.218  Sum_probs=38.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          201 SIDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      .+...|.+.|.... .....=+ +..+|++.|+.+...|++|+..|.++|.|+..
T Consensus        15 ~i~~~l~~~I~~g~-~~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   68 (126)
T 3ic7_A           15 QIADRICDDILLGQ-YEEEGRIPSVREYASIVEVNANTVMRSYEYLQSQEVIYNK   68 (126)
T ss_dssp             HHHHHHHHHHHTTS-SCBTSEECCTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEE
T ss_pred             HHHHHHHHHHHhCC-CCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            45555555555431 1223345 78899999999999999999999999999873

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=86.76  E-value=0.82  Score=36.09  Aligned_cols=56  Identities=16%  Similarity=0.216  Sum_probs=45.9

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC--ceeec
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF--HYKSA  262 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~--hyk~t  262 (265)
                      .+.+..||.+|..       ..+++.+|++.|+++...|...|..|.+.|.|-. -+..  .|..|
T Consensus        57 ~p~R~~IL~~L~~-------~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~Gr~~~y~lt  115 (151)
T 3f6v_A           57 EPTRRRLVQLLTS-------GEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRKDGRFRYYRLD  115 (151)
T ss_dssp             SHHHHHHHHHGGG-------CCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEC
T ss_pred             CHHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEC
Confidence            3678889999863       2589999999999999999999999999999987 5543  44444

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=86.73  E-value=0.69  Score=38.22  Aligned_cols=53  Identities=11%  Similarity=0.026  Sum_probs=46.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|.. .|.
T Consensus        45 gLt~~q~~iL~~L~~~------~~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~~~   98 (207)
T 2fxa_A           45 DLNINEHHILWIAYQL------NGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRL   98 (207)
T ss_dssp             TCCHHHHHHHHHHHHH------TSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC-
T ss_pred             CCCHHHHHHHHHHHHC------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            5778888999999753      3799999999999999999999999999999998 654

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=86.72  E-value=0.81  Score=27.63  Aligned_cols=40  Identities=8%  Similarity=-0.092  Sum_probs=31.1

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCC
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENS  249 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG  249 (265)
                      .+..|+.++.        .|++..+|++.|+++...|...+......|
T Consensus        10 ~~~~i~~~~~--------~g~s~~~IA~~lgis~~Tv~~~~~~~~~~g   49 (51)
T 1tc3_C           10 ERAQLDVMKL--------LNVSLHEMSRKISRSRHCIRVYLKDPVSYG   49 (51)
T ss_dssp             HHHHHHHHHH--------TTCCHHHHHHHHTCCHHHHHHHHHCSTTTT
T ss_pred             HHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHhhHHhcC
Confidence            3345665552        388999999999999999999988766655

>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis}

Probab=86.61  E-value=2.5  Score=31.62  Aligned_cols=79  Identities=18%  Similarity=0.310  Sum_probs=48.6

Q ss_pred             EeEEEEEEEEEE---eeeC---CCeEEEEEE--c----CCC-----eEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           67 VNTITVVGIVCD---MQDK---EPQFIFLID--D----GTG-----RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~~---~t~~~y~Ld--D----gTG-----~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      ++.|.|+|.|..   +...   ...+.|.|.  .    ..|     -|.|..|...+.  .....++.|+.|.|.|+|+.
T Consensus         5 mN~v~l~G~l~~dpe~r~t~~G~~v~~f~la~~~~~~~~~g~~~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~l~~   82 (116)
T 3vdy_A            5 FNQVMLVGRLTKDPDLRYTSAGAAVAHVTLAVNRSFKNASGEIEADYVNCTLWRKTAE--NTALYCQKGSLVGVSGRIQT   82 (116)
T ss_dssp             CCCEEEEEEESSCCEEEECTTSCEEEEEEEEEECSSCCSSSCCCEEEEEEEEEHHHHH--HHHHHCCTTCEEEEEEEEEE
T ss_pred             EeEEEEEEEEccCcEEEECCCCCEEEEEEEEEeccccCCCCccccEEEEEEEECHHHH--HHHHhCCCCCEEEEEEEEEe
Confidence            567888888854   2221   235566652  1    122     388999976432  12234899999999999985


Q ss_pred             --eC---Cc----cEEEEEEeeeCCCh
Q 024592          130 --FQ---DK----RSLNAYSLRPIIDF  147 (265)
Q Consensus       130 --f~---~~----~~i~~~~i~~v~d~  147 (265)
                        |.   |+    ..|.+..|..+...
T Consensus        83 ~~~~d~dG~~~~~~ev~a~~i~~l~~~  109 (116)
T 3vdy_A           83 RSYENEEGVNVYVTEVLADTVRFMDPK  109 (116)
T ss_dssp             EEEC----CCEEEEEEEEEEEEECC--
T ss_pred             eEEECCCCCEEEEEEEEEEEEEEccCC
Confidence              54   22    35777777777653

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=86.60  E-value=1.1  Score=35.60  Aligned_cols=46  Identities=17%  Similarity=0.153  Sum_probs=41.3

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-+++||++|+ .+      .+++.+|++.|+++=.+++-+|-.|..||.|.+
T Consensus        11 erk~~ILE~Lk-~G------~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~   56 (165)
T 2vxz_A           11 VRLRDILALLA-DG------CKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTR   56 (165)
T ss_dssp             HHHHHHHHHHT-TC------CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEE
T ss_pred             HHHHHHHHHHH-hC------CccHHHHHHHhCCcHHHHHHHHHHHHhcCceEE
Confidence            46788999998 32      579999999999999999999999999999987

>2l01_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides vulgatus}

Probab=86.59  E-value=2  Score=30.15  Aligned_cols=46  Identities=15%  Similarity=0.215  Sum_probs=40.3

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCC-CHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNL-PMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~-~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..-.|+.+|.+.      ...++.+|.+..++ +.+++.-||-.|..|+.|.-
T Consensus        11 nAG~VW~~L~~~------~~~s~~el~k~t~l~~d~el~lAiGWLaREdKI~~   57 (77)
T 2l01_A           11 LAGQIWEALNGT------EGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVT   57 (77)
T ss_dssp             HHHHHHHHHTTS------SCEEHHHHHHHHTCSCHHHHHHHHHHHHHTTCEEE
T ss_pred             HHHHHHHHHhcC------CCCCHHHHHHHHCCCCHHHHHHHHHHHhhcCceEE
Confidence            345689999763      37899999999999 99999999999999999987

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=86.56  E-value=0.7  Score=36.13  Aligned_cols=49  Identities=20%  Similarity=0.226  Sum_probs=42.6

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++..+..||++|.+.     + -++.++|.+.+     +++...|..+|+.|.+.|.|-.
T Consensus        17 ~T~qR~~Il~~l~~~-----~-h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~   70 (145)
T 3eyy_A           17 LTPQRQLVLEAVDTL-----E-HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSH   70 (145)
T ss_dssp             CCHHHHHHHHHHHHH-----S-SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             cCHHHHHHHHHHHhc-----C-CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEE
Confidence            567888899999763     3 68999999988     4899999999999999999977

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=86.50  E-value=1.4  Score=31.53  Aligned_cols=43  Identities=19%  Similarity=0.249  Sum_probs=36.5

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE  247 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~  247 (265)
                      ..|+.-+..||.++.        +|.+..+|++.|++++..|+.-+..+..
T Consensus        28 ~~Lt~rE~~Vl~l~~--------~G~s~~eIA~~L~iS~~TV~~~~~~i~~   70 (90)
T 3ulq_B           28 DVLTPRECLILQEVE--------KGFTNQEIADALHLSKRSIEYSLTSIFN   70 (90)
T ss_dssp             -CCCHHHHHHHHHHH--------TTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            568899999999885        3899999999999999999988877653

>3rn5_A Interferon-inducible protein AIM2; OB fold, DNA binding, cytosolic, immune system-DNA complex; HET: DNA; 2.50A {Homo sapiens} PDB: 3rn2_A*

Probab=86.44  E-value=5.8  Score=32.76  Aligned_cols=58  Identities=24%  Similarity=0.321  Sum_probs=37.8

Q ss_pred             EEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeeeCCccEEEE
Q 024592           76 VCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSLNA  138 (265)
Q Consensus        76 V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i~~  138 (265)
                      |........++.|.|.|.||.++|..+-.-.     .-..++||-+|.+.= |+...++++|..
T Consensus       131 v~KK~v~~~~~~YeI~DnTG~MeVvv~G~~~-----~i~CEeGDKLrL~cFeL~~~~~~~qL~s  189 (208)
T 3rn5_A          131 VQKVTEKKKNILFDLSDNTGKMEVLGVRNED-----TMKCKEGDKVRLTFFTLSKNGEKLQLTS  189 (208)
T ss_dssp             EEEEEECSSEEEEEEEETTEEEEEEEECSTG-----GGSCCTTCEEEEEEEEEEECSSSEEEEC
T ss_pred             EEEEEeccceEEEEEecCCCcEEEEEeccCc-----ccccCCCCeeEEEEEEEeccCCeeeEEE
Confidence            3344566789999999999999999764321     234577886665542 444455555443

>1jb7_A Telomere-binding protein alpha subunit; DNA-protein interactions, DNA HYDR sodium ION, quadruplex DNA, DNA-binding protein-DNA complex; 1.86A {Sterkiella nova} SCOP: b.40.4.3 b.40.4.3 b.40.4.3 PDB: 1kix_A 1otc_A* 2i0q_A 1ph6_A 1ph1_A 1phj_A* 1ph3_A 1pa6_A 1ph4_A 1ph7_A 1ph8_A 1ph9_A 1ph5_A* 1ph2_A* 1k8g_A

Probab=86.43  E-value=2.4  Score=40.10  Aligned_cols=68  Identities=21%  Similarity=0.194  Sum_probs=50.4

Q ss_pred             eEEEEEEEEEEeee-----C-CCeEEEEEEcCC-C-------eE-----EEEEeccccccccccccc-CCCCEEEEE-EE
Q 024592           68 NTITVVGIVCDMQD-----K-EPQFIFLIDDGT-G-------RI-----ECSRWAHEQMEFNEVNQI-SKGMYVRVY-GH  126 (265)
Q Consensus        68 ~~V~iVG~V~~v~~-----~-~t~~~y~LdDgT-G-------~I-----~~~~w~~~~~~~~~~~~~-~~g~yVrV~-G~  126 (265)
                      ..|.|+|+|+++..     . .-.++|+|-|.+ .       -|     .|.+|....   +..+.+ ..||.|++. -+
T Consensus        50 ~~VnviGVVvd~~~P~~T~G~D~~~t~tI~D~S~~~~~~~~~Gl~~~~~~v~iF~~~~---e~LP~V~~~GDII~Lhrvk  126 (495)
T 1jb7_A           50 QPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRF---EDLPIIHRAGDIIRVHRAT  126 (495)
T ss_dssp             SCEEEEEEEEEECCCEECSSSCEEEEEEEEBTTBSBCCTTSSCSCBCCEEEEEEESSG---GGSCCCCEETCEEEEEEEE
T ss_pred             CeEEEEEEEeecCCceecCCCeEEEEEEEEeCCCCcccccccccccCceEEEEECCCh---HHCCCCCCCCCEEEEEEEE
Confidence            35899999998742     1 236899999955 2       16     999997644   246777 699999994 57


Q ss_pred             eeeeCCccEEEE
Q 024592          127 LKAFQDKRSLNA  138 (265)
Q Consensus       127 i~~f~~~~~i~~  138 (265)
                      |+.|+++.++.+
T Consensus       127 Iq~~ng~~~~v~  138 (495)
T 1jb7_A          127 LRLYNGQRQFNA  138 (495)
T ss_dssp             EEEETTEEEEEE
T ss_pred             EEEECCcEEEEe
Confidence            999999987644

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69

Probab=86.14  E-value=1.3  Score=32.38  Aligned_cols=55  Identities=11%  Similarity=0.146  Sum_probs=43.5

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC-CCHHHHHHHHHHHhhCCeEEe-ecCC-----ceeecc
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLN-LPMDKLMEALESLNENSLVYS-IDEF-----HYKSAV  263 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~-~~~~~v~~al~~L~~eG~IYs-iDd~-----hyk~t~  263 (265)
                      ....||..|..       .++++.+|++.++ ++...+...|..|.+.|.|-. .|..     .|..|.
T Consensus        26 ~~~~IL~~L~~-------~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~   87 (107)
T 2fsw_A           26 WTLLIIFQINR-------RIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTP   87 (107)
T ss_dssp             SHHHHHHHHTT-------SCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECH
T ss_pred             cHHHHHHHHHh-------CCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEECc
Confidence            44567777742       3689999999995 999999999999999999988 6643     465554

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=86.11  E-value=0.72  Score=40.70  Aligned_cols=36  Identities=17%  Similarity=0.283  Sum_probs=33.1

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE-eec
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVY-SID  255 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY-siD  255 (265)
                      .++++++|+++|++++..||.-|++|.++|.|- .+.
T Consensus        20 ~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~iri~   56 (315)
T 2w48_A           20 QDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAIN   56 (315)
T ss_dssp             SCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEec
Confidence            489999999999999999999999999999997 354

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=86.11  E-value=0.25  Score=41.66  Aligned_cols=62  Identities=15%  Similarity=0.199  Sum_probs=46.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCH--HHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHR--NVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV  263 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~--~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~  263 (265)
                      +++..+..+|++|-...    +.|++.  .+|+++++++...|..+|+.|..+|.|.-..+..+..|.
T Consensus         3 ~lt~~~e~yL~~i~~l~----~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~GlV~r~~~~~v~LT~   66 (226)
T 2qq9_A            3 DLVATTEMYLRTIYELE----EEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTP   66 (226)
T ss_dssp             CHHHHHHHHHHHHHHHH----HHTCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTTSBEEECH
T ss_pred             CCCHHHHHHHHHHHHHh----hcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCCeEECH
Confidence            35667777888775431    236665  999999999999999999999999999873334555554

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=86.03  E-value=1.5  Score=32.36  Aligned_cols=50  Identities=16%  Similarity=0.177  Sum_probs=41.9

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      ..+..||..|.+       .++++.+|++.++++...|...|..|.+.|.|.. -+..
T Consensus        32 ~~~~~il~~L~~-------~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~~~~~r   82 (119)
T 2lkp_A           32 PSRLMILTQLRN-------GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAGR   82 (119)
T ss_dssp             HHHHHHHHHHHH-------CCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEEEEETT
T ss_pred             HHHHHHHHHHHH-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCC
Confidence            466778887753       2579999999999999999999999999999977 5544

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=85.83  E-value=1.6  Score=30.38  Aligned_cols=42  Identities=10%  Similarity=0.298  Sum_probs=35.2

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      ..|++.+++|+.++.        +|.+..+|++.|++++..|+..+..+.
T Consensus        20 ~~Lt~~e~~vl~l~~--------~g~s~~eIA~~l~is~~tV~~~l~r~~   61 (82)
T 1je8_A           20 NQLTPRERDILKLIA--------QGLPNKMIARRLDITESTVKVHVKHML   61 (82)
T ss_dssp             GGSCHHHHHHHHHHT--------TTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            458889999998862        389999999999999999988777654

>1v1q_A Primosomal replication protein N; primosome, DNA replication, DNA binding; 2.1A {Escherichia coli} SCOP: b.40.4.3 PDB: 2ccz_A

Probab=85.81  E-value=7.5  Score=30.06  Aligned_cols=33  Identities=18%  Similarity=0.266  Sum_probs=25.0

Q ss_pred             EEEEEecccccccccccccCCCCEEEEEEEeeeeC
Q 024592           97 IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ  131 (265)
Q Consensus        97 I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~  131 (265)
                      |.|..|-..++  ....-+..|+.|.|.|+|+.-.
T Consensus        67 i~vv~wGk~AE--~~~~yl~KGs~V~VeGrL~tr~   99 (134)
T 1v1q_A           67 MPVIVSGHENQ--AITHSITVGSRITVQGFISCHK   99 (134)
T ss_dssp             EEEEEESTGGG--GGGTTCCTTCEEEEEEEEEEEC
T ss_pred             EEEEEEhHHHH--HHHHhcCCCCEEEEEEEEEEEE
Confidence            88999976442  1234589999999999999863

>3en2_A Probable primosomal replication protein N; PRIB RSR213C NESG X-RAY Q8XZT7 Q8XZT7_ralso, structural genomics, PSI-2; 2.30A {Ralstonia solanacearum}

Probab=85.71  E-value=1.9  Score=31.82  Aligned_cols=34  Identities=21%  Similarity=0.229  Sum_probs=23.3

Q ss_pred             EEEEEecccccccccccccCCCCEEEEEEEeee--eCCc
Q 024592           97 IECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQDK  133 (265)
Q Consensus        97 I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~~~  133 (265)
                      |.|..|-.-++   ....+..|+.|.|.|+|+.  ++++
T Consensus        50 i~vv~wGk~AE---~~~~~~kGs~V~VeGrL~trs~~s~   85 (101)
T 3en2_A           50 IEALGAGKMAS---VLDRIAPGTVLECVGFLARKHRSSK   85 (101)
T ss_dssp             EEEEEETHHHH---HHTTSCTTCEEEEEEEEEECC----
T ss_pred             EEEEEEhHHHH---HHhhcCCCCEEEEEEEEEeCcCCCC
Confidence            78889975432   2445889999999999985  4444

>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47

Probab=85.58  E-value=0.62  Score=32.32  Aligned_cols=51  Identities=12%  Similarity=0.238  Sum_probs=43.4

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .+-+...++|+..      .=+.+++++..|++..+++.+.|+.|.++|.|-= +||.
T Consensus         7 ~ll~~Fi~yIk~~------Kvv~LedLA~~F~l~t~~~i~RI~~Le~~g~ltGViDDR   58 (72)
T 1wi9_A            7 GFLTEFINYIKKS------KVVLLEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDR   58 (72)
T ss_dssp             CHHHHHHHHHHHC------SEECHHHHHHHHCSCHHHHHHHHHHHHHHSSSCEEECTT
T ss_pred             HHHHHHHHHHHHc------CeeeHHHHHHHhCCChHHHHHHHHHHHHCCCeEEEEeCC
Confidence            3446677888874      3579999999999999999999999999999988 8874

>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA replication, phosphoprotein; 2.14A {Streptomyces coelicolor}

Probab=85.51  E-value=3.7  Score=34.02  Aligned_cols=75  Identities=27%  Similarity=0.432  Sum_probs=44.5

Q ss_pred             EeEEEEEEEEEE---eeeC---CCeEEEEEEc---------------CCCeEEEEEecccccccccccccCCCCEEEEEE
Q 024592           67 VNTITVVGIVCD---MQDK---EPQFIFLIDD---------------GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG  125 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~~---~t~~~y~LdD---------------gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G  125 (265)
                      ++.|.|+|+|..   ++..   ...+.|+|-=               .|--|.|..|...++  .....|+.|+.|.|.|
T Consensus         4 ~N~V~LiGrL~~DPElR~T~~G~~Va~FsLAvn~R~~d~~~Ge~~d~~T~wi~VvawgklAE--~v~~~L~KG~~V~VeG   81 (199)
T 3eiv_A            4 ETVITVVGNLVDDPELRFTPSGAAVAKFRVASTPRTFDRQTNEWKDGESLFLTCSVWRQAAE--NVAESLQRGMRVIVQG   81 (199)
T ss_dssp             CCEEEEEEEESSCCEEEECTTCCEEEEEEEEECC-----------CCCCEEEEEEEETHHHH--HHHHHCCTTCEEEEEE
T ss_pred             ccEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCcccccCCCcEecCccEEEEEEEEhHHHH--HHHHhcCCCCEEEEEE
Confidence            467888888854   2221   2345555531               233488999976432  1234589999999999


Q ss_pred             Eeee--eCCc-------cEEEEEEeee
Q 024592          126 HLKA--FQDK-------RSLNAYSLRP  143 (265)
Q Consensus       126 ~i~~--f~~~-------~~i~~~~i~~  143 (265)
                      +|+.  |.++       ..|.+..|.+
T Consensus        82 rL~~rswedkdG~kr~~~eVvA~~Ig~  108 (199)
T 3eiv_A           82 RLKQRSYEDREGVKRTVYELDVDEVGA  108 (199)
T ss_dssp             EEEEEC--------CCEEEEEEEEEEE
T ss_pred             EEEeeEEECCCCCEEEEEEEEEEEEec
Confidence            9986  4322       3455555554

>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3

Probab=85.49  E-value=3.5  Score=36.35  Aligned_cols=77  Identities=23%  Similarity=0.380  Sum_probs=50.3

Q ss_pred             EeEEEEEEEEEE---eee---CCCeEEEEEE------cCCC-------eEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592           67 VNTITVVGIVCD---MQD---KEPQFIFLID------DGTG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGHL  127 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld------DgTG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i  127 (265)
                      ++.|.|+|.|..   ++.   ....+.|.|.      |..|       -|.|..|...+.  .... ++.|+.|.|.|+|
T Consensus       129 mN~V~L~GrL~~dPelr~t~~G~~v~~f~lAv~~~~~d~~Ge~~~~t~~i~vvawg~~Ae--~~~~-l~KG~~V~V~GrL  205 (301)
T 1se8_A          129 MNEVLVLGNVTRDPEIRYTPAGDAVLSLSIAVNENYQDRQGQRQEKVHYIDATLWRDLAE--NMKE-LRKGDPVMIMGRL  205 (301)
T ss_dssp             EEEEEEEEEECSCCEEEECTTCCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHHH--HHTT-CCTTCEEEEEEEE
T ss_pred             eeEEEEEEEECcCCEEEECCCCCEEEEEEEEEcCceEcCCCCcccccEEEEEEECCHHHH--HHHh-cCCCCEEEEEEEE
Confidence            688999999965   222   1245666663      2223       488889975432  1234 9999999999999


Q ss_pred             ee--eCCc-------cEEEEEEeeeCCC
Q 024592          128 KA--FQDK-------RSLNAYSLRPIID  146 (265)
Q Consensus       128 ~~--f~~~-------~~i~~~~i~~v~d  146 (265)
                      +.  |.++       ..|.+..|..+..
T Consensus       206 ~~~~y~dkdG~~r~~~ev~a~~i~~l~~  233 (301)
T 1se8_A          206 VNEGWTDKDGNKRNSTRVEATRVEALAR  233 (301)
T ss_dssp             EEEECC------CEEEEEEEEEEEECCC
T ss_pred             eeeeEECCCCcEEEEEEEEEEEEEEecc
Confidence            86  5432       3577777777654

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=85.44  E-value=2.8  Score=30.64  Aligned_cols=61  Identities=21%  Similarity=0.162  Sum_probs=47.7

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .+++..+=.||..|.+......+..++..+|++++.++...+...|..|...|+|=. .++|
T Consensus        12 ~gl~~~q~~vL~~L~~~~~~~~g~~~s~~eLa~~l~l~~stLsR~l~rLe~~GLV~r~~~~D   73 (96)
T 2obp_A           12 DGIDPAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVSVEAD   73 (96)
T ss_dssp             -CCCHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTT
T ss_pred             cCCCHHHHHHHHHHHHHHhhCCCCCcCHHHHHHHhCCchhhHHHHHHHHHHCCCEEeecCCC
Confidence            457778888888776542212334589999999999999999999999999999988 6644

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=85.26  E-value=1.4  Score=35.21  Aligned_cols=49  Identities=18%  Similarity=0.169  Sum_probs=38.5

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..-.+|-+|...   ..+.-++.++|++++++++.-++++|..|...|.|.+
T Consensus        28 yAlr~L~~LA~~---~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s   76 (159)
T 3lwf_A           28 YGLTITLELAKR---IGDGPISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKS   76 (159)
T ss_dssp             HHHHHHHHHHHT---TTSCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhc---CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEE
Confidence            334455555432   1233589999999999999999999999999999998

>3afp_A Single-stranded DNA-binding protein; OB-fold, quaternary structure and stability, changes on oligomerisation, water-bridges, DNA damage; 2.05A {Mycobacterium leprae} PDB: 3afq_A 1ue1_A 1ue5_A 1ue6_A 1ue7_A 1x3e_A 1x3f_A 1x3g_A 3a5u_A*

Probab=85.12  E-value=1.6  Score=35.18  Aligned_cols=61  Identities=25%  Similarity=0.389  Sum_probs=40.0

Q ss_pred             EeEEEEEEEEEE---eeeC---CCeEEEEEEc---------------CCCeEEEEEecccccccccccccCCCCEEEEEE
Q 024592           67 VNTITVVGIVCD---MQDK---EPQFIFLIDD---------------GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG  125 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~~---~t~~~y~LdD---------------gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G  125 (265)
                      ++.|.|+|.|..   ++..   ...+.|+|.=               .|--|.|..|...+.  .....|+.|+.|.|.|
T Consensus         4 ~N~V~LiG~L~~dPelr~t~~G~~va~f~lAv~~~~~~~~~Ge~~d~~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~VeG   81 (168)
T 3afp_A            4 DTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDRQSGEWKDGEALFLRCNIWREAAE--NVAESLTRGARVIVTG   81 (168)
T ss_dssp             CCEEEEEEEESSSCCCEECTTSCEEEEEEEEECC--------CCCCCCCEEEEEEEEHHHHH--HHHHHCCTTCEEEEEE
T ss_pred             cCEEEEEEEECCCCEEEECCCCCEEEEEEEEEccccccccCCcEecCCcEEEEEEEehHHHH--HHHHhCCCCCEEEEEE
Confidence            467888998854   2211   2355666641               133489999975432  1234689999999999


Q ss_pred             Eeee
Q 024592          126 HLKA  129 (265)
Q Consensus       126 ~i~~  129 (265)
                      +|+.
T Consensus        82 rL~~   85 (168)
T 3afp_A           82 RLKQ   85 (168)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            9986

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=85.07  E-value=3  Score=32.05  Aligned_cols=57  Identities=11%  Similarity=0.086  Sum_probs=45.4

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEe-ecCC-----ceeeccC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDEF-----HYKSAVN  264 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYs-iDd~-----hyk~t~~  264 (265)
                      .....||..|..       ..+.+.+|++.+ +++...+...|..|.++|.|-- .+.+     .|..|.-
T Consensus        26 kW~l~IL~~L~~-------g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT~~   89 (131)
T 4a5n_A           26 KWKGILFYHMID-------GKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEF   89 (131)
T ss_dssp             SSHHHHHHHHTT-------SCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTT
T ss_pred             cCHHHHHHHHhc-------CCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEECHh
Confidence            355667777642       257999999999 9999999999999999999998 6653     5666654

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=85.07  E-value=1.9  Score=34.38  Aligned_cols=50  Identities=16%  Similarity=0.232  Sum_probs=42.5

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-------CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-------NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-------~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++..+..||++|.+.     +.-++.++|.+.+       +++...|-.+|+.|.+.|.|-.
T Consensus        31 ~T~qR~~IL~~L~~~-----~~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~~   87 (162)
T 4ets_A           31 YTKQREVLLKTLYHS-----DTHYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVTS   87 (162)
T ss_dssp             CCHHHHHHHHHHHSC-----CSCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHhC-----CCCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEEE
Confidence            467888899999863     3468999998766       3889999999999999999977

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=84.71  E-value=1.5  Score=37.65  Aligned_cols=55  Identities=18%  Similarity=0.193  Sum_probs=42.5

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCcee
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYK  260 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk  260 (265)
                      +...|++.+++.+.    .--.+.+|+..+++++.++++.|..|..+|.|..++++.|-
T Consensus       142 ~~~~i~~~~~~~g~----~pp~~~dl~~~l~~~~~~~~~~l~~l~~~g~lv~l~~~~~~  196 (258)
T 1lva_A          142 LLKDLEDKYRVSRW----QPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYW  196 (258)
T ss_dssp             HHHHHHHHHHHHTT----SCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEESSSSBEE
T ss_pred             HHHHHHHHHHHCCC----CCCCHHHHHhHhCCCHHHHHHHHHHHHHCCCEEEecCCeEE
Confidence            44556666654321    12378999999999999999999999999999997676664

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=84.65  E-value=0.1  Score=41.56  Aligned_cols=49  Identities=16%  Similarity=0.297  Sum_probs=42.4

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +..+...|++.|+..      .-++..+|+++++++...|+++|..|.++|.|..
T Consensus        11 ~d~l~~~Il~~l~~~------~~ls~~eLa~~lgvSr~~vr~al~~L~~~Gli~~   59 (163)
T 2gqq_A           11 LDRIDRNILNELQKD------GRISNVELSKRVGLSPTPCLERVRRLERQGFIQG   59 (163)
T ss_dssp             CCSHHHHHHHHHHHC------SSCCTTGGGTSSSCCTTTSSSTHHHHHHHTSEEE
T ss_pred             hhHHHHHHHHHHHhC------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence            567899999987642      3568999999999999999999999999999963

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=84.37  E-value=1.6  Score=34.66  Aligned_cols=49  Identities=10%  Similarity=0.015  Sum_probs=40.3

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC-CCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLN-LPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~-~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-+..||..|...+    ..-.++++|++.+. ++...|...|+.|.+.|.|-.
T Consensus        29 ~tR~~IL~~Ll~~p----~~~~ta~eL~~~l~~lS~aTVyrhL~~L~eaGLV~~   78 (151)
T 3u1d_A           29 ETRLDVLHQILAQP----DGVLSVEELLYRNPDETEANLRYHVDELVDRGIVEK   78 (151)
T ss_dssp             HHHHHHHHHHHHST----TSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             hHHHHHHHHHHcCC----CCCCCHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEE
Confidence            45667888876531    22379999999997 999999999999999999986

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=84.23  E-value=0.87  Score=45.52  Aligned_cols=66  Identities=14%  Similarity=0.230  Sum_probs=47.3

Q ss_pred             eEEEEEEEEEEeee----CCCeEEEEEEcCCCeEEEEEecccccccccccccCC--CCEEEEEEEeeee--CCccEEE
Q 024592           68 NTITVVGIVCDMQD----KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISK--GMYVRVYGHLKAF--QDKRSLN  137 (265)
Q Consensus        68 ~~V~iVG~V~~v~~----~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~--g~yVrV~G~i~~f--~~~~~i~  137 (265)
                      ..|+|.|.|.+...    ....+...+.|+||.|.+.+|.. ..   ....++.  |..+.|+|+++.+  .+..++.
T Consensus       166 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~f~~-~~---~~~~~~~~~g~~~~~~G~~~~~~~~~~~~~~  239 (780)
T 1gm5_A          166 EKVTTQGKIVSVETKKFQNMNILTAVLSDGLVHVPLKWFNQ-DY---LQTYLKQLTGKEVFVTGTVKSNAYTGQYEIH  239 (780)
T ss_dssp             CCCEEEECCCCCEEEECSSCEEEEEEECCSSCCEEEEECSC-CT---THHHHHTTCSSCEEEEEEECSCCTTSSCCEE
T ss_pred             CEEEEEEEEEEEEeecCCCCeEEEEEEEECCceEEEEEECc-HH---HHhhCccCCCCEEEEEEEEEEccCCCcEEEE
Confidence            37889999977632    23467788999999999887752 11   2345678  9999999999985  4544443

>2hs5_A Putative transcriptional regulator GNTR; APC6050, rhodococcus SP. RH structural genomics, PSI-2, protein structure initiative; 2.20A {Rhodococcus SP} SCOP: a.4.5.6 a.78.1.1

Probab=84.02  E-value=1.6  Score=36.82  Aligned_cols=53  Identities=23%  Similarity=0.237  Sum_probs=39.3

Q ss_pred             hhHHHHHHHhcCc---CCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRP---EFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~---~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+...|++.|++.   +......=++..+|+++|+++..-||+||..|..+|.|..
T Consensus        28 ~~~~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~   83 (239)
T 2hs5_A           28 SRTTRVAGILRDAIIDGTFRPGARLSEPDICAALDVSRNTVREAFQILIEDRLVAH   83 (239)
T ss_dssp             HHHHHHHHHHHHHHHHTSSCTTCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cHHHHHHHHHHHHHHcCCCCCcCEeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            3455555555421   1123344579999999999999999999999999999976

>1z9f_A Single-strand binding protein; TM0604, single stranded DNA-binding protein, structural GENO joint center for structural genomics, JCSG; 2.30A {Thermotoga maritima}

Probab=83.96  E-value=4  Score=32.30  Aligned_cols=78  Identities=18%  Similarity=0.220  Sum_probs=45.9

Q ss_pred             EeEEEEEEEEEE---eee---CCCeEEEEEE--c-----C------CCeEEEEEecccccccccccccCCCCEEEEEEEe
Q 024592           67 VNTITVVGIVCD---MQD---KEPQFIFLID--D-----G------TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHL  127 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld--D-----g------TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i  127 (265)
                      ++.|.|+|+|..   ++.   ....+.|+|.  .     .      |--|.|..|...+.  .....++.|+.|.|.|+|
T Consensus        16 ~N~V~LiGrL~~DPelr~t~~G~~va~f~lAv~~r~~~~~~Ge~~~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~VeGrL   93 (153)
T 1z9f_A           16 FNKIILIGRLVRDPEERYTLSGTPVTTFTIAVDRVPRKNAPDDAQTTDFFRIVTFGRLAE--FARTYLTKGRLVLVEGEM   93 (153)
T ss_dssp             CCCEEEEEEESSCCEEEECC--CEEEEEEEEEEC-----------CEEEEEEEEEHHHHH--HHHHHCCTTCEEEEEEEE
T ss_pred             eeEEEEEEEECCCCEEEECCCCCEEEEEEEEEcCCccccCCCCEeeeEEEEEEEECHHHH--HHHhhCCCCCEEEEEEEE
Confidence            567888888854   221   1234555553  1     1      23488889965332  123458999999999999


Q ss_pred             ee--eC---Cc----cEEEEEEeeeCCC
Q 024592          128 KA--FQ---DK----RSLNAYSLRPIID  146 (265)
Q Consensus       128 ~~--f~---~~----~~i~~~~i~~v~d  146 (265)
                      +.  |.   |+    ..|.+..|..+..
T Consensus        94 ~~~~~~dkdG~~r~~~eV~a~~i~~l~~  121 (153)
T 1z9f_A           94 RMRRWETPTGEKRVSPEVVANVVRFMDR  121 (153)
T ss_dssp             EEEC-------CCCEEEEEEEEEEECC-
T ss_pred             EeceEECCCCCEEEEEEEEEEEEEEccC
Confidence            86  43   22    2577777776654

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0

Probab=83.60  E-value=2.4  Score=31.36  Aligned_cols=58  Identities=14%  Similarity=0.163  Sum_probs=44.0

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEe-ec-CCceeecc
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-ID-EFHYKSAV  263 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYs-iD-d~hyk~t~  263 (265)
                      .....||..|...     +.-+++.+|++.+ +++...+...|..|.+.|.|-. .+ .-.|..|.
T Consensus        27 ~wrl~IL~~L~~g-----~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~r~~~y~LT~   87 (111)
T 3df8_A           27 KYTMLIISVLGNG-----STRQNFNDIRSSIPGISSTILSRRIKDLIDSGLVERRSGQITTYALTE   87 (111)
T ss_dssp             TTHHHHHHHHTSS-----SSCBCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEEESSSEEEEECH
T ss_pred             ccHHHHHHHHhcC-----CCCCCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEeecCcEEEEECc
Confidence            4566788888631     2225599999999 8999999999999999999988 55 22455443

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=83.60  E-value=1.6  Score=37.35  Aligned_cols=56  Identities=11%  Similarity=0.119  Sum_probs=48.4

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      .+++.-|-.||.+|...+    +.+++..+|++.++++...|-.+|+.|...|.|.- -|+
T Consensus       154 ~gLt~~q~~vL~~L~~~~----~~~~t~~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~~~~  210 (250)
T 1p4x_A          154 LTLSFVEFTILAIITSQN----KNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERST  210 (250)
T ss_dssp             CSSCHHHHHHHHHHHTTT----TCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECS
T ss_pred             CCCCHHHHHHHHHHHhCC----CCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCCC
Confidence            468888999999997631    23699999999999999999999999999999998 654

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=83.02  E-value=2.4  Score=30.34  Aligned_cols=42  Identities=14%  Similarity=0.239  Sum_probs=34.6

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      ..|++.++.|+.++ .       +|.+..+|++.|++++..|+..+..+.
T Consensus        26 ~~Lt~~e~~vl~l~-~-------~g~s~~eIA~~l~is~~tV~~~l~r~~   67 (95)
T 3c57_A           26 SGLTDQERTLLGLL-S-------EGLTNKQIADRMFLAEKTVKNYVSRLL   67 (95)
T ss_dssp             -CCCHHHHHHHHHH-H-------TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHH-H-------cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            46888999999887 2       389999999999999999888776554

>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=82.96  E-value=0.86  Score=41.14  Aligned_cols=43  Identities=19%  Similarity=0.224  Sum_probs=38.9

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..||++|+ .+      .++..+|++.++++...|.+.+++|+++|.|..
T Consensus        23 ~~il~~l~-~~------~~sr~~la~~~gls~~tv~~~v~~L~~~gli~~   65 (380)
T 2hoe_A           23 SRILKRIM-KS------PVSRVELAEELGLTKTTVGEIAKIFLEKGIVVE   65 (380)
T ss_dssp             CCSHHHHH-HS------CBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHH-cC------CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            34888888 62      689999999999999999999999999999987

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=82.95  E-value=1.4  Score=34.43  Aligned_cols=43  Identities=9%  Similarity=0.036  Sum_probs=35.2

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      .-++.++|++++++++.-+++++..|...|.|.+ --.--|..+
T Consensus        29 ~~~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~rG~GGy~L~   72 (149)
T 1ylf_A           29 SLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRGPGGAGLL   72 (149)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---CCEEES
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEccCCCceEeC
Confidence            3589999999999999999999999999999998 333345544

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=82.77  E-value=0.95  Score=37.25  Aligned_cols=44  Identities=9%  Similarity=0.075  Sum_probs=37.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSL  250 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~  250 (265)
                      .=|+.|++.|++.      .-++++++++.|+.+++.||.-|.+|...+.
T Consensus        12 eR~~~i~~~l~~~------~~~~~~~la~~~~vs~~TiRrDl~eL~~~~l   55 (190)
T 4a0z_A           12 KRREAIRQQIDSN------PFITDHELSDLFQVSIQTIRLDRTYLNIPEL   55 (190)
T ss_dssp             HHHHHHHHHHHHC------TTCCHHHHHHHHTSCHHHHHHHHHHHTCCCH
T ss_pred             HHHHHHHHHHHHC------CCEeHHHHHHHHCCCHHHHHHHHHHhcCcch
Confidence            3567799999874      3589999999999999999999999988764

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=82.57  E-value=1.8  Score=33.10  Aligned_cols=55  Identities=13%  Similarity=0.202  Sum_probs=43.3

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEe-ecCC-----ceeecc
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDEF-----HYKSAV  263 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYs-iDd~-----hyk~t~  263 (265)
                      ..-.||..|. .      .++++.+|++.+ +++...+...|+.|.+.|.|-. .|..     .|..|.
T Consensus        36 w~l~IL~~L~-~------g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~   97 (131)
T 1yyv_A           36 WGVLILVALR-D------GTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTP   97 (131)
T ss_dssp             HHHHHHHHGG-G------CCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECH
T ss_pred             cHHHHHHHHH-c------CCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEECc
Confidence            4455676664 2      368999999999 7999999999999999999998 6642     455553

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=82.37  E-value=2  Score=31.40  Aligned_cols=42  Identities=17%  Similarity=0.201  Sum_probs=35.3

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      ..|++-+.+||.++.        +|++..||++.|++++..|+.-+..+.
T Consensus        33 ~~Lt~re~~Vl~l~~--------~G~s~~EIA~~L~iS~~TV~~~l~ri~   74 (99)
T 1p4w_A           33 KRLSPKESEVLRLFA--------EGFLVTEIAKKLNRSIKTISSQKKSAM   74 (99)
T ss_dssp             SSCCHHHHHHHHHHH--------HTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            568899999998864        389999999999999999888776554

>1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1

Probab=82.31  E-value=1.3  Score=40.83  Aligned_cols=56  Identities=16%  Similarity=0.144  Sum_probs=48.5

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      -+++.-|-.||.+|.+.    .+.|++..+|+++++++...|...|+.|+..|.|.- -|+
T Consensus       400 ~~lt~~q~~vl~~l~~~----~~~~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~~~~  456 (487)
T 1hsj_A          400 FNLNYEEIYILNHILRS----ESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSL  456 (487)
T ss_dssp             CCCCHHHHHHHHHHHTC----SCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECC
T ss_pred             cCCCHHHHHHHHHHHhC----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCC
Confidence            46888888899999763    246899999999999999999999999999999988 554

>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3

Probab=82.24  E-value=4  Score=35.98  Aligned_cols=77  Identities=14%  Similarity=0.218  Sum_probs=45.7

Q ss_pred             EeEEEEEEEEEE---eee---CCCeEEEEEE------cCCC-------eEEEEEecccccccccccc-cCCCCEEEEEEE
Q 024592           67 VNTITVVGIVCD---MQD---KEPQFIFLID------DGTG-------RIECSRWAHEQMEFNEVNQ-ISKGMYVRVYGH  126 (265)
Q Consensus        67 v~~V~iVG~V~~---v~~---~~t~~~y~Ld------DgTG-------~I~~~~w~~~~~~~~~~~~-~~~g~yVrV~G~  126 (265)
                      ++.|.|+|.|..   ++.   ....+.|.|.      |.+|       -|.|..|...+.  ..... ++.|+.|.|.|+
T Consensus         5 mN~V~LiGrL~~dPelr~t~~G~~v~~f~LAv~r~~~~~~G~~~~~t~~i~vv~~g~~Ae--~~~~~~l~KG~~V~VeG~   82 (301)
T 1se8_A            5 MNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGRERNLPWYHRVSILGKPAE--WQAERNLKGGDAVVVEGT   82 (301)
T ss_dssp             EEEEEEEEEESSCCEEEECTTSCEEEEEEEEEEEEC-------CEEEEEEEEEEESHHHH--HHHHTCCCTTCEEEEEEE
T ss_pred             eeEEEEEEEECCCceEEECCCCCEEEEEEEEEcCceECCCCCEecceEEEEEEEEcHHHH--HHHhhCCCCCCEEEEEEE
Confidence            688999999854   221   2245666662      1223       378888865332  12234 799999999999


Q ss_pred             eee--eCCc---c----EEEEEEeeeCC
Q 024592          127 LKA--FQDK---R----SLNAYSLRPII  145 (265)
Q Consensus       127 i~~--f~~~---~----~i~~~~i~~v~  145 (265)
                      |+.  |.++   +    .|.+..|..+.
T Consensus        83 L~~r~~~dkdG~~r~~~ev~a~~i~~l~  110 (301)
T 1se8_A           83 LEYRQWEAPEGGKRSAVNVKALRMEQLG  110 (301)
T ss_dssp             EEEEEEC-----CEEEEEEEEEEEEECS
T ss_pred             EEeeeEECCCCCEEEEEEEEEeEEEEee
Confidence            984  6543   2    35566665554

>2fxq_A Single-strand binding protein; strand beta-sheet extended loops, DNA binding protein; 1.85A {Thermus aquaticus} PDB: 2ihe_A 2cwa_A 2ihf_A

Probab=82.07  E-value=5.9  Score=33.96  Aligned_cols=78  Identities=15%  Similarity=0.224  Sum_probs=51.6

Q ss_pred             EEeEEEEEEEEEE---eeeC---CCeEEEEEE----------cCCCeEEEEEecccccccccccccCCCCEEEEEEEeee
Q 024592           66 DVNTITVVGIVCD---MQDK---EPQFIFLID----------DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA  129 (265)
Q Consensus        66 ~v~~V~iVG~V~~---v~~~---~t~~~y~Ld----------DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~  129 (265)
                      .++.|.|+|+|..   ++..   ...+.|.|.          |.|--|.|..|...+.  ... .++.|+.|.|.|+|+.
T Consensus       127 ~~N~v~l~G~l~~dpe~r~t~~G~~v~~f~lAv~~~~~g~~~~~t~~~~v~~wg~~Ae--~~~-~l~KG~~V~V~G~l~~  203 (264)
T 2fxq_A          127 ALNQVILMGNLTRDPDLRYTPQGTAVVRLGLAVNERRRGQEEERTHFLEVQAWRELAE--WAS-ELRKGDGLLVIGRLVN  203 (264)
T ss_dssp             CCEEEEEEEEESSCCCCEECTTCCEEEEEEEEEECCC-------EEEEEEEEEHHHHH--HHT-TCCTTCEEEEEEEEEE
T ss_pred             ceEEEEEEEEECCCCEEEECCCCCEEEEEEEEEcCCcCCCCccccEEEEEEEEChHHH--Hhh-hcCCCCEEEEEEEEEe
Confidence            3689999999965   2221   245667663          2233599999965432  224 8899999999999986


Q ss_pred             --eC---Cc----cEEEEEEeeeCCC
Q 024592          130 --FQ---DK----RSLNAYSLRPIID  146 (265)
Q Consensus       130 --f~---~~----~~i~~~~i~~v~d  146 (265)
                        |.   |+    ..|.+..|..+..
T Consensus       204 ~~~~~~dG~~~~~~ev~a~~i~~l~~  229 (264)
T 2fxq_A          204 DSWTSSSGERRFQTRVEALRLERPTR  229 (264)
T ss_dssp             EEEECTTSCEEEEEEEEEEEEECCCC
T ss_pred             eEEECCCCCEEEEEEEEEEEEEECcc
Confidence              43   33    2477777777754

>3cuq_B Vacuolar protein-sorting-associated protein 36; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_B

Probab=82.03  E-value=2  Score=36.12  Aligned_cols=50  Identities=6%  Similarity=0.053  Sum_probs=44.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .++..+..|+++++..      .++++.++++.++.+..-.+++|+.|+.+|.+.-
T Consensus       151 ~~~~~~~~il~~~~~~------g~vt~~~la~~l~ws~~~a~e~L~~~e~~G~l~~  200 (218)
T 3cuq_B          151 KEEEMVASALETVSEK------GSLTSEEFAKLVGMSVLLAKERLLLAEKMGHLCR  200 (218)
T ss_dssp             CGGGGHHHHHHHHHHT------SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             chHHHHHHHHHHHHHC------CCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCEEE
Confidence            4567899999999753      4899999999999999999999999999999886

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=81.92  E-value=1.4  Score=37.71  Aligned_cols=55  Identities=15%  Similarity=0.203  Sum_probs=47.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++.-|=.||.+|.+.    .+.|++..+|++.+.++...|...|+.|+..|.|.- -|+
T Consensus        31 ~lt~~q~~vL~~L~~~----~~~~~~~~el~~~l~~~~~t~t~~l~rLe~~G~i~R~~~~   86 (250)
T 1p4x_A           31 DMTIKEFILLTYLFHQ----QENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSK   86 (250)
T ss_dssp             SSCHHHHHHHHHHHSC----SCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECS
T ss_pred             CCCHHHHHHHHHHHhc----CCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCC
Confidence            5778888899999763    235899999999999999999999999999999998 554

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=81.53  E-value=5.1  Score=26.40  Aligned_cols=47  Identities=9%  Similarity=0.031  Sum_probs=35.1

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      ..|++-++.|+...---   ...+|.+..||++.+++++..|+..+....
T Consensus         4 ~~L~~~er~il~l~~~l---~~~~g~s~~eIA~~lgis~~tV~~~~~ra~   50 (68)
T 2p7v_B            4 AGLTAREAKVLRMRFGI---DMNTDYTLEEVGKQFDVTRERIRQIEAKAL   50 (68)
T ss_dssp             CCCCHHHHHHHHHHTTT---TSSSCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHcc---CCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            34778888888776421   113599999999999999999888766543

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=81.49  E-value=4.4  Score=27.19  Aligned_cols=47  Identities=13%  Similarity=0.205  Sum_probs=34.9

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHH----HHHHHh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLME----ALESLN  246 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~----al~~L~  246 (265)
                      ..|++-++.|+...---   ..++|.+..+|++.+++++..|+.    ++..|-
T Consensus         9 ~~L~~~er~il~l~~~l---~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A            9 SKLSEREAMVLKMRKGL---IDGREHTLEEVGAYFGVTRERIRQIENKALRKLK   59 (73)
T ss_dssp             TTSCHHHHHHHHHHHTT---TTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHhc---ccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            45778888888765421   223699999999999999999887    445554

>3c7j_A Transcriptional regulator, GNTR family; structural genomics, PSI-2, protein structure initiative, midwest center for STR genomics; HET: MSE; 2.10A {Pseudomonas syringae PV}

Probab=81.37  E-value=3.5  Score=34.64  Aligned_cols=36  Identities=17%  Similarity=0.262  Sum_probs=32.6

Q ss_pred             CCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          218 NNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       218 ~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ...=++..+|+++|+.+..-||+||..|..+|.|..
T Consensus        46 pG~~L~e~~La~~lgVSr~~VReAL~~L~~~Glv~~   81 (237)
T 3c7j_A           46 SGTALRQQELATLFGVSRMPVREALRQLEAQSLLRV   81 (237)
T ss_dssp             TTCBCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CcCeeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            345679999999999999999999999999999976

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=81.25  E-value=2.6  Score=27.01  Aligned_cols=36  Identities=17%  Similarity=0.344  Sum_probs=28.7

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      +..|+.++.        +|.+..+|++.|++++..|+..+..+.
T Consensus         3 e~~vl~l~~--------~g~s~~eIA~~l~is~~tV~~~~~~~~   38 (61)
T 2jpc_A            3 ERQVLKLID--------EGYTNHGISEKLHISIKTVETHRMNMM   38 (61)
T ss_dssp             HHHHHHHHH--------TSCCSHHHHHHTCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHH--------cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            456777653        388999999999999999988776654

>3ulp_A Single-strand binding protein; OB-fold, DNA binding, single-stranded DNA, apicoplast, DNA B protein-DNA complex; HET: DNA; 2.10A {Plasmodium falciparum}

Probab=81.23  E-value=2.6  Score=31.96  Aligned_cols=66  Identities=20%  Similarity=0.182  Sum_probs=42.5

Q ss_pred             eEEeEEEEEEEEEE---eee--C-CCeEEEEEE------cC-CC-------eEEEEEec-ccccccccccccCCCCEEEE
Q 024592           65 ADVNTITVVGIVCD---MQD--K-EPQFIFLID------DG-TG-------RIECSRWA-HEQMEFNEVNQISKGMYVRV  123 (265)
Q Consensus        65 ~~v~~V~iVG~V~~---v~~--~-~t~~~y~Ld------Dg-TG-------~I~~~~w~-~~~~~~~~~~~~~~g~yVrV  123 (265)
                      ..++.|.|+|.|..   ++.  . ...+.|.|-      |. +|       -|.|..|. ..+.  .....++.|+.|.|
T Consensus         4 ~~~N~v~l~Grl~~dpelr~t~~G~~v~~f~lA~~~~~~~~~~G~~~~~t~~~~v~~wg~~~Ae--~~~~~l~KG~~V~V   81 (124)
T 3ulp_A            4 KSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVD--LIDKYLRKGRRVYV   81 (124)
T ss_dssp             CCEEEEEEEEEECSCCEEEECTTSCEEEEEEEEEEEEEECTTTCCEEEEEEEEEEEECCHHHHH--HHHHHCCTTCEEEE
T ss_pred             ccceEEEEEEEECCCcEEEECCCCCEEEEEEEEEccceecccCCcEecccEEEEEEEEEchHHH--HHHhhcCCCCEEEE
Confidence            34789999999965   222  1 235666662      21 34       38888887 4332  12335899999999


Q ss_pred             EEEee--eeCC
Q 024592          124 YGHLK--AFQD  132 (265)
Q Consensus       124 ~G~i~--~f~~  132 (265)
                      .|+|+  .|.+
T Consensus        82 ~G~L~~~~~~d   92 (124)
T 3ulp_A           82 QGSLHTRKWHT   92 (124)
T ss_dssp             EEEEEEEEECC
T ss_pred             EEEEEeEEEeC
Confidence            99997  4654

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=81.18  E-value=0.3  Score=43.79  Aligned_cols=48  Identities=13%  Similarity=0.126  Sum_probs=0.0

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..-+..||..|..      ..+++..+|+++|++++..|+..|+.|.++|.|..
T Consensus        19 ~~r~~~iL~~l~~------~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~Glv~~   66 (345)
T 2o0m_A           19 LQERFQILRNIYW------MQPIGRRSLSETMGITERVLRTETDVLKQLNLIEP   66 (345)
T ss_dssp             ------------------------------------------------------
T ss_pred             hHHHHHHHHHHHH------cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            3456668888765      34899999999999999999999999999999974

>4dam_A Single-stranded DNA-binding protein 1; OB-fold; 1.70A {Streptomyces coelicolor}

Probab=81.09  E-value=1.9  Score=33.18  Aligned_cols=63  Identities=22%  Similarity=0.223  Sum_probs=40.5

Q ss_pred             eEEeEEEEEEEEEE---ee--eCCCeEEEEEE------c-CCC--------eEEEEEecccccccccccccCCCCEEEEE
Q 024592           65 ADVNTITVVGIVCD---MQ--DKEPQFIFLID------D-GTG--------RIECSRWAHEQMEFNEVNQISKGMYVRVY  124 (265)
Q Consensus        65 ~~v~~V~iVG~V~~---v~--~~~t~~~y~Ld------D-gTG--------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~  124 (265)
                      ..++.|.|+|.|..   +.  .....+.|.|-      | .+|        -+.|..|...++  .....++.|+.|.|.
T Consensus        13 ~~~N~V~LiGrL~~dPelr~t~~G~v~~fslAv~~~~~d~~~Ge~~d~~t~w~~v~~wg~~Ae--~~~~~l~KG~~V~Ve   90 (128)
T 4dam_A           13 MNEIMICAVGNVATTPVFRDLANGPSVRFRLAVTARYWDREKNAWTDGHTNFFTVWANRQLAT--NASGSLAVGDPVVVQ   90 (128)
T ss_dssp             BCCCEEEEEEEECSCCEEEEETTEEEEEEEEEEEEEEEETTTTEEEEEEEEEEEEEEEHHHHH--HHHHHCCTTCEEEEE
T ss_pred             cceeEEEEEEEECCCCEEEEcCCCCEEEEEEEEcCceecccCCceecCCcEEEEEEEEcHHHH--HHHHhcCCCCEEEEE
Confidence            45788999999854   11  11245666662      2 123        377888865332  123458999999999


Q ss_pred             EEeee
Q 024592          125 GHLKA  129 (265)
Q Consensus       125 G~i~~  129 (265)
                      |+|+.
T Consensus        91 GrL~~   95 (128)
T 4dam_A           91 GRLKV   95 (128)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            99975

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=80.85  E-value=2.5  Score=35.00  Aligned_cols=48  Identities=21%  Similarity=0.332  Sum_probs=42.2

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +.+..||.+|..       ..+++.+|++.++++...|...|..|.+.|.|-. .+
T Consensus        15 ~~rl~IL~~L~~-------~~~s~~eLa~~l~is~stvs~hLk~Le~~GLV~~~~~   63 (202)
T 2p4w_A           15 ETRRRILFLLTK-------RPYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVE   63 (202)
T ss_dssp             HHHHHHHHHHHH-------SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEee
Confidence            567789998853       2589999999999999999999999999999988 55

>4hik_A Protection of telomeres protein 1; specificity, plasticity, promiscuity, OB-fold, ssDNA binding stranded telomeric DNA; HET: DNA; 1.64A {Schizosaccharomyces pombe} PDB: 4hid_A* 4him_A* 4hio_A* 4hj5_A* 4hj7_A* 4hj8_A* 4hj9_A* 4hja_A*

Probab=80.56  E-value=4.8  Score=31.56  Aligned_cols=55  Identities=24%  Similarity=0.375  Sum_probs=38.1

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCC---------------------C--eEEEEEecccccccccccccCCCCEEEEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGT---------------------G--RIECSRWAHEQMEFNEVNQISKGMYVRVY  124 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgT---------------------G--~I~~~~w~~~~~~~~~~~~~~~g~yVrV~  124 (265)
                      .-+.+++.|+.+-.....+++.+.|.|                     |  +|.+..|.+-+.  -..+.+++|+||++.
T Consensus        15 ~F~Dl~~qVv~~~~~~~~~~LyVTDYT~N~~~~~~~~~~~~~~W~Gp~G~~tlqVtlwd~ha~--~ar~~lk~Gd~v~L~   92 (143)
T 4hik_A           15 QRCSFYAQVIKTWYSDKNFTLYVTDYTENELFFPMSPYTSSSRWRGPFGRFSIRCILWDEHDF--YCRNYIKEGDYVVMK   92 (143)
T ss_dssp             CEEEEEEEEEEEEECSSCEEEEEECSCCCTTSCCBCTTCTTCSCCCCCBSCCEEEEECHHHHH--HHTTTCCTTCEEEEE
T ss_pred             CeEEEEEEEEEEEcCCCeEEEEEecCCCCCcccccccCCCCccccCCCCcEEEEEEEECcHHH--HHHhhCCCCCEEEEE
Confidence            457788888887655588888888887                     2  456777765332  112458999999974

>3rlo_A Gamma-interferon-inducible protein 16; HIN200/OB fold/DNA binding, DNA binding/cytosolic DNA sensor cytosol, DNA binding protein; 1.80A {Homo sapiens} PDB: 3rnu_A* 3b6y_A 3rln_A

Probab=80.51  E-value=5.3  Score=32.89  Aligned_cols=58  Identities=16%  Similarity=0.164  Sum_probs=37.2

Q ss_pred             EEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEE-eeee-CCccEEEE
Q 024592           76 VCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAF-QDKRSLNA  138 (265)
Q Consensus        76 V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f-~~~~~i~~  138 (265)
                      |........++.|.|.|.||.++|..+-.-.     .-..++||-+|.+.= |+.- .++++|..
T Consensus       127 v~KK~v~~~~~~YeI~DnTG~MeVvv~G~~~-----~i~CEeGDKLrL~cFeL~~~~~~~~qL~s  186 (204)
T 3rlo_A          127 VHKKNVRGEFTYYEIQDNTGKMEVVVHGRLT-----TINCEEGDKLKLTCFELAPKSGNTGELRS  186 (204)
T ss_dssp             EEEEEEETTEEEEEEEETTEEEEEEECGGGG-----GCCCCTTCEEEEEEEEEECCTTTTCEEEE
T ss_pred             EEEEEeccceEEEEEecCCCcEEEEEeccCc-----ccccCCCCeeEEEEEEEecccCCceeEEE
Confidence            3344556679999999999999999764321     234578887766553 4432 24444443

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=80.41  E-value=2.8  Score=30.56  Aligned_cols=58  Identities=12%  Similarity=0.047  Sum_probs=47.9

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHH-hcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeec
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQ-QLNLPMDKLMEALESLNENSLVYS-IDEFHYKSA  262 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~-~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t  262 (265)
                      .+++..|-.||-+|...     + .++..+|++ .++++...|-..|+-|+.+|.|=. -||  ...|
T Consensus        12 ~~L~~~QfsiL~~L~~~-----~-~~t~~~Lae~~l~~drstvsrnl~~L~r~GlVe~~~~D--l~LT   71 (95)
T 1bja_A           12 DVLNEKTATILITIAKK-----D-FITAAEVREVHPDLGNAVVNSNIGVLIKKGLVEKSGDG--LIIT   71 (95)
T ss_dssp             TSSCHHHHHHHHHHHHS-----T-TBCHHHHHHTCTTSCHHHHHHHHHHHHTTTSEEEETTE--EEEC
T ss_pred             cCCCHHHHHHHHHHHHC-----C-CCCHHHHHHHHhcccHHHHHHHHHHHHHCCCeecCCCC--eeeC
Confidence            46788899999999763     2 889999999 889999999999999999999954 333  5444

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=80.24  E-value=1.5  Score=34.91  Aligned_cols=49  Identities=14%  Similarity=0.196  Sum_probs=39.3

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      ..-.+|-+|...    .+.-++.++|++++++++.-|+++|..|...|.|-+.
T Consensus        13 yAlr~l~~La~~----~~~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~   61 (162)
T 3k69_A           13 VAVHSILYLDAH----RDSKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGT   61 (162)
T ss_dssp             HHHHHHHHHHTT----TTSCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEE
T ss_pred             HHHHHHHHHHhC----CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            334566666653    1345899999999999999999999999999999773

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=80.14  E-value=2.6  Score=29.79  Aligned_cols=42  Identities=7%  Similarity=0.151  Sum_probs=35.0

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      ..|++.++.|+.++.        +|.+..+|++.|++++..|+..+..+.
T Consensus        28 ~~Lt~~e~~vl~l~~--------~g~s~~eIA~~l~is~~tV~~~l~r~~   69 (91)
T 2rnj_A           28 EMLTEREMEILLLIA--------KGYSNQEIASASHITIKTVKTHVSNIL   69 (91)
T ss_dssp             GGCCSHHHHHHHHHH--------TTCCTTHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            457888999998862        389999999999999999988876654

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=80.12  E-value=3  Score=28.20  Aligned_cols=41  Identities=12%  Similarity=0.129  Sum_probs=33.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      .|++.+..|+.++ .       .|.+..+|++.+++++..|+..+..+.
T Consensus        16 ~L~~~e~~vl~l~-~-------~g~s~~eIA~~l~is~~tV~~~~~r~~   56 (79)
T 1x3u_A           16 TLSERERQVLSAV-V-------AGLPNKSIAYDLDISPRTVEVHRANVM   56 (79)
T ss_dssp             HHCHHHHHHHHHH-T-------TTCCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHH-H-------cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3667888888876 2       389999999999999999998776654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	265
d2pi2a1	128	b.40.4.3 (A:44-171) Replication protein A 32 KDa s	1e-40
d1dpua_	69	a.4.5.16 (A:) C-terminal domain of RPA32 {Human (H	4e-08

>d2pi2a1 b.40.4.3 (A:44-171) Replication protein A 32 KDa subunit (RPA32) fragment {Human (Homo sapiens) [TaxId: 9606]} Length = 128

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 32 KDa subunit (RPA32) fragment
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  134 bits (340), Expect = 1e-40
 Identities = 37/128 (28%), Positives = 68/128 (53%), Gaps = 2/128 (1%)

Query: 40  TLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGR-IE 98
            ++P T+ QL   +  DE    I   +++ +T+VGI+   +      ++ IDD T   ++
Sbjct: 2   HIVPCTISQLLSATLVDEVF-RIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMD 60

Query: 99  CSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECI 158
             +W       +E   +    YV+V GHL++FQ+K+SL A+ + P+ D NE T+H +E I
Sbjct: 61  VRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVI 120

Query: 159 YVQLYNTR 166
              +  ++
Sbjct: 121 NAHMVLSK 128

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]} Length = 69

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (112), Expect = 4e-08
 Identities = 13/63 (20%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 204 QMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDEFHYKS 261
             VL+ ++         G++   +  QL ++ +  + +A++ L+    +YS +D+ H+KS
Sbjct: 9   NQVLNLIKA---CPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFKS 65

Query: 262 AVN 264
              
Sbjct: 66  TDA 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	265
d2pi2a1	128	Replication protein A 32 KDa subunit (RPA32) fragm	100.0
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	99.86
d1o7ia_	115	Archaeal ssDNA-binding protein {Archaeon Sulfolobu	97.8
d1c0aa1	106	Aspartyl-tRNA synthetase (AspRS) {Escherichia coli	97.74
d1n9wa1	93	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	97.69
d1nnxa_	106	Hypothetical protein YgiW {Escherichia coli [TaxId	97.61
d1b8aa1	103	Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ	97.5
d1wjja_	145	Hypothetical protein At4g28440 (F20O9.120) {Thale	97.5
d1l0wa1	104	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	97.48
d1eova1	134	Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S	97.46
d1e1oa1	143	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	97.12
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	96.92
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	96.77
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.72
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	96.6
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	96.57
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.55
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	96.52
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	96.29
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.26
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.25
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	95.95
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	95.79
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	95.7
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	95.5
d1gm5a2	180	RecG "wedge" domain {Thermotoga maritima [TaxId: 2	95.39
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	95.3
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	95.28
d1jmca2	122	Replication protein A 70 KDa subunit (RPA70) {Huma	94.69
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	94.65
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	94.64
d1jmca1	116	Replication protein A 70 KDa subunit (RPA70) {Huma	94.57
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	94.45
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	94.41
d1v1qa_	111	Primosomal replication protein N, PriB {Escherichi	94.32
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	94.31
d1xjva1	140	Protection of telomeres protein 1, Pot1 {Human (Ho	94.12
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	94.05
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	93.72
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	93.6
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	93.18
d1qzga_	170	Protection of telomeres protein 1, Pot1 {Fission y	93.15
d2oq0a1	88	Gamma-interferon-inducible protein Ifi-16 {Human (	93.11
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	92.94
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	92.87
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	92.7
d1l1oc_	178	Replication protein A 70 KDa subunit (RPA70) {Huma	92.68
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	92.67
d2pi2e1	115	Replication protein A 14 KDa (RPA14) subunit {Huma	92.64
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	92.51
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	92.27
d1zyba1	73	Probable transcription regulator BT4300, C-termina	92.19
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	92.16
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	92.01
d1qvca_	145	ssDNA-binding protein {Escherichia coli [TaxId: 56	91.94
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	91.92
d1y0ua_	89	Putative arsenical resistance operon repressor AF0	91.79
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	91.75
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	91.7
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	91.68
d1oyia_	62	dsRNA-binding protein E3 (E3L) {Vaccinia virus [Ta	91.5
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	91.41
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	91.37
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	91.12
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	90.99
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	90.88
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	90.55
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	90.42
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	89.97
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	89.88
d2dk8a1	68	DNA-directed RNA polymerase III subunit RPC6, RPO3	89.86
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	89.72
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	89.61
d1jb7a1	169	Telomere end binding protein alpha subunit {Oxytri	89.35
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	89.35
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	88.97
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	88.53
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	88.35
d1se8a_	231	ssDNA-binding protein {Deinococcus radiodurans [Ta	88.33
d2v9va2	73	C-terminal fragment of elongation factor SelB {Moo	88.16
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	88.15
d1sr3a_	114	Heme chaperone CcmE {Escherichia coli [TaxId: 562]	88.0
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	87.72
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	87.7
d1ue1a_	118	ssDNA-binding protein {Mycobacterium tuberculosis	87.57
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	87.08
d1ucra_	74	Dissimilatory sulfite reductase DsvD {Desulfovibri	86.29
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	85.83
d1j75a_	57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	85.78
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	84.53
d1in4a1	75	Holliday junction helicase RuvB {Thermotoga mariti	84.41
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	84.21
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	84.12
d1se8a_	231	ssDNA-binding protein {Deinococcus radiodurans [Ta	84.06
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	83.87
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	83.82
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	83.79
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	83.41
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	82.49
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	82.11
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	81.93
d1zara1	89	Rio2 serine protein kinase N-terminal domain {Arch	81.87
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	81.4
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	81.39
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	81.16
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	81.03
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	80.53
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	80.15
d3ulla_	115	ssDNA-binding protein {Human (Homo sapiens), mitoc	80.07

>d2pi2a1 b.40.4.3 (A:44-171) Replication protein A 32 KDa subunit (RPA32) fragment {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 32 KDa subunit (RPA32) fragment
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=7.7e-40  Score=258.98  Aligned_cols=127  Identities=28%  Similarity=0.536  Sum_probs=113.7

Q ss_pred             cceeeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCC-eEEEEEecccccccccccccCC
Q 024592           39 RTLLPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISK  117 (265)
Q Consensus        39 ~~~~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~  117 (265)
                      |+|+|||||||++|+. +++.|+++|+++++|+|||+|+++++.++++.|+|+|+|| .|+|++|.+++.+....+.+++
T Consensus         1 q~i~PvtI~ql~~a~~-~~~~f~i~g~~v~~V~iVG~V~~i~~~~t~~~y~idDgTG~~i~v~~w~~~~~~~~~~~~i~~   79 (128)
T d2pi2a1           1 QHIVPCTISQLLSATL-VDEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPP   79 (128)
T ss_dssp             CCCEECCHHHHHHCEE-ETTEEEETTEEESEEEEEEEEEEEEECSSEEEEEEECSSSSCEEEEEECC-------CCCCCT
T ss_pred             CceeeEEHHHHhcCcC-CCCCEEECCEEEEEEEEEEEEEEEEecCCEEEEEEECCCCCcEEEEEECCCCCCccccccccC
Confidence            6899999999999943 2568999999999999999999999999999999999999 5999999876655555678999


Q ss_pred             CCEEEEEEEeeeeCCccEEEEEEeeeCCChhHHHHHHHHHHHHHHHhcc
Q 024592          118 GMYVRVYGHLKAFQDKRSLNAYSLRPIIDFNEITSHFVECIYVQLYNTR  166 (265)
Q Consensus       118 g~yVrV~G~i~~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~~l~~~~  166 (265)
                      |+||||+|+||.|+++++|++++|+||+|+||+++|+|||+++||+++|
T Consensus        80 g~yVrV~G~lk~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~hL~~tk  128 (128)
T d2pi2a1          80 ETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSK  128 (128)
T ss_dssp             TCEEEEEEEEEEETTEEEEEEEEEEECSCTHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEEEeeCCeEEEEEEEEEEeCCcCHHHHHHHHHHHHHHhhcC
Confidence            9999999999999999999999999999999999999999999999975

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=2e-22  Score=140.35  Aligned_cols=65  Identities=20%  Similarity=0.393  Sum_probs=61.4

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEe-ecCCceeeccC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDEFHYKSAVN  264 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t~~  264 (265)
                      ++|++.|++||++||.+   .+++|+|+++|+++| ++|..+|++|+++|++|||||| |||+|||+|++
T Consensus         2 nGLs~~q~~V~~~i~s~---~~~eGi~~~el~~~l~~~~~~~i~~aid~L~~eG~IYsTiDddHfkstd~   68 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKAC---PRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFKSTDA   68 (69)
T ss_dssp             CCSCHHHHHHHHHHHHC---CCTTTEEHHHHHHHSTTSCHHHHHHHHHHHHHTTSEEECSSTTEEEESSC
T ss_pred             CCCCHHHHHHHHHHHhC---CCccCcCHHHHHHHccCCCHHHHHHHHHHHHhCCceecccccchhcccCC
Confidence            57999999999999976   468999999999999 6999999999999999999999 99999999986

>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Archaeal ssDNA-binding protein
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=97.80  E-value=8.6e-05  Score=55.12  Aligned_cols=73  Identities=22%  Similarity=0.351  Sum_probs=56.7

Q ss_pred             eEEEEEEEEEEeeeC--------C-CeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEE-EEeeeeCCccEEE
Q 024592           68 NTITVVGIVCDMQDK--------E-PQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY-GHLKAFQDKRSLN  137 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~--------~-t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~-G~i~~f~~~~~i~  137 (265)
                      ..|+|+|+|.++.+.        . ......|-|.||+|.+..|.+.      ...+++|+.|++. +.++.|++...|+
T Consensus        13 ~~v~i~~~V~~~~~~r~~~~~~g~~~v~~~~i~DeTG~i~~~~W~~~------~~~l~~Gdvv~i~na~v~~~~g~~el~   86 (115)
T d1o7ia_          13 ESVNVTVRVLEASEARQIQTKNGVRTISEAIVGDETGRVKLTLWGKH------AGSIKEGQVVKIENAWTTAFKGQVQLN   86 (115)
T ss_dssp             SSEEEEEEEEEECCCEEECCTTCCEEEEEEEEEETTEEEEEEEEGGG------TTCCCTTCEEEEEEEEEEEETTEEEEE
T ss_pred             CCEEEEEEEEECCCCceeecCCCCEEEEEEEEEcCCCeEEEEEeccc------cccCCCCCEEEEeeEEEEEECCeEEEE
Confidence            458899999887321        1 2367889999999999999653      3468999999996 7899999999888


Q ss_pred             EEE---eeeCCC
Q 024592          138 AYS---LRPIID  146 (265)
Q Consensus       138 ~~~---i~~v~d  146 (265)
                      +..   |.++.|
T Consensus        87 ~~~~s~i~~~~d   98 (115)
T d1o7ia_          87 AGSKTKIAEASE   98 (115)
T ss_dssp             ECTTCEEEECCC
T ss_pred             ECCCeEEEECCC
Confidence            844   666655

>d1c0aa1 b.40.4.1 (A:1-106) Aspartyl-tRNA synthetase (AspRS) {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Escherichia coli [TaxId: 562]

Probab=97.74  E-value=9.5e-05  Score=54.18  Aligned_cols=78  Identities=17%  Similarity=0.179  Sum_probs=58.8

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC----------CccEEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ----------DKRSLN  137 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~----------~~~~i~  137 (265)
                      ..|+|.|||..++.......+.|-|+||.+.|..-.+.....+....+...+.|.|.|+|+.-.          |...|.
T Consensus        16 ~~V~v~GWv~~~R~~g~i~Fi~LRD~~G~~Q~v~~~~~~~~~~~~~~l~~Es~v~V~G~V~~r~~~~~n~~~~tg~iEi~   95 (106)
T d1c0aa1          16 QQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNEFCIQVTGTVRARDEKNINRDMATGEIEVL   95 (106)
T ss_dssp             CEEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECGGGHHHHHHHTTCCTTCEEEEEEEEEECCTTTCCTTSTTTTEEEE
T ss_pred             CEEEEEEEEEEeeeCCCcEEEEEEcCCeEEeEEecccchhHHHHHHhhCccceEEEEeEEeccCccccCCCCCCCcEEEE
Confidence            6899999999999888888889999999999976544322122345688899999999997521          235777


Q ss_pred             EEEeeeCC
Q 024592          138 AYSLRPII  145 (265)
Q Consensus       138 ~~~i~~v~  145 (265)
                      +..+..+.
T Consensus        96 v~~i~vl~  103 (106)
T d1c0aa1          96 ASSLTIIN  103 (106)
T ss_dssp             EEEEEEEE
T ss_pred             EeEEEEEe
Confidence            77776553

>d1n9wa1 b.40.4.1 (A:1-93) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Thermus thermophilus, AspRS-2 [TaxId: 274]

Probab=97.69  E-value=0.00023  Score=50.74  Aligned_cols=71  Identities=13%  Similarity=0.113  Sum_probs=56.9

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC---CccEEEEEEeeeC
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ---DKRSLNAYSLRPI  144 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~---~~~~i~~~~i~~v  144 (265)
                      ..|+|.|||.+++.......+.|.|+||.+.|..=..        ..+..++.|.|.|.+..-.   +...|.+..+..+
T Consensus        14 ~~V~v~GwV~~~R~~gk~~Fi~LrD~sg~iQ~v~~~~--------~~~~~e~~v~v~G~v~~~~~~~~~~Ei~v~~i~il   85 (93)
T d1n9wa1          14 QEVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGGL--------KLPLPESALRVRGLVVENAKAPGGLEVQAKEVEVL   85 (93)
T ss_dssp             SEEEEEEEEEEEEECSSEEEEEEEETTEEEEEEEESC--------CCCCTTCEEEEEEEEEECTTSTTSEEEEEEEEEEE
T ss_pred             CEEEEEEEEEeEEeCCCcEEEEEEcCCccceEEeccc--------cccccceEEEEEEEEEECCCCCCCEEEEEeEEEEE
Confidence            5799999999999988888889999999999875322        3456789999999998754   5678888887766


Q ss_pred             CC
Q 024592          145 ID  146 (265)
Q Consensus       145 ~d  146 (265)
                      ..
T Consensus        86 ~~   87 (93)
T d1n9wa1          86 SP   87 (93)
T ss_dssp             EC
T ss_pred             ec
Confidence            43

>d1nnxa_ b.40.10.1 (A:) Hypothetical protein YgiW {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Hypothetical protein YgiW
family: Hypothetical protein YgiW
domain: Hypothetical protein YgiW
species: Escherichia coli [TaxId: 562]

Probab=97.61  E-value=0.00056  Score=49.86  Aligned_cols=83  Identities=13%  Similarity=0.226  Sum_probs=60.8

Q ss_pred             eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEE
Q 024592           43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVR  122 (265)
Q Consensus        43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVr  122 (265)
                      ..|+++++++..  +          ..|.|-|.|++.-...   .|...|+||+|.+-.=.+.    -.-..+.+++.|+
T Consensus        24 ~~tV~~a~~~~D--d----------t~V~L~G~Iv~~l~~d---~Y~F~D~TG~I~VeId~~~----w~g~~v~p~~kV~   84 (106)
T d1nnxa_          24 VTTVESAKSLRD--D----------TWVTLRGNIVERISDD---LYVFKDASGTINVDIDHKR----WNGVTVTPKDTVE   84 (106)
T ss_dssp             CCCHHHHTTSCS--S----------EEEEEEEEEEEEEETT---EEEEEETTEEEEEECCGGG----STTCCCCTTSCEE
T ss_pred             EEhHHHHhhCcC--C----------CeEEEEEEEEEEeCCc---eEEEECCCCcEEEEEChhh----cCCcccCCCCEEE
Confidence            468999988642  3          6799999888766544   4678999999988752111    0123678899999


Q ss_pred             EEEEeeeeCCccEEEEEEeeeC
Q 024592          123 VYGHLKAFQDKRSLNAYSLRPI  144 (265)
Q Consensus       123 V~G~i~~f~~~~~i~~~~i~~v  144 (265)
                      |+|.+..-.....|-+.+|+.|
T Consensus        85 i~GevDk~~~~~eIdV~~I~~l  106 (106)
T d1nnxa_          85 IQGEVDKDWNSVEIDVKQIRKV  106 (106)
T ss_dssp             EEEEEEEETTEEEEEEEEEEEC
T ss_pred             EEEEEcCCCCceEEEEEEEEEC
Confidence            9999996556678888888764

>d1b8aa1 b.40.4.1 (A:1-103) Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococcus kodakaraensis [TaxId: 311400]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Archaeon Pyrococcus kodakaraensis [TaxId: 311400]

Probab=97.50  E-value=0.00043  Score=50.24  Aligned_cols=77  Identities=16%  Similarity=0.170  Sum_probs=57.2

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccc--cccccccCCCCEEEEEEEeeee-CCc--cEEEEEEee
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQME--FNEVNQISKGMYVRVYGHLKAF-QDK--RSLNAYSLR  142 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~g~yVrV~G~i~~f-~~~--~~i~~~~i~  142 (265)
                      ..|+|.|||.+++.....+.+.|.|+||.|.|..-.+...+  .+....+..++.|.|.|.++.- +.+  ..|.+..+.
T Consensus        17 ~~V~v~Gwv~~~R~~g~i~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~l~~es~v~V~G~v~~~~~~~~~iEi~v~~i~   96 (103)
T d1b8aa1          17 QKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIV   96 (103)
T ss_dssp             CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSCHHHHHHGGGCCTTCEEEEEEEEEECTTSTTSEEEEEEEEE
T ss_pred             CEEEEEEEEehhccCCCcEEEEEEcCCEeeeEEEeccccchhhhhHHhhCCcceEEEEEEEEEECCCCCccEEEEeeEEE
Confidence            46999999999998888888899999999998865433211  1234578999999999999763 222  347776665


Q ss_pred             eC
Q 024592          143 PI  144 (265)
Q Consensus       143 ~v  144 (265)
                      -+
T Consensus        97 il   98 (103)
T d1b8aa1          97 VL   98 (103)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Hypothetical protein At4g28440 (F20O9.120)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.50  E-value=0.00034  Score=53.97  Aligned_cols=85  Identities=19%  Similarity=0.152  Sum_probs=63.7

Q ss_pred             eeeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeC-------------------CCeEEEEEEcCCCeEEEEEe
Q 024592           42 LPMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDK-------------------EPQFIFLIDDGTGRIECSRW  102 (265)
Q Consensus        42 ~PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~-------------------~t~~~y~LdDgTG~I~~~~w  102 (265)
                      ..++|++|....              ..|.|+++|.++...                   ..-....|-|.||+|.+..|
T Consensus        15 ~~~kI~dL~pg~--------------~~vnl~vkVl~~~~~~~~~r~~~~~~~~~~~g~~~~v~~~~v~DeTG~i~~tlW   80 (145)
T d1wjja_          15 VFVKVEQLKPGT--------------TGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETGCILFTAR   80 (145)
T ss_dssp             SSCCSTTCCTTC--------------CCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSCEEEEEEC
T ss_pred             ceeEHHHCCCCC--------------CCceEEEEEEEcccceeecccccccccccccCCCcEEEEEEEEccCCeEEEEEE
Confidence            356788875431              568899999887521                   12556799999999999999


Q ss_pred             cccccccccccccCCCCEEEEEEE-eeeeCCccEEEEEE---eeeCCC
Q 024592          103 AHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKRSLNAYS---LRPIID  146 (265)
Q Consensus       103 ~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~~i~~~~---i~~v~d  146 (265)
                      .+.      .+.+++|+.|++.+. ++.|++...|.+-.   |.++.+
T Consensus        81 ~~~------~~~l~~Gd~v~i~na~v~~~~G~~~L~vg~~g~I~~~~e  122 (145)
T d1wjja_          81 NDQ------VDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGA  122 (145)
T ss_dssp             TTH------HHHTCTTCEEEEEEEEEEEETTEEEEEECTTCCBCCCSC
T ss_pred             ecc------ccccCcCCEEEEeeEEEEEECCEEEEEECCCEEEEECCC
Confidence            763      245899999998865 77899999999864   555544

>d1l0wa1 b.40.4.1 (A:1-104) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-1 [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Thermus thermophilus, AspRS-1 [TaxId: 274]

Probab=97.48  E-value=0.00052  Score=49.91  Aligned_cols=76  Identities=12%  Similarity=0.193  Sum_probs=57.7

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeeeeC--------CccEEEEE
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQ--------DKRSLNAY  139 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~--------~~~~i~~~  139 (265)
                      ..|+|.|||.+++.....+.+.|-|+||.|.|..-.+.+ ..+....+...+.|.|.|.|+.-.        |...|.+.
T Consensus        17 ~~V~l~GWV~~~R~~g~i~Fi~LRD~~G~iQ~v~~~~~~-~~~~~~~l~~Es~I~V~G~V~~r~~~n~~~~tG~iEi~v~   95 (104)
T d1l0wa1          17 EEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASP-AYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELS   95 (104)
T ss_dssp             CEEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECTTST-THHHHTTCCTTCEEEEEEEEEECSSCCTTSTTTTEEEEEE
T ss_pred             CEEEEEEEEEehhcCCCeEEEEEECCCCceEEecccchh-HHHHHhhcCcccEEEEEEEEeeCCccCCCCCCCCEEEEEe
Confidence            589999999999998988899999999999988743322 123356788899999999997411        23577777


Q ss_pred             EeeeC
Q 024592          140 SLRPI  144 (265)
Q Consensus       140 ~i~~v  144 (265)
                      .+..+
T Consensus        96 ~i~iL  100 (104)
T d1l0wa1          96 ALEVL  100 (104)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            66554

>d1eova1 b.40.4.1 (A:71-204) Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Aspartyl-tRNA synthetase (AspRS)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.46  E-value=0.00052  Score=52.10  Aligned_cols=93  Identities=11%  Similarity=0.116  Sum_probs=67.6

Q ss_pred             eeeHHHHhcCCCCCCCCeEECCeEEeEEEEEEEEEEeeeCCC-eEEEEEEcCCCeEEEEEeccccccc-----ccccccC
Q 024592           43 PMTVKQLSELSSNDESSASIDGADVNTITVVGIVCDMQDKEP-QFIFLIDDGTGRIECSRWAHEQMEF-----NEVNQIS  116 (265)
Q Consensus        43 PvtIkqi~~a~~~~~~~f~i~g~~v~~V~iVG~V~~v~~~~t-~~~y~LdDgTG~I~~~~w~~~~~~~-----~~~~~~~  116 (265)
                      ...|+++..+... +          ..|+|.|||..++..+. ...+.|.|+||.|.|..-.+...+.     +....+.
T Consensus        23 r~~i~dl~~~~~~-g----------~~V~v~GwV~~~R~~G~kl~F~~LrD~sg~iQ~~v~~~~~~~~~~~~~~~~~~l~   91 (134)
T d1eova1          23 RVKFVDLDEAKDS-D----------KEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLN   91 (134)
T ss_dssp             CCCGGGCCTTTTT-T----------CEEEEEEEEEEEEECSSSEEEEEEEETTEEEEEEEECCSSSSSCHHHHHHHTTCC
T ss_pred             EEEeccccchhcC-C----------CEEEEEEEEEEEEeCCCcEEEEEEEcCCCcEEEEEEeccccchhHHHHHHHhcCC
Confidence            3557777654221 1          57899999999998765 5688999999999999886543321     1235789


Q ss_pred             CCCEEEEEEEeeeeC--------CccEEEEEEeeeCCC
Q 024592          117 KGMYVRVYGHLKAFQ--------DKRSLNAYSLRPIID  146 (265)
Q Consensus       117 ~g~yVrV~G~i~~f~--------~~~~i~~~~i~~v~d  146 (265)
                      .|+.|.|.|.|+.-.        +...|.+..|..|..
T Consensus        92 ~es~V~V~G~v~~~~~~~~~~~~~~~Ei~v~~i~vls~  129 (134)
T d1eova1          92 LESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISE  129 (134)
T ss_dssp             TTCEEEEEEEEEECSSCCTTSSEEEEEEEEEEEEEEEC
T ss_pred             CCCEEEEEEEEEeCCccCCCCCCCcEEEEEEEEEEEeC
Confidence            999999999997643        235788887776654

>d1e1oa1 b.40.4.1 (A:11-153) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Anticodon-binding domain
domain: Lysyl-tRNA synthetase (LysRS)
species: Escherichia coli, gene lysU [TaxId: 562]

Probab=97.12  E-value=0.0021  Score=49.19  Aligned_cols=77  Identities=17%  Similarity=0.143  Sum_probs=60.7

Q ss_pred             EEEEEEEEEEeeeCCCeEEEEEEcCCCeEEEEEeccccccc---ccccccCCCCEEEEEEEeeee-CCccEEEEEEeeeC
Q 024592           69 TITVVGIVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEF---NEVNQISKGMYVRVYGHLKAF-QDKRSLNAYSLRPI  144 (265)
Q Consensus        69 ~V~iVG~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~g~yVrV~G~i~~f-~~~~~i~~~~i~~v  144 (265)
                      .|+|.|+|..++....-+.+.|.|.||.|.+..-.+.-.+.   .....+..||.|-|.|.+..= .|+..|.+..+..+
T Consensus        56 ~V~vaGRI~~~R~~Gk~~F~~i~D~~g~iQi~~~~~~~~~~~~~~~~k~ld~GDiIgv~G~~~~TktGElsi~~~~~~lL  135 (143)
T d1e1oa1          56 EVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLL  135 (143)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSSTTHHHHTGGGCCTTCEEEEEEEEEECTTCCEEEEEEEEEEE
T ss_pred             eEEEEEEEEEEcccCCeeEEEEEeCCceEEEEEccccchhhhHHHHHhcCCcccEEEeecccEECCCCcEEEEeeEEEEe
Confidence            59999999999988888899999999999988765432221   123568999999999998654 48888988887765


Q ss_pred             C
Q 024592          145 I  145 (265)
Q Consensus       145 ~  145 (265)
                      +
T Consensus       136 s  136 (143)
T d1e1oa1         136 T  136 (143)
T ss_dssp             E
T ss_pred             c
Confidence            4

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=96.92  E-value=0.00098  Score=43.84  Aligned_cols=48  Identities=13%  Similarity=0.252  Sum_probs=43.2

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      ++.+..+||+.|++++      -++..+|++.+++++++|...++.|.++|.|-
T Consensus         3 lD~~D~~IL~~L~~n~------r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI~   50 (63)
T d2cfxa1           3 LDQIDLNIIEELKKDS------RLSMRELGRKIKLSPPSVTERVRQLESFGIIK   50 (63)
T ss_dssp             CCHHHHHHHHHHHHCS------CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHHHHHcC------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            5678999999998753      46999999999999999999999999999993

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=96.77  E-value=0.0014  Score=43.28  Aligned_cols=55  Identities=18%  Similarity=0.172  Sum_probs=46.1

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCce
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHY  259 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hy  259 (265)
                      .+..+|..++++.+    -.--.+.+|+..+++++.+++..|..|..+|.+.-|.+|+|
T Consensus         7 ~l~~~I~~~~~~~g----~~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI~~d~y   61 (64)
T d1lvaa3           7 KLLKDLEDKYRVSR----WQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFY   61 (64)
T ss_dssp             HHHHHHHHHHHHHT----TSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEESSSSBE
T ss_pred             HHHHHHHHHHHHcC----CCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeccccc
Confidence            47778888887743    12348999999999999999999999999999999666665

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=96.72  E-value=0.00094  Score=43.89  Aligned_cols=48  Identities=10%  Similarity=0.218  Sum_probs=43.5

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      +..+..+||+.|+++      .-++..+|+++++++++.|+..++.|.++|.|-
T Consensus         3 lD~~D~~IL~~L~~~------~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~   50 (63)
T d2cg4a1           3 IDNLDRGILEALMGN------ARTAYAELAKQFGVSPETIHVRVEKMKQAGIIT   50 (63)
T ss_dssp             CCHHHHHHHHHHHHC------TTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            567899999999874      356999999999999999999999999999994

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.60  E-value=0.0024  Score=43.32  Aligned_cols=53  Identities=19%  Similarity=0.361  Sum_probs=45.2

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeec
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSA  262 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t  262 (265)
                      +||++|...     +.++++.||++.++++.+.+...|..|++.|.+...++..|..+
T Consensus         9 ~IL~~~a~~-----~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~~g~y~lG   61 (75)
T d1mkma1           9 EILDFIVKN-----PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRYVPG   61 (75)
T ss_dssp             HHHHHHHHC-----SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECTTSCEEEC
T ss_pred             HHHHHHHhC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCCEeec
Confidence            578887653     46899999999999999999999999999999999445678764

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.57  E-value=0.0011  Score=43.10  Aligned_cols=48  Identities=19%  Similarity=0.277  Sum_probs=42.6

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      +..+..+|++.|+++      .-+++.+|++++++++..|...++.|.++|.|-
T Consensus         1 lD~~D~~Il~~L~~n------~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1           1 LDEIDKKIIKILQND------GKAPLREISKITGLAESTIHERIRKLRESGVIK   48 (60)
T ss_dssp             CCHHHHHHHHHHHHC------TTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            357889999999874      246999999999999999999999999999884

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=96.55  E-value=0.0016  Score=43.54  Aligned_cols=45  Identities=13%  Similarity=0.195  Sum_probs=40.6

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ...||++|+..      ..++..+|++.++++...|...++.|+++|.|..
T Consensus         8 ~~~Il~~l~~~------g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e   52 (71)
T d1z05a1           8 AGRVYKLIDQK------GPISRIDLSKESELAPASITKITRELIDAHLIHE   52 (71)
T ss_dssp             HHHHHHHHHHH------CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            35699999874      3799999999999999999999999999999986

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.52  E-value=0.0012  Score=42.96  Aligned_cols=48  Identities=15%  Similarity=0.307  Sum_probs=42.6

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      +..+..+|+.+|++++      =++..+|+++++++++.|...++.|.++|.|-
T Consensus         1 lD~~D~kIl~~L~~n~------r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI~   48 (60)
T d1i1ga1           1 IDERDKIILEILEKDA------RTPFTEIAKKLGISETAVRKRVKALEEKGIIE   48 (60)
T ss_dssp             CCSHHHHHHHHHHHCT------TCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHHHHHcC------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            3568899999998752      46999999999999999999999999999984

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=96.29  E-value=0.0014  Score=44.14  Aligned_cols=53  Identities=23%  Similarity=0.302  Sum_probs=44.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCC--cCHHHHHHhcCC-CHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNG--VHRNVISQQLNL-PMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~G--v~~~~I~~~l~~-~~~~v~~al~~L~~eG~IYs  253 (265)
                      .|++-|++||++|++--   .++|  .++.||++.|++ +...|...|..|.+.|.|-.
T Consensus         2 ~LT~rQ~~vL~~I~~~~---~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r   57 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHI---SQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEI   57 (71)
T ss_dssp             CCCHHHHHHHHHHHHHH---HHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHHHH---HHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeec
Confidence            47889999999998642   2234  589999999997 78899999999999999965

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.26  E-value=0.0057  Score=39.97  Aligned_cols=54  Identities=9%  Similarity=0.253  Sum_probs=43.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCe-EEeecCCcee
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSL-VYSIDEFHYK  260 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~-IYsiDd~hyk  260 (265)
                      ..+.+||++|++      +.-++.++|++.|+++...|+..|+.|.+.|. |++.-.--|.
T Consensus         5 ~~~~~iL~~L~~------~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~I~~~~g~GY~   59 (63)
T d1biaa1           5 TVPLKLIALLAN------GEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYS   59 (63)
T ss_dssp             HHHHHHHHHHTT------SSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEEETTTEEE
T ss_pred             HHHHHHHHHHHH------CCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCcEEEeCCCeEE
Confidence            567789999975      24689999999999999999999999999998 5444333444

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.25  E-value=0.0038  Score=41.66  Aligned_cols=45  Identities=18%  Similarity=0.192  Sum_probs=40.8

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ...||.+|++.      ..++..+|++.++++...|...+++|+++|.|.+
T Consensus         7 ~~~Il~~i~~~------g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e   51 (70)
T d1z6ra1           7 AGAVYRLIDQL------GPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQE   51 (70)
T ss_dssp             HHHHHHHHHSS------CSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            35699999874      3789999999999999999999999999999987

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.95  E-value=0.0041  Score=40.89  Aligned_cols=53  Identities=11%  Similarity=0.234  Sum_probs=42.5

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCe-EEeecCCceee
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSL-VYSIDEFHYKS  261 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~-IYsiDd~hyk~  261 (265)
                      +..|+++|++.     +..++.++|++.|+.+...|+.-|+.|.+.|. |++... -|..
T Consensus         9 ~~~Il~~L~~~-----~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~~I~~~~g-GY~L   62 (65)
T d1j5ya1           9 LKSIVRILERS-----KEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPR-GYVL   62 (65)
T ss_dssp             HHHHHHHHHHC-----SSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEEETT-EEEC
T ss_pred             HHHHHHHHHHc-----CCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEEeCC-CEEe
Confidence            45688888652     34699999999999999999999999999997 766433 5543

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.79  E-value=0.014  Score=39.21  Aligned_cols=51  Identities=10%  Similarity=0.211  Sum_probs=39.8

Q ss_pred             hHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.+.|.+.|.... .....=+ +..+|+++|+++...|++|++.|.++|.|+.
T Consensus         8 ~~e~i~~~I~~g~-~~~G~~LPs~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~   59 (74)
T d1hw1a1           8 AEEYIIESIWNNR-FPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTI   59 (74)
T ss_dssp             HHHHHHHHHHTTS-SCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHcCC-CCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            3445666665532 2334456 7899999999999999999999999999997

>d2dk5a1 a.4.5.85 (A:8-85) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.70  E-value=0.0066  Score=41.44  Aligned_cols=54  Identities=17%  Similarity=0.424  Sum_probs=48.3

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEee
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSI  254 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsi  254 (265)
                      .++++-...||++|++.    .+.||-..+|..+.+++..+|.++|..|++.++|=++
T Consensus         9 ~~l~~~E~lVY~~I~~a----g~~GIW~~dir~ktnL~~~~l~K~LK~Lesk~lIK~V   62 (78)
T d2dk5a1           9 KGSDNQEKLVYQIIEDA----GNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAV   62 (78)
T ss_dssp             CCSCSSHHHHHHHHHHH----CTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             hCCCHHHHHHHHHHHHc----cccceeHHHHHHHcCCCHHHHHHHHHHHHhcCCceee
Confidence            45677788999999985    4679999999999999999999999999999999773

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=95.50  E-value=0.016  Score=39.21  Aligned_cols=50  Identities=10%  Similarity=0.302  Sum_probs=38.1

Q ss_pred             HHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+.|.+.|.+.. ....+=+ +..++++.|+.+...|++||..|.++|.|++
T Consensus         4 ~~~i~~~I~~g~-l~~G~~LPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~   54 (78)
T d3bwga1           4 ATEIETYIEEHQ-LQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQ   54 (78)
T ss_dssp             HHHHHHHHHHTT-CCTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHcCC-CCCcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            344444444321 2334456 7899999999999999999999999999998

>d1gm5a2 b.40.4.9 (A:106-285) RecG "wedge" domain {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RecG "wedge" domain
domain: RecG "wedge" domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.39  E-value=0.0086  Score=46.96  Aligned_cols=73  Identities=12%  Similarity=0.235  Sum_probs=49.3

Q ss_pred             eEEEEEEEEEEeee----CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEeee--eCCccEEEEEEe
Q 024592           68 NTITVVGIVCDMQD----KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKA--FQDKRSLNAYSL  141 (265)
Q Consensus        68 ~~V~iVG~V~~v~~----~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~--f~~~~~i~~~~i  141 (265)
                      ..|++.|.|..+..    .-..+...+.|+||.|++++|...-.  ........|+.|.|.|+++.  |+++.++.-..+
T Consensus        61 ~~vti~g~V~~~~~~~~~~~~~~~~~v~D~~g~i~l~fFn~~~~--~~~~k~~~G~~v~v~Gkvk~~~~~~~~q~~~p~~  138 (180)
T d1gm5a2          61 EKVTTQGKIVSVETKKFQNMNILTAVLSDGLVHVPLKWFNQDYL--QTYLKQLTGKEVFVTGTVKSNAYTGQYEIHNAEV  138 (180)
T ss_dssp             CCCEEEECCCCCEEEECSSCEEEEEEECCSSCCEEEEECSCCTT--HHHHHTTCSSCEEEEEEECSCCTTSSCCEEEEEE
T ss_pred             eeeeeeeEEEeeccccccccceeEEEEEeccceEEEEEeCcHHH--HHHHhhhcCceEEEEEEEeeccccceeeccCcee
Confidence            35788898876542    12456889999999999987753211  11112346999999999965  777777665544


Q ss_pred             e
Q 024592          142 R  142 (265)
Q Consensus       142 ~  142 (265)
                      .
T Consensus       139 ~  139 (180)
T d1gm5a2         139 T  139 (180)
T ss_dssp             E
T ss_pred             c
Confidence            3

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=95.30  E-value=0.005  Score=40.14  Aligned_cols=42  Identities=19%  Similarity=0.256  Sum_probs=37.3

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +||+.|++.       .++..||++.++++...|...+++|+++|.|..
T Consensus         3 ~Il~~i~~~-------pisr~eLa~~~gls~~TVs~~v~~L~~~GlV~e   44 (62)
T d2hoea1           3 RILKRIMKS-------PVSRVELAEELGLTKTTVGEIAKIFLEKGIVVE   44 (62)
T ss_dssp             CSHHHHHHS-------CBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHC-------CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            367777641       489999999999999999999999999999988

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=95.28  E-value=0.024  Score=37.55  Aligned_cols=53  Identities=17%  Similarity=0.149  Sum_probs=45.0

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDE  256 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd  256 (265)
                      ++++.|-+++-+.   ...++++..+|+++|+++..+|..+|-.|...|.|+..++
T Consensus         7 ~i~~lvk~~l~~L---~~~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~~~   59 (70)
T d1sfua_           7 EIFSLVKKEVLSL---NTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPS   59 (70)
T ss_dssp             HHHHHHHHHHHTS---CTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHHHHHHHHHhc---CCCCCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecCCC
Confidence            5777777777665   3467999999999999999999999999999999998444

>d1jmca2 b.40.4.3 (A:299-420) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.69  E-value=0.072  Score=38.97  Aligned_cols=67  Identities=16%  Similarity=0.365  Sum_probs=46.0

Q ss_pred             eEEEEEEEEEEeee------C-----CCeEEEEEEcCCCe-EEEEEecccccccccccccCCCCEEEEEEE-eeeeCCcc
Q 024592           68 NTITVVGIVCDMQD------K-----EPQFIFLIDDGTGR-IECSRWAHEQMEFNEVNQISKGMYVRVYGH-LKAFQDKR  134 (265)
Q Consensus        68 ~~V~iVG~V~~v~~------~-----~t~~~y~LdDgTG~-I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~-i~~f~~~~  134 (265)
                      ..|-|+|+|.++..      .     .....++|.|.||. |++.+|-+.+..    .....+..|.+.|- ++.|+++ 
T Consensus        17 ~~vDViGvv~~v~~~~~i~~k~~g~~~~kR~i~i~D~t~~~i~vtLWg~~a~~----~~~~~~~Vi~~k~~~v~~~~g~-   91 (122)
T d1jmca2          17 SLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDADK----FDGSRQPVLAIKGARVSDFGGR-   91 (122)
T ss_dssp             CEEEEEEEEEEECCCEEEEETTTTEEEEEEEEEEECTTCCEEEEEEEHHHHHH----CCCTTCCEEEEEEEEEECTTSS-
T ss_pred             CeEEEEEEEEEccCcEEEEEcCCCCceeEEEEEEEcCCCCEEEEEEEchHhhh----hCCCCCCEEEEeeeEEeeccCc-
Confidence            35888899988742      1     13579999999995 999999765421    12345666666665 6789986 


Q ss_pred             EEEEE
Q 024592          135 SLNAY  139 (265)
Q Consensus       135 ~i~~~  139 (265)
                      .|...
T Consensus        92 sL~~~   96 (122)
T d1jmca2          92 SLSVL   96 (122)
T ss_dssp             EEECC
T ss_pred             eEecc
Confidence            56553

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.65  E-value=0.033  Score=39.86  Aligned_cols=53  Identities=23%  Similarity=0.275  Sum_probs=46.9

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++.-+-.||.+|.+.      .++++.+|++.++++...|..+|+.|.+.|.|-. .++
T Consensus        17 Glt~~e~~v~~~L~~~------g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~~~   70 (109)
T d1sfxa_          17 SFKPSDVRIYSLLLER------GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVE   70 (109)
T ss_dssp             CCCHHHHHHHHHHHHH------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             CCCHHHHHHHHHHHhc------CCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEecc
Confidence            6888999999998764      3789999999999999999999999999999976 543

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=94.64  E-value=0.035  Score=36.54  Aligned_cols=35  Identities=23%  Similarity=0.285  Sum_probs=32.2

Q ss_pred             CCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          219 NNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       219 ~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ..=++..+++++++.+...|++|+..|.++|.|+.
T Consensus        23 G~~l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~   57 (69)
T d2hs5a1          23 GARLSEPDICAALDVSRNTVREAFQILIEDRLVAH   57 (69)
T ss_dssp             TCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCccCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            34478999999999999999999999999999987

>d1jmca1 b.40.4.3 (A:183-298) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.57  E-value=0.019  Score=41.86  Aligned_cols=62  Identities=15%  Similarity=0.126  Sum_probs=43.7

Q ss_pred             eEEEEEEEEEEee------eC---CCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEE-EeeeeC
Q 024592           68 NTITVVGIVCDMQ------DK---EPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQ  131 (265)
Q Consensus        68 ~~V~iVG~V~~v~------~~---~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~  131 (265)
                      +.++|.|+|.+..      ..   ...+.+.|.|.||.|.|..|.+...  .....|++|+.+.+.+ +|+..+
T Consensus        13 ~~~~I~~RV~~k~~~r~f~~~~~~g~v~~~~l~De~G~I~~t~~~~~~~--~f~~~l~~G~vy~i~~~~V~~~~   84 (116)
T d1jmca1          13 SKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRATAFNEQVD--KFFPLIEVNKVYYFSKGTLKIAN   84 (116)
T ss_dssp             CCCEEEEEEEEECCCEEEECSSCEEEEEEEEEECSSCEEEEEEEHHHHH--HHGGGCCTTCEEEEECCEEEECC
T ss_pred             CCEEEEEEEEEeccceEEECCCCCceEEEEEEEcCCCCEEEEEchhhhh--hhHhhcccCCEEEEcceEEEEcc
Confidence            4577888886642      11   1347889999999999999976542  2345699999888865 466544

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.45  E-value=0.014  Score=40.57  Aligned_cols=54  Identities=15%  Similarity=0.188  Sum_probs=43.0

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC--CCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN--LPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~--~~~~~v~~al~~L~~eG~IYs  253 (265)
                      |++-|+.||++|.+.- .....-++..+|++.++  ++...||..|..|..+|.|+.
T Consensus         2 Lt~Rq~~IL~~Ive~y-~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~   57 (87)
T d1stza1           2 LNDRQRKVLYCIVREY-IENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQ   57 (87)
T ss_dssp             CCHHHHHHHHHHHHHH-HHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEEC
T ss_pred             cCHHHHHHHHHHHHHH-HHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccC
Confidence            5677888998776531 12245678899999975  689999999999999999986

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=94.41  E-value=0.019  Score=40.36  Aligned_cols=51  Identities=20%  Similarity=0.176  Sum_probs=44.5

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      ++.+..||.+|...      ..+++.+|++.++++...+...|..|.+.|.|-. -+.
T Consensus        15 ~p~r~~IL~~L~~~------~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~~   66 (100)
T d1ub9a_          15 NPVRLGIMIFLLPR------RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVI   66 (100)
T ss_dssp             SHHHHHHHHHHHHH------SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred             CHHHHHHHHHhccC------CCeeHHHHHHHHhhccccccHHHHHHhhhceeEEEEcC
Confidence            46788899999653      3689999999999999999999999999999987 554

>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Primosomal replication protein N, PriB
species: Escherichia coli [TaxId: 562]

Probab=94.32  E-value=0.21  Score=35.72  Aligned_cols=83  Identities=20%  Similarity=0.337  Sum_probs=53.9

Q ss_pred             eEEeEEEEEEEEEEee---e---CCCeEEEEEEcC-----CC-------eEEEEEecccccccccccccCCCCEEEEEEE
Q 024592           65 ADVNTITVVGIVCDMQ---D---KEPQFIFLIDDG-----TG-------RIECSRWAHEQMEFNEVNQISKGMYVRVYGH  126 (265)
Q Consensus        65 ~~v~~V~iVG~V~~v~---~---~~t~~~y~LdDg-----TG-------~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~  126 (265)
                      .-.+.|.|+|.|..-.   .   ....+.|.|.=.     .|       .|+|..|-..+.  .-...++.|+.|.|.|+
T Consensus         4 mm~N~v~L~G~l~~dpelr~T~~G~~v~~f~la~~~~~~e~~~~r~~~~~i~vv~~g~~Ae--~~~~~l~kG~~v~v~G~   81 (111)
T d1v1qa_           4 LMTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQ--AITHSITVGSRITVQGF   81 (111)
T ss_dssp             GCCEEEEEEEEEEEEEEEEECTTCCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESTGGG--GGGTTCCTTCEEEEEEE
T ss_pred             cceEEEEEEEEecCCcceEECCCCCEEEEEEEEeccEEecccceEEEEEEEEEEEeCHHHH--HHHHHhcCCCEEEEEEE
Confidence            3457888999887642   1   124566666410     12       278888866442  22357899999999999


Q ss_pred             eeee--CC---ccEEEEEEeeeCCChhH
Q 024592          127 LKAF--QD---KRSLNAYSLRPIIDFNE  149 (265)
Q Consensus       127 i~~f--~~---~~~i~~~~i~~v~d~Ne  149 (265)
                      |+..  ++   +..|.+..|.-++.-++
T Consensus        82 L~~~~~~~~~~r~v~~a~~ie~l~s~~~  109 (111)
T d1v1qa_          82 ISCHKAKNGLSKMVLHAEQIELIDSVDK  109 (111)
T ss_dssp             EEEECTTTTSCEEEEEEEEEEETTSCSC
T ss_pred             EEEecccCCCCEEEEEEEEEEEecCCCc
Confidence            9974  33   34566888887766554

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=94.31  E-value=0.032  Score=39.81  Aligned_cols=51  Identities=18%  Similarity=0.158  Sum_probs=44.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++..+-.||.+|-..     +..+++.+|++.++++...|...|+.|.+.|.|..
T Consensus        18 gLs~~~~~iL~~L~~~-----~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r   68 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEI-----EKPITSEELADIFKLSKTTVENSLKKLIELGLVVR   68 (109)
T ss_dssp             TCCHHHHHHHHHHHHH-----CSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CcCHHHHHHHHHHHHc-----CCCCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEE
Confidence            5778888999877432     23589999999999999999999999999999987

>d1xjva1 b.40.4.3 (A:6-145) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Protection of telomeres protein 1, Pot1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.12  E-value=0.39  Score=35.81  Aligned_cols=69  Identities=17%  Similarity=0.230  Sum_probs=52.2

Q ss_pred             eEEEEEEEEEEeee----CC-C-eEEEEEEcCCC-eEEEEEeccccccccccccc-CCCCEEEEEEE-eeeeCCccEEEE
Q 024592           68 NTITVVGIVCDMQD----KE-P-QFIFLIDDGTG-RIECSRWAHEQMEFNEVNQI-SKGMYVRVYGH-LKAFQDKRSLNA  138 (265)
Q Consensus        68 ~~V~iVG~V~~v~~----~~-t-~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~-~~g~yVrV~G~-i~~f~~~~~i~~  138 (265)
                      ..|.++|+|.+...    +. . .++++|-|.|- .|.|.+|....+   ..+.+ ..||.|++..- |+.|+++.+...
T Consensus        16 ~~vnv~gVV~~~~~p~~s~g~D~~~tl~I~D~S~~gl~v~iF~~~~~---~LP~v~~~GDII~l~r~~v~~~~~~~~~~~   92 (140)
T d1xjva1          16 TIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNYE---ALPIIYKNGDIVRFHRLKIQVYKKETQGIT   92 (140)
T ss_dssp             EEEEEEEEEEEEEEEEECSSSSEEEEEEEECTTCCEEEEEEEESSGG---GSCCCCSTTCEEEEEEEEEEEETTEEEEEE
T ss_pred             CEEEEEEEEeecCCCEEcCCCeEEEEEEEEeCCCCCeEEEEECCChH---HCCCCCCCCCEEEEEEEEEEEECCeEEEEe
Confidence            46889999988752    22 2 46789999884 399999976542   46666 57999999885 889999987766


Q ss_pred             E
Q 024592          139 Y  139 (265)
Q Consensus       139 ~  139 (265)
                      .
T Consensus        93 ~   93 (140)
T d1xjva1          93 S   93 (140)
T ss_dssp             E
T ss_pred             c
Confidence            4

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=94.05  E-value=0.059  Score=39.56  Aligned_cols=56  Identities=14%  Similarity=0.301  Sum_probs=48.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++.-+-.||.+|...    .+.+++..+|++.++++...+..+|+.|++.|.|.. .|++
T Consensus        26 glt~~q~~vL~~l~~~----~~~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~   82 (135)
T d3broa1          26 DLTGTQMTIIDYLSRN----KNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGK   82 (135)
T ss_dssp             TCCHHHHHHHHHHHHT----TTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             CCCHHHHHHHHHHHHc----CCCCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHHhhhh
Confidence            5778888999998763    245799999999999999999999999999999998 6543

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.72  E-value=0.05  Score=40.00  Aligned_cols=55  Identities=13%  Similarity=0.163  Sum_probs=47.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...    .+.|+++.+|++.++++.+.+...++.|.+.|.|.- -|.
T Consensus        30 ~Ls~~q~~vL~~l~~~----~~~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~~~~   85 (125)
T d1p4xa2          30 TLSFVEFTILAIITSQ----NKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERST   85 (125)
T ss_dssp             SSCHHHHHHHHHHHTT----TTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECS
T ss_pred             CCCHHHHHHHHHHHHc----cCCCccHHHHHHHHCCCcchHHHHHHHHHhccCEeeeecC
Confidence            4667888899999653    356899999999999999999999999999999987 444

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=93.60  E-value=0.059  Score=39.81  Aligned_cols=62  Identities=11%  Similarity=0.143  Sum_probs=48.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC-----ceeeccC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF-----HYKSAVN  264 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~-----hyk~t~~  264 (265)
                      +++..+-.||.+|.+.     +.|++..+|++.++++...|...|+.|++.|.|.. -|.+     +...|.-
T Consensus        28 glt~~~~~~L~~l~~~-----~~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~~   95 (140)
T d3deua1          28 ELTQTHWVTLHNIHQL-----PPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEK   95 (140)
T ss_dssp             TCCHHHHHHHHHHHHS-----CSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC--------CEEEECGG
T ss_pred             CCCHHHHHHHHHHHHc-----CCCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEecccCCCCCceeeEECHH
Confidence            5677888899988652     34899999999999999999999999999999998 5543     4555543

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=93.18  E-value=0.05  Score=35.02  Aligned_cols=44  Identities=7%  Similarity=0.182  Sum_probs=36.1

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.|+++.++      ...+...+|++.|+++.+.|.+++..|.++|.|-.
T Consensus        10 k~I~~l~~~------~~~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~   53 (61)
T d2ev0a1          10 EQIYMLIEE------KGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY   53 (61)
T ss_dssp             HHHHHHHHH------HSSCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHhc------CCCccHHHHHHHhCCCchhHHHHHHHHHHCCCEEE
Confidence            345665543      23689999999999999999999999999999853

>d1qzga_ b.40.4.3 (A:) Protection of telomeres protein 1, Pot1 {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Protection of telomeres protein 1, Pot1
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=93.15  E-value=0.78  Score=35.27  Aligned_cols=69  Identities=14%  Similarity=0.221  Sum_probs=52.1

Q ss_pred             eEEEEEEEEEEee---e--CCC---eEEEEEEcCC----C-eEEEEEeccccccccccccc-CCCCEEEEEE-EeeeeCC
Q 024592           68 NTITVVGIVCDMQ---D--KEP---QFIFLIDDGT----G-RIECSRWAHEQMEFNEVNQI-SKGMYVRVYG-HLKAFQD  132 (265)
Q Consensus        68 ~~V~iVG~V~~v~---~--~~t---~~~y~LdDgT----G-~I~~~~w~~~~~~~~~~~~~-~~g~yVrV~G-~i~~f~~  132 (265)
                      ..|.++|+|....   .  +.+   .++++|-|.|    . .|.|.+|.....   ..+.+ +.||.|++.. +++.|++
T Consensus        37 ~~VnviGVV~~~~~P~rs~~G~~Dy~~tl~I~D~S~~~~~~gl~v~iF~~~~e---~LP~V~~vGDII~l~rvkvq~~~g  113 (170)
T d1qzga_          37 TIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFSKQGN---DLPVIKQVGQPLLLHQITLRSYRD  113 (170)
T ss_dssp             EEEEEEEEEEEEEEEEECSSTTCCEEEEEEEECTTSCTTSCCEEEEEEESSSS---CSCCCCSTTCEEEEEEEEEEEETT
T ss_pred             CEEEEEEEEeeccCceecCCCCCcEEEEEEEEcCCCCCCCCceEEEEECCChH---HCCCcCCCCCEEEEEEEEEEEECC
Confidence            5789999998864   1  222   5779999977    3 399999987542   46776 5799999987 4889999


Q ss_pred             ccEEEEE
Q 024592          133 KRSLNAY  139 (265)
Q Consensus       133 ~~~i~~~  139 (265)
                      +.+....
T Consensus       114 ~~q~v~~  120 (170)
T d1qzga_         114 RTQGLSK  120 (170)
T ss_dssp             EEEEEEE
T ss_pred             ceEEEec
Confidence            9885554

>d2oq0a1 b.40.16.1 (A:115-202) Gamma-interferon-inducible protein Ifi-16 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: HIN-2000 domain-like
family: HIN-200/IF120x domain
domain: Gamma-interferon-inducible protein Ifi-16
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.11  E-value=0.63  Score=31.66  Aligned_cols=57  Identities=12%  Similarity=0.213  Sum_probs=37.2

Q ss_pred             EEEEeeeCCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEE-EeeeeCCccEE
Q 024592           75 IVCDMQDKEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYG-HLKAFQDKRSL  136 (265)
Q Consensus        75 ~V~~v~~~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G-~i~~f~~~~~i  136 (265)
                      .|-.......++.|.|.|.||.|+|...-.-.     .-..++||-+|.+- .|+.-+++++|
T Consensus        20 ~v~KK~~~~~~~~YeI~D~TG~MeVvv~G~~~-----ni~CeeGDKLrL~cFeL~~~~~~~qL   77 (88)
T d2oq0a1          20 MLHKKTVNQKTTIYEIQDDRGKMDVVGTGQCH-----NIPCEEGDKLQLFCFRLRKKNQMSKL   77 (88)
T ss_dssp             EEEEEEECSSEEEEEEEETTEEEEEEEEGGGS-----SCCCCTTCEEEEEEEEEEEETTEEEE
T ss_pred             EEEEEEEcCCeEEEEEecCCCcEEEEEeccEe-----ecccCCCCeEEEEEEEEEecCCeEEE
Confidence            34445677899999999999999999764321     23457787665543 24444444444

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.94  E-value=0.14  Score=37.80  Aligned_cols=53  Identities=15%  Similarity=0.212  Sum_probs=46.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .|+++.+|++.++++...|...|+.|++.|.|.. -|.
T Consensus        33 ~lt~~q~~vL~~l~~~------~~~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~~~~   86 (141)
T d1lnwa_          33 DLTPPDVHVLKLIDEQ------RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNP   86 (141)
T ss_dssp             CCCHHHHHHHHHHHSS------TTCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCccHhHHHHHHHHHHHhhceeeeccC
Confidence            5778888999999753      4799999999999999999999999999999987 543

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.87  E-value=0.11  Score=38.12  Aligned_cols=55  Identities=18%  Similarity=0.153  Sum_probs=45.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++.-+-.||.+|...     ..|+++.+|++.++++...|..+++.|+..|.|.. .|.+
T Consensus        25 glt~~q~~iL~~l~~~-----~~~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~~~~~   80 (137)
T d2fbha1          25 GLSQARWLVLLHLARH-----RDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVAE   80 (137)
T ss_dssp             CCTTTHHHHHHHHHHC-----SSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCBT
T ss_pred             CCCHHHHHHHHHHHHc-----CCCCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccccCCCC
Confidence            4556677788777542     24899999999999999999999999999999998 6654

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.70  E-value=0.044  Score=37.66  Aligned_cols=38  Identities=16%  Similarity=0.257  Sum_probs=35.7

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .=++++.|++.|+++++++...|..|+.+|.|.. ||..
T Consensus        29 ~~Isl~~la~~l~l~~~evE~~l~~mI~~~~i~akIDq~   67 (84)
T d1ufma_          29 NNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQI   67 (84)
T ss_dssp             SEEEHHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETT
T ss_pred             ceeeHHHHHHHHCCCHHHHHHHHHHHHhcCeEEEEEeCC
Confidence            4589999999999999999999999999999999 9975

>d1l1oc_ b.40.4.3 (C:) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 70 KDa subunit (RPA70)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.68  E-value=0.15  Score=39.85  Aligned_cols=75  Identities=13%  Similarity=0.092  Sum_probs=49.1

Q ss_pred             eEEEEEEcCCCeEEEEEecccccc----------------ccc---ccccCCCCEEEEEEEe--eeeCCc--cEEEEEEe
Q 024592           85 QFIFLIDDGTGRIECSRWAHEQME----------------FNE---VNQISKGMYVRVYGHL--KAFQDK--RSLNAYSL  141 (265)
Q Consensus        85 ~~~y~LdDgTG~I~~~~w~~~~~~----------------~~~---~~~~~~g~yVrV~G~i--~~f~~~--~~i~~~~i  141 (265)
                      .+.+.|.|+||.+.+..|.+.+..                ...   .-.-..|.-+.+.+++  ..|+++  ...++..+
T Consensus        77 ~l~~~i~D~Tg~~~~~~F~~~a~~l~G~sA~EL~~~~~~d~~~~~~~~~~l~~k~~~f~~~~k~~~yn~e~r~k~~v~~i  156 (178)
T d1l1oc_          77 ILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELKDKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDV  156 (178)
T ss_dssp             EEEEEEECSSCEEEEEEEHHHHHHHHSSCHHHHHHHTTSCHHHHHHHHHHTTTCEEEEEEEEECCCC-----CEEEEEEE
T ss_pred             EEEEEEecCCCCEEEEEehhhHHHHhCCCHHHHHHHhhcCHHHHHHHHHHhcCcEEEEEEEEEecccCCeeEEEEEEEEe
Confidence            477789999999999999753320                000   0011345555555554  467764  46888999


Q ss_pred             eeCCChhHHHHHHHHHHHH
Q 024592          142 RPIIDFNEITSHFVECIYV  160 (265)
Q Consensus       142 ~~v~d~Nei~~H~Levi~~  160 (265)
                      .|| |+.+..-|+|+-|..
T Consensus       157 ~pv-d~~~e~~~L~~~I~~  174 (178)
T d1l1oc_         157 KPV-DYREYGRRLVMSIRR  174 (178)
T ss_dssp             EEC-CHHHHHHHHHHHHHH
T ss_pred             EeC-CHHHHHHHHHHHHHH
Confidence            998 588888999988764

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.67  E-value=0.04  Score=36.83  Aligned_cols=52  Identities=13%  Similarity=0.195  Sum_probs=43.7

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCH-HHHHHHHHHHhhCCeEEeecC
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPM-DKLMEALESLNENSLVYSIDE  256 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~-~~v~~al~~L~~eG~IYsiDd  256 (265)
                      +++++.+|+++|.+.+      ....-+|++.|+++- .+|+.+|-.|...|.||..++
T Consensus         3 ~~d~eekI~~~L~~~g------~~~Al~iak~lGl~kakeVN~~LY~L~k~g~v~k~~~   55 (73)
T d1xmka1           3 MAEIKEKICDYLFNVS------DSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQGT   55 (73)
T ss_dssp             HHHHHHHHHHHHHHTC------CEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEECS
T ss_pred             hHHHHHHHHHHHHHcC------CchHHHHHHHhCCCcHHHHhHHHHHHHHCCCeecCCC
Confidence            3578999999998752      356788999999998 589999999999999998443

>d2pi2e1 b.40.4.3 (E:3-117) Replication protein A 14 KDa (RPA14) subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Replication protein A 14 KDa (RPA14) subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.64  E-value=0.66  Score=33.27  Aligned_cols=64  Identities=17%  Similarity=0.212  Sum_probs=43.3

Q ss_pred             eEEEEEEEEEEeeeCCCeEEEEEEcCCC-eEEEEEecccccccccccccCCCCEEEEEEEeeeeCCccEEEEEEeeeC
Q 024592           68 NTITVVGIVCDMQDKEPQFIFLIDDGTG-RIECSRWAHEQMEFNEVNQISKGMYVRVYGHLKAFQDKRSLNAYSLRPI  144 (265)
Q Consensus        68 ~~V~iVG~V~~v~~~~t~~~y~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~~f~~~~~i~~~~i~~v  144 (265)
                      ..|+|||+|.++......  +++.+.-| .+.|..-.+        .....+.||.|+|++   .++..|.+..+...
T Consensus        21 k~V~ivGkV~~v~~~g~~--~~~~s~D~~~V~v~l~~~--------~~~~~~~~vEViG~V---~~~~sI~~~~~~~f   85 (115)
T d2pi2e1          21 KPVCFVGRLEKIHPTGKM--FILSDGEGKNGTIELMEP--------LDEEISGIVEVVGRV---TAKATILCTSYVQF   85 (115)
T ss_dssp             CEEEEEEEEEEECTTSSE--EEEECTTSCEEEEECSSC--------CSSCCCSEEEEEEEE---CTTSCEEEEEEEEC
T ss_pred             CeEEEEEEEEEEcCCCCE--EEEEcCCCCEEEEEeCCC--------CCCccCCeEEEEEEE---CCCCcEEEEEEEEc
Confidence            589999999988654444  45666554 576664432        123567899999999   45666777766554

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=92.51  E-value=0.086  Score=34.11  Aligned_cols=33  Identities=12%  Similarity=0.214  Sum_probs=30.7

Q ss_pred             CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          221 GVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+...+|++.|+.+.+.|.+++..|.++|.|=.
T Consensus        23 ~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~~   55 (63)
T d2isya1          23 TPLRARIAERLDQSGPTVSQTVSRMERDGLLRV   55 (63)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcHHHHHHHhCCCchhHHHHHHHHHHCCCEEE
Confidence            589999999999999999999999999999843

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=92.27  E-value=0.077  Score=36.91  Aligned_cols=45  Identities=13%  Similarity=0.126  Sum_probs=38.7

Q ss_pred             CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeeccCC
Q 024592          220 NGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAVNA  265 (265)
Q Consensus       220 ~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~~~  265 (265)
                      +|+.+..|....+++-+.+.+.|+.|.+.|.| .-++..|..|.-|
T Consensus        17 ~g~~kT~i~~~aNLs~~~~~kyl~~L~~~GLI-~~~~~~Y~iT~kG   61 (90)
T d1r7ja_          17 SGSPKTRIMYGANLSYALTGRYIKMLMDLEII-RQEGKQYMLTKKG   61 (90)
T ss_dssp             TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSE-EEETTEEEECHHH
T ss_pred             CCCCccHHHHHcCCCHHHHHHHHHHHHHCCCe-eecCCEEEECccH
Confidence            47789999999999999999999999999999 4355688888643

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=92.19  E-value=0.16  Score=33.63  Aligned_cols=51  Identities=14%  Similarity=0.207  Sum_probs=39.2

Q ss_pred             hhHHHHHHHhcCcCCCCC-C--CCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          201 SIDQMVLDFLRRPEFLAN-N--NGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~-~--~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      ++..+|..+|-....... +  --++.++|++.++.+.+.|..+|..|.++|.|
T Consensus         4 dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~lg~sr~tvsr~l~~l~~~g~I   57 (73)
T d1zyba1           4 DLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLI   57 (73)
T ss_dssp             SHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSC
T ss_pred             CHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence            467778777654321111 1  23689999999999999999999999999998

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=92.16  E-value=0.12  Score=38.35  Aligned_cols=52  Identities=15%  Similarity=0.134  Sum_probs=45.0

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      -|++..+-+|+.+|-..     +.+++..+|++.++++...|...|+.|.+.|+|..
T Consensus        22 ~Gl~~~~~~i~~~L~~~-----~~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r   73 (151)
T d1ku9a_          22 HGLNKSVGAVYAILYLS-----DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRK   73 (151)
T ss_dssp             TTCCHHHHHHHHHHHHC-----SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCCHHHHHHHHHHHhC-----CCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEE
Confidence            35778888899887531     34799999999999999999999999999999986

>d2gxba1 a.4.5.19 (A:140-198) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.01  E-value=0.16  Score=32.04  Aligned_cols=48  Identities=21%  Similarity=0.316  Sum_probs=40.7

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++|+.+|++..   ...-.+..+++.+|+++-.+|+.+|-.|...|.+..
T Consensus         1 Eq~vl~~l~~lg---~~~~~tA~~LA~kl~vpKk~iNr~LYsL~~kgkl~k   48 (59)
T d2gxba1           1 EQRILKFLEELG---EGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQK   48 (59)
T ss_dssp             HHHHHHHHHHHC---TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ChHHHHHHHhcC---CccchhHHHHHHHhCCcHHHHHHHHHHHHHccchhh
Confidence            367899998753   235789999999999999999999999999998754

>d1qvca_ b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Escherichia coli [TaxId: 562]

Probab=91.94  E-value=0.18  Score=37.76  Aligned_cols=66  Identities=17%  Similarity=0.232  Sum_probs=45.2

Q ss_pred             eEEeEEEEEEEEEE---ee---eCCCeEEEEEE--------------cCCCeEEEEEecccccccccccccCCCCEEEEE
Q 024592           65 ADVNTITVVGIVCD---MQ---DKEPQFIFLID--------------DGTGRIECSRWAHEQMEFNEVNQISKGMYVRVY  124 (265)
Q Consensus        65 ~~v~~V~iVG~V~~---v~---~~~t~~~y~Ld--------------DgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~  124 (265)
                      +-++.|.|+|.|..   ++   .....+.|.|-              +.|-=+.|..|...+.  .....++.|+.|.|.
T Consensus         3 ~~mN~v~LiG~l~~dpe~r~~~~G~~v~~f~va~~~~~~~~~~~~~~~~t~w~~v~~~g~~Ae--~~~~~l~KG~~V~V~   80 (145)
T d1qvca_           3 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAE--VASEYLRKGSQVYIE   80 (145)
T ss_dssp             CCEEEEEEEEEESSCCEEECCSSSCCEEEEEEEECCCCSCCSSSSCCCCCEEEEEEEETHHHH--HHHHHCCTTCEEEEE
T ss_pred             CcceEEEEEEECCCCCEEEECCCCCEEEEEEEEecccccccccccccccceEEeeEEecchhh--hHhhhcccCCEEEEE
Confidence            45789999999965   22   12356788873              2233489999965332  223568999999999


Q ss_pred             EEeee--eCC
Q 024592          125 GHLKA--FQD  132 (265)
Q Consensus       125 G~i~~--f~~  132 (265)
                      |+|+.  |.+
T Consensus        81 G~l~~~~~~~   90 (145)
T d1qvca_          81 GQLRTRKWTD   90 (145)
T ss_dssp             EEEEEEEECS
T ss_pred             EEEEEeeeEC
Confidence            99875  653

>d1v4ra1 a.4.5.6 (A:1-100) Transcriptional repressor TraR, N-terminal domain {Streptomyces sp. [TaxId: 1931]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional repressor TraR, N-terminal domain
species: Streptomyces sp. [TaxId: 1931]

Probab=91.92  E-value=0.059  Score=38.07  Aligned_cols=52  Identities=21%  Similarity=0.280  Sum_probs=39.8

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCc-CHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGV-HRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv-~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .+...|.+.|.+.. ....+=+ +..+++++|+.+...|++|+..|.++|.|++
T Consensus        13 qi~~~i~~~I~~g~-l~~G~~LPs~r~La~~~~vSr~tvr~Al~~L~~~Gli~~   65 (100)
T d1v4ra1          13 DVATHFRTLIKSGE-LAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSS   65 (100)
T ss_dssp             HHHHHHHHHTTTTS-CCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEE
T ss_pred             HHHHHHHHHHHcCC-CCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            34555555555432 2333446 7899999999999999999999999999997

>d1y0ua_ a.4.5.5 (A:) Putative arsenical resistance operon repressor AF0168 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Putative arsenical resistance operon repressor AF0168
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.79  E-value=0.28  Score=32.75  Aligned_cols=55  Identities=20%  Similarity=0.317  Sum_probs=46.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCCceeeccCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEFHYKSAVNA  265 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~hyk~t~~~  265 (265)
                      +++++||.+|-+        |-+.++|-+.|+++..+.+=-|.-|. -|.+.. +|+ -|+.|.-|
T Consensus        31 PvRrkiLrmi~k--------grsedEIm~~l~LSkkqldYHLk~LE-~GfciErvge-~w~~T~~G   86 (89)
T d1y0ua_          31 PVRRKILRMLDK--------GRSEEEIMQTLSLSKKQLDYHLKVLE-AGFCIERVGE-RWVVTDAG   86 (89)
T ss_dssp             HHHHHHHHHHHT--------TCCHHHHHHHHTCCHHHHHHHHHHHH-HTTSEEEETT-EEEECTTT
T ss_pred             HHHHHHHHHHHc--------cCCHHHHHHHhccCHHHHHHHHHHHH-ccceeEecCC-ceeecccc
Confidence            699999999953        77899999999999999998887664 588888 877 78888755

>d1u5ta2 a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.75  E-value=0.14  Score=33.67  Aligned_cols=48  Identities=15%  Similarity=0.158  Sum_probs=40.7

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +.-|..||++....      --+++..+...|+-+....+.+|+.|+.||.+.-
T Consensus         2 s~Dqt~vLe~a~~~------G~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~Wv   49 (68)
T d1u5ta2           2 TSDQTKILEICSIL------GYSSISLLKANLGWEAVRSKSALDEMVANGLLWI   49 (68)
T ss_dssp             CTTHHHHHHTTTTT------SCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEE
T ss_pred             CchHHHHHHHHHHc------CceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEEE
Confidence            34578899887642      2689999999999999999999999999998764

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=91.70  E-value=0.091  Score=35.91  Aligned_cols=39  Identities=10%  Similarity=0.215  Sum_probs=35.5

Q ss_pred             CCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          218 NNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       218 ~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      ...++++.+|++.++++...|...|+.|.++|+|-. .|-
T Consensus        18 ~~~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~~D~   57 (85)
T d3ctaa1          18 NRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVTK   57 (85)
T ss_dssp             SEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeccc
Confidence            345899999999999999999999999999999988 664

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=91.68  E-value=0.17  Score=39.23  Aligned_cols=47  Identities=21%  Similarity=0.317  Sum_probs=42.0

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++...+||.+|+.       ..+++.+|++.++++.+.|...|..|.+.|.|.+
T Consensus        18 ~p~R~~Il~~L~~-------~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~   64 (190)
T d1ulya_          18 EDTRRKILKLLRN-------KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEV   64 (190)
T ss_dssp             SHHHHHHHHHHTT-------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            3678889999964       2479999999999999999999999999999987

>d1oyia_ a.4.5.19 (A:) dsRNA-binding protein E3 (E3L) {Vaccinia virus [TaxId: 10245]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: dsRNA-binding protein E3 (E3L)
species: Vaccinia virus [TaxId: 10245]

Probab=91.50  E-value=0.1  Score=32.08  Aligned_cols=48  Identities=25%  Similarity=0.423  Sum_probs=41.0

Q ss_pred             HHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecC
Q 024592          205 MVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDE  256 (265)
Q Consensus       205 ~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd  256 (265)
                      .|-+.|+.-+    -+|...-++.++|++...+|.++|-.|-....+|+.||
T Consensus         6 ivceaik~ig----~egata~qltrqlnmekrevnkalydlqrsamvy~s~d   53 (62)
T d1oyia_           6 IVCEAIKTIG----IEGATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDD   53 (62)
T ss_dssp             HHHHHHHHHS----SSTEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECSS
T ss_pred             HHHHHHHhcc----ccchHHHHHHHHHhHHHHHHHHHHHHHHHhhheecCCC
Confidence            4566676642    46999999999999999999999999999999999665

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=91.41  E-value=0.15  Score=40.00  Aligned_cols=49  Identities=20%  Similarity=0.333  Sum_probs=42.6

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +...+||.+|+.       .-+++.+|++.|+++...|+.-|..|.+.|.|.+ .+.
T Consensus        15 ~~R~~Il~~L~~-------~~~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~~~~~~   64 (194)
T d2p4wa1          15 ETRRRILFLLTK-------RPYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVEK   64 (194)
T ss_dssp             HHHHHHHHHHHH-------SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             HHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEee
Confidence            577889999964       1479999999999999999999999999999988 553

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.37  E-value=0.081  Score=38.05  Aligned_cols=56  Identities=14%  Similarity=0.159  Sum_probs=47.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++.-|-.||.+|...    .+.+++..+|++.++++...|...|+.|.+.|+|.- .|.+
T Consensus        30 ~Ls~~q~~vL~~l~~~----~~~~~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~~~~   86 (115)
T d2frha1          30 SISFEEFAVLTYISEN----KEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEH   86 (115)
T ss_dssp             CCCHHHHHHHHHHHHT----CCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSS
T ss_pred             CCCHHHHHHHHHHHcC----CCCCCCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeeeccc
Confidence            4667778888888653    245699999999999999999999999999999998 6554

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.12  E-value=0.16  Score=37.09  Aligned_cols=54  Identities=13%  Similarity=0.118  Sum_probs=47.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++.-+-.||.+|...      .++++.+|++.++++...|..+|+.|...|+|.. -|.+
T Consensus        27 glt~~q~~vL~~l~~~------~~~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~~~~~   81 (136)
T d2fbia1          27 GLTEQQWRVIRILRQQ------GEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAPK   81 (136)
T ss_dssp             TCCHHHHHHHHHHHHH------CSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeecCc
Confidence            5777888899999753      3799999999999999999999999999999998 6554

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=90.99  E-value=0.19  Score=37.24  Aligned_cols=53  Identities=15%  Similarity=0.214  Sum_probs=46.4

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..|-.||.+|.+.      .|++..+|++.++++...|...|+.|...|.|.. .|.
T Consensus        26 ~lt~~q~~iL~~i~~~------~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~~~   79 (144)
T d1lj9a_          26 SLTRGQYLYLVRVCEN------PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDA   79 (144)
T ss_dssp             TCTTTHHHHHHHHHHS------TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHhC------CCCCHHHHHHHHCccHhhHHHHHHHHHhhhcccccCCC
Confidence            4667888899888653      4899999999999999999999999999999998 654

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=90.88  E-value=0.16  Score=37.51  Aligned_cols=54  Identities=11%  Similarity=0.180  Sum_probs=47.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++.-+-.||.+|...      .|+++.+|++.++++...|...++.|+..|.|.. .|.+
T Consensus        32 glt~~q~~iL~~l~~~------~~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~~~~~   86 (143)
T d1s3ja_          32 GVTPAQLFVLASLKKH------GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTK   86 (143)
T ss_dssp             TCCHHHHHHHHHHHHH------SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheeeeecC
Confidence            5777888899999753      3899999999999999999999999999999998 6644

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.55  E-value=0.44  Score=30.66  Aligned_cols=31  Identities=19%  Similarity=0.322  Sum_probs=29.5

Q ss_pred             cCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          222 VHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       222 v~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      ++.++|+..++.+.+.|..+|..|.++|.|-
T Consensus        30 lt~~~lA~~~G~sRetvsr~L~~l~~~glI~   60 (69)
T d1i5za1          30 ITRQEIGQIVGCSRETVGRILKMLEDQNLIS   60 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            7899999999999999999999999999883

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=90.42  E-value=0.24  Score=36.24  Aligned_cols=53  Identities=9%  Similarity=0.036  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++.-+-.||..|...      .|+++.+|++.++++...|...|+.|+..|+|-. -+.
T Consensus        27 glt~~q~~iL~~i~~~------~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~~~~   80 (139)
T d2a61a1          27 GITPAQFDILQKIYFE------GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDP   80 (139)
T ss_dssp             TCCHHHHHHHHHHHHH------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHhCCCcccchHHHHHHHhcCeeeeeecc
Confidence            4677788899999653      3789999999999999999999999999999987 543

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=89.97  E-value=0.2  Score=35.93  Aligned_cols=55  Identities=16%  Similarity=0.174  Sum_probs=46.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...    .+.|+++.+|++.++++...+-.+|+.|.+.|.|-- .|+
T Consensus        29 ~Lt~~q~~vL~~l~~~----~~~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~~~~   84 (115)
T d1hsja1          29 NLNYEEIYILNHILRS----ESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSL   84 (115)
T ss_dssp             CCCHHHHHHHHHHHTC----SCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECC
T ss_pred             CCCHHHHHHHHHHHcc----CCCCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEEeec
Confidence            5677787899888642    245899999999999999999999999999999986 443

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=89.88  E-value=0.4  Score=30.61  Aligned_cols=42  Identities=10%  Similarity=0.036  Sum_probs=36.1

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      ..|++-+.+||.++-        .|.+..+|++.|++++..|+..+..+.
T Consensus         3 ~~Lt~rE~~vl~l~~--------~G~s~~eIA~~l~iS~~TV~~~~~~i~   44 (65)
T d1l3la1           3 AWLDPKEATYLRWIA--------VGKTMEEIADVEGVKYNSVRVKLREAM   44 (65)
T ss_dssp             CCCCHHHHHHHHHHT--------TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHH--------hcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            357889999999985        399999999999999999998887664

>d2dk8a1 a.4.5.85 (A:8-75) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.86  E-value=0.18  Score=32.92  Aligned_cols=48  Identities=13%  Similarity=0.263  Sum_probs=42.5

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEE
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IY  252 (265)
                      -.+..+|+++++..     ..|++=++|.+.+ .++.++=-++|..|...|+|=
T Consensus         6 ~~ie~~Ilel~k~~-----P~GitD~dl~~a~p~v~~~qRv~aiN~LLs~g~id   54 (68)
T d2dk8a1           6 VEIENRIIELCHQF-----PHGITDQVIQNEMPHIEAQQRAVAINRLLSMGQLD   54 (68)
T ss_dssp             HHHHHHHHHHHHHC-----SSCEEHHHHHHHCTTSCHHHHHHHHHHHHHHTSEE
T ss_pred             HhHHHHHHHHHHhC-----CCCCChHHHHHHCcCCCHHHHHHHHHHHHHcCCeE
Confidence            36889999999964     4699999999999 699999999999999999873

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=89.72  E-value=0.36  Score=32.65  Aligned_cols=56  Identities=7%  Similarity=0.070  Sum_probs=46.8

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCceeecc
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHYKSAV  263 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hyk~t~  263 (265)
                      .++-.|++.|..       ..++.++|+++++.+++-+...|+.|..-|.+=...++.|+.|.
T Consensus        21 av~L~ifd~l~~-------gp~s~~eLA~~~g~~~~~l~rlLr~l~a~gl~~e~~~~~y~lt~   76 (85)
T d1tw3a1          21 AATLRLVDHILA-------GARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTE   76 (85)
T ss_dssp             HHHTTHHHHHHT-------TCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEETTEEEECT
T ss_pred             HHHcCcHHHhcc-------CCCCHHHHHHHhCcChhHHHHHHHHHHHCCCeEecCCCeEecCH
Confidence            356678888853       25899999999999999999999999999977557778998774

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=89.61  E-value=0.42  Score=30.66  Aligned_cols=41  Identities=10%  Similarity=0.106  Sum_probs=35.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      .|++-+.+|+.++.        .|.+..+|++.|++++..|+..+..+.
T Consensus         4 ~LT~rE~~vl~l~~--------~G~s~~eIA~~L~is~~TV~~~~~~i~   44 (67)
T d1fsea_           4 LLTKREREVFELLV--------QDKTTKEIASELFISEKTVRNHISNAM   44 (67)
T ss_dssp             CCCHHHHHHHHHHT--------TTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH--------ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            47889999999985        399999999999999999998877654

>d1jb7a1 b.40.4.3 (A:36-204) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Telomere end binding protein alpha subunit
species: Oxytricha nova [TaxId: 200597]

Probab=89.35  E-value=1.5  Score=33.53  Aligned_cols=69  Identities=20%  Similarity=0.192  Sum_probs=52.1

Q ss_pred             eEEEEEEEEEEeee----C--CCeEEEEEEcCC------------C-eEEEEEeccccccccccccc-CCCCEEEEEE-E
Q 024592           68 NTITVVGIVCDMQD----K--EPQFIFLIDDGT------------G-RIECSRWAHEQMEFNEVNQI-SKGMYVRVYG-H  126 (265)
Q Consensus        68 ~~V~iVG~V~~v~~----~--~t~~~y~LdDgT------------G-~I~~~~w~~~~~~~~~~~~~-~~g~yVrV~G-~  126 (265)
                      ..|.|.|+|.+...    +  .=.++++|-|.|            + .|.|.+|.....   ..+.+ +.||.|++.. +
T Consensus        15 ~~vNv~GVV~~~~~p~~s~g~D~~~tl~I~D~S~~~~~~~~~~~~~~~l~v~~F~~~~~---~LP~V~~~GDII~l~rv~   91 (169)
T d1jb7a1          15 QPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRFE---DLPIIHRAGDIIRVHRAT   91 (169)
T ss_dssp             SCEEEEEEEEEECCCEECSSSCEEEEEEEEBTTBSBCCTTSSCSCBCCEEEEEEESSGG---GSCCCCEETCEEEEEEEE
T ss_pred             CeEEEEEEEeecCCceecCCCcEEEEEEEEeCCCCccccccccccCCceEEEEECCCHH---HCCCCCCCCCEEEEEEEE
Confidence            34789999998642    2  236889999976            2 489999977542   46666 5799999987 4


Q ss_pred             eeeeCCccEEEEE
Q 024592          127 LKAFQDKRSLNAY  139 (265)
Q Consensus       127 i~~f~~~~~i~~~  139 (265)
                      |+.|+++.+..+.
T Consensus        92 i~~~~g~~~~v~~  104 (169)
T d1jb7a1          92 LRLYNGQRQFNAN  104 (169)
T ss_dssp             EEEETTEEEEEEE
T ss_pred             EEEECCceeEEEc
Confidence            9999999887764

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=89.35  E-value=0.2  Score=36.42  Aligned_cols=55  Identities=15%  Similarity=0.203  Sum_probs=47.3

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...    .+.++++.+|++.++++...+..+|+.|...|.|.- -|.
T Consensus        31 ~Lt~~q~~iL~~l~~~----~~~~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~~~~   86 (125)
T d1p4xa1          31 DMTIKEFILLTYLFHQ----QENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSK   86 (125)
T ss_dssp             SSCHHHHHHHHHHHSC----SCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECS
T ss_pred             CCCHHHHHHHHHHHHh----ccCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCceeeccc
Confidence            5778888999988663    245799999999999999999999999999999988 443

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.97  E-value=0.25  Score=32.53  Aligned_cols=51  Identities=12%  Similarity=0.238  Sum_probs=43.8

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .+-...+++|+..      .=+.+++++.+|++..+++.+.|++|..+|.|-= +||.
T Consensus         7 ~lL~~FI~~Ik~~------Kvv~LedLAa~F~lktqd~i~RIq~Le~~g~ltGViDDR   58 (72)
T d1wi9a_           7 GFLTEFINYIKKS------KVVLLEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDR   58 (72)
T ss_dssp             CHHHHHHHHHHHC------SEECHHHHHHHHCSCHHHHHHHHHHHHHHSSSCEEECTT
T ss_pred             HHHHHHHHHHHHC------CEeeHHHHHHHcCCcHHHHHHHHHHHHHCCCeeeEEcCC
Confidence            4556677788764      3679999999999999999999999999999988 8884

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=88.53  E-value=0.44  Score=30.62  Aligned_cols=43  Identities=9%  Similarity=0.307  Sum_probs=36.7

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNE  247 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~  247 (265)
                      ..|++-+.+|+.++.+        |.+..+|+++|++++..|+.-+..+..
T Consensus         5 ~~LT~rE~~vl~ll~~--------G~s~~eIA~~l~iS~~TV~~~~~~i~~   47 (67)
T d1a04a1           5 NQLTPRERDILKLIAQ--------GLPNKMIARRLDITESTVKVHVKHMLK   47 (67)
T ss_dssp             GGSCHHHHHHHHHHHT--------TCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHh--------CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3578889999999853        999999999999999999988877653

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=88.35  E-value=0.33  Score=35.44  Aligned_cols=54  Identities=15%  Similarity=0.211  Sum_probs=47.1

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++.-+-.||..|...      .++++.+|++.++++.+.+...|..|++.|.|-. .|..
T Consensus        29 ~lt~~q~~iL~~l~~~------~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~~   83 (140)
T d2etha1          29 DMKTTELYAFLYVALF------GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPV   83 (140)
T ss_dssp             HSBHHHHHHHHHHHHH------CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTT
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeeeccc
Confidence            4677888899999763      3789999999999999999999999999999998 6554

>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Deinococcus radiodurans [TaxId: 1299]

Probab=88.33  E-value=0.96  Score=36.10  Aligned_cols=61  Identities=21%  Similarity=0.360  Sum_probs=41.9

Q ss_pred             EEeEEEEEEEEEE---eee--C-CCeEEEEEE------cC-------CCeEEEEEecccccccccccccCCCCEEEEEEE
Q 024592           66 DVNTITVVGIVCD---MQD--K-EPQFIFLID------DG-------TGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH  126 (265)
Q Consensus        66 ~v~~V~iVG~V~~---v~~--~-~t~~~y~Ld------Dg-------TG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~  126 (265)
                      .+++|.|+|.+..   +..  . ...+.|.|-      |.       |--+.|..|-..+.   ....++.|+.|.|.|+
T Consensus       126 ~~N~v~l~G~l~~dpe~r~t~~G~~~~~f~va~~~~~~~~~g~~~~~t~~~~v~~~g~~Ae---~~~~l~KG~~V~V~G~  202 (231)
T d1se8a_         126 AMNEVLVLGNVTRDPEIRYTPAGDAVLSLSIAVNENYQDRQGQRQEKVHYIDATLWRDLAE---NMKELRKGDPVMIMGR  202 (231)
T ss_dssp             CEEEEEEEEEECSCCEEEECTTCCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHHH---HHTTCCTTCEEEEEEE
T ss_pred             cceeEEEEEEeCCCcEEEECCCCCEEEEEEEEECCCeECCCCceeeeeEEEEeEecCcHHH---HhhhCCCCCEEEEEEE
Confidence            3689999999966   222  2 246777772      22       33488889965432   2346899999999999


Q ss_pred             eee
Q 024592          127 LKA  129 (265)
Q Consensus       127 i~~  129 (265)
                      |+.
T Consensus       203 l~~  205 (231)
T d1se8a_         203 LVN  205 (231)
T ss_dssp             EEE
T ss_pred             eEe
Confidence            964

>d2v9va2 a.4.5.35 (A:438-510) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=88.16  E-value=0.28  Score=32.18  Aligned_cols=52  Identities=17%  Similarity=0.114  Sum_probs=39.8

Q ss_pred             hHHHHHHHhcCcC-CCCCCCCcCHHHHHHhc--CCCHHHHHHHHHHHhhCCeEEe
Q 024592          202 IDQMVLDFLRRPE-FLANNNGVHRNVISQQL--NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       202 ~~~~Vl~~i~~~~-~~~~~~Gv~~~~I~~~l--~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      +++.|++.|++=. ......|++.+++.+++  ++++.-+...|+.|+.+|.|-.
T Consensus         6 l~~~i~~~L~~fH~~~P~~~G~~keeLr~~l~~~~~~~~f~~lL~~l~~~g~l~~   60 (73)
T d2v9va2           6 WWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQL   60 (73)
T ss_dssp             HHHHHHHHHHHHHHHCTTSSCEEHHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHHHHCccccCCCHHHHHHHhcccCCHHHHHHHHHHHHHCCChhe
Confidence            5556666653211 11346899999999999  6999999999999999999865

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=88.15  E-value=0.46  Score=34.65  Aligned_cols=53  Identities=15%  Similarity=0.115  Sum_probs=46.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++.-+-.||.+|...      .|++..+|++.++++...+...++.|.+.|.|-. -|.
T Consensus        31 ~Lt~~q~~vL~~l~~~------~~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~~~~   84 (138)
T d1jgsa_          31 DITAAQFKVLCSIRCA------ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP   84 (138)
T ss_dssp             TSCHHHHHHHHHHHHH------SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             CCCHHHHHHHHhHHhC------cCCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEeecc
Confidence            5677888899999653      3799999999999999999999999999999987 554

>d1sr3a_ b.40.9.1 (A:) Heme chaperone CcmE {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Heme chaperone CcmE
family: Heme chaperone CcmE
domain: Heme chaperone CcmE
species: Escherichia coli [TaxId: 562]

Probab=88.00  E-value=1.4  Score=31.51  Aligned_cols=55  Identities=25%  Similarity=0.312  Sum_probs=42.2

Q ss_pred             eEEEEEEEEEE--eee--CCCeEEEEEEcCCCeEEEEEecccccccccccccCCCCEEEEEEEee
Q 024592           68 NTITVVGIVCD--MQD--KEPQFIFLIDDGTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGHLK  128 (265)
Q Consensus        68 ~~V~iVG~V~~--v~~--~~t~~~y~LdDgTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~i~  128 (265)
                      .+++|=|.|..  +..  .+..+.|.|.|+.+.|.|.+---      .++-|++|.-|-|.|++.
T Consensus        29 ~~iRvgG~V~~gSi~~~~~~~~~~F~itD~~~~i~V~Y~Gi------lPdlF~eg~~VVveG~~~   87 (114)
T d1sr3a_          29 QRLRVGGMVMPGSVQRDPNSLKVTFTIYDAEGSVDVSYEGI------LPDLFREGQGVVVQGELE   87 (114)
T ss_dssp             SEEEEEEEECTTTCEECSSSSEEEEEEECSSCEEEEEEESC------CCTTCCTTSEEEEEEEEC
T ss_pred             cEEEEeeEEEEeEEEeecCcceEEEEEccCCcEEEEEecCC------CChhhcCCCeEEEEEEEC
Confidence            46778888854  433  34689999999999999886421      356789999999999974

>d2obpa1 a.4.5.71 (A:12-92) Putative DNA-binding protein ReutB4095 {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ReutB4095-like
domain: Putative DNA-binding protein ReutB4095
species: Ralstonia eutropha [TaxId: 106590]

Probab=87.72  E-value=1  Score=29.78  Aligned_cols=58  Identities=21%  Similarity=0.173  Sum_probs=44.8

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      .+.--.||..|.+.....+..--+...|.++-++|++.+|..|..|.+-|.+-. ++||
T Consensus         3 DP~lvavL~~L~eA~~e~~g~~WSLaklsKra~~PMS~LRR~LTqL~~aGl~~t~~~ed   61 (81)
T d2obpa1           3 DPAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVSVEAD   61 (81)
T ss_dssp             CHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTT
T ss_pred             ChHHHHHHHHHHHHhccCCCCCccHHHHHhhcCCcHHHHHHHHHHHhhcCceeeeeccC
Confidence            344456677776653212223358999999999999999999999999999999 9887

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=87.70  E-value=0.27  Score=35.90  Aligned_cols=53  Identities=17%  Similarity=0.181  Sum_probs=46.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .|++..+|++.++++...+...++.|+..|.|-. -|+
T Consensus        31 glt~~q~~vL~~i~~~------~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~~~   84 (136)
T d2bv6a1          31 NLTYPQFLVLTILWDE------SPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSE   84 (136)
T ss_dssp             TCCHHHHHHHHHHHHS------SEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHcC------CCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEeecC
Confidence            5778888999999763      4899999999999999999999999999999987 443

>d1ue1a_ b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.57  E-value=0.48  Score=33.85  Aligned_cols=60  Identities=25%  Similarity=0.392  Sum_probs=40.7

Q ss_pred             eEEEEEEEEEE---eee--C-CCeEEEEEE--c-------------CCCeEEEEEecccccccccccccCCCCEEEEEEE
Q 024592           68 NTITVVGIVCD---MQD--K-EPQFIFLID--D-------------GTGRIECSRWAHEQMEFNEVNQISKGMYVRVYGH  126 (265)
Q Consensus        68 ~~V~iVG~V~~---v~~--~-~t~~~y~Ld--D-------------gTG~I~~~~w~~~~~~~~~~~~~~~g~yVrV~G~  126 (265)
                      ++|.|+|.|..   +..  . ...+.|.|-  +             .|--+.|..|...+.  .-...++.|+.|.|.|+
T Consensus         3 N~V~L~G~l~~dpe~r~~~~G~~v~~f~lA~~~~~~~~~~~~~~~~~t~~~~v~~~g~~Ae--~~~~~l~KG~~V~V~G~   80 (118)
T d1ue1a_           3 TTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDRQTGEWKDGEALFLRCNIWREAAE--NVAESLTRGARVIVSGR   80 (118)
T ss_dssp             CEEEEEEEESSCCEEEECTTSCEEEEEEEEECCCCCC-----CCCCCCEEEEEEEEHHHHH--HHHHHCCTTCEEEEEEE
T ss_pred             CEEEEEEEcCcCCEEEECCCCCEEEEEEEEecccccccCCCcccccceeeEEEEeChHHHH--HHHHhccCCCEEEEEeE
Confidence            68999999964   222  2 246678873  1             123499999975432  12346899999999999


Q ss_pred             eee
Q 024592          127 LKA  129 (265)
Q Consensus       127 i~~  129 (265)
                      |+.
T Consensus        81 L~~   83 (118)
T d1ue1a_          81 LKQ   83 (118)
T ss_dssp             EEE
T ss_pred             eee
Confidence            986

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=87.08  E-value=0.26  Score=36.02  Aligned_cols=54  Identities=17%  Similarity=0.155  Sum_probs=47.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +++.-+-.||.+|...      .|++..+|++.++++...+..+++.|+..|.|.- -|.+
T Consensus        30 gLt~~q~~vL~~l~~~------~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~~~~~   84 (137)
T d1z91a1          30 NITYPQYLALLLLWEH------ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEE   84 (137)
T ss_dssp             CCCHHHHHHHHHHHHH------SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCSS
T ss_pred             CcCHHHHHHHHHHHcC------CCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEeecCC
Confidence            5778888899999763      4899999999999999999999999999999988 5543

>d1ucra_ a.4.5.45 (A:) Dissimilatory sulfite reductase DsvD {Desulfovibrio vulgaris [TaxId: 881]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Dissimilatory sulfite reductase DsvD
domain: Dissimilatory sulfite reductase DsvD
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=86.29  E-value=0.41  Score=31.39  Aligned_cols=51  Identities=16%  Similarity=0.229  Sum_probs=39.8

Q ss_pred             ChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEE
Q 024592          200 KSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       200 ~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IY  252 (265)
                      .++++.|+++|+....  +-.=.=+.++.+.+ ..-+.+|.+++..|++||.+-
T Consensus         2 ee~k~~Ive~l~~k~~--~KsKfYfkDf~k~~Pd~k~R~vKK~~~~lV~e~~L~   53 (74)
T d1ucra_           2 EEAKQKVVDFLNSKSG--SKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVLE   53 (74)
T ss_dssp             CHHHHHHHHHHSSHHH--HSSCEEHHHHHHHCTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             cHHHHHHHHHHHhccC--CcCceeHHHHHHHCCCccHHHHHHHHHHHhccceEE
Confidence            4688999999976431  12234568888888 689999999999999999874

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=85.83  E-value=0.89  Score=29.37  Aligned_cols=41  Identities=17%  Similarity=0.182  Sum_probs=35.7

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      .|++-+.+|+.++..        |.+..+|+..|++++..|+.-+..+.
T Consensus        12 ~LT~rE~~vl~~l~~--------G~s~~eIA~~l~iS~~TV~~~~~~i~   52 (70)
T d1yioa1          12 SLTGREQQVLQLTIR--------GLMNKQIAGELGIAEVTVKVHRHNIM   52 (70)
T ss_dssp             TSCHHHHHHHHHHTT--------TCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHc--------CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            588899999999853        89999999999999999998877654

>d1j75a_ a.4.5.19 (A:) Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Dlm-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.78  E-value=0.58  Score=28.82  Aligned_cols=48  Identities=21%  Similarity=0.302  Sum_probs=40.7

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++.++||.+|+..+     .-+-..+|++.|..|..++++.|-.|..|+.+-.
T Consensus         1 ~LEQkILQVL~dag-----spvk~~ql~k~cqVpkk~lNqVL~rlkke~kVsl   48 (57)
T d1j75a_           1 NLEQKILQVLSDDG-----GPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSS   48 (57)
T ss_dssp             CHHHHHHHHHHHHC-----SCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHhcC-----CchHHHHHHHHHCCCHHHHHHHHHHHHhcccccc
Confidence            36789999999752     2467789999999999999999999999998654

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=84.53  E-value=0.54  Score=34.45  Aligned_cols=47  Identities=13%  Similarity=0.229  Sum_probs=38.4

Q ss_pred             HHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          203 DQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       203 ~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      .-.+|-+|...    .+.-++.++|++++++|..-++++|..|...|.|-+
T Consensus         9 Av~~L~~la~~----~~~~vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S   55 (138)
T d1ylfa1           9 AVHILSILKNN----PSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYV   55 (138)
T ss_dssp             HHHHHHHHHHS----CGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHhC----CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            34456666542    234689999999999999999999999999999987

>d1in4a1 a.4.5.11 (A:255-329) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=84.41  E-value=0.91  Score=30.03  Aligned_cols=52  Identities=19%  Similarity=0.204  Sum_probs=42.6

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHH-HHhhCCeEE
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALE-SLNENSLVY  252 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~-~L~~eG~IY  252 (265)
                      +|+.+++++|+.|-+.-   ..--+.++-|+..++.+.+.|.+.++ +|+..|.|-
T Consensus         2 GLd~~Dr~yL~~l~~~f---~ggPvGl~tlAa~l~e~~~TiEdviEPyLiq~G~i~   54 (75)
T d1in4a1           2 GLDEFDRKILKTIIEIY---RGGPVGLNALAASLGVEADTLSEVYEPYLLQAGFLA   54 (75)
T ss_dssp             CCCHHHHHHHHHHHHHS---TTCCBCHHHHHHHHTSCHHHHHHHTHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHHHHHHh---CCCCCcHHHHHHHHcCChhHHHHHhhHHHHHhhHHh
Confidence            57889999999876542   22347899999999999999999998 899998874

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=84.21  E-value=1.4  Score=30.38  Aligned_cols=50  Identities=18%  Similarity=0.162  Sum_probs=42.4

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecCC
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDEF  257 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd~  257 (265)
                      +.+.+|+..|..       ..+++.+|++.++++.+.|-.-|..|.+.|.|.+ -+..
T Consensus        23 p~Rl~Il~~L~~-------~~~~v~ela~~l~is~stvS~HL~~L~~aglV~~~r~G~   73 (98)
T d1r1ta_          23 PNRLRLLSLLAR-------SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGR   73 (98)
T ss_dssp             HHHHHHHHHHTT-------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             HHHHHHHHHHHc-------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEECC
Confidence            567788888854       2479999999999999999999999999999977 5443

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=84.12  E-value=1  Score=30.35  Aligned_cols=42  Identities=17%  Similarity=0.197  Sum_probs=36.7

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHh
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLN  246 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~  246 (265)
                      ..|++-+.+|+.+|..        |.+..+|++.|++++..|+..+..+.
T Consensus        21 ~~LT~rE~~vl~ll~~--------G~s~~eIA~~l~iS~~TV~~~~~~i~   62 (87)
T d1p4wa_          21 KRLSPKESEVLRLFAE--------GFLVTEIAKKLNRSIKTISSQKKSAM   62 (87)
T ss_dssp             SSCCHHHHHHHHHHHH--------TCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHc--------CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            4588999999999964        89999999999999999998887664

>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Deinococcus radiodurans [TaxId: 1299]

Probab=84.06  E-value=1.6  Score=34.78  Aligned_cols=79  Identities=13%  Similarity=0.151  Sum_probs=49.6

Q ss_pred             EEeEEEEEEEEEE---eee--C-CCeEEEEEE------cCC-------CeEEEEEecccccccccc-cccCCCCEEEEEE
Q 024592           66 DVNTITVVGIVCD---MQD--K-EPQFIFLID------DGT-------GRIECSRWAHEQMEFNEV-NQISKGMYVRVYG  125 (265)
Q Consensus        66 ~v~~V~iVG~V~~---v~~--~-~t~~~y~Ld------DgT-------G~I~~~~w~~~~~~~~~~-~~~~~g~yVrV~G  125 (265)
                      -+++|.|+|.|.+   +..  . ...+.|.|-      |..       --+.|..|-..+.  ... ..++.|+.|.|.|
T Consensus         2 ~mN~v~l~G~l~~dpe~r~t~~G~~~~~f~lA~~~~~~~~~g~~~~~t~~~~v~~~g~~Ae--~~~~~~l~KG~~V~V~G   79 (231)
T d1se8a_           2 GMNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGRERNLPWYHRVSILGKPAE--WQAERNLKGGDAVVVEG   79 (231)
T ss_dssp             CEEEEEEEEEESSCCEEEECTTSCEEEEEEEEEEEEC-------CEEEEEEEEEEESHHHH--HHHHTCCCTTCEEEEEE
T ss_pred             CccEEEEEEEECcCCEEEECCCCCEEEEEEEEECCcEECCCCCEEeeeeeeeEEEeCchhh--hhhhhccCCCCEEEEEE
Confidence            3688999999964   322  2 246778772      222       2378888865432  112 3589999999999


Q ss_pred             Eeee--eC---Cc----cEEEEEEeeeCCC
Q 024592          126 HLKA--FQ---DK----RSLNAYSLRPIID  146 (265)
Q Consensus       126 ~i~~--f~---~~----~~i~~~~i~~v~d  146 (265)
                      +|+.  |.   |+    ..|.+..|..+..
T Consensus        80 ~l~~~~~~~~dG~~r~~~~i~a~~v~~l~~  109 (231)
T d1se8a_          80 TLEYRQWEAPEGGKRSAVNVKALRMEQLGT  109 (231)
T ss_dssp             EEEEEEEC-----CEEEEEEEEEEEEECSS
T ss_pred             EEEeeeeECCCCCEEEEEEEEEEEEEEccC
Confidence            9874  54   22    3567777777655

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=83.87  E-value=0.2  Score=38.35  Aligned_cols=57  Identities=19%  Similarity=0.123  Sum_probs=47.8

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      .+++.-|=.||..|...   ..+.|++..+|++.++++...|...|+.|+..|.|.- .|.
T Consensus        58 ~gLt~~q~~vL~~L~~~---~~~~~lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~~~  115 (172)
T d2fbka1          58 SGLNAAGWDLLLTLYRS---APPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDE  115 (172)
T ss_dssp             TTCCHHHHHHHHHHHHH---CCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC--
T ss_pred             cCCCHHHHHHHHHHHhh---CCCCCcCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeeccc
Confidence            46788888899888654   2356899999999999999999999999999999998 543

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=83.82  E-value=0.61  Score=30.75  Aligned_cols=32  Identities=9%  Similarity=0.233  Sum_probs=29.5

Q ss_pred             CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEE
Q 024592          221 GVHRNVISQQLNLPMDKLMEALESLNENSLVY  252 (265)
Q Consensus       221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IY  252 (265)
                      -++.++|+..++.+.+.|..+|..|.++|.|-
T Consensus        29 ~lt~~eLA~~~G~sretvsr~L~~l~~~glI~   60 (81)
T d2gaua1          29 YLSREELATLSNMTVSNAIRTLSTFVSERMLA   60 (81)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            36889999999999999999999999999874

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=83.79  E-value=0.57  Score=35.50  Aligned_cols=53  Identities=11%  Similarity=0.026  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ecC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-IDE  256 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iDd  256 (265)
                      +++..+-.||.+|...      .|+++.+|++.++++...|..++..|++.|+|-- -|+
T Consensus        38 ~Lt~~q~~vL~~l~~~------~~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~~~   91 (162)
T d2fxaa1          38 DLNINEHHILWIAYQL------NGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRL   91 (162)
T ss_dssp             TCCHHHHHHHHHHHHH------TSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC-
T ss_pred             CCCHHHHHHHhhhccC------CCcCHHHHHHHHcCCchhhHHHHHHHHHCCCceeeccc
Confidence            5677888899999753      3899999999999999999999999999999987 553

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.41  E-value=0.82  Score=29.24  Aligned_cols=43  Identities=21%  Similarity=0.298  Sum_probs=37.4

Q ss_pred             hhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          201 SIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       201 ~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      ++.++|++++.        +|++..+|+++|+++..-|.+.+..--+.|.|
T Consensus        18 DLR~Riv~~~~--------~G~s~r~aA~rf~VS~s~v~k~l~r~reTG~i   60 (63)
T d1k78a1          18 VVRQRIVELAH--------QGVRPCDISRQLRVSHGCVSKILGRYYETGSI   60 (63)
T ss_dssp             HHHHHHHHHHH--------TTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHH--------cCCCHHHHHHHhCCCHHHHHHHHHHHHHhcCC
Confidence            79999999985        38999999999999999999999887776654

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=82.49  E-value=0.72  Score=30.38  Aligned_cols=38  Identities=11%  Similarity=0.149  Sum_probs=30.2

Q ss_pred             CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEeecCCce
Q 024592          221 GVHRNVISQQLNLPMDKLMEALESLNENSLVYSIDEFHY  259 (265)
Q Consensus       221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYsiDd~hy  259 (265)
                      -++.++|+..++.+.+.|..+|..|.++|.| +++..++
T Consensus        30 ~lt~~elA~~~g~sretvsr~l~~l~~~glI-~~~~~~i   67 (80)
T d3e5ua1          30 PLSQKSIGEITGVHHVTVSRVLASLKRENIL-DKKKNKI   67 (80)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSE-EC----C
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCcE-EecCCEE
Confidence            3677999999999999999999999999988 4444443

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=81.93  E-value=0.69  Score=33.86  Aligned_cols=53  Identities=17%  Similarity=0.200  Sum_probs=44.2

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe-ec
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS-ID  255 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs-iD  255 (265)
                      +++.-+-.||.+|...     +.++++.+|++.++++...|...|+.|...|+|.. -+
T Consensus        31 glt~~q~~vL~~L~~~-----~g~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~~   84 (145)
T d2hr3a1          31 PVQFSQLVVLGAIDRL-----GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHT-----TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             CCCHHHHHHHHHHHHc-----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeeeC
Confidence            4566788898888532     22599999999999999999999999999999987 55

>d1zara1 a.4.5.56 (A:2-90) Rio2 serine protein kinase N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rio2 serine protein kinase N-terminal domain
domain: Rio2 serine protein kinase N-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=81.87  E-value=1.8  Score=29.53  Aligned_cols=66  Identities=14%  Similarity=0.021  Sum_probs=53.5

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe--ecCCceeeccCC
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS--IDEFHYKSAVNA  265 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs--iDd~hyk~t~~~  265 (265)
                      .+++..=+||..|...-  ..-+=|+.+.|.+..+++..++...|..|...+.|.-  ..-+-|+.|..|
T Consensus         8 ~L~~~dfRvL~aiE~gm--rnhE~VP~~lI~~~a~l~~~~~~~~L~~L~k~kLv~~~~~~Y~GYrLT~~G   75 (89)
T d1zara1           8 KMGKHSWRIMDAIFKNL--WDYEYVPLQLISSHARIGEEKARNILKYLSDLRVVQNRQKDYEGSTFTFIG   75 (89)
T ss_dssp             TCCHHHHHHHHHHHTTT--TTCSSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECSSSCEEEECHHH
T ss_pred             HcCHHHHHHHHHHHhcc--ccCccccHHHHHHHHCCCHHHHHHHHHHHHHcCCeeccCCCcceEEeeccC
Confidence            35667778888886642  3346899999999999999999999999999999976  555788888654

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=81.40  E-value=1.5  Score=28.67  Aligned_cols=31  Identities=16%  Similarity=0.168  Sum_probs=28.7

Q ss_pred             CcCHHHHHHhcCCCHHHHHHHHHHHhhCCeE
Q 024592          221 GVHRNVISQQLNLPMDKLMEALESLNENSLV  251 (265)
Q Consensus       221 Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~I  251 (265)
                      .++.++|+..++.+.+.|..+|..|.++|.|
T Consensus        30 ~~t~~eiA~~lG~sretvsr~l~~l~~~g~I   60 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTALNSLIKEGYI   60 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHHHHHHHTTSS
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence            3578899999999999999999999999987

>d2hzta1 a.4.5.69 (A:4-98) Putative transcriptional regulator YtcD {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtcD
species: Bacillus subtilis [TaxId: 1423]

Probab=81.39  E-value=1.5  Score=30.13  Aligned_cols=57  Identities=12%  Similarity=0.198  Sum_probs=44.7

Q ss_pred             hHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-CCCHHHHHHHHHHHhhCCeEEe-ecCCc-----eeeccCC
Q 024592          202 IDQMVLDFLRRPEFLANNNGVHRNVISQQL-NLPMDKLMEALESLNENSLVYS-IDEFH-----YKSAVNA  265 (265)
Q Consensus       202 ~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-~~~~~~v~~al~~L~~eG~IYs-iDd~h-----yk~t~~~  265 (265)
                      ..-.|+..|...       -....+|.+.+ +++..-+.+.|.+|+++|.|.- +.+..     |..|.-|
T Consensus        12 W~l~Il~~L~~g-------~~rF~el~~~l~gis~~~Ls~rLk~Le~~glv~r~~~~~~p~~veY~LT~~G   75 (95)
T d2hzta1          12 WKCVILCHLTHG-------KKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYG   75 (95)
T ss_dssp             THHHHHHHHTTC-------CBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTG
T ss_pred             CHHHHHHHHHcC-------CCCHHHHHHHhhcCChhHHHHHHHHHHHhHHHhheeccccccchhhhhhhhH
Confidence            445566666421       24799999999 8999999999999999999998 66654     8877654

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.16  E-value=2.5  Score=30.06  Aligned_cols=61  Identities=20%  Similarity=0.311  Sum_probs=47.8

Q ss_pred             CCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcC----CCHHHHHHHHHHHhhCCeEEe-ec--CCceeecc
Q 024592          198 EGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLN----LPMDKLMEALESLNENSLVYS-ID--EFHYKSAV  263 (265)
Q Consensus       198 ~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~----~~~~~v~~al~~L~~eG~IYs-iD--d~hyk~t~  263 (265)
                      .|+++...||++|=..     ...+++.+|.+.|.    .....|+..|..|.+-|.|-. -+  -..|.++.
T Consensus         4 ~L~~~E~~IM~~lW~~-----g~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~~gr~~~Y~~~i   71 (122)
T d2g9wa1           4 RLGDLERAVMDHLWSR-----TEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDDRAHRYAPVH   71 (122)
T ss_dssp             GCCHHHHHHHHHHHTC-----SSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC---CCEEEESS
T ss_pred             CCCHHHHHHHHHHHcC-----CCCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEeecCCeEEEEeCC
Confidence            4678999999999653     34689999999993    678899999999999999976 44  34566543

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=81.03  E-value=1.4  Score=28.00  Aligned_cols=41  Identities=5%  Similarity=0.156  Sum_probs=32.7

Q ss_pred             CCCChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHH
Q 024592          197 DEGKSIDQMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALES  244 (265)
Q Consensus       197 ~~l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~  244 (265)
                      ..|++.++.|+.+.--       +|++..+|++.+++++..|+..+..
T Consensus        20 ~~L~~~~r~v~~l~~~-------~~~s~~eIA~~lgis~~tv~~~~~r   60 (71)
T d1rp3a2          20 SKLPEREKLVIQLIFY-------EELPAKEVAKILETSVSRVSQLKAK   60 (71)
T ss_dssp             TTSCHHHHHHHHHHHT-------SCCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHh-------HhCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3577888888876543       4899999999999999998876643

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=80.53  E-value=1.7  Score=31.14  Aligned_cols=44  Identities=11%  Similarity=0.209  Sum_probs=37.3

Q ss_pred             HHHHHHhcCcCCCCCCCCcCHHHHHHhcCCCHHHHHHHHHHHhhCCeEEe
Q 024592          204 QMVLDFLRRPEFLANNNGVHRNVISQQLNLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       204 ~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      -.+|-+|..      ++.++.++|++.++.++.-|+++|..|...|.|-+
T Consensus         7 v~~L~~la~------~~~~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s   50 (127)
T d1xd7a_           7 IHILSLISM------DEKTSSEIIADSVNTNPVVVRRMISLLKKADILTS   50 (127)
T ss_dssp             HHHHHHHHT------CSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHhc------CCCCCHHHHHHHhCcCHHHHHHHHHHHHHhCcccc
Confidence            346667754      23599999999999999999999999999999876

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=80.15  E-value=2.1  Score=30.84  Aligned_cols=51  Identities=12%  Similarity=0.188  Sum_probs=41.9

Q ss_pred             CChhHHHHHHHhcCcCCCCCCCCcCHHHHHHhc-----CCCHHHHHHHHHHHhhCCeEEe
Q 024592          199 GKSIDQMVLDFLRRPEFLANNNGVHRNVISQQL-----NLPMDKLMEALESLNENSLVYS  253 (265)
Q Consensus       199 l~~~~~~Vl~~i~~~~~~~~~~Gv~~~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  253 (265)
                      ++.-+..||++|.+.    ...=+++++|.+.+     .++...|-..|+.|.+.|.|=.
T Consensus        14 ~T~qR~~Il~~L~~~----~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~~   69 (134)
T d1mzba_          14 VTLPRVKILQMLDSA----EQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVR   69 (134)
T ss_dssp             CCHHHHHHHHHHHCC-----CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHHHHHhC----CCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEEE
Confidence            467888899999763    12358999999888     3889999999999999999965

>d3ulla_ b.40.4.3 (A:) ssDNA-binding protein {Human (Homo sapiens), mitochondria [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Human (Homo sapiens), mitochondria [TaxId: 9606]

Probab=80.07  E-value=1.6  Score=30.65  Aligned_cols=64  Identities=19%  Similarity=0.302  Sum_probs=37.6

Q ss_pred             eEEeEEEEEEEEEE---eee---CCCeEEEEEE------c------CCC-e------EEEEEecccccccccccccCCCC
Q 024592           65 ADVNTITVVGIVCD---MQD---KEPQFIFLID------D------GTG-R------IECSRWAHEQMEFNEVNQISKGM  119 (265)
Q Consensus        65 ~~v~~V~iVG~V~~---v~~---~~t~~~y~Ld------D------gTG-~------I~~~~w~~~~~~~~~~~~~~~g~  119 (265)
                      +.+++|.|+|.|.+   +..   ....+.|.|-      |      ..| .      +.|..|.....+ .....++.|+
T Consensus         3 ~~mN~V~L~G~l~~dpe~r~t~~G~~v~~f~vAv~~~~~~~~~~~~~~g~~~~~t~w~~v~~~g~~~a~-~~~~~l~KG~   81 (115)
T d3ulla_           3 RSLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVYQLGDVSQKTTWHRISVFRPGLRD-VAYQYVKKGS   81 (115)
T ss_dssp             CCEEEEEEEEEECSCCEEECCTTSCCEEEEEEEEEEEECC---------CCEEEEEEEEEEECSTTHHH-HHHHHCCTTC
T ss_pred             CceeEEEEEEECCCCCEEEEeCCCCEEEEEEEEcccccccccccccccccceeeeeeeeeeeeecccch-hhhhhccCCC
Confidence            45789999999965   322   2345678773      1      122 1      444444332110 0112479999


Q ss_pred             EEEEEEEeee
Q 024592          120 YVRVYGHLKA  129 (265)
Q Consensus       120 yVrV~G~i~~  129 (265)
                      .|.|.|+|+.
T Consensus        82 ~V~V~Grl~~   91 (115)
T d3ulla_          82 RIYLEGKIDY   91 (115)
T ss_dssp             EEEEEEEEEC
T ss_pred             EEEEEEEEee
Confidence            9999999986