Citrus Sinensis ID: 023576

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280
Protein Sequence
MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFARG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccEEEEEHHHHHcccccccccccEEEccEEEEEEEEEEEEEEEEEcccEEEEEEEcccccEEEEEcccccccHHHHcccccccEEEEEEEEEEEccEEEEEEEEEEEcccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccHHHHHHHccccHHHHHHHHHHHHHccEEEEEccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccEEEHHHHHHcccccccccEEEEccEEEEEEEEEEEEEEEcccccEEEEEEEcccccEEEEEEEccccccHcccccccccEEEEEEEEEEccccEEEEEEEEEEcccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccHHHHHHHHcccHHHHHHHHHHHHHcccEEEcccccccccccc
Coil and Loop (DISEMBL)
mfsssqfdasnafsgggfmpsqppqsadypsstarsrdsqglVPVTVKMISeashsgddksnfminGLEITNVTLVGLvynkeerasdvnftlddgtgrvvCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSvrpvtnfdevtCHYIECIYFHlqnsksqvqgfpssqpqmvdsslntsartglsgyqtaptnlssqfgvdglkdCDQMILDYlqqpssserergvhvnelseqlkipqkKIMDSIASLEnegliystiDEFHYKFARG
Flexible Loop (DISEMBL)
MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEAshsgddksnFMINGLEITNVTLVGLVYNKEerasdvnftlddgtgrvvCKRWasevfdtremeaIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQpssserergVHVNelseqlkipqkkIMDSIASLENegliystidEFHYKFARG
Low Complexity Region (SEG)
MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFARG
Disordered region (IsUnstruct)
*************************************************************NFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQ******************************************FGVDGLKDCDQMILDYL*****************************DSIASLENEGLIYSTIDEFHYKF***
Disordered Region (DISOPRED)
*******************************************PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQN**************************************************DQMILDYLQ**************ELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF***
Disordered Region (DISEMBL)
*********SNAFSGGGFMP********************GLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKS*****************NTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQP***********NELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFARG
Disordered Region (DISPRO)
***************************************QGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKS******************************************GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHY*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFARG
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	280	2.2.26 [Sep-21-2011]
Q9ZQ19	279	Replication protein A 32	yes	no	0.967	0.971	0.553	2e-83
Q8LFJ8	278	Replication protein A 32	no	no	0.939	0.946	0.436	2e-59
Q63528	270	Replication protein A 32	yes	no	0.860	0.892	0.286	5e-22
P15927	270	Replication protein A 32	yes	no	0.846	0.877	0.286	2e-21
Q62193	270	Replication protein A 32	yes	no	0.903	0.937	0.279	2e-21
Q92373	279	Replication factor A prot	yes	no	0.882	0.885	0.297	4e-21
Q5RC43	270	Replication protein A 32	yes	no	0.846	0.877	0.282	5e-21
P26754	273	Replication factor A prot	yes	no	0.903	0.926	0.246	1e-15
Q13156	261	Replication protein A 30	no	no	0.685	0.735	0.221	1e-09

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

 Score =  308 bits (790), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/280 (55%), Positives = 211/280 (75%), Gaps = 9/280 (3%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDK 60
           MFSSSQF+ ++ FSGGGFM SQP Q+ +  SSTA++RD QGLVPVTVK I+E   S  +K
Sbjct: 1   MFSSSQFEPNSGFSGGGFMSSQPSQAYESSSSTAKNRDFQGLVPVTVKQITECFQSSGEK 60

Query: 61  SNFMINGLEITNVTLVGLVYNKEE-RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQ 119
           S  +ING+ +TNV+LVGLV +K+E + ++V FTLDDGTGR+ CKRW SE FD REME+++
Sbjct: 61  SGLVINGISLTNVSLVGLVCDKDESKVTEVRFTLDDGTGRIDCKRWVSETFDAREMESVR 120

Query: 120 DGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQ 179
           DG YVRL G+LK+FQGK Q++ FSVRP+ +F+EVT HYIECI+F+ QNS+SQ Q     Q
Sbjct: 121 DGTYVRLSGHLKTFQGKTQLLVFSVRPIMDFNEVTFHYIECIHFYSQNSESQRQ-----Q 175

Query: 180 PQMVDSSLNTSARTGLSGYQTAPTN--LSSQFG-VDGLKDCDQMILDYLQQPSSSERERG 236
              V  S+NT+ + G +  Q    N  +SSQ    +G K+ D MILDYL+QP+ + R++G
Sbjct: 176 VGDVTQSVNTTFQGGSNTNQATLLNPVVSSQNNDGNGRKNLDDMILDYLKQPACTARQQG 235

Query: 237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
           +H++E+++QLKIP+ K+   + SLE +GLIYSTIDE+H+K
Sbjct: 236 IHIDEIAQQLKIPKNKLEGVVQSLEGDGLIYSTIDEYHFK 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|Q8LFJ8|RFA2B_ARATH Replication protein A 32 kDa subunit B OS=Arabidopsis thaliana GN=RPA2B PE=2 SV=1

 Score =  229 bits (584), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 120/275 (43%), Positives = 176/275 (64%), Gaps = 12/275 (4%)

Query: 7   FDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMIN 66
           FD + AF+GGGFMPSQ    A   SS+ ++RD + L+P+T+K +S AS +G+  SNF I+
Sbjct: 6   FDGNAAFAGGGFMPSQATTQAHESSSSLKNRDVRTLLPLTLKQLSSASTTGE--SNFSID 63

Query: 67  GLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRL 126
           G++I  V +VG +   E R + V+F +DDGTG V C RW     +T EMEA++ GMYVRL
Sbjct: 64  GVDIKTVVIVGRISRMENRITQVDFVVDDGTGWVDCVRWCHARQETEEMEAVKLGMYVRL 123

Query: 127 IGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSK----SQVQGFPSSQPQM 182
            G+LK FQGK+ +  FSVRPVT+F+E+  H+ EC+Y H+ N+K    S  Q   + +PQM
Sbjct: 124 HGHLKIFQGKRSVNVFSVRPVTDFNEIVHHFTECMYVHMYNTKLRGGSITQDTATPRPQM 183

Query: 183 VDSSLNTSARTGLSGYQTAPTN-LSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNE 241
             S++ T A+     YQT P+N   +QF  D +    Q +L+YL QP     E GVH + 
Sbjct: 184 PYSTMPTPAKP----YQTGPSNQFPNQFN-DSMHGVKQTVLNYLNQPMHIVSEAGVHCDI 238

Query: 242 LSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
           ++ +L+IP  ++ +++  L N+G IYST+DE  +K
Sbjct: 239 IARELRIPLLQVKEALEQLSNDGCIYSTLDETCFK 273

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

 Score =  105 bits (261), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 76/265 (28%), Positives = 133/265 (50%), Gaps = 24/265 (9%)

Query: 14  SGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNV 73
           S GGF    P Q+       +R+R +Q +VP T+  +  A+ + +    F I  +EI+ V
Sbjct: 23  SPGGFGSPTPSQA----EKKSRAR-AQHIVPCTISQLLSATLTDE---VFKIGDVEISQV 74

Query: 74  TLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKS 132
           T+VG++ + E+  +++ + +DD T   +  ++W      + E   +    YV++ G+L+S
Sbjct: 75  TIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSGENTVVPPETYVKVAGHLRS 134

Query: 133 FQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQPQMVDSSLNTSAR 192
           FQ KK +VAF + P+ + +E T H +E +  HL  SK+  Q     +P M +  +     
Sbjct: 135 FQNKKSLVAFKIIPLEDMNEFTAHILEVVNSHLMLSKANSQA-SVGRPSMSNPGMGEPGN 193

Query: 193 TGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK-IPQK 251
              SG    P N        GL      +L+ ++   +  R  G++  +L  QL+ +P  
Sbjct: 194 --FSGNNFMPAN--------GLTVVQNQVLNLIK---ACPRPEGLNFQDLRSQLQHMPVA 240

Query: 252 KIMDSIASLENEGLIYSTIDEFHYK 276
            I  ++  L NEG IYST+D+ H+K
Sbjct: 241 SIKQAVDFLCNEGHIYSTVDDDHFK 265

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

 Score =  103 bits (256), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 131/269 (48%), Gaps = 32/269 (11%)

Query: 14  SGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNV 73
           S GGF    P Q+       +R+R +Q +VP T+  +  A+   +    F I  +EI+ V
Sbjct: 23  SPGGFGSPAPSQA----EKKSRAR-AQHIVPCTISQLLSATLVDEV---FRIGNVEISQV 74

Query: 74  TLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKS 132
           T+VG++ + E+  +++ + +DD T   +  ++W      + E   +    YV++ G+L+S
Sbjct: 75  TIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRS 134

Query: 133 FQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQG----FPSSQPQMVDSSLN 188
           FQ KK +VAF + P+ + +E T H +E I  H+  SK+  Q      P S P M ++   
Sbjct: 135 FQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAG-- 192

Query: 189 TSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK- 247
                   G    P N        GL      +L+ ++   +  R  G++  +L  QLK 
Sbjct: 193 -----NFGGNSFMPAN--------GLTVAQNQVLNLIK---ACPRPEGLNFQDLKNQLKH 236

Query: 248 IPQKKIMDSIASLENEGLIYSTIDEFHYK 276
           +    I  ++  L NEG IYST+D+ H+K
Sbjct: 237 MSVSSIKQAVDFLSNEGHIYSTVDDDHFK 265

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

 Score =  102 bits (255), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/279 (27%), Positives = 139/279 (49%), Gaps = 26/279 (9%)

Query: 2   FSSSQFDASNAF--SGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDD 59
           F+SS +     +  S GGF    P Q+       +R R +Q +VP T+  +  A+ + + 
Sbjct: 9   FTSSTYGGRGGYTQSPGGFGSPTPSQA----EKKSRVR-AQHIVPCTISQLLSATLTDE- 62

Query: 60  KSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREMEAI 118
              F I  +EI+ VT+VG++ + E+  +++ + +DD T   +  ++W      + E   +
Sbjct: 63  --VFRIGDVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAPPMDVRQWVDTDDASGENAVV 120

Query: 119 QDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSS 178
               YV++ G+L+SFQ KK +VAF + P+ + +E T H +E +  H+  SK   Q   + 
Sbjct: 121 PPETYVKVAGHLRSFQNKKSLVAFKIIPLEDMNEFTAHILEVVNSHMMLSKPNSQA-SAG 179

Query: 179 QPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVH 238
           +P M +  ++ S     SG    P N         L      +L+ ++   +  R  G++
Sbjct: 180 RPSMSNPGMSESF--NFSGNNFMPANR--------LTVVQNQVLNLIK---ACPRPEGLN 226

Query: 239 VNELSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYK 276
             +L  QL+ +P   I  ++  L NEG IYST+D+ H+K
Sbjct: 227 FQDLRSQLQHMPVPSIKQAVDFLCNEGHIYSTVDDDHFK 265

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

 Score =  102 bits (253), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 84/282 (29%), Positives = 136/282 (48%), Gaps = 35/282 (12%)

Query: 8   DASNAFS---GGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFM 64
           D ++AFS   GGG   ++  QS+  PS   +      L PVT+K I  AS    D + F 
Sbjct: 14  DFNSAFSPGMGGGAGFNEYDQSSQ-PSVDRQQGAGNKLRPVTIKQILNASQVHAD-AEFK 71

Query: 65  INGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYV 124
           I+G+E+  VT VG++ N   + ++  + ++DGTG +  + W  E  D   +  +    YV
Sbjct: 72  IDGVEVGQVTFVGVLRNIHAQTTNTTYQIEDGTGMIEVRHW--EHIDA--LSELATDTYV 127

Query: 125 RLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQPQMVD 184
           R+ GN+K F GK  I +  +R + + +EV  H++E I  HL  ++       ++ P    
Sbjct: 128 RVYGNIKIFSGKIYIASQYIRTIKDHNEVHFHFLEAIAVHLHFTQKANAVNGANAP---- 183

Query: 185 SSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQP----------SSSERE 234
               TS   G +       N+SS    + L   +Q + +Y   P          S+ E  
Sbjct: 184 -GYGTSNALGYN-------NISSNGAANSL---EQKLAEYSLTPAQMTVMQAIHSAPETN 232

Query: 235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
            GVHV +L++ +  P   +      L+ EG+IY+TIDE H+K
Sbjct: 233 EGVHVRQLAQSVG-PGIDLTAVTDFLQQEGIIYTTIDENHFK 273

Binds to single-stranded sequences.

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

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

 Score =  101 bits (252), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 76/269 (28%), Positives = 131/269 (48%), Gaps = 32/269 (11%)

Query: 14  SGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNV 73
           S GGF    P Q+       +R+R +Q +VP T+  +  A+   +    F I  +EI+ V
Sbjct: 23  SPGGFGSPAPSQA----EKKSRAR-AQHIVPCTISQLLSATLVDEV---FRIGNVEISQV 74

Query: 74  TLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKS 132
           T+VG++ + E+  +++ + +DD T   +  ++W      + E   +    YV++ G+L+S
Sbjct: 75  TIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDASSENTVVPPETYVKVAGHLRS 134

Query: 133 FQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQG----FPSSQPQMVDSSLN 188
           FQ KK +VAF + P+ + +E T H +E I  H+  SK+  Q      P S P M ++   
Sbjct: 135 FQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAG-- 192

Query: 189 TSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK- 247
                   G    P N        GL      +L+ ++   +  R  G++  +L  QLK 
Sbjct: 193 -----NFGGNSFMPAN--------GLTVAQNQVLNLIK---ACPRPEGLNFQDLKNQLKH 236

Query: 248 IPQKKIMDSIASLENEGLIYSTIDEFHYK 276
           +    +  ++  L NEG IYST+D+ H+K
Sbjct: 237 MSVSSVKQAMDFLSNEGHIYSTVDDDHFK 265

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

 Score = 83.6 bits (205), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/292 (24%), Positives = 136/292 (46%), Gaps = 39/292 (13%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQP-PQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDD 59
           M +   ++  ++ +GGGF  S+  P S +  ++T  +     L PVT+K I E+     D
Sbjct: 1   MATYQPYNEYSSVTGGGFENSESRPGSGESETNTRVNT----LTPVTIKQILESKQDIQD 56

Query: 60  KSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-------- 111
              F+ +  E+ +V  VG+V N  +  +++  T++DGTG++  ++W+ +  D        
Sbjct: 57  GP-FVSHNQELHHVCFVGVVRNITDHTANIFLTIEDGTGQIEVRKWSEDANDLAAGNDDS 115

Query: 112 ------TREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHL 165
                 ++  +  + G YV++ G LK F GKK I    ++P+ +F+EV  H++E I  H 
Sbjct: 116 SGKGYGSQVAQQFEIGGYVKVFGALKEFGGKKNIQYAVIKPIDSFNEVLTHHLEVIKCHS 175

Query: 166 QNSKSQVQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYL 225
             S    Q   S+           S   G S +     + SS  G   L    Q IL++ 
Sbjct: 176 IASGMMKQPLESA-----------SNNNGQSLFVKDDNDTSS--GSSPL----QRILEFC 218

Query: 226 QQPSSSERER--GVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHY 275
           ++    +      V +  +S+ L + +  + +   +L ++G IY T D+ ++
Sbjct: 219 KKQCEGKDANSFAVPIPLISQSLNLDETTVRNCCTTLTDQGFIYPTFDDNNF 270

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

 Score = 63.5 bits (153), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 49/221 (22%), Positives = 99/221 (44%), Gaps = 29/221 (13%)

Query: 63  FMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGM 122
           F + G+ ++ V++VG++   E+ ++ + + +DD T + +  R        +++  +  G+
Sbjct: 64  FKVRGIIVSQVSIVGVIRGAEKASNHICYKIDDMTAKPIEARQWFGREKVKQVTPLSVGV 123

Query: 123 YVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQ----VQGFPSS 178
           YV++ G LK   G K +    +  + + +E T H +E +  H+   K++    V+  P S
Sbjct: 124 YVKVFGILKCPTGTKSLEVLKIHVLEDMNEFTVHILETVNAHMMLDKARRDTTVESVPVS 183

Query: 179 QPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVH 238
             ++ D+  N  +                      ++D      + L+       + G  
Sbjct: 184 PSEVNDAGDNDESHRNF------------------IQD------EVLRLIHECPHQEGKS 219

Query: 239 VNELSEQL-KIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278
           ++EL  QL  +  K I ++I  L  EG IY T+D  H+K A
Sbjct: 220 IHELRAQLCDLSVKAIKEAIDYLTVEGHIYPTVDREHFKSA 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	280
224121196	282	predicted protein [Populus trichocarpa]	0.964	0.957	0.615	8e-96
31790111	273	RPA 32kDa [Pisum sativum]	0.971	0.996	0.598	7e-91
297735401	277	unnamed protein product [Vitis vinifera]	0.967	0.978	0.574	1e-88
449437074	271	PREDICTED: replication protein A 32 kDa	0.957	0.988	0.592	9e-88
359485014	275	PREDICTED: replication protein A 32 kDa	0.960	0.978	0.570	5e-87
225429793	268	PREDICTED: replication factor A protein	0.85	0.888	0.624	1e-86
356563809	277	PREDICTED: replication protein A 32 kDa	0.985	0.996	0.569	6e-85
255574103	242	Replication protein A 30 kDa subunit, pu	0.817	0.946	0.580	3e-84
356552567	292	PREDICTED: replication factor A protein	0.982	0.941	0.557	3e-82
18400560	279	replicon protein A2 [Arabidopsis thalian	0.967	0.971	0.553	1e-81

>gi|224121196|ref|XP_002330767.1| predicted protein [Populus trichocarpa] gi|222872569|gb|EEF09700.1| predicted protein [Populus trichocarpa]

 Score =  355 bits (912), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 176/286 (61%), Positives = 225/286 (78%), Gaps = 16/286 (5%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQ---------GLVPVTVKMIS 51
           MFSSSQFDA++AFSGGGFMPSQ  Q  D   S A++             G+VPVTVK IS
Sbjct: 1   MFSSSQFDATSAFSGGGFMPSQSTQLTDSTPSPAKASLLSLSLSSRNSLGVVPVTVKQIS 60

Query: 52  EASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD 111
           +AS SGD+KS+F+ING+++TNVT+VG+V+NK E+++DV+F +DDGTGR+ C+RW +E FD
Sbjct: 61  QASQSGDEKSSFVINGVDVTNVTVVGMVFNKAEKSTDVSFVIDDGTGRIGCRRWVTENFD 120

Query: 112 TREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQ 171
             EMEA+QDGMYVR+IG+L+ FQ  KQ+VAFSVRPVTNFDE+T H+I+CI+ HLQNSK  
Sbjct: 121 KLEMEAVQDGMYVRVIGHLRVFQDVKQLVAFSVRPVTNFDEITFHFIDCIHSHLQNSK-- 178

Query: 172 VQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNL-SSQFGVDGLKDCDQMILDYLQQPSS 230
           +QG  S+Q  MV+SS+NT  R G    QT  +NL S QF VDGLKDCDQ++LD LQQ SS
Sbjct: 179 LQGGASTQLHMVESSMNTPVRNG----QTFTSNLMSKQFDVDGLKDCDQLVLDRLQQSSS 234

Query: 231 SERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
             +E+G+H++EL +QLK+P +KI +SI SLE+EGLIYSTIDEFHYK
Sbjct: 235 IGQEKGMHMDELCQQLKLPMEKIKESIRSLEDEGLIYSTIDEFHYK 280

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|31790111|gb|AAP58374.1| RPA 32kDa [Pisum sativum]

 Score =  339 bits (870), Expect = 7e-91,   Method: Compositional matrix adjust.
 Identities = 167/279 (59%), Positives = 220/279 (78%), Gaps = 7/279 (2%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDK 60
           MFSSSQFD+SNAFSGGGF  SQ  +S+  P+   +SRDSQGLVPVTVK ISEAS SGD+K
Sbjct: 1   MFSSSQFDSSNAFSGGGFTSSQLNESSPAPT---KSRDSQGLVPVTVKQISEASQSGDEK 57

Query: 61  SNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQD 120
           SNF ING+++TNVTLVG+VY K ER +DVNF LDDGTGR+ C+RW +E FD++EME + +
Sbjct: 58  SNFAINGVDLTNVTLVGMVYEKTERNTDVNFVLDDGTGRIKCRRWVNETFDSKEMEEVSN 117

Query: 121 GMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQP 180
            MYVR+ GNLKSFQG KQ+ AFSVRPVTNFDE+  H+I+CI+ HL  +K +++G PS+ P
Sbjct: 118 DMYVRVYGNLKSFQGVKQLGAFSVRPVTNFDEIPFHFIDCIHSHLL-AKVKLEGTPSTYP 176

Query: 181 QMVDSSLNTSARTGLSGYQTAPTNLS-SQFGVDGLKDCDQMILDYLQQPSSSERERGVHV 239
              +SS+NT  ++ L+G Q AP+N   +Q+  DGL+DCD++++DYLQQ SS   ERG+HV
Sbjct: 177 P-TNSSINTPVKSALNGSQ-APSNPGYTQYSTDGLEDCDKLVIDYLQQHSSMLDERGIHV 234

Query: 240 NELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278
            EL+ +LK+P  +I  S+ +LE++GL+YSTID+ HYK A
Sbjct: 235 EELARELKLPLDRIRLSVKALEDDGLVYSTIDDSHYKQA 273

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  332 bits (850), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 159/277 (57%), Positives = 207/277 (74%), Gaps = 6/277 (2%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDK 60
           M+S SQFD + AFSGGGFMPSQ  Q+A+   S AR+RD+Q L+P+TVK ISEA  S DDK
Sbjct: 1   MYSHSQFDGNAAFSGGGFMPSQATQAAEPGFSPARNRDTQALLPLTVKQISEAFLSSDDK 60

Query: 61  SNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQD 120
           SNF+I+G+E+ NVTLVG+V+NK ER +DV F LDDGTGR+ C RW +E  DT+EME I D
Sbjct: 61  SNFLIDGVEVNNVTLVGMVFNKAERVTDVGFMLDDGTGRIDCNRWVNEAVDTKEMEGILD 120

Query: 121 GMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQP 180
           GMYVR+ G+LK FQGK+ +  FS+RPVT+F+E+  H+IECIY H+ N+KS+VQ    +Q 
Sbjct: 121 GMYVRVHGHLKGFQGKRHLNVFSIRPVTDFNEIASHFIECIYVHIYNTKSRVQAGGPTQS 180

Query: 181 QMVDSSLNTSARTGLSGYQTA-PTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHV 239
            + + ++ T     L GYQ + P   S Q+G  GLK  DQ+++DYLQQP S  R++GV  
Sbjct: 181 HVTNPAIGTP----LKGYQASQPNQFSGQYGA-GLKGVDQLVIDYLQQPQSLARDQGVGR 235

Query: 240 NELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
           +EL++QL +P  KIM+SI SLE EGLIYSTIDE+HYK
Sbjct: 236 DELAQQLNVPVDKIMESIRSLEEEGLIYSTIDEWHYK 272

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437074|ref|XP_004136317.1| PREDICTED: replication protein A 32 kDa subunit A-like [Cucumis sativus] gi|449519474|ref|XP_004166760.1| PREDICTED: replication protein A 32 kDa subunit A-like [Cucumis sativus]

 Score =  329 bits (843), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 166/280 (59%), Positives = 211/280 (75%), Gaps = 12/280 (4%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDK 60
           MFSS+QFD     S  GF  SQ   S     S+A+SR+S GL+PVTVK ISEASHSG++K
Sbjct: 1   MFSSTQFD-----SASGFTSSQTNDS-----SSAKSRESPGLIPVTVKQISEASHSGEEK 50

Query: 61  SNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQD 120
           +NF+ING++ITNVT+VG V  K ER +D+ FT+DDGTG + CKRW ++ FDT +ME IQD
Sbjct: 51  ANFVINGVDITNVTIVGKVSEKAERNTDITFTVDDGTGTIGCKRWVNDTFDTNQMEEIQD 110

Query: 121 GMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQ-VQGFPSSQ 179
           GMYVR+ G+LK FQ  KQI AFSVRPVTNFDE+T H+IECI+ HL+NSK Q ++G  S+Q
Sbjct: 111 GMYVRVNGHLKMFQSNKQIFAFSVRPVTNFDEITFHFIECIHDHLRNSKLQNLKGNGSTQ 170

Query: 180 PQMVDSSLNTSARTGLSGYQTAPTNL-SSQFGVDGLKDCDQMILDYLQQPSSSERERGVH 238
            Q  DS + T  + G +GY T  + + S Q  VD  K CD+++LDYLQ PSS  +ERG+H
Sbjct: 171 LQTSDSIVKTPVQNGSNGYHTTSSAIPSEQHTVDVKKSCDELVLDYLQLPSSVAKERGIH 230

Query: 239 VNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278
            +ELS+QLK+P +KI+DSI SLE+EGLIYSTIDEFH+K A
Sbjct: 231 KDELSQQLKLPMEKILDSIRSLEDEGLIYSTIDEFHFKSA 270

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  326 bits (836), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 158/277 (57%), Positives = 206/277 (74%), Gaps = 8/277 (2%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDK 60
           M+S SQFD + AFSGGGFMPSQ  Q+A+   S AR+RD+Q L+P+TVK ISEA  S DDK
Sbjct: 1   MYSHSQFDGNAAFSGGGFMPSQATQAAEPGFSPARNRDTQALLPLTVKQISEAFLSSDDK 60

Query: 61  SNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQD 120
           SNF+I+G+E+ NVTLVG+V+NK ER +DV F LDDGTGR+ C RW +E  DT+EME I D
Sbjct: 61  SNFLIDGVEVNNVTLVGMVFNKAERVTDVGFMLDDGTGRIDCNRWVNEAVDTKEMEGILD 120

Query: 121 GMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQP 180
           GMYVR+ G+LK FQGK+ +  FS+RPVT+F+E+  H+IECIY H+ N+KS+  G   +Q 
Sbjct: 121 GMYVRVHGHLKGFQGKRHLNVFSIRPVTDFNEIASHFIECIYVHIYNTKSRAGG--PTQS 178

Query: 181 QMVDSSLNTSARTGLSGYQTA-PTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHV 239
            + + ++ T     L GYQ + P   S Q+G  GLK  DQ+++DYLQQP S  R++GV  
Sbjct: 179 HVTNPAIGTP----LKGYQASQPNQFSGQYGA-GLKGVDQLVIDYLQQPQSLARDQGVGR 233

Query: 240 NELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
           +EL++QL +P  KIM+SI SLE EGLIYSTIDE+HYK
Sbjct: 234 DELAQQLNVPVDKIMESIRSLEEEGLIYSTIDEWHYK 270

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429793|ref|XP_002282796.1| PREDICTED: replication factor A protein 2 [Vitis vinifera] gi|296081770|emb|CBI20775.3| unnamed protein product [Vitis vinifera]

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 153/245 (62%), Positives = 199/245 (81%), Gaps = 7/245 (2%)

Query: 32  STARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNF 91
           S+A+SR++QGL+PVTVK ISEASHSGDDKSNF I+G+++TN+TLVG+V++K ER +DV+F
Sbjct: 26  SSAKSRETQGLIPVTVKQISEASHSGDDKSNFQIDGVDVTNITLVGMVFDKSERVTDVSF 85

Query: 92  TLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFD 151
            LDDGTGR+ CKRW +E FDTREME I DG+YVRL G+L+S  G +Q+VAFSVRPVTNFD
Sbjct: 86  ALDDGTGRIECKRWVNEAFDTREMENISDGIYVRLNGHLRSSGGNRQLVAFSVRPVTNFD 145

Query: 152 EVTCHYIECIYFHLQNSKSQVQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGV 211
           E+  H+IE I+ HL+NSK+++     +QP      L+ S +T  +GYQT  + LS+Q  V
Sbjct: 146 EIAFHFIEVIHLHLKNSKTRLPSDALTQP------LSASVKTESTGYQTPSSQLSAQ-SV 198

Query: 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID 271
           DG+K  DQM+LDYLQQPS+ +RE+G+H +ELS+QLKI  +KIM+SI +LE EGLIYSTID
Sbjct: 199 DGVKGLDQMVLDYLQQPSNYDREKGIHRDELSQQLKISTEKIMESIRTLEEEGLIYSTID 258

Query: 272 EFHYK 276
           EFHYK
Sbjct: 259 EFHYK 263

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356563809|ref|XP_003550151.1| PREDICTED: replication protein A 32 kDa subunit-like [Glycine max]

 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 159/279 (56%), Positives = 212/279 (75%), Gaps = 3/279 (1%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDK 60
           MFS SQFDA+ AFSGGGFM SQP    D   + ++SR++QGLVPVTVK ISEAS SGD+K
Sbjct: 1   MFSGSQFDATTAFSGGGFMSSQPSTLNDSSPAPSKSRETQGLVPVTVKQISEASQSGDEK 60

Query: 61  SNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQD 120
           SNF+ING+++ NVTL+G+V+ K ER +DVNF LDDGTGR+ C+RW +E FDT+EMEA+ +
Sbjct: 61  SNFVINGVDLNNVTLLGMVFEKVERNTDVNFVLDDGTGRIKCRRWVNEAFDTKEMEAVMN 120

Query: 121 GMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQP 180
           GMYVR+ G+LKSFQG KQ+V FS RPVTNFDE+  H+I+CI+ HL+ SK +++G  +S  
Sbjct: 121 GMYVRVYGHLKSFQGVKQLVTFSARPVTNFDEIPFHFIDCIHNHLR-SKIKMEGI-TSSN 178

Query: 181 QMVDSSLNTSARTGLSGYQTAPTN-LSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHV 239
               SSLNT  ++  +G Q   +N +S+Q  VDGLK  D++I+DYL+Q S     RG+HV
Sbjct: 179 PSSGSSLNTPGKSAPNGSQAPSSNPVSAQHSVDGLKGIDKLIMDYLEQHSDMSDGRGIHV 238

Query: 240 NELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278
           +ELS +LK+P +KI  S+ +L ++G IYSTID+ HYK A
Sbjct: 239 DELSRELKLPMEKIKLSLKTLADDGEIYSTIDDDHYKKA 277

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255574103|ref|XP_002527967.1| Replication protein A 30 kDa subunit, putative [Ricinus communis] gi|223532593|gb|EEF34379.1| Replication protein A 30 kDa subunit, putative [Ricinus communis]

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 152/262 (58%), Positives = 194/262 (74%), Gaps = 33/262 (12%)

Query: 15  GGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVT 74
           GGGFM SQ  Q  D   S A+SRDSQGLVPVTVK IS+ASHSGD+ SN++I+G+++TNVT
Sbjct: 12  GGGFMSSQSSQPTDSAPSPAKSRDSQGLVPVTVKQISQASHSGDENSNYVIDGVDVTNVT 71

Query: 75  LVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ 134
           +VG+V++K ++ +DVNFT+DDGTGR+ CKRW +E FD+ EME IQDGMYVR+ G+L+SFQ
Sbjct: 72  VVGMVFDKAQKVTDVNFTVDDGTGRIGCKRWVNENFDSSEMETIQDGMYVRVSGHLRSFQ 131

Query: 135 GKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQPQMVDSSLNTSARTG 194
           G +Q+ AFSVRPV NFDEVT H+I+CI+ HL NSKSQ                       
Sbjct: 132 GVRQLGAFSVRPVMNFDEVTFHFIDCIHTHLLNSKSQ----------------------- 168

Query: 195 LSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIM 254
                      + Q+ VDGLKDCDQ++LDYLQQ SS  +E+G+H++ELS+QLK+P  KI 
Sbjct: 169 ----------FTKQYSVDGLKDCDQLVLDYLQQSSSMGQEKGIHMDELSQQLKLPMDKIK 218

Query: 255 DSIASLENEGLIYSTIDEFHYK 276
           ++I SLE+EGLIYSTIDEFHYK
Sbjct: 219 ETIRSLEDEGLIYSTIDEFHYK 240

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552567|ref|XP_003544637.1| PREDICTED: replication factor A protein 2-like [Glycine max]

 Score =  310 bits (795), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 155/278 (55%), Positives = 207/278 (74%), Gaps = 3/278 (1%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDK 60
           MFS SQFDA+ AFSGGGF  SQP    D   + + SR++ GLVPVTVK ISEAS SGD+K
Sbjct: 18  MFSGSQFDATTAFSGGGFTSSQPSTLNDSSPAPSNSRETPGLVPVTVKQISEASQSGDEK 77

Query: 61  SNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQD 120
           SNF+ING+++ NVTLVG+++ K ER +DV+F LDDGTGR+ C+RW +E FDT+EMEA+ +
Sbjct: 78  SNFVINGVDLNNVTLVGMMFEKVERNTDVSFVLDDGTGRIKCRRWINEAFDTKEMEAVMN 137

Query: 121 GMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQP 180
            MYVR+ G+LKSFQG KQ+VAFSVRPVTNFDE+  H+I+CI+ HL+ SK +V+G  S+ P
Sbjct: 138 DMYVRVYGHLKSFQGVKQLVAFSVRPVTNFDEIPFHFIDCIHNHLR-SKIKVEGITSANP 196

Query: 181 QMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVN 240
               SSL T  ++  +  Q A   + +Q  VDGLK  D++++DYL+Q S     RG+HV+
Sbjct: 197 SS-GSSLETPVKSAPNRSQ-ASNPVCAQHSVDGLKGIDKLVMDYLEQHSDRSDGRGIHVD 254

Query: 241 ELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278
           ELS +LK+P +KI  S+ +L ++G IYSTID+ HYK A
Sbjct: 255 ELSRELKLPIEKIKLSLKTLADDGEIYSTIDDDHYKKA 292

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18400560|ref|NP_565571.1| replicon protein A2 [Arabidopsis thaliana] gi|186502765|ref|NP_001118376.1| replicon protein A2 [Arabidopsis thaliana] gi|75338841|sp|Q9ZQ19.2|RFA2A_ARATH RecName: Full=Replication protein A 32 kDa subunit A; Short=AtRPA32A; Short=RP-A p32 A; AltName: Full=DNA replication protein A2 subunit A; AltName: Full=Protein SUPPRESSOR OF ROS1; AltName: Full=Replication factor A protein 2 A; Short=AtRPA2 A; Short=RF-A protein 2 A; AltName: Full=Replicon protein A2 A gi|20197764|gb|AAD18120.2| putative replication protein A1 [Arabidopsis thaliana] gi|21594953|gb|AAM66059.1| putative replication protein A1 [Arabidopsis thaliana] gi|26450159|dbj|BAC42198.1| putative replication protein A1 [Arabidopsis thaliana] gi|28973057|gb|AAO63853.1| putative replication protein A1 [Arabidopsis thaliana] gi|82621223|gb|ABB86293.1| DNA replication protein A2 subunit [Arabidopsis thaliana] gi|330252488|gb|AEC07582.1| replicon protein A2 [Arabidopsis thaliana] gi|330252489|gb|AEC07583.1| replicon protein A2 [Arabidopsis thaliana]

 Score =  308 bits (790), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 155/280 (55%), Positives = 211/280 (75%), Gaps = 9/280 (3%)

Query: 1   MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDK 60
           MFSSSQF+ ++ FSGGGFM SQP Q+ +  SSTA++RD QGLVPVTVK I+E   S  +K
Sbjct: 1   MFSSSQFEPNSGFSGGGFMSSQPSQAYESSSSTAKNRDFQGLVPVTVKQITECFQSSGEK 60

Query: 61  SNFMINGLEITNVTLVGLVYNKEE-RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQ 119
           S  +ING+ +TNV+LVGLV +K+E + ++V FTLDDGTGR+ CKRW SE FD REME+++
Sbjct: 61  SGLVINGISLTNVSLVGLVCDKDESKVTEVRFTLDDGTGRIDCKRWVSETFDAREMESVR 120

Query: 120 DGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQ 179
           DG YVRL G+LK+FQGK Q++ FSVRP+ +F+EVT HYIECI+F+ QNS+SQ Q     Q
Sbjct: 121 DGTYVRLSGHLKTFQGKTQLLVFSVRPIMDFNEVTFHYIECIHFYSQNSESQRQ-----Q 175

Query: 180 PQMVDSSLNTSARTGLSGYQTAPTN--LSSQFG-VDGLKDCDQMILDYLQQPSSSERERG 236
              V  S+NT+ + G +  Q    N  +SSQ    +G K+ D MILDYL+QP+ + R++G
Sbjct: 176 VGDVTQSVNTTFQGGSNTNQATLLNPVVSSQNNDGNGRKNLDDMILDYLKQPACTARQQG 235

Query: 237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
           +H++E+++QLKIP+ K+   + SLE +GLIYSTIDE+H+K
Sbjct: 236 IHIDEIAQQLKIPKNKLEGVVQSLEGDGLIYSTIDEYHFK 275

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	280
TAIR|locus:2061072	279	RPA2 "replicon protein A2" [Ar	0.967	0.971	0.553	2.1e-77
UNIPROTKB|Q6H7J5	298	OJ1643_A10.19 "Putative replic	0.939	0.882	0.414	3.1e-51
UNIPROTKB|Q9AVM2	279	OsRPA32 "Replication protein A	0.942	0.946	0.419	9.5e-50
UNIPROTKB|Q5Z8L1	438	P0550B04.15 "Putative replicat	0.503	0.321	0.433	8.8e-30
RGD|619714	270	Rpa2 "replication protein A2"	0.903	0.937	0.301	1.4e-25
UNIPROTKB|E2RQP7	293	RPA2 "Uncharacterized protein"	0.921	0.880	0.289	1.8e-25
UNIPROTKB|G4MT45	275	MGG_07124 "Replication protein	0.917	0.934	0.289	2.6e-24
UNIPROTKB|P15927	270	RPA2 "Replication protein A 32	0.903	0.937	0.293	4.2e-24
UNIPROTKB|Q2KI86	270	RPA2 "Uncharacterized protein"	0.903	0.937	0.290	5.3e-24
POMBASE|SPCC1753.01c	279	ssb2 "single-stranded DNA bind	0.910	0.913	0.299	8.7e-24

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

 Score = 779 (279.3 bits), Expect = 2.1e-77, P = 2.1e-77
 Identities = 155/280 (55%), Positives = 211/280 (75%)

Query:     1 MFSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDK 60
             MFSSSQF+ ++ FSGGGFM SQP Q+ +  SSTA++RD QGLVPVTVK I+E   S  +K
Sbjct:     1 MFSSSQFEPNSGFSGGGFMSSQPSQAYESSSSTAKNRDFQGLVPVTVKQITECFQSSGEK 60

Query:    61 SNFMINGLEITNVTLVGLVYNKEE-RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQ 119
             S  +ING+ +TNV+LVGLV +K+E + ++V FTLDDGTGR+ CKRW SE FD REME+++
Sbjct:    61 SGLVINGISLTNVSLVGLVCDKDESKVTEVRFTLDDGTGRIDCKRWVSETFDAREMESVR 120

Query:   120 DGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQ 179
             DG YVRL G+LK+FQGK Q++ FSVRP+ +F+EVT HYIECI+F+ QNS+SQ Q     Q
Sbjct:   121 DGTYVRLSGHLKTFQGKTQLLVFSVRPIMDFNEVTFHYIECIHFYSQNSESQRQ-----Q 175

Query:   180 PQMVDSSLNTSARTGLSGYQTAPTN--LSSQFGV-DGLKDCDQMILDYLQQPSSSERERG 236
                V  S+NT+ + G +  Q    N  +SSQ    +G K+ D MILDYL+QP+ + R++G
Sbjct:   176 VGDVTQSVNTTFQGGSNTNQATLLNPVVSSQNNDGNGRKNLDDMILDYLKQPACTARQQG 235

Query:   237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
             +H++E+++QLKIP+ K+   + SLE +GLIYSTIDE+H+K
Sbjct:   236 IHIDEIAQQLKIPKNKLEGVVQSLEGDGLIYSTIDEYHFK 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 = 532 (192.3 bits), Expect = 3.1e-51, P = 3.1e-51
 Identities = 116/280 (41%), Positives = 172/280 (61%)

Query:     8 DASNAFSGGGFMPSQPPQSADYPSSTA----RSRDSQGLVPVTVKMISEASHSGDDKSNF 63
             +AS+ F GGGFMPSQ   +A+  S       +SR++Q L+P+TVK I +AS + DDKSNF
Sbjct:    20 NASSLFGGGGFMPSQATNAAEGTSGGGGGFPKSRNAQALLPLTVKQIMDASQTNDDKSNF 79

Query:    64 MINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMY 123
              +NG+E++ V LVG + NK +R +DV+FTLDDGTGRV   RW ++  DT+EM  IQ+G Y
Sbjct:    80 AVNGMEVSTVRLVGRMLNKLDRVTDVSFTLDDGTGRVPVNRWENDSTDTKEMADIQNGDY 139

Query:   124 VRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQ--NSKSQVQ-----GFP 176
             V + G LK FQGK+Q+VA+SVR +TNF++VT H++ C++ HL+    KSQV      G P
Sbjct:   140 VIVNGGLKGFQGKRQVVAYSVRRITNFNDVTHHFLHCVHVHLELTRPKSQVNANTATGTP 199

Query:   177 SSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERG 236
             +        + N S  T  +   +AP N  +     G    D ++L+    P+    + G
Sbjct:   200 NQTMPRDSMAYNQSPLTNQASTFSAPQNTGT-----GTNMID-LVLNVFHDPAVMNDDHG 253

Query:   237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
             V V+ +S +L +P++ +   I    + G +Y+TID+ HYK
Sbjct:   254 VGVDYVSRRLNLPEETVGKIIIDQVDLGHLYATIDDHHYK 293

GO:0005515 "protein binding" evidence=IPI

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

 Score = 518 (187.4 bits), Expect = 9.5e-50, P = 9.5e-50
 Identities = 118/281 (41%), Positives = 182/281 (64%)

Query:     7 FDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSG--DDK-SNF 63
             F   +AFS   F  SQ   +AD  ++ ++SR +   +P+TVK ISEA  SG   +K + F
Sbjct:     4 FSQPDAFSPSQFTSSQNA-AAD-STTPSKSRGASSTMPLTVKQISEAQQSGITGEKGAPF 61

Query:    64 MINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMY 123
             +++G+E  NV LVGLV  K ER +DV+F +DDGTGR+   RW ++  D+ E  A+Q+GMY
Sbjct:    62 VVDGVETANVRLVGLVSGKTERNTDVSFMIDDGTGRLDFIRWVNDGADSAETAAVQNGMY 121

Query:   124 VRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQPQMV 183
             V +IG+LK  Q +K+  AF++RPVT+++EVT H+I+C+  HL+N+KSQ+ G P+      
Sbjct:   122 VSVIGSLKGLQERKRATAFAIRPVTDYNEVTLHFIQCVRMHLENTKSQI-GSPAK----T 176

Query:   184 DSSLNTSARTGLSGYQTAPTNLSSQ----FGV-DGLK-DCDQMILDYLQQPSSSERERGV 237
              S++ +S+  G S   T PT++ S       V +G K D +  +L+  ++P++ E E GV
Sbjct:   177 YSAMGSSSSNGFSE-MTTPTSVKSNPAPVLSVTNGSKTDLNTEVLNVFREPANVESEHGV 235

Query:   238 HVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA 278
             H++E+ ++L++P+ KI  +I  L + G IYSTIDE HYK A
Sbjct:   236 HIDEIVKRLRLPEAKIKVAIDYLADIGHIYSTIDESHYKSA 276

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|Q5Z8L1 P0550B04.15 "Putative replication protein A2" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 295 (108.9 bits), Expect = 8.8e-30, Sum P(2) = 8.8e-30
 Identities = 65/150 (43%), Positives = 96/150 (64%)

Query:    32 STARSRDSQ--GLVPVTVKMISE------ASHSGDDKSNFMINGLEITNVTLVGLVYNKE 83
             S ++ RD +  G VP TV  IS       A+  G D   F I+G+E TNV ++G V +  
Sbjct:    38 SPSKPRDPRFSGCVPATVLHISRSFAAALAADGGGDPV-FSIDGVETTNVRVLGRVVSVV 96

Query:    84 ERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFS 143
              R +DV FTLDD TG++   RW ++  DTR+   IQ+G+YV++  NL  FQ KKQ +A S
Sbjct:    97 SRDTDVCFTLDDSTGKIPLVRWITDQSDTRDTSYIQEGVYVKVQVNLMGFQAKKQGLARS 156

Query:   144 VRPVTNFDEVTCHYIECIYFHLQNSKSQVQ 173
             +RP+ NF+EV  H+IEC++ HL++ +S++Q
Sbjct:   157 IRPINNFNEVVLHFIECMHVHLESVQSKMQ 186

GO:0005515 "protein binding" evidence=IPI

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

 Score = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 84/279 (30%), Positives = 143/279 (51%)

Query:     2 FSSSQFDASNAF--SGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDD 59
             FSSS + A+  +  S GGF  S  P  A+  S   R+R +Q +VP T+  +  A+ + D+
Sbjct:     9 FSSSSYGAAGGYTQSPGGF-GSPTPSQAEKKS---RAR-AQHIVPCTISQLLSATLT-DE 62

Query:    60 KSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREMEAI 118
                F I  +EI+ VT+VG++ + E+  +++ + +DD T   +  ++W      + E   +
Sbjct:    63 V--FKIGDVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSGENTVV 120

Query:   119 QDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSS 178
                 YV++ G+L+SFQ KK +VAF + P+ + +E T H +E +  HL  SK+  Q     
Sbjct:   121 PPETYVKVAGHLRSFQNKKSLVAFKIIPLEDMNEFTAHILEVVNSHLMLSKANSQA-SVG 179

Query:   179 QPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVH 238
             +P M +  +        SG    P N        GL      +L+ ++   +  R  G++
Sbjct:   180 RPSMSNPGMGEPGN--FSGNNFMPAN--------GLTVVQNQVLNLIK---ACPRPEGLN 226

Query:   239 VNELSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYK 276
               +L  QL+ +P   I  ++  L NEG IYST+D+ H+K
Sbjct:   227 FQDLRSQLQHMPVASIKQAVDFLCNEGHIYSTVDDDHFK 265

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

UNIPROTKB|E2RQP7 RPA2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 289 (106.8 bits), Expect = 1.8e-25, P = 1.8e-25
 Identities = 81/280 (28%), Positives = 143/280 (51%)

Query:     2 FSSSQFDASNAFSG-GGFMPSQPPQSADYPSSTAR-SRD-SQGLVPVTVKMISEASHSGD 58
             F  S+   S+AFSG GG+  S     +  PS   + SR  +Q +VP T+  +  A+   D
Sbjct:    27 FGGSESYGSSAFSGAGGYTQSPGGFGSPTPSQAEKKSRARAQHIVPCTISQLLSATLV-D 85

Query:    59 DKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREMEA 117
             +   F I  +EI+ VT+VG++ + E+  +++ + +DD T   +  ++W      + E   
Sbjct:    86 EM--FKIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDASSENTV 143

Query:   118 IQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPS 177
             +    YV++ G+L+SFQ KK +VAF + P+ + +E T H +E +  H+  SKS  Q  P+
Sbjct:   144 VPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTAHILEVVNAHMILSKSNSQP-PA 202

Query:   178 SQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGV 237
              +  + +  +  +   G  G  + P N        GL      +L+ ++   +  R  G+
Sbjct:   203 GRAPISNPGMGETGNFG--GISSIPAN--------GLTVAQNQVLNLIK---ACPRPEGL 249

Query:   238 HVNELSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYK 276
             +  +L  QL+ +    I  ++  L NEG IYST+D+ H+K
Sbjct:   250 NFQDLKNQLQHMSVASIKQAVDFLSNEGHIYSTVDDDHFK 289

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 79/273 (28%), Positives = 129/273 (47%)

Query:     2 FSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKS 61
             FS + ++A  A  GGGFM      S   P    +S   + L PVTVK + +      D +
Sbjct:     9 FSRTGYNAQGAEDGGGFMGGSQQGSQGGPGG--KSYQDECLKPVTVKQLLDVQAPYPD-A 65

Query:    62 NFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWAS--EVFDTREMEAIQ 119
             +F+++G  IT +TLVG V +   + +++ + +DDGTG +  KRW    +  D       Q
Sbjct:    66 DFLLDGRAITQITLVGQVRSINPQPTNITYRIDDGTGTIDVKRWIDPEKAEDADAASQHQ 125

Query:   120 DGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQ 179
                YVR+ G LK+F  ++ + A  VRPV +F+EV  H +E  Y HL   +    G   + 
Sbjct:   126 PDSYVRVWGKLKAFNNRRHVGALFVRPVEDFNEVNYHMLEVAYVHLDAVRQSSGGGGGAG 185

Query:   180 PQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHV 239
                 D+    S   G  G  +   N S+           Q + ++LQ  +SS    G+  
Sbjct:   186 GGGDDNMFVDSYGGGGGGGGSKAANCSTNA---------QRLFNHLQ--NSSAGNEGLEA 234

Query:   240 NELSEQLKIPQKKIMDSIASLENEGLIYSTIDE 272
             N ++  + +  + +  +   L + GLIY T+D+
Sbjct:   235 NIIARGINMSVRDVEAAADELLSAGLIYPTVDD 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 = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 82/279 (29%), Positives = 140/279 (50%)

Query:     2 FSSSQFDASNAF--SGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDD 59
             + SS +  +  +  S GGF  S  P  A+  S   R+R +Q +VP T+  +  A+   D+
Sbjct:     9 YGSSSYGGAGGYTQSPGGF-GSPAPSQAEKKS---RAR-AQHIVPCTISQLLSATLV-DE 62

Query:    60 KSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREMEAI 118
                F I  +EI+ VT+VG++ + E+  +++ + +DD T   +  ++W      + E   +
Sbjct:    63 V--FRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVV 120

Query:   119 QDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSS 178
                 YV++ G+L+SFQ KK +VAF + P+ + +E T H +E I  H+  SK+  Q  PS+
Sbjct:   121 PPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQ--PSA 178

Query:   179 QPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVH 238
                 + S+   S      G    P N        GL      +L+ ++   +  R  G++
Sbjct:   179 GRAPI-SNPGMSEAGNFGGNSFMPAN--------GLTVAQNQVLNLIK---ACPRPEGLN 226

Query:   239 VNELSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYK 276
               +L  QLK +    I  ++  L NEG IYST+D+ H+K
Sbjct:   227 FQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFK 265

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|Q2KI86 RPA2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 81/279 (29%), Positives = 138/279 (49%)

Query:     2 FSSSQFDASNAF--SGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDD 59
             +S+S F  +  +  S GGF    P  S     S AR+   Q +VP T+  +  A+   D+
Sbjct:     9 YSTSSFGGAGGYTQSPGGF--GSPTASQAEKKSRARA---QHIVPCTISQLLSATLV-DE 62

Query:    60 KSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREMEAI 118
                F I  +EI+ VT+VG++ N E+ A+++ + +DD T   +  ++W      + E   +
Sbjct:    63 V--FRIGNVEISQVTIVGIIRNAEKAATNIVYKIDDMTAAPMDVRQWVDTDDASSENTVV 120

Query:   119 QDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSS 178
                 YV++ G+L+SFQ KK +VAF + P+ + +E T H +E +  H+  SKS  Q     
Sbjct:   121 PPETYVKVAGHLRSFQNKKSLVAFKIIPLEDMNEFTTHILEVVNAHMMLSKSNSQPSAGR 180

Query:   179 QPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVH 238
              P + +  +  +   G  G    P N        GL      +L+ ++   +  R  G++
Sbjct:   181 AP-ISNPGMGEAGNFG--GNNFIPAN--------GLTVAQNQVLNLIK---ACPRPEGLN 226

Query:   239 VNELSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYK 276
               +L  QL+ +    I  ++  L NEG IYST+D+ H+K
Sbjct:   227 FQDLKNQLQHMSVASIKLAVDFLSNEGHIYSTVDDDHFK 265

GO:0019903 "protein phosphatase binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 82/274 (29%), Positives = 135/274 (49%)

Query:     8 DASNAFS---GGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFM 64
             D ++AFS   GGG   ++  QS+  PS   +      L PVT+K I  AS    D + F 
Sbjct:    14 DFNSAFSPGMGGGAGFNEYDQSSQ-PSVDRQQGAGNKLRPVTIKQILNASQVHAD-AEFK 71

Query:    65 INGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYV 124
             I+G+E+  VT VG++ N   + ++  + ++DGTG +  + W  E  D   +  +    YV
Sbjct:    72 IDGVEVGQVTFVGVLRNIHAQTTNTTYQIEDGTGMIEVRHW--EHIDA--LSELATDTYV 127

Query:   125 RLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSK--SQVQGFPSSQPQM 182
             R+ GN+K F GK  I +  +R + + +EV  H++E I  HL  ++  + V G  ++ P  
Sbjct:   128 RVYGNIKIFSGKIYIASQYIRTIKDHNEVHFHFLEAIAVHLHFTQKANAVNG--ANAPGY 185

Query:   183 VDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNEL 242
               S  N      +S    A  +L  +     L      ++  +   S+ E   GVHV +L
Sbjct:   186 GTS--NALGYNNISS-NGAANSLEQKLAEYSLTPAQMTVMQAIH--SAPETNEGVHVRQL 240

Query:   243 SEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK 276
             ++ +  P   +      L+ EG+IY+TIDE H+K
Sbjct:   241 AQSVG-PGIDLTAVTDFLQQEGIIYTTIDENHFK 273

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

---

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)
Q9ZQ19	RFA2A_ARATH	No assigned EC number	0.5535	0.9678	0.9713	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	280
cd04478	95	cd04478, RPA2_DBD_D, RPA2_DBD_D: A subfamily of OB	1e-41
COG5235	258	COG5235, RFA2, Single-stranded DNA-binding replica	8e-32
pfam08784	103	pfam08784, RPA_C, Replication protein A C terminal	3e-17
pfam01336	75	pfam01336, tRNA_anti, OB-fold nucleic acid binding	4e-09
cd04492	83	cd04492, YhaM_OBF_like, YhaM_OBF_like: A subfamily	2e-06
cd03524	75	cd03524, RPA2_OBF_family, RPA2_OBF_family: A famil	1e-05
cd04483	92	cd04483, hOBFC1_like, hOBFC1_like: A subfamily of	3e-04
COG2176	1444	COG2176, PolC, DNA polymerase III, alpha subunit (	6e-04
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	0.001
cd00090	78	cd00090, HTH_ARSR, Arsenical Resistance Operon Rep	0.001
smart00418	66	smart00418, HTH_ARSR, helix_turn_helix, Arsenical	0.002

>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 =  138 bits (349), Expect = 1e-41
 Identities = 52/95 (54%), Positives = 74/95 (77%), Gaps = 1/95 (1%)

Query: 72  NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNL 130
            VTLVG+V N EE+++++ +T+DDGTG +  ++W  +  D + E+E I++G YVR+ GNL
Sbjct: 1   QVTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNL 60

Query: 131 KSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHL 165
           KSFQGKK I+AFS+RPVT+F+EVT H +E IY HL
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|227560 COG5235, RFA2, Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]

 Score =  118 bits (296), Expect = 8e-32
 Identities = 64/263 (24%), Positives = 123/263 (46%), Gaps = 21/263 (7%)

Query: 14  SGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNV 73
           + G    +  P   D             L PVT+K I        D S F+++  E+TNV
Sbjct: 14  TRGQIFGTGSPPPMDRSEGGYIVNT---LRPVTIKQILSCDQDETD-STFLVDSAEVTNV 69

Query: 74  TLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF 133
             VG+V N +   ++  F ++DGTG +  + W    ++  + + +++  YV++ G+LK+F
Sbjct: 70  QFVGVVRNIKTSTTNSMFVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTF 129

Query: 134 QGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGFPSSQPQMVDSSLNTSART 193
            GK+ I A  +  + + +EVT H++ECIY HL  ++ Q+Q       + ++  +    ++
Sbjct: 130 NGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTR-QLQ-------RPLEEEVKNDGQS 181

Query: 194 GLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKI 253
             +      ++ SS+   D + +C +   D   +         V +  LS+     + ++
Sbjct: 182 LFAKLDNDTSSGSSRLQED-ILECYRRNQD---ENGLHI---NVVIKMLSQSYSEDETRV 234

Query: 254 MDSIASLENEGLIYSTIDEFHYK 276
             +I  L  +G IY T+D   +K
Sbjct: 235 --NIDVLLRDGHIYPTVDGNEFK 255

Length = 258

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

 Score = 74.7 bits (184), Expect = 3e-17
 Identities = 34/114 (29%), Positives = 51/114 (44%), Gaps = 15/114 (13%)

Query: 164 HLQNSKSQVQ---GFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQM 220
           HL+ +K +     G          S++ T         Q A +   +     GL      
Sbjct: 1   HLRLTKGRSGSSAGGAGPSVANTGSAMGT---------QGAFSGGDASVANPGLTPLQDQ 51

Query: 221 ILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYSTIDEF 273
           +L+ ++Q  S   E GVHV+EL+ QL  +P   I  ++  L NEG IYSTID+ 
Sbjct: 52  VLNLIKQ--SCPGEEGVHVDELAAQLNGLPVNDIRQAVDFLSNEGHIYSTIDDD 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|216440 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain

 Score = 51.9 bits (125), Expect = 4e-09
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 73  VTLVGLVYNKEERASDVNF-TLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK 131
           VT+ G V +       V F TL DGTG +    +  E    +  + +++G  V + G +K
Sbjct: 1   VTVAGRVTSVRRSGGKVAFLTLRDGTGSIQVVLFKEEAE--KLAKKLKEGDVVLVTGKVK 58

Query: 132 SFQGKK-QIVAFSVRPV 147
              G + ++V   +  +
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|239938 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)

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 7/66 (10%)

Query: 90  NFTLDDGTGRVVCKRWASEVFDTRE--MEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPV 147
             TL D TG +  K W     D  E   E  + G  V + G ++ ++G+ Q+    +R V
Sbjct: 22  ALTLQDKTGEIEAKLW-----DASEEDEEKFKPGDIVHVKGRVEEYRGRLQLKIQRIRLV 76

Query: 148 TNFDEV 153
           T  D V
Sbjct: 77  TEEDGV 82

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. Length = 83

>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 = 42.3 bits (100), Expect = 1e-05
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 74  TLVGLVYNKEERASD---VNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGN 129
           T+VG+V   EE  ++   + FTL DGTG  +    +  E+ +  E   +++G  V + G 
Sbjct: 1   TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLF-GELAEELENL-LKEGQVVYIKGK 58

Query: 130 LKSFQGKKQIVAFSVRP 146
           +K F+G+ Q++  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 = 39.0 bits (91), Expect = 3e-04
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 18/87 (20%)

Query: 76  VGLVYNKEERASDVNFTLDDGTGRVVCKRW-----------------ASEVFDTREMEA- 117
           +G V ++ ER +  +F +DDGTG V C  W                         +    
Sbjct: 3   LGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKV 62

Query: 118 IQDGMYVRLIGNLKSFQGKKQIVAFSV 144
           ++ G  +R+ G++++++G+++I A  V
Sbjct: 63  LEIGDLLRVRGSIRTYRGEREINASVV 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

>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]

 Score = 41.2 bits (97), Expect = 6e-04
 Identities = 25/121 (20%), Positives = 51/121 (42%), Gaps = 13/121 (10%)

Query: 69  EITNVTLVGLVYNKEER-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMY 123
           E T V + G ++  E +      + +N  + D T  ++ K++  +  D ++ + I+ GM+
Sbjct: 238 EETRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGIKKGMW 297

Query: 124 VRLIGN--LKSFQGKKQIVAFSVRPVTNF---DEVTCHYIECIYFHLQNSKSQVQGFPSS 178
           V+  GN  L +F     ++   +  + N    D      +E    H     SQ+    S 
Sbjct: 298 VKARGNVQLDTFTRDLTMIINDINEIENAKRKDLAKEKRVE---LHFHTKMSQMDAITSV 354

Query: 179 Q 179
           +
Sbjct: 355 E 355

Length = 1444

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 40.2 bits (95), Expect = 0.001
 Identities = 22/117 (18%), Positives = 52/117 (44%), Gaps = 8/117 (6%)

Query: 69  EITNVTLVGLVYNKEERASD-----VNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMY 123
           E   V + G V+  E +        + F + D T  ++ K+++ +  D ++ + I+ G +
Sbjct: 235 EERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDW 294

Query: 124 VRLIGNLK--SFQGKKQIVAFSVRPVTNFDEV-TCHYIECIYFHLQNSKSQVQGFPS 177
           V++ G+++  +F     + A  +  + + +   T    + +  HL    S +   PS
Sbjct: 295 VKVRGSVQNDTFTRDLVMNAQDINEIKHPERKDTAEEEKRVELHLHTKMSTMDAIPS 351

Length = 1437

>gnl|CDD|238042 cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 7/46 (15%)

Query: 221 ILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI 266
           IL  L        E  + V+EL+E+L + Q  +   +  LE  GL+
Sbjct: 12  ILRLL-------LEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLV 50

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. Length = 78

>gnl|CDD|197713 smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon Repressor

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 7/51 (13%)

Query: 221 ILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID 271
           IL  L        E  + V EL+E L + Q  +   +  L   GL+ S  +
Sbjct: 2   ILKLL-------AEGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45

Length = 66

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	280
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	99.74
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	99.73
PF10451	256	Stn1: Telomere regulation protein Stn1; InterPro:	99.56
PF01336	75	tRNA_anti-codon: OB-fold nucleic acid binding doma	99.23
cd04492	83	YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol	98.87
PRK13480	314	3'-5' exoribonuclease YhaM; Provisional	98.85
COG3390	196	Uncharacterized protein conserved in archaea [Func	98.68
cd03524	75	RPA2_OBF_family RPA2_OBF_family: A family of oligo	98.61
cd04485	84	DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp	98.54
PRK06461	129	single-stranded DNA-binding protein; Reviewed	98.51
cd04489	78	ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol	98.45
cd04491	82	SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil	98.3
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	98.2
PF13742	99	tRNA_anti_2: OB-fold nucleic acid binding domain	98.13
cd04488	75	RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f	98.04
cd04484	82	polC_OBF polC_OBF: A subfamily of OB folds corresp	98.02
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	97.73
cd04321	86	ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, a	97.62
KOG3416	134	consensus Predicted nucleic acid binding protein [	97.55
PF04076	103	BOF: Bacterial OB fold (BOF) protein; InterPro: IP	97.54
cd04323	84	AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, a	97.51
cd04100	85	Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, ant	97.51
COG4085	204	Predicted RNA-binding protein, contains TRAM domai	97.5
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.45
cd04490	79	PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds	97.43
cd04317	135	EcAspRS_like_N EcAspRS_like_N: N-terminal, anticod	97.43
TIGR00156	126	conserved hypothetical protein TIGR00156. As of th	97.34
PRK00286	438	xseA exodeoxyribonuclease VII large subunit; Revie	97.32
cd04316	108	ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, a	97.28
PRK05673	1135	dnaE DNA polymerase III subunit alpha; Validated	97.28
COG1570	440	XseA Exonuclease VII, large subunit [DNA replicati	97.26
cd04320	102	AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r	97.26
cd04322	108	LysRS_N LysRS_N: N-terminal, anticodon recognition	97.21
cd04319	103	PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticod	97.18
PRK10053	130	hypothetical protein; Provisional	97.1
PRK03932	450	asnC asparaginyl-tRNA synthetase; Validated	97.09
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.06
COG3481	287	Predicted HD-superfamily hydrolase [General functi	97.03
cd04318	82	EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticod	97.03
TIGR00237	432	xseA exodeoxyribonuclease VII, large subunit. This	97.0
PRK07373	449	DNA polymerase III subunit alpha; Reviewed	96.96
PRK07211	485	replication factor A; Reviewed	96.94
PRK07218	423	replication factor A; Provisional	96.77
COG3111	128	Periplasmic protein with OB-fold [Function unknown	96.73
TIGR00457	453	asnS asparaginyl-tRNA synthetase. In a multiple se	96.62
PF13730	55	HTH_36: Helix-turn-helix domain	96.46
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	96.41
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	96.39
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	96.39
PRK07217	311	replication factor A; Reviewed	96.38
PRK14699	484	replication factor A; Provisional	96.36
PRK07211	485	replication factor A; Reviewed	96.25
TIGR01405	1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	96.24
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	96.19
PRK00448	1437	polC DNA polymerase III PolC; Validated	96.17
PRK08402	355	replication factor A; Reviewed	96.16
PRK07218	423	replication factor A; Provisional	96.16
PRK12445	505	lysyl-tRNA synthetase; Reviewed	96.11
PRK05672	1046	dnaE2 error-prone DNA polymerase; Validated	96.11
TIGR00458	428	aspS_arch aspartyl-tRNA synthetase, archaeal type.	96.1
PRK12366	637	replication factor A; Reviewed	96.04
PRK14699	484	replication factor A; Provisional	96.03
PRK06920	1107	dnaE DNA polymerase III DnaE; Reviewed	96.01
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	96.0
PRK07374	1170	dnaE DNA polymerase III subunit alpha; Validated	95.99
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	95.96
PRK05159	437	aspC aspartyl-tRNA synthetase; Provisional	95.9
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	95.81
PRK06826	1151	dnaE DNA polymerase III DnaE; Reviewed	95.76
cd04497	138	hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f	95.74
COG0017	435	AsnS Aspartyl/asparaginyl-tRNA synthetases [Transl	95.73
PRK00484	491	lysS lysyl-tRNA synthetase; Reviewed	95.71
PRK15491	374	replication factor A; Provisional	95.7
TIGR00459	583	aspS_bact aspartyl-tRNA synthetase, bacterial type	95.7
PTZ00401	550	aspartyl-tRNA synthetase; Provisional	95.65
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.6
TIGR00499	496	lysS_bact lysyl-tRNA synthetase, eukaryotic and no	95.56
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.54
PRK06386	358	replication factor A; Reviewed	95.53
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.53
PLN02903	652	aminoacyl-tRNA ligase	95.52
PRK00476	588	aspS aspartyl-tRNA synthetase; Validated	95.45
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	95.41
PLN02502	553	lysyl-tRNA synthetase	95.38
PRK07279	1034	dnaE DNA polymerase III DnaE; Reviewed	95.35
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	95.32
PRK15491	374	replication factor A; Provisional	95.3
PRK12820	706	bifunctional aspartyl-tRNA synthetase/aspartyl/glu	95.29
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	95.27
PLN02603	565	asparaginyl-tRNA synthetase	95.19
PRK11169	164	leucine-responsive transcriptional regulator; Prov	95.09
PRK08402	355	replication factor A; Reviewed	95.06
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	95.06
PLN02850	530	aspartate-tRNA ligase	95.05
PF02765	146	POT1: Telomeric single stranded DNA binding POT1/C	95.04
PLN02221	572	asparaginyl-tRNA synthetase	94.98
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	94.94
COG2176	1444	PolC DNA polymerase III, alpha subunit (gram-posit	94.94
COG1571	421	Predicted DNA-binding protein containing a Zn-ribb	94.94
COG1522	154	Lrp Transcriptional regulators [Transcription]	94.93
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	94.92
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	94.92
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	94.91
cd04479	101	RPA3 RPA3: A subfamily of OB folds similar to huma	94.81
COG3355	126	Predicted transcriptional regulator [Transcription	94.68
PRK12366	637	replication factor A; Reviewed	94.64
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	94.59
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	94.47
PRK05813	219	single-stranded DNA-binding protein; Provisional	94.45
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	94.29
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	94.18
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	94.16
PTZ00385	659	lysyl-tRNA synthetase; Provisional	94.16
PRK08486	182	single-stranded DNA-binding protein; Provisional	94.06
PF08661	109	Rep_fac-A_3: Replication factor A protein 3; Inter	93.99
cd04481	106	RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of unc	93.98
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	93.97
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	93.96
PRK06386	358	replication factor A; Reviewed	93.88
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	93.84
PRK07275	162	single-stranded DNA-binding protein; Provisional	93.6
cd04486	78	YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fol	93.49
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	93.48
cd04474	104	RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor	93.45
PRK02983	1094	lysS lysyl-tRNA synthetase; Provisional	93.43
PRK12423	202	LexA repressor; Provisional	93.37
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	93.33
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	93.26
cd04475	101	RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor	93.21
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	93.18
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	93.07
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	93.02
PRK06751	173	single-stranded DNA-binding protein; Provisional	93.01
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	92.94
PTZ00425	586	asparagine-tRNA ligase; Provisional	92.93
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	92.91
PRK07459	121	single-stranded DNA-binding protein; Provisional	92.79
COG2345	218	Predicted transcriptional regulator [Transcription	92.72
PRK03573	144	transcriptional regulator SlyA; Provisional	92.71
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	92.54
COG1190	502	LysU Lysyl-tRNA synthetase (class II) [Translation	92.54
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	92.53
PRK02801	101	primosomal replication protein N; Provisional	92.5
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	92.49
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	92.46
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	92.42
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	92.35
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	92.32
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	92.3
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	92.3
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	92.02
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	92.02
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	92.01
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	91.99
PTZ00417	585	lysine-tRNA ligase; Provisional	91.88
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	91.86
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	91.78
PRK06752	112	single-stranded DNA-binding protein; Validated	91.72
PRK14999	241	histidine utilization repressor; Provisional	91.7
PF08679	67	DsrD: Dissimilatory sulfite reductase D (DsrD); In	91.67
PRK06293	161	single-stranded DNA-binding protein; Provisional	91.64
PF03100	131	CcmE: CcmE; InterPro: IPR004329 CcmE is the produc	91.63
PRK06863	168	single-stranded DNA-binding protein; Provisional	91.6
PRK10079	241	phosphonate metabolism transcriptional regulator P	91.44
PF10771	65	DUF2582: Protein of unknown function (DUF2582); In	91.38
PRK06958	182	single-stranded DNA-binding protein; Provisional	91.34
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	91.34
PF00436	104	SSB: Single-strand binding protein family; InterPr	91.29
COG1414	246	IclR Transcriptional regulator [Transcription]	91.24
TIGR00621	164	ssb single stranded DNA-binding protein (ssb). Thi	91.24
PF06969	66	HemN_C: HemN C-terminal domain; InterPro: IPR01072	91.02
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	90.9
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	90.89
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	90.88
PF08646	146	Rep_fac-A_C: Replication factor-A C terminal domai	90.81
COG2188	236	PhnF Transcriptional regulators [Transcription]	90.78
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	90.52
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	90.5
PRK09954	362	putative kinase; Provisional	90.41
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	90.37
PRK05813	219	single-stranded DNA-binding protein; Provisional	90.35
PRK11569	274	transcriptional repressor IclR; Provisional	90.34
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	90.22
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	90.2
PRK08763	164	single-stranded DNA-binding protein; Provisional	90.08
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	90.07
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	89.76
cd04476	166	RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds cor	89.69
cd04496	100	SSB_OBF SSB_OBF: A subfamily of OB folds similar t	89.66
PF02295	66	z-alpha: Adenosine deaminase z-alpha domain; Inter	89.42
PHA02943	165	hypothetical protein; Provisional	89.28
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	89.12
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	89.08
smart00753	88	PAM PCI/PINT associated module.	89.08
COG1725	125	Predicted transcriptional regulators [Transcriptio	88.98
PRK13254	148	cytochrome c-type biogenesis protein CcmE; Reviewe	88.75
PRK07772	186	single-stranded DNA-binding protein; Provisional	88.74
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	88.48
PF10264	80	Stork_head: Winged helix Storkhead-box1 domain; In	88.47
PRK13509	251	transcriptional repressor UlaR; Provisional	88.45
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	88.33
PRK09010	177	single-stranded DNA-binding protein; Provisional	88.25
PRK10870	176	transcriptional repressor MprA; Provisional	88.07
PRK09462	148	fur ferric uptake regulator; Provisional	88.03
KOG0554	446	consensus Asparaginyl-tRNA synthetase (mitochondri	87.94
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	87.83
PRK08182	148	single-stranded DNA-binding protein; Provisional	87.81
PRK07274	131	single-stranded DNA-binding protein; Provisional	87.79
TIGR03337	231	phnR transcriptional regulator protein. This famil	87.79
PRK13732	175	single-stranded DNA-binding protein; Provisional	87.78
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	87.71
PRK05733	172	single-stranded DNA-binding protein; Provisional	87.55
PRK11014	141	transcriptional repressor NsrR; Provisional	87.45
PRK00215	205	LexA repressor; Validated	87.37
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	87.32
PRK13777	185	transcriptional regulator Hpr; Provisional	86.93
PRK04984	239	fatty acid metabolism regulator; Provisional	86.86
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	86.78
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	86.77
PF14502	48	HTH_41: Helix-turn-helix domain	86.75
KOG0555	545	consensus Asparaginyl-tRNA synthetase [Translation	86.65
PRK10046	225	dpiA two-component response regulator DpiA; Provis	86.46
TIGR03338	212	phnR_burk phosphonate utilization associated trans	86.41
PF05331	114	DUF742: Protein of unknown function (DUF742); Inte	86.09
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	85.88
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	85.87
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	85.69
PRK03902	142	manganese transport transcriptional regulator; Pro	85.67
PRK06266	178	transcription initiation factor E subunit alpha; V	85.66
PRK03837	241	transcriptional regulator NanR; Provisional	85.52
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	85.51
PRK07217	311	replication factor A; Reviewed	85.35
PRK06642	152	single-stranded DNA-binding protein; Provisional	85.27
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	85.24
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	85.08
PF15072	86	DUF4539: Domain of unknown function (DUF4539)	85.05
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	85.01
PRK10681	252	DNA-binding transcriptional repressor DeoR; Provis	84.79
PRK13165	160	cytochrome c-type biogenesis protein CcmE; Reviewe	84.56
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	84.4
PRK07135	973	dnaE DNA polymerase III DnaE; Validated	84.12
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	84.09
PRK14165	217	winged helix-turn-helix domain-containing protein/	84.07
PF02760	170	HIN: HIN-200/IF120x domain; InterPro: IPR004021 Th	84.01
COG3888	321	Predicted transcriptional regulator [Transcription	83.8
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	83.78
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	83.67
PRK13150	159	cytochrome c-type biogenesis protein CcmE; Reviewe	83.55
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	83.54
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	83.54
TIGR00617	608	rpa1 replication factor-a protein 1 (rpa1). This f	83.47
PRK11639	169	zinc uptake transcriptional repressor; Provisional	83.42
TIGR00617	608	rpa1 replication factor-a protein 1 (rpa1). This f	83.33
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	83.17
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	83.14
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	83.03
COG2512	258	Predicted membrane-associated trancriptional regul	82.79
COG4742	260	Predicted transcriptional regulator [Transcription	82.75
PF09106	59	SelB-wing_2: Elongation factor SelB, winged helix	82.29
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	82.18
PF12869	144	tRNA_anti-like: tRNA_anti-like; InterPro: IPR02442	82.1
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	82.09
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	82.07
PRK04036	504	DNA polymerase II small subunit; Validated	81.91
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	81.9
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	81.88
PF05491	76	RuvB_C: Holliday junction DNA helicase ruvB C-term	81.83
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	81.82
COG1654	79	BirA Biotin operon repressor [Transcription]	81.8
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	81.76
PF04255	56	DUF433: Protein of unknown function (DUF433); Inte	81.53
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	81.27
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	81.2
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	81.08
COG1497	260	Predicted transcriptional regulator [Transcription	81.07
COG1846	126	MarR Transcriptional regulators [Transcription]	80.86
PRK15481	431	transcriptional regulatory protein PtsJ; Provision	80.73
PHA00738	108	putative HTH transcription regulator	80.67
PRK11050	152	manganese transport regulator MntR; Provisional	80.52
PF04492	100	Phage_rep_O: Bacteriophage replication protein O ;	80.07

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

Probab=100.00  E-value=3.9e-49  Score=330.32  Aligned_cols=244  Identities=24%  Similarity=0.451  Sum_probs=190.9

Q ss_pred             cCccccCCCCCCCCCCCCCCcccCCCCCceeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEE
Q 023576           13 FSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFT   92 (280)
Q Consensus        13 ~~ggGf~~~~~~~~~~~~~~~~k~~~~~~~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~   92 (280)
                      ..+|||.+.+++.+   ...+....+.++|+|||||||+++.+.. .++.|.+++.++.+|++||+||++....++..|+
T Consensus        13 it~g~~~~~~s~p~---~drseg~~~vntLrpvTIKQIl~~~qd~-~d~~f~vd~~Ev~~V~fVGvvrni~~~ttn~~~~   88 (258)
T COG5235          13 ITRGQIFGTGSPPP---MDRSEGGYIVNTLRPVTIKQILSCDQDE-TDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFV   88 (258)
T ss_pred             eeccceecCCCCCC---CCccccCceeeeeeeeEHHHhhcccccc-cCCceeecceEEeeEEEEEEEEeeeecccceEEE
Confidence            45889986655421   2233445678999999999999999976 6789999999999999999999999999999999


Q ss_pred             EEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHhcCCCC
Q 023576           93 LDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQV  172 (280)
Q Consensus        93 LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~~~~~~  172 (280)
                      |+||||.|+|++|...+.+.+.+....++.||||+|.||.|+||+.|.+..|++|+|+||+++|+||||+.||.+++...
T Consensus        89 iEDGTG~Ievr~W~~~~~~~e~~~d~~~~~yvkV~G~lk~F~GK~~I~~~~i~~I~d~NeV~~HfLe~I~~Hl~~t~~~~  168 (258)
T COG5235          89 IEDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTRQLQ  168 (258)
T ss_pred             EecCCceEEEEecCCCchHHHhccccccccEEEEecceeeeCCeeEEehhheeeccccchhHHHHHHHHHHHHHHHHHhc
Confidence            99999999999998777666777888999999999999999999999999999999999999999999999999988654


Q ss_pred             CCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCchhHHHHHHhcCCC-CCCCCCccCHHHHHHHhCCCHH
Q 023576          173 QGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPS-SSERERGVHVNELSEQLKIPQK  251 (280)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~Vl~~i~~~~-~~~~e~Gv~v~~I~~~l~~~~~  251 (280)
                      .      |..+.  .+.++.+.+..+.+.     +   +.+...||+.++.++|... ......+|++..|++.++.+  
T Consensus       169 ~------ple~~--~~n~GqSlf~k~dNd-----t---Ssgss~lq~~~~~c~~~~~~~~~~~~~V~I~~lsqs~~~d--  230 (258)
T COG5235         169 R------PLEEE--VKNDGQSLFAKLDND-----T---SSGSSRLQEDILECYRRNQDENGLHINVVIKMLSQSYSED--  230 (258)
T ss_pred             c------hhhhh--cCCCccceeeeccCc-----c---ccccccccHHHHHHHHHhcCCCCcccceeehHhhhhcCcc--
Confidence            3      21110  001111101112211     0   1234679999999988752 22334677777777777755  


Q ss_pred             HHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          252 KIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       252 ~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      +.+..++.|..+|+||.|+|++|||++
T Consensus       231 et~v~~d~L~~~g~iYpTvD~n~fkt~  257 (258)
T COG5235         231 ETRVNIDVLLRDGHIYPTVDGNEFKTT  257 (258)
T ss_pred             ceeeeeeeehhCceEEeeecCcceeec
Confidence            444459999999999999999999986

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

Probab=100.00  E-value=3.2e-48  Score=343.26  Aligned_cols=263  Identities=35%  Similarity=0.561  Sum_probs=202.7

Q ss_pred             CCCCcCCCCCCcCccccCCCCCCCCCCCCCCcccCCCCCceeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEE
Q 023576            2 FSSSQFDASNAFSGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYN   81 (280)
Q Consensus         2 ~~~~~~~~~~~~~ggGf~~~~~~~~~~~~~~~~k~~~~~~~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~   81 (280)
                      +.+..|....++.+|++++++.......+....+.++..+++|+||+||.++....+  ..|.+++.++.+|.+||+|++
T Consensus         2 f~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~v~~~ti~qi~s~~~~~~--~~~~i~~~~v~~v~~VGivr~   79 (265)
T KOG3108|consen    2 FSSYTFEDYNGQSSGGQGPGQFTTSRPPSSQSITNRRVQGVVPLTIKQILSSTQDDD--SVFKIGGVEVSAVSIVGIVRN   79 (265)
T ss_pred             cccccceecccccccccCCCcccccCCccccccccceeccccccceeeecccccccc--ccEEEccEEEEEEEEEEEEEe
Confidence            344455555566777776555332211222233456889999999999999988652  299999999999999999999


Q ss_pred             eeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHH
Q 023576           82 KEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECI  161 (280)
Q Consensus        82 ~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i  161 (280)
                      +++..+.+.|+|+|+||.|+|++|...+.+..+...+++|.||||.|.|+.|+|+++|.+++|+||.|+||+++|+|||+
T Consensus        80 ~e~~~t~i~y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~~yVkv~G~Lk~f~Gk~sl~~fkI~pv~D~Nevt~h~LE~i  159 (265)
T KOG3108|consen   80 IEKSATNITYEIEDGTGQIDVRQWFHDNAESEEMPALETGTYVKVYGHLKPFQGKKSLQVFKIRPVEDFNEVTTHFLEVI  159 (265)
T ss_pred             ceecCcceEEEEecCcccEEEEEeccccchhhhCcccccCcEEEeeecccCCCCceeEEEEeeeeeecCCceeEEeehhh
Confidence            99999999999999999999999998776666678999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCchhHHHHHHhcCCCCCCCCCccCHHH
Q 023576          162 YFHLQNSKSQVQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNE  241 (280)
Q Consensus       162 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~  241 (280)
                      ++|+.+++.+..   +.....   +.+.+..+ .+.-...  ++++ ..+..|..+++.|++.+++..+   .+|+|+.+
T Consensus       160 ~~hl~~s~~~~~---~sa~~~---~~~~~~~s-~~~~~~~--~~~s-~~~~~l~~i~~~v~~~~~~~~h---~eGv~~~~  226 (265)
T KOG3108|consen  160 NAHLSLSKSPSQ---SSAGND---PVGFPGMS-EAADSGY--SQES-GQSSQLERIQQRVLQAIESGLH---IEGVHIKE  226 (265)
T ss_pred             HHHHHhhhcccc---cccccC---CCCCcccc-ccccccc--Cccc-ccchhhhHHHHHHHHhhhcCcc---cccccHHH
Confidence            999999987654   111000   00000000 0000000  0111 1112378899999999999753   47999999


Q ss_pred             HHHHhC-CCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          242 LSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       242 I~~~l~-~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      |+++|+ .....+++++++|++|||||+|+||+|||+|+
T Consensus       227 i~~~l~~~~~~~~~~~~~~l~~eG~iy~TvD~~hFks~~  265 (265)
T KOG3108|consen  227 IAAQLREPSVSELREAVDFLLNEGHIYSTVDEEHFKSTN  265 (265)
T ss_pred             HHHHhcccchhhHHHHHHHHhcCCeEEEeechhheeecC
Confidence            999997 66778999999999999999999999999985

>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=4.6e-25  Score=168.64  Aligned_cols=94  Identities=55%  Similarity=0.986  Sum_probs=86.2

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCc
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNF  150 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~  150 (280)
                      +|++||+|++++..++++.|+|+|+||+|+|++|.+.+.+ ....+.+++|+||+|.|+++.|++++||+++.++|++|+
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            4899999999999999999999999999999999876531 123678999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHH
Q 023576          151 DEVTCHYIECIYFHL  165 (280)
Q Consensus       151 Nei~~H~Le~i~~~l  165 (280)
                      ||+++|+|||+++||
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=99.74  E-value=2.1e-17  Score=125.59  Aligned_cols=73  Identities=27%  Similarity=0.578  Sum_probs=64.5

Q ss_pred             EEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh------------------hhhccCCCCCEEEEEEEEeeeCC
Q 023576           74 TLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT------------------REMEAIQDGMYVRLIGNLKSFQG  135 (280)
Q Consensus        74 ~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~------------------~~~~~~~~G~yVrV~G~l~~f~~  135 (280)
                      .|||+|+++++.++|+.|+|||+||+|+|++|.+...+.                  ...+.+++|+||||.|+|+.|++
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             eeEEEEEEEee
Q 023576          136 KKQIVAFSVRP  146 (280)
Q Consensus       136 ~~~i~~~~ir~  146 (280)
                      ++||++..|..
T Consensus        81 ~~ql~i~~~~~   91 (92)
T cd04483          81 EREINASVVYK   91 (92)
T ss_pred             eeEEEEEEEEe
Confidence            99999998864

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=99.73  E-value=4e-18  Score=132.06  Aligned_cols=59  Identities=37%  Similarity=0.682  Sum_probs=50.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      ++++++++||++|++.  +..++|||+++|+++|++++++|++||++|++||+||+|||||
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            6899999999999992  3578899999999999999999999999999999999999996

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=99.56  E-value=9.4e-14  Score=123.94  Aligned_cols=126  Identities=19%  Similarity=0.313  Sum_probs=95.4

Q ss_pred             cee-eeeHHHHhhcccC----------CCCCCCeEECCEEEeeEEEEEEEEEeeec----CCeeEEEEEcCCc--eEEEE
Q 023576           41 GLV-PVTVKMISEASHS----------GDDKSNFMINGLEITNVTLVGLVYNKEER----ASDVNFTLDDGTG--RVVCK  103 (280)
Q Consensus        41 ~~~-PvtIkqi~~a~~~----------~~~~~~~~i~g~~i~~V~iVG~V~~~~~~----~t~~~~~LdDgTG--~I~~~  103 (280)
                      .+. ||+|+||+.....          ....+.|.+.++||..|+|||.|+.+...    ..++.|+|||+||  .|+|+
T Consensus        26 ~~~~PlfI~DI~~~~~~Sr~~~~~y~~~~~~~~~f~~NhPI~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~  105 (256)
T PF10451_consen   26 KVTVPLFISDIHKRLKQSRKVCENYYAPQQQNIYFYNNHPIRWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECK  105 (256)
T ss_dssp             SEE-E--HHHHCT----C--THHHHGGGG-TT-EEETTEEE-EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEE
T ss_pred             cccCcEEHHHhhhhcccccchhhhhhhhccCCEEEECCcccEEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEE
Confidence            344 9999999982211          01256889999999999999999999865    7899999999999  89999


Q ss_pred             EecccccC-hhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHhcC
Q 023576          104 RWASEVFD-TREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSK  169 (280)
Q Consensus       104 ~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~~~  169 (280)
                      .|.+.... .-....+ .|+.|+|.|.++  ++.++|.+..|..+.+++++..||.+++..+-.|.+
T Consensus       106 ~~~~~~~~~~l~~~~~-~G~~V~VkG~vs--r~~~ql~ve~i~~~~~l~~Ei~fW~~~~~~R~~L~~  169 (256)
T PF10451_consen  106 CSKSSYLSMGLPINDL-IGKVVEVKGTVS--RNERQLDVERIELVRDLNAEIEFWKERMRFRKELSK  169 (256)
T ss_dssp             EEHHHHHCCCHHCTT--TT-EEEEEEEEE--SSSEEEEEEEEEEETSCCHHHHHHHHHHHHHHHCCC
T ss_pred             EEcccccccCCCccCC-CCcEEEEEEEEc--cCcEEEEEEEEEccCChHHHHHHHHHHHHHHHHcCC
Confidence            99763211 1112344 999999999999  899999999999999999999999999998755543

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=99.23  E-value=1.2e-10  Score=84.01  Aligned_cols=73  Identities=29%  Similarity=0.430  Sum_probs=63.5

Q ss_pred             EEEEEEEEEe-eecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCe-eEEEEEEEeeC
Q 023576           73 VTLVGLVYNK-EERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGK-KQIVAFSVRPV  147 (280)
Q Consensus        73 V~iVG~V~~~-~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~-~~i~~~~ir~v  147 (280)
                      |+|.|+|.++ .....++.|+|+|+||.|+|++|.+..  ......+++|+.|+|.|+++.+++. .+|.+.+++++
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 778899999999999999999998321  2346789999999999999999987 99999999864

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=98.87  E-value=3.5e-08  Score=72.44  Aligned_cols=76  Identities=25%  Similarity=0.390  Sum_probs=61.7

Q ss_pred             EEEEEEEee--ecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchH
Q 023576           75 LVGLVYNKE--ERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDE  152 (280)
Q Consensus        75 iVG~V~~~~--~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Ne  152 (280)
                      +|-.++...  .+..++.++|+|.||.|+|++|.+..   .....+++|.+|.|.|+++.|++..++.+..|.+++++|+
T Consensus         5 ~v~~~~~~~tk~g~~~~~~~l~D~tg~i~~~~f~~~~---~~~~~l~~g~~v~v~G~v~~~~~~~~l~~~~i~~l~~~~~   81 (83)
T cd04492           5 LIKSKELRTAKNGKPYLALTLQDKTGEIEAKLWDASE---EDEEKFKPGDIVHVKGRVEEYRGRLQLKIQRIRLVTEEDG   81 (83)
T ss_pred             EEEEeeeecccCCCcEEEEEEEcCCCeEEEEEcCCCh---hhHhhCCCCCEEEEEEEEEEeCCceeEEEEEEEECCcccC
Confidence            444444432  23368999999999999999997543   2246799999999999999999999999999999999886


Q ss_pred             H
Q 023576          153 V  153 (280)
Q Consensus       153 i  153 (280)
                      .
T Consensus        82 ~   82 (83)
T cd04492          82 V   82 (83)
T ss_pred             C
Confidence            4

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=98.85  E-value=1.9e-08  Score=92.66  Aligned_cols=79  Identities=16%  Similarity=0.311  Sum_probs=63.8

Q ss_pred             EEEeeEEEEEEEEEe--eecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEe
Q 023576           68 LEITNVTLVGLVYNK--EERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVR  145 (280)
Q Consensus        68 ~~i~~V~iVG~V~~~--~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir  145 (280)
                      ..|..+.+|-.+.-.  +.+.+|+.++|.|.||.|+|++|...+   +....+++|++|+|.|++..|+++.|+++..|+
T Consensus        12 ~~v~~~~lv~~~~~~~~knG~~yl~l~l~D~tG~I~ak~W~~~~---~~~~~~~~g~vv~v~G~v~~y~g~~Ql~i~~i~   88 (314)
T PRK13480         12 EQVDHFLLIKSATKGVASNGKPFLTLILQDKSGDIEAKLWDVSP---EDEATYVPETIVHVKGDIINYRGRKQLKVNQIR   88 (314)
T ss_pred             CEeeEEEEEEEceeeecCCCCeEEEEEEEcCCcEEEEEeCCCCh---hhHhhcCCCCEEEEEEEEEEECCcceEEEEEeE
Confidence            445666655555432  234579999999999999999998754   236779999999999999999999999999999


Q ss_pred             eCCC
Q 023576          146 PVTN  149 (280)
Q Consensus       146 ~v~d  149 (280)
                      +++.
T Consensus        89 ~~~~   92 (314)
T PRK13480         89 LATE   92 (314)
T ss_pred             ECCC
Confidence            8754

>COG3390 Uncharacterized protein conserved in archaea [Function unknown]

Probab=98.68  E-value=1.3e-07  Score=79.35  Aligned_cols=126  Identities=22%  Similarity=0.332  Sum_probs=93.4

Q ss_pred             eeeeHHHHhhcccCCC--C---CCCeE--ECCEEEeeEEEEEEEEEeee---cCCeeEEEEEcCCceEEEEEeccccc--
Q 023576           43 VPVTVKMISEASHSGD--D---KSNFM--INGLEITNVTLVGLVYNKEE---RASDVNFTLDDGTGRVVCKRWASEVF--  110 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~--~---~~~~~--i~g~~i~~V~iVG~V~~~~~---~~t~~~~~LdDgTG~I~~~~w~~~~~--  110 (280)
                      +-|+++.|.++..+..  +   ...+.  -=|..+++|.|||.+.+...   +.++..+++.|.||.+.+  |...-.  
T Consensus        11 ~rVFa~El~e~~~s~~e~~e~~sp~yliTPlG~k~nRifivGtltek~~i~ed~~~~R~rVvDpTGsF~V--yag~yqPE   88 (196)
T COG3390          11 YRVFAKELRESKFSKKEEDEERSPNYLITPLGLKVNRIFIVGTLTEKEGIGEDREYWRIRVVDPTGSFYV--YAGQYQPE   88 (196)
T ss_pred             HHHHHHHHhhcceeccccccccCCcEEechhhhheeEEEEEEEEEeccCcCCcccEEEEEEecCCceEEE--EcCCCChH
Confidence            3477889988766541  1   12333  46899999999999999764   457999999999999888  322111  


Q ss_pred             ChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee----CCCchHHHHHHHHHHHHHHHhcCC
Q 023576          111 DTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP----VTNFDEVTCHYIECIYFHLQNSKS  170 (280)
Q Consensus       111 ~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~----v~d~Nei~~H~Le~i~~~l~~~~~  170 (280)
                      +....+.++.+++|.|.|++++|+..--...++|||    ..|++-..+|-+++.+..+..-+.
T Consensus        89 a~a~l~~ve~~~~VaViGKi~~y~~d~g~~~~siRpE~vs~vde~~r~~Wv~eta~~tl~Ri~a  152 (196)
T COG3390          89 AKAFLEDVEVPDLVAVIGKIRTYRTDEGVVLFSIRPELVSKVDEEARDLWVLETAEQTLERIKA  152 (196)
T ss_pred             HHHHHHhccCCceEEEecccceeecCCCceEEEechhhhhhcCHHHHHHHHHHHHHHHHHHHHH
Confidence            123457789999999999999999876666667766    345677789999999988776554

>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=98.61  E-value=3.6e-07  Score=64.44  Aligned_cols=71  Identities=30%  Similarity=0.446  Sum_probs=58.6

Q ss_pred             EEEEEEEEeeecC---CeeEEEEEcCC-ceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576           74 TLVGLVYNKEERA---SDVNFTLDDGT-GRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus        74 ~iVG~V~~~~~~~---t~~~~~LdDgT-G~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~  146 (280)
                      +++|.|.++....   .+..++|+|+| |.|+|.+|.+...  .....+++|++|.|.|+++.+++++++.+..++|
T Consensus         1 ~v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~--~~~~~~~~g~~v~v~g~v~~~~~~~~l~~~~~~~   75 (75)
T cd03524           1 TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAE--ELENLLKEGQVVYIKGKVKKFRGRLQLIVESIEL   75 (75)
T ss_pred             CeEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHH--HHHhhccCCCEEEEEEEEEecCCeEEEEeeeecC
Confidence            3789999987654   68999999999 9999999986532  1235689999999999999999999999876653

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=98.54  E-value=3.2e-07  Score=66.88  Aligned_cols=72  Identities=15%  Similarity=0.223  Sum_probs=57.0

Q ss_pred             EEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCC
Q 023576           75 LVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVT  148 (280)
Q Consensus        75 iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~  148 (280)
                      ++|.|.++..     ...++.++|+|+||.++|++|.+.-.  .....+++|.+|.|.|+++.|++..++.+..+.++.
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            5677766532     22479999999999999999964311  124578999999999999999999999998887775

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.

>PRK06461 single-stranded DNA-binding protein; Reviewed

Probab=98.51  E-value=1.1e-06  Score=70.86  Aligned_cols=84  Identities=19%  Similarity=0.268  Sum_probs=65.2

Q ss_pred             eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeee-------c--CCeeEEEEEcCCceEEEEEecccccChhh
Q 023576           44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEE-------R--ASDVNFTLDDGTGRVVCKRWASEVFDTRE  114 (280)
Q Consensus        44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~-------~--~t~~~~~LdDgTG~I~~~~w~~~~~~~~~  114 (280)
                      ++.|++|...                ...|.+++.|.++..       .  ..+..++|.|.||+|.+++|.+..     
T Consensus         4 ~~kI~dL~~g----------------~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~I~~tlW~~~a-----   62 (129)
T PRK06461          4 ITKIKDLKPG----------------MERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQA-----   62 (129)
T ss_pred             ceEHHHcCCC----------------CCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCEEEEEEeCCcc-----
Confidence            5678888532                134566667765421       1  238889999999999999998642     


Q ss_pred             hccCCCCCEEEEE-EEEeeeCCeeEEEEE---EEeeCCC
Q 023576          115 MEAIQDGMYVRLI-GNLKSFQGKKQIVAF---SVRPVTN  149 (280)
Q Consensus       115 ~~~~~~G~yVrV~-G~l~~f~~~~~i~~~---~ir~v~d  149 (280)
                       ..|++|+.|+|. |.++.|+++.+|++.   .|+++.+
T Consensus        63 -~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~  100 (129)
T PRK06461         63 -GSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD  100 (129)
T ss_pred             -ccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence             468999999999 888999999999998   6888875

>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=98.45  E-value=3.6e-06  Score=61.32  Aligned_cols=73  Identities=25%  Similarity=0.434  Sum_probs=59.5

Q ss_pred             EEEEEEEEEeee-cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC--CeeEEEEEEEeeC
Q 023576           73 VTLVGLVYNKEE-RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ--GKKQIVAFSVRPV  147 (280)
Q Consensus        73 V~iVG~V~~~~~-~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~--~~~~i~~~~ir~v  147 (280)
                      +++.|.|.+++. +.....++|+|.||.|+|.+|.+...  .....+++|+.|.|.|++..+.  ++.+|.+..|.|.
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            578899988764 33478999999999999999986431  1236789999999999999874  7899999998774

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.

>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=98.30  E-value=3.4e-06  Score=62.33  Aligned_cols=53  Identities=17%  Similarity=0.330  Sum_probs=47.3

Q ss_pred             CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEEEEEE
Q 023576           86 ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQIVAFS  143 (280)
Q Consensus        86 ~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i~~~~  143 (280)
                      ..+..++|.|.||+|.+++|.+.+     ...+++|+.|++. |.++.|++..+|.+..
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            468999999999999999998753     4679999999999 9999999999998764

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=1.2e-05  Score=60.83  Aligned_cols=73  Identities=18%  Similarity=0.275  Sum_probs=59.4

Q ss_pred             EEEEEEEEeee--cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576           74 TLVGLVYNKEE--RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN  149 (280)
Q Consensus        74 ~iVG~V~~~~~--~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d  149 (280)
                      +|.|.|.+...  .+..+-|+|.|.++.|.|.+|............+++||-|.|.|.++.|.   ||.+.+++++.-
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            67899988765  45679999999999999999976521112346789999999999999998   899999998754

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=98.20  E-value=1.9e-05  Score=57.32  Aligned_cols=72  Identities=25%  Similarity=0.314  Sum_probs=59.5

Q ss_pred             EEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576           73 VTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus        73 V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~  146 (280)
                      |++-|.|.+....+..+-|+|.|.++.|.|.+|......  ....+++|+-|.|.|++...+++-|+.+..|+.
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 VHIEGEVVQIKQTSGPTIFTLRDETGTVWAAAFEEAGVR--AYPEVEVGDIVRVTGEVEPRDGQLQIEVESLEV   72 (73)
T ss_pred             CEEEEEEeccccCCCCEEEEEEcCCEEEEEEEEchhccC--CcCCCCCCCEEEEEEEEecCCeEEEEEEeeEEE
Confidence            467898887655556799999999999999999765421  245789999999999999988899999998875

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=98.13  E-value=3.3e-05  Score=59.36  Aligned_cols=75  Identities=24%  Similarity=0.385  Sum_probs=64.3

Q ss_pred             EeeEEEEEEEEEeee-cCCeeEEEEEcCCceEEEEEecccccChhhh-ccCCCCCEEEEEEEEeeeC--CeeEEEEEEEe
Q 023576           70 ITNVTLVGLVYNKEE-RASDVNFTLDDGTGRVVCKRWASEVFDTREM-EAIQDGMYVRLIGNLKSFQ--GKKQIVAFSVR  145 (280)
Q Consensus        70 i~~V~iVG~V~~~~~-~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~-~~~~~G~yVrV~G~l~~f~--~~~~i~~~~ir  145 (280)
                      +..|+|.|.|.++.. ....+=|+|-|+...|.|.+|.....  .-. ..+++|+-|.|.|++..|.  |+.++.+..|+
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            589999999999987 67788899999999999999986542  112 4689999999999999995  78999999998


Q ss_pred             e
Q 023576          146 P  146 (280)
Q Consensus       146 ~  146 (280)
                      |
T Consensus        99 P   99 (99)
T PF13742_consen   99 P   99 (99)
T ss_pred             C
Confidence            7

>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=98.04  E-value=5.7e-05  Score=53.70  Aligned_cols=63  Identities=30%  Similarity=0.400  Sum_probs=49.1

Q ss_pred             EEEEEEEeee----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEE
Q 023576           75 LVGLVYNKEE----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIV  140 (280)
Q Consensus        75 iVG~V~~~~~----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~  140 (280)
                      +.|.|.++..    ...++.++|.|+||.|+|+.|....   .....+++|+.+.|.|+++.|++..++.
T Consensus         2 i~~~V~~~~~~~~~~~~~~~~~~~D~~g~i~~~~F~~~~---~~~~~~~~G~~~~v~Gkv~~~~~~~qi~   68 (75)
T cd04488           2 VEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNFQP---YLKKQLPPGTRVRVSGKVKRFRGGLQIV   68 (75)
T ss_pred             EEEEEEEEEeccCCCccEEEEEEEcCCCEEEEEEECCCH---HHHhcCCCCCEEEEEEEEeecCCeeEEe
Confidence            4566665432    2358999999999999999996321   2346799999999999999999887775

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

>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=98.02  E-value=9.1e-05  Score=54.96  Aligned_cols=73  Identities=23%  Similarity=0.447  Sum_probs=56.6

Q ss_pred             eEEEEEEEEEeeecC-----CeeEEEEEcCCceEEEEEecccccChhhhccCC-CCCEEEEEEEEe--eeCCeeEEEEEE
Q 023576           72 NVTLVGLVYNKEERA-----SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQ-DGMYVRLIGNLK--SFQGKKQIVAFS  143 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~-----t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~-~G~yVrV~G~l~--~f~~~~~i~~~~  143 (280)
                      .|.|-|.|-.++.+.     .-++|.|.|.|.+|.|+.|.. + +......++ +|++|+|.|++.  .|.....+.+..
T Consensus         1 ~v~i~G~Vf~~e~re~k~g~~i~~~~itD~t~Si~~K~F~~-~-~~~~~~~ik~~G~~v~v~G~v~~D~f~~e~~~~i~~   78 (82)
T cd04484           1 NVVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLR-K-DEKDKEELKSKGDWVRVRGKVQYDTFSKELVLMIND   78 (82)
T ss_pred             CEEEEEEEEEEEEEEecCCCEEEEEEEEcCCCCEEEEEecc-C-ChhHHhhcccCCCEEEEEEEEEEccCCCceEEEeee
Confidence            367889997775422     356899999999999999985 2 223456789 999999999987  577888888877


Q ss_pred             Eee
Q 023576          144 VRP  146 (280)
Q Consensus       144 ir~  146 (280)
                      |.+
T Consensus        79 i~~   81 (82)
T cd04484          79 IEE   81 (82)
T ss_pred             EEE
Confidence            765

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.

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

Probab=97.73  E-value=0.00015  Score=70.63  Aligned_cols=78  Identities=24%  Similarity=0.312  Sum_probs=68.9

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCc
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNF  150 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~  150 (280)
                      ..|.|.|.|..+...+.-..|+|.|+||.|+|--|....-  ...+.+++|++|+|+|.++.-.++.||-+..+.+++-.
T Consensus       214 ~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGv--RAyP~IevGdiV~ViG~V~~r~g~lQiE~~~me~L~G~  291 (715)
T COG1107         214 KTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGV--RAYPEIEVGDIVEVIGEVTRRDGRLQIEIEAMEKLTGD  291 (715)
T ss_pred             ceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCc--ccCCCCCCCceEEEEEEEeecCCcEEEeehhhHHhhCc
Confidence            6899999999999888889999999999999998875431  23578999999999999999999999999999888763

>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=97.62  E-value=0.00096  Score=49.74  Aligned_cols=76  Identities=17%  Similarity=0.143  Sum_probs=54.8

Q ss_pred             eEEEEEEEEEeee-cCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC-------CeeEEEEE
Q 023576           72 NVTLVGLVYNKEE-RASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ-------GKKQIVAF  142 (280)
Q Consensus        72 ~V~iVG~V~~~~~-~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~-------~~~~i~~~  142 (280)
                      .|+|.|+|.+++. .....-+.|.|+|| .|.|.. ......-.....+..|+.|.|.|.+..-.       +...|.+.
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            3789999999987 55666669999999 588754 32211112235689999999999998743       55678887


Q ss_pred             EEeeCC
Q 023576          143 SVRPVT  148 (280)
Q Consensus       143 ~ir~v~  148 (280)
                      .+..+.
T Consensus        80 ~i~il~   85 (86)
T cd04321          80 DIQTLN   85 (86)
T ss_pred             EEEEec
Confidence            776653

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

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

Probab=97.55  E-value=0.00044  Score=54.67  Aligned_cols=83  Identities=23%  Similarity=0.207  Sum_probs=62.4

Q ss_pred             eeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEE
Q 023576           45 VTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYV  124 (280)
Q Consensus        45 vtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yV  124 (280)
                      ..||||..+.+.-          ..+..|...|.++...+......+.+-|.||+|.+-+|.+.      ...|++||.|
T Consensus         5 i~ikdi~P~~kN~----------~v~fIvl~~g~~tkTkdg~~v~~~kVaD~TgsI~isvW~e~------~~~~~PGDIi   68 (134)
T KOG3416|consen    5 IFIKDIKPGLKNI----------NVTFIVLEYGRATKTKDGHEVRSCKVADETGSINISVWDEE------GCLIQPGDII   68 (134)
T ss_pred             hhHhhcChhhhcc----------eEEEEEEeeceeeeccCCCEEEEEEEecccceEEEEEecCc------CcccCCccEE
Confidence            4588887775532          22344555666666666668999999999999999999854      3679999999


Q ss_pred             EEEEEEee-eCCeeEEEEEE
Q 023576          125 RLIGNLKS-FQGKKQIVAFS  143 (280)
Q Consensus       125 rV~G~l~~-f~~~~~i~~~~  143 (280)
                      |..|...+ |++.+.|.+-+
T Consensus        69 rLt~Gy~Si~qg~LtL~~GK   88 (134)
T KOG3416|consen   69 RLTGGYASIFQGCLTLYVGK   88 (134)
T ss_pred             EecccchhhhcCceEEEecC
Confidence            99988875 67877776543

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

Probab=97.54  E-value=0.0029  Score=48.98  Aligned_cols=83  Identities=20%  Similarity=0.201  Sum_probs=56.7

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCC
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGM  122 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~  122 (280)
                      ...|++|++++.    ++          ..|.|-|.|+..-..+   .|...|.||+|.+.+=.+.    ..-..+.+++
T Consensus        21 ~~~TV~~a~~~~----Dd----------~~V~L~G~Iv~~l~~d---~Y~F~D~TG~I~VeId~~~----w~g~~vt~~~   79 (103)
T PF04076_consen   21 TVTTVAQAKNAK----DD----------TPVTLEGNIVKQLGDD---KYLFRDATGEIEVEIDDDV----WRGQTVTPDD   79 (103)
T ss_dssp             ----HHHHTTS-----SS----------EEEEEEEEEEEEEETT---EEEEEETTEEEEEE--GGG----STT----TTS
T ss_pred             CeEeHHHHhhCc----CC----------CeEEEEEEEEEEecCC---EEEEECCCCcEEEEEChhh----cCCcccCCCC
Confidence            447899998762    12          6889999998877666   6789999999998752221    1124578889


Q ss_pred             EEEEEEEEeeeCCeeEEEEEEEee
Q 023576          123 YVRLIGNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus       123 yVrV~G~l~~f~~~~~i~~~~ir~  146 (280)
                      .|+|.|.+..--.+..|-+.+|++
T Consensus        80 ~Vri~GeVDk~~~~~~IdV~~I~K  103 (103)
T PF04076_consen   80 KVRISGEVDKDWNKTEIDVDRIEK  103 (103)
T ss_dssp             EEEEEEEEEEETTEEEEEEEEEEE
T ss_pred             EEEEEEEEeCCCCceEEEEEEEEC
Confidence            999999999766788899888864

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.

>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=97.51  E-value=0.0021  Score=47.56  Aligned_cols=76  Identities=17%  Similarity=0.197  Sum_probs=55.0

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCe------eEEEEEEEe
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGK------KQIVAFSVR  145 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~------~~i~~~~ir  145 (280)
                      .|+|.|+|.+++......-+.|.|+||.|.|..-.+...+......+..|+.|.|.|.+..-...      ..|.+..+.
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            47899999999887777777999999999986533321111234578999999999999975433      456666665


Q ss_pred             eC
Q 023576          146 PV  147 (280)
Q Consensus       146 ~v  147 (280)
                      .+
T Consensus        81 vl   82 (84)
T cd04323          81 II   82 (84)
T ss_pred             EE
Confidence            44

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

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

Probab=97.51  E-value=0.0015  Score=48.37  Aligned_cols=76  Identities=22%  Similarity=0.281  Sum_probs=56.1

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeee------CCeeEEEEEEE
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSF------QGKKQIVAFSV  144 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f------~~~~~i~~~~i  144 (280)
                      .|+|.|+|.+++......-+.|.|+||.+.|..-.+...+ ......+..|++|.|.|.+..-      .+...|.+..+
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            3789999999988777666799999999999764332211 1234679999999999999863      34466777766


Q ss_pred             eeC
Q 023576          145 RPV  147 (280)
Q Consensus       145 r~v  147 (280)
                      +.+
T Consensus        81 ~il   83 (85)
T cd04100          81 EVL   83 (85)
T ss_pred             EEE
Confidence            654

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

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

Probab=97.50  E-value=0.00063  Score=57.67  Aligned_cols=84  Identities=21%  Similarity=0.334  Sum_probs=63.8

Q ss_pred             CCEEEeeEEEEEEEEEeee--cCCeeEEEEEcCCceEEEEEecccccC---hhhhccCCCCCEEEEEEEEeeeCCeeEEE
Q 023576           66 NGLEITNVTLVGLVYNKEE--RASDVNFTLDDGTGRVVCKRWASEVFD---TREMEAIQDGMYVRLIGNLKSFQGKKQIV  140 (280)
Q Consensus        66 ~g~~i~~V~iVG~V~~~~~--~~t~~~~~LdDgTG~I~~~~w~~~~~~---~~~~~~~~~G~yVrV~G~l~~f~~~~~i~  140 (280)
                      +|.-+.-|.+=|.|.+.+.  ...-..+.|+|+||.|++..+...+..   ..-++.+.+|++|.|.|+++.|+++.+|.
T Consensus        47 ~G~l~e~v~vkg~V~~~~n~~~~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~~~eGe~veVtGrv~~yrG~~eVk  126 (204)
T COG4085          47 DGRLNEEVTVKGEVTADQNAIGGGIESLVLNDGTGTITVVASRSTEETLELNEGMPVTVEGEIVEVTGRVEEYRGSSEVK  126 (204)
T ss_pred             CceeeccceeeeEEEeeecccccceEEEEEECCCCcEEEEEecChhHhHhhcCCCCccccCcEEEEEEEEEEeCCCceee
Confidence            3455667888888888763  446778899999999999999765431   11234678999999999999999999998


Q ss_pred             EEE---EeeCCC
Q 023576          141 AFS---VRPVTN  149 (280)
Q Consensus       141 ~~~---ir~v~d  149 (280)
                      +..   +||+.-
T Consensus       127 vnq~~d~~~l~k  138 (204)
T COG4085         127 VNQPNDSRPLPK  138 (204)
T ss_pred             ccCccccccccc
Confidence            654   455544

>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=97.45  E-value=0.00027  Score=46.65  Aligned_cols=47  Identities=32%  Similarity=0.572  Sum_probs=39.4

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      |+..+.+||++|.+.      .+++..+|++.++++...|...|..|.++|.|
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            356788999999974      37999999999999999999999999999987

...

>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=97.43  E-value=0.0017  Score=47.74  Aligned_cols=69  Identities=22%  Similarity=0.278  Sum_probs=49.1

Q ss_pred             EEEEEEEEEee--ecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEE
Q 023576           73 VTLVGLVYNKE--ERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSV  144 (280)
Q Consensus        73 V~iVG~V~~~~--~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~i  144 (280)
                      |.++|.|.+++  ..... .++|+|.||+++|.+|.+.-.--.....+.++..|-|.|++.. ++. .+.+..|
T Consensus         2 v~i~GiI~~v~~TK~g~~-~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g~v~~-~~~-~l~~~~I   72 (79)
T cd04490           2 VSIIGMVNDVRSTKNGHR-IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVSGTVSK-DGG-LIFADEI   72 (79)
T ss_pred             EEEEEEEeEEEEcCCCCE-EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEEEEEec-CCC-EEEEEEe
Confidence            57888888775  22234 9999999999999999765320012357899999999999966 444 5555544

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.

>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=97.43  E-value=0.0014  Score=52.99  Aligned_cols=78  Identities=19%  Similarity=0.265  Sum_probs=57.1

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee----------CCeeEEEE
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF----------QGKKQIVA  141 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f----------~~~~~i~~  141 (280)
                      .|+|.|+|.+++......-+.|.|++|.+.|.+-.....+......+..|++|.|.|.+..-          .+...|.+
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            49999999999887766667999999999987643322111234579999999999998852          23466777


Q ss_pred             EEEeeCCC
Q 023576          142 FSVRPVTN  149 (280)
Q Consensus       142 ~~ir~v~d  149 (280)
                      ..+..+..
T Consensus        96 ~~i~vl~~  103 (135)
T cd04317          96 SELEVLNK  103 (135)
T ss_pred             eEEEEEEC
Confidence            77766654

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

>TIGR00156 conserved hypothetical protein TIGR00156

Probab=97.34  E-value=0.007  Score=48.45  Aligned_cols=82  Identities=17%  Similarity=0.202  Sum_probs=58.5

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCC
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGM  122 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~  122 (280)
                      ...|++|++++.    ++          ..|.|-|.|+..-..+   .|...|+||.|.+.+=.+.    ..-..+.+++
T Consensus        44 ~~~tV~~a~~~~----Dd----------t~V~L~G~Iv~~l~~d---~Y~F~D~TG~I~VeId~~~----w~G~~v~p~d  102 (126)
T TIGR00156        44 KKMTVDFAKSMH----DG----------ASVTLRGNIISHIGDD---RYVFRDKSGEINVVIPAAV----WNGREVQPKD  102 (126)
T ss_pred             ceEeHHHHhhCC----CC----------CEEEEEEEEEEEeCCc---eEEEECCCCCEEEEECHHH----cCCCcCCCCC
Confidence            368999998862    23          5788888888766554   6789999999888751110    1123578899


Q ss_pred             EEEEEEEEeeeCCeeEEEEEEEe
Q 023576          123 YVRLIGNLKSFQGKKQIVAFSVR  145 (280)
Q Consensus       123 yVrV~G~l~~f~~~~~i~~~~ir  145 (280)
                      -|||.|.|..--....|-+.+|+
T Consensus       103 ~V~I~GeVDk~~~~~~IdV~~I~  125 (126)
T TIGR00156       103 MVNISGSLDKKSAPAEVDVTHIQ  125 (126)
T ss_pred             EEEEEEEECCCCCCeEEEEEEEE
Confidence            99999999854345677777765

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

>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed

Probab=97.32  E-value=0.001  Score=64.25  Aligned_cols=112  Identities=17%  Similarity=0.216  Sum_probs=83.0

Q ss_pred             eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeec-CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCC
Q 023576           44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEER-ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGM  122 (280)
Q Consensus        44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~-~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~  122 (280)
                      |+++++|...-+.-       ++.. +..|+|.|.|.+.... +..+=|+|-|.+..|.|.+|......  -...+++|+
T Consensus         5 ~~svsel~~~ik~~-------le~~-~~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~~--~~~~~~~G~   74 (438)
T PRK00286          5 ILSVSELNRYVKSL-------LERD-LGQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSARR--LKFKPEEGM   74 (438)
T ss_pred             cCcHHHHHHHHHHH-------HHhh-CCcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhhc--CCCCCCCCC
Confidence            57888887654321       1222 6899999999998765 45788999999999999999865321  124579999


Q ss_pred             EEEEEEEEeeeC--CeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHh
Q 023576          123 YVRLIGNLKSFQ--GKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQN  167 (280)
Q Consensus       123 yVrV~G~l~~f~--~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~  167 (280)
                      -|.|.|++..|.  |.-||.|..|.|.-- -++ +--+|-+...|..
T Consensus        75 ~v~v~g~~~~y~~~g~~ql~v~~i~~~g~-G~l-~~~~~~lk~~L~~  119 (438)
T PRK00286         75 KVLVRGKVSLYEPRGDYQLIVEEIEPAGI-GAL-AAAFEQLKEKLAA  119 (438)
T ss_pred             EEEEEEEEEEECCCCCEEEEEEEeeeCCc-cHH-HHHHHHHHHHHHH
Confidence            999999999985  679999999998764 454 4445555555543

>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=97.28  E-value=0.0035  Score=48.69  Aligned_cols=80  Identities=15%  Similarity=0.148  Sum_probs=58.6

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC--hhhhccCCCCCEEEEEEEEeeeCC---eeEEEEEEEe
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD--TREMEAIQDGMYVRLIGNLKSFQG---KKQIVAFSVR  145 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~G~yVrV~G~l~~f~~---~~~i~~~~ir  145 (280)
                      ..|+|.|+|.+++......-+.|.|+||.|.|.+-......  ......+..|+.|.|.|.+..-..   ...|.+..++
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            35899999999988777777799999999998664322111  123456899999999999887432   3667778777


Q ss_pred             eCCCc
Q 023576          146 PVTNF  150 (280)
Q Consensus       146 ~v~d~  150 (280)
                      .+...
T Consensus        93 il~~~   97 (108)
T cd04316          93 VLSEA   97 (108)
T ss_pred             EEeCC
Confidence            76654

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.

>PRK05673 dnaE DNA polymerase III subunit alpha; Validated

Probab=97.28  E-value=0.00086  Score=71.64  Aligned_cols=76  Identities=20%  Similarity=0.237  Sum_probs=61.8

Q ss_pred             eEEEEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576           72 NVTLVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus        72 ~V~iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~  146 (280)
                      .|.++|.|.+++.     +..+..++|+|.||.|++++|.+.-.  .....+.+|..|.|.|++..++++.+|.+..|.+
T Consensus       979 ~V~v~G~I~~vk~~~TKkG~~mafltLeD~TG~iEvviFp~~ye--~~~~~L~~g~iV~V~GkVe~~~~~~qlii~~I~~ 1056 (1135)
T PRK05673        979 VVTVAGLVVSVRRRVTKRGNKMAIVTLEDLSGRIEVMLFSEALE--KYRDLLEEDRIVVVKGQVSFDDGGLRLTAREVMD 1056 (1135)
T ss_pred             eEEEEEEEEEEEecccCCCCeEEEEEEEeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeeccc
Confidence            5788888888754     23578899999999999999975421  2235689999999999999988889999999988


Q ss_pred             CCC
Q 023576          147 VTN  149 (280)
Q Consensus       147 v~d  149 (280)
                      +.+
T Consensus      1057 L~~ 1059 (1135)
T PRK05673       1057 LEE 1059 (1135)
T ss_pred             HHH
Confidence            854

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

Probab=97.26  E-value=0.0036  Score=59.91  Aligned_cols=95  Identities=23%  Similarity=0.270  Sum_probs=77.0

Q ss_pred             EeeEEEEEEEEEeeecC-CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee--CCeeEEEEEEEee
Q 023576           70 ITNVTLVGLVYNKEERA-SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF--QGKKQIVAFSVRP  146 (280)
Q Consensus        70 i~~V~iVG~V~~~~~~~-t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f--~~~~~i~~~~ir~  146 (280)
                      +.+|+|-|.|.+++... ..+=|+|-|....|.|.+|.....-  -...+++|+.|-|.|+|..|  +|+-||.+..|+|
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 LGQVWVRGEISNFTRPASGHLYFTLKDERAQIRCVMFKGNNRR--LKFRPEEGMQVLVRGKISLYEPRGDYQIVAESMEP  100 (440)
T ss_pred             CCeEEEEEEecCCccCCCccEEEEEccCCceEEEEEEcCcccc--cCCCccCCCEEEEEEEEEEEcCCCceEEEEecCCc
Confidence            78999999999998544 3788999999999999999876421  12457999999999999999  5789999999998


Q ss_pred             CCCchHHHHHHHHHHHHHHHhc
Q 023576          147 VTNFDEVTCHYIECIYFHLQNS  168 (280)
Q Consensus       147 v~d~Nei~~H~Le~i~~~l~~~  168 (280)
                      .-. -. .+--+|.++..|...
T Consensus       101 ~G~-G~-L~~~~E~lK~kL~aE  120 (440)
T COG1570         101 AGL-GA-LYLAFEQLKAKLAAE  120 (440)
T ss_pred             CCh-hH-HHHHHHHHHHHHHhC
Confidence            765 33 366778888887654

>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=97.26  E-value=0.0035  Score=48.11  Aligned_cols=79  Identities=11%  Similarity=0.010  Sum_probs=58.4

Q ss_pred             eEEEEEEEEEeeecC-CeeEEEEEcCCceEEEEEecccc--cCh--hhhccCCCCCEEEEEEEEeeeC--------CeeE
Q 023576           72 NVTLVGLVYNKEERA-SDVNFTLDDGTGRVVCKRWASEV--FDT--REMEAIQDGMYVRLIGNLKSFQ--------GKKQ  138 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~-t~~~~~LdDgTG~I~~~~w~~~~--~~~--~~~~~~~~G~yVrV~G~l~~f~--------~~~~  138 (280)
                      .|+|.|+|.+++... ...-+.|.|+||.|.|.+-.+..  .+.  .....+..|+.|.|.|.+..-.        +...
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            378999999998876 66777999999999999864421  111  1235689999999999998631        3467


Q ss_pred             EEEEEEeeCCCc
Q 023576          139 IVAFSVRPVTNF  150 (280)
Q Consensus       139 i~~~~ir~v~d~  150 (280)
                      |.+..++.+...
T Consensus        81 l~~~~i~il~~~   92 (102)
T cd04320          81 LHIEKIYVVSEA   92 (102)
T ss_pred             EEEEEEEEEecC
Confidence            788887777543

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.

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

Probab=97.21  E-value=0.0038  Score=48.44  Aligned_cols=77  Identities=13%  Similarity=0.188  Sum_probs=54.2

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh--hhhcc-CCCCCEEEEEEEEeee-CCeeEEEEEEEeeC
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT--REMEA-IQDGMYVRLIGNLKSF-QGKKQIVAFSVRPV  147 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~--~~~~~-~~~G~yVrV~G~l~~f-~~~~~i~~~~ir~v  147 (280)
                      .|+|.|+|.+++.....+-+.|-|+||.|.|.+-.....+.  ..... +..|+.|.|.|.+..- .+...|.+..+.-+
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            47899999999988777778999999999997643321111  11234 8999999999998854 34455555555444


Q ss_pred             C
Q 023576          148 T  148 (280)
Q Consensus       148 ~  148 (280)
                      .
T Consensus        81 s   81 (108)
T cd04322          81 S   81 (108)
T ss_pred             e
Confidence            3

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=97.18  E-value=0.0042  Score=47.82  Aligned_cols=79  Identities=24%  Similarity=0.205  Sum_probs=56.6

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeeeCC---eeEEEEEEEeeC
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSFQG---KKQIVAFSVRPV  147 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f~~---~~~i~~~~ir~v  147 (280)
                      .|+|.|+|.+++......-+.|.|+||.+.|.+-.+...+ ......+..|+.|.|.|.+..-..   ...|.+..+..+
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            3789999999988777777799999999998764331111 122356899999999999986432   245677777666


Q ss_pred             CCc
Q 023576          148 TNF  150 (280)
Q Consensus       148 ~d~  150 (280)
                      ...
T Consensus        81 ~~a   83 (103)
T cd04319          81 QNV   83 (103)
T ss_pred             ecC
Confidence            554

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.

>PRK10053 hypothetical protein; Provisional

Probab=97.10  E-value=0.024  Score=45.67  Aligned_cols=78  Identities=14%  Similarity=0.251  Sum_probs=57.0

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEE----ecccccChhhhccC
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKR----WASEVFDTREMEAI  118 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~----w~~~~~~~~~~~~~  118 (280)
                      ...|++|.+++.    ++          ..|.|-|.|+..-..+   .|...|+||.|.+.+    |..        ..+
T Consensus        48 ~~~tV~~a~~~~----Dd----------~~V~L~G~Iv~~lg~d---~Y~F~D~tG~I~VeID~~~w~G--------~~v  102 (130)
T PRK10053         48 RKMTVEQAKTMH----DG----------ATVSLRGNLIDHKGDD---RYVFRDKSGEINVIIPAAVFDG--------REV  102 (130)
T ss_pred             ceEEHHHhhcCc----CC----------CeEEEEEEEEEEeCCc---eEEEECCCCcEEEEeCHHHcCC--------CcC
Confidence            357999988752    23          5677788887765554   678999999988875    532        357


Q ss_pred             CCCCEEEEEEEEeeeCCeeEEEEEEEe
Q 023576          119 QDGMYVRLIGNLKSFQGKKQIVAFSVR  145 (280)
Q Consensus       119 ~~G~yVrV~G~l~~f~~~~~i~~~~ir  145 (280)
                      .+.+.|||.|.+..=.....|-+.+|+
T Consensus       103 ~p~~kV~I~GevDk~~~~~~IdV~~i~  129 (130)
T PRK10053        103 QPDQMININGSLDKKSAPPVVRVTHLQ  129 (130)
T ss_pred             CCCCEEEEEEEECCCCCCeEEEEEEEe
Confidence            889999999999864445677777765

>PRK03932 asnC asparaginyl-tRNA synthetase; Validated

Probab=97.09  E-value=0.0069  Score=58.80  Aligned_cols=94  Identities=18%  Similarity=0.193  Sum_probs=67.8

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCC
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDG  121 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G  121 (280)
                      .+++|++|+.....          |   ..|+|.|+|.+++......-+.|.|+||.|.+.+-.+...+ -.....+..|
T Consensus         2 ~~~~~~~~~~~~~~----------~---~~V~i~G~v~~~R~~g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~   68 (450)
T PRK03932          2 MRVSIKDILKGKYV----------G---QEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTG   68 (450)
T ss_pred             CcEEHHHhcccccC----------C---CEEEEEEEEEEEEeCCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCC
Confidence            46789998732111          1   67999999999988776667799999998877764433111 1234568999


Q ss_pred             CEEEEEEEEeeeC---CeeEEEEEEEeeCCC
Q 023576          122 MYVRLIGNLKSFQ---GKKQIVAFSVRPVTN  149 (280)
Q Consensus       122 ~yVrV~G~l~~f~---~~~~i~~~~ir~v~d  149 (280)
                      +.|.|.|.+..-.   +...|.+..++.+..
T Consensus        69 s~v~v~G~v~~~~~~~~~~el~~~~i~vl~~   99 (450)
T PRK03932         69 SSVIVTGTVVESPRAGQGYELQATKIEVIGE   99 (450)
T ss_pred             cEEEEEEEEEcCCCCCCCEEEEEEEEEEccC
Confidence            9999999999743   356788888877664

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

Probab=97.06  E-value=0.0023  Score=45.63  Aligned_cols=59  Identities=20%  Similarity=0.394  Sum_probs=48.5

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC-ccccc
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE-FHYKF  277 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd-~hfk~  277 (280)
                      ...+++||.+|+..+    +.|++..+|++.++++...|+..|..|.++|.|...-+. -.|..
T Consensus         5 ~~~~~~IL~~L~~~g----~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~i   64 (68)
T smart00550        5 DSLEEKILEFLENSG----DETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWKL   64 (68)
T ss_pred             hHHHHHHHHHHHHCC----CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceEe
Confidence            357889999999852    337999999999999999999999999999999875433 34443

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

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

Probab=97.03  E-value=0.00048  Score=62.41  Aligned_cols=63  Identities=29%  Similarity=0.481  Sum_probs=56.3

Q ss_pred             ecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576           84 ERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN  149 (280)
Q Consensus        84 ~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d  149 (280)
                      ....++.++++|.||.|+++.|+-...   ....+..|..|++.|....|++.+|+.+..+|++++
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            355799999999999999999987653   256799999999999999999999999999999887

>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=97.03  E-value=0.017  Score=42.39  Aligned_cols=74  Identities=18%  Similarity=0.154  Sum_probs=54.9

Q ss_pred             EEEEEEEEEeeecCCeeEEEEEcCCce--EEEEEecccccChhhhccCCCCCEEEEEEEEeeeC---CeeEEEEEEEeeC
Q 023576           73 VTLVGLVYNKEERASDVNFTLDDGTGR--VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ---GKKQIVAFSVRPV  147 (280)
Q Consensus        73 V~iVG~V~~~~~~~t~~~~~LdDgTG~--I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~~~ir~v  147 (280)
                      |++.|+|.+++......-+.|.|+|+.  |.|..-.+.. .......+..|+.|.|.|.+..-.   +...|.+..+..+
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            789999999998777777789999994  9997643321 112346789999999999988753   3466777776654

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

>TIGR00237 xseA exodeoxyribonuclease VII, large subunit

Probab=97.00  E-value=0.0049  Score=59.56  Aligned_cols=94  Identities=21%  Similarity=0.251  Sum_probs=73.4

Q ss_pred             EeeEEEEEEEEEeeec-CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC--CeeEEEEEEEee
Q 023576           70 ITNVTLVGLVYNKEER-ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ--GKKQIVAFSVRP  146 (280)
Q Consensus        70 i~~V~iVG~V~~~~~~-~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~--~~~~i~~~~ir~  146 (280)
                      +..|+|.|.|.+.... +..+=|+|-|....|.|.+|......  -...+++|+-|.|.|++..|.  |+-||.+..|.|
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 FLQVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNNR--LKFRPQNGQQVLVRGGISVYEPRGDYQIICFEMQP   94 (432)
T ss_pred             CCcEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhhC--CCCCCCCCCEEEEEEEEEEECCCCcEEEEEEEecc
Confidence            5689999999998754 45788899999999999999875421  124579999999999999995  779999999999


Q ss_pred             CCCchHHHHHHHHHHHHHHHh
Q 023576          147 VTNFDEVTCHYIECIYFHLQN  167 (280)
Q Consensus       147 v~d~Nei~~H~Le~i~~~l~~  167 (280)
                      .- .-++ +--+|-+...|..
T Consensus        95 ~G-~G~l-~~~~~~lk~~L~~  113 (432)
T TIGR00237        95 AG-EGLL-QLAYEQLKEKLAA  113 (432)
T ss_pred             CC-hHHH-HHHHHHHHHHHHH
Confidence            75 4454 4455556666653

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.

>PRK07373 DNA polymerase III subunit alpha; Reviewed

Probab=96.96  E-value=0.0041  Score=60.25  Aligned_cols=76  Identities=14%  Similarity=0.181  Sum_probs=60.4

Q ss_pred             eEEEEEEEEEeeec-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576           72 NVTLVGLVYNKEER-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus        72 ~V~iVG~V~~~~~~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~  146 (280)
                      .|+++|.|.+++..     .....++|+|.||.|++.+|.+.-.  .....+.++..|-|.|++..-.+..+|.+..|.+
T Consensus       282 ~v~vaG~I~~ik~~~TKkG~~maf~~leD~tG~ie~vvFp~~y~--~~~~~l~~~~~v~v~G~v~~~~~~~~liv~~i~~  359 (449)
T PRK07373        282 KVSAVVMLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPKSYE--RISELLQVDARLIIWGKVDRRDDQVQLIVEDAEP  359 (449)
T ss_pred             EEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeEEEEEeEeec
Confidence            58899999887642     3467789999999999999976421  2235689999999999998755678899999888


Q ss_pred             CCC
Q 023576          147 VTN  149 (280)
Q Consensus       147 v~d  149 (280)
                      +.+
T Consensus       360 l~~  362 (449)
T PRK07373        360 IEE  362 (449)
T ss_pred             Hhh
Confidence            765

>PRK07211 replication factor A; Reviewed

Probab=96.94  E-value=0.0058  Score=59.47  Aligned_cols=76  Identities=28%  Similarity=0.451  Sum_probs=60.3

Q ss_pred             eeEEEEEEEEEeee----------cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEE
Q 023576           71 TNVTLVGLVYNKEE----------RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~----------~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i  139 (280)
                      ..|.|.|+|.++..          ......++|-|.||+|.+.+|.+...   ..+.+++|+.|+|. ++++.|++...|
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            45788888876532          11357899999999999999987642   23569999999995 899999999999


Q ss_pred             EEE---EEeeCCC
Q 023576          140 VAF---SVRPVTN  149 (280)
Q Consensus       140 ~~~---~ir~v~d  149 (280)
                      ++.   .|.++.+
T Consensus       249 sl~~~s~I~~~~d  261 (485)
T PRK07211        249 HVGDRGAVEEVDE  261 (485)
T ss_pred             EECCCceEEECCc
Confidence            886   7888766

>PRK07218 replication factor A; Provisional

Probab=96.77  E-value=0.011  Score=56.91  Aligned_cols=72  Identities=22%  Similarity=0.356  Sum_probs=57.9

Q ss_pred             eeEEEEEEEEEeeec--------CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEEEE
Q 023576           71 TNVTLVGLVYNKEER--------ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQIVA  141 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~--------~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i~~  141 (280)
                      ..|.|.|+|.++..+        .......|.|.||+|....|.+.       +.+.+|+.|+|.+ .++.|++..+|++
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            458888888877431        13556689999999999999863       3589999999998 7788999999999


Q ss_pred             E---EEeeCCC
Q 023576          142 F---SVRPVTN  149 (280)
Q Consensus       142 ~---~ir~v~d  149 (280)
                      .   .|.++++
T Consensus       246 ~~~t~I~~~d~  256 (423)
T PRK07218        246 SEFTTVEALDR  256 (423)
T ss_pred             CCceEEEECCC
Confidence            8   7777765

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

Probab=96.73  E-value=0.042  Score=43.50  Aligned_cols=81  Identities=16%  Similarity=0.243  Sum_probs=59.2

Q ss_pred             eeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEE----EecccccChhhhcc
Q 023576           42 LVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCK----RWASEVFDTREMEA  117 (280)
Q Consensus        42 ~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~----~w~~~~~~~~~~~~  117 (280)
                      ..-.|+++-+++.    ++          ..|.|.|.|+..-...   .|..-|+||+|.+-    .|..        ..
T Consensus        43 ~~~~TV~~Ak~~~----Dd----------a~V~l~GnIv~qi~~D---~y~FrD~sGeI~VeIdd~~w~g--------~t   97 (128)
T COG3111          43 AKVTTVDQAKTLH----DD----------AWVSLEGNIVRQIGDD---RYVFRDASGEINVDIDDKVWNG--------QT   97 (128)
T ss_pred             cceeEHHHhhccc----cC----------CeEEEEeeEEEeeCCc---eEEEEcCCccEEEEecccccCC--------cc
Confidence            3446788877662    22          5788999988866555   56899999987765    4543        35


Q ss_pred             CCCCCEEEEEEEEeeeCCeeEEEEEEEeeC
Q 023576          118 IQDGMYVRLIGNLKSFQGKKQIVAFSVRPV  147 (280)
Q Consensus       118 ~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v  147 (280)
                      +.+.+.|++.|.+-.=-.+..|-+.+|+++
T Consensus        98 v~P~dkV~I~GevDk~~~~~eIdV~~I~k~  127 (128)
T COG3111          98 VTPKDKVRIQGEVDKDWNSVEIDVKHIEKL  127 (128)
T ss_pred             cCcccEEEEEeEEcCCCccceeEhhheEec
Confidence            788899999999987555677777777765

>TIGR00457 asnS asparaginyl-tRNA synthetase

Probab=96.62  E-value=0.021  Score=55.51  Aligned_cols=94  Identities=16%  Similarity=0.179  Sum_probs=63.9

Q ss_pred             eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCC--ceEEEEEecccccC-hhhhccCCC
Q 023576           44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGT--GRVVCKRWASEVFD-TREMEAIQD  120 (280)
Q Consensus        44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgT--G~I~~~~w~~~~~~-~~~~~~~~~  120 (280)
                      |.+|+.++.-....        .|   ..|+|.|+|.+++.....+-+.|.|+|  |.|.|.+-.....+ ......+..
T Consensus         1 ~~~~~~~~~~~~~~--------~g---~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~   69 (453)
T TIGR00457         1 SAAIKDLLQQVYKF--------VG---DEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTT   69 (453)
T ss_pred             CccHHHHHhcchhc--------CC---CEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCC
Confidence            56788888521111        12   569999999999976666667999999  99999764331111 123457999


Q ss_pred             CCEEEEEEEEeee---CCeeEEEEEEEeeCC
Q 023576          121 GMYVRLIGNLKSF---QGKKQIVAFSVRPVT  148 (280)
Q Consensus       121 G~yVrV~G~l~~f---~~~~~i~~~~ir~v~  148 (280)
                      |+.|.|.|.+..-   .+...|.+..++.+.
T Consensus        70 gs~V~v~G~v~~~~~~~~~~El~~~~i~vl~  100 (453)
T TIGR00457        70 GSSVSVTGKVVESPGKGQPVELQVKKIEVVG  100 (453)
T ss_pred             CcEEEEEEEEEcCCCCCCCEEEEEeEEEEEe
Confidence            9999999998863   234566666665554

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.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=96.46  E-value=0.01  Score=40.03  Aligned_cols=54  Identities=20%  Similarity=0.342  Sum_probs=42.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      +|++....|+-+|..........-.+.+.|++.++++.+.|+.+|.+|.+.|+|
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            467777888888877542222233489999999999999999999999999986

>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=96.41  E-value=0.0072  Score=41.51  Aligned_cols=46  Identities=35%  Similarity=0.537  Sum_probs=40.7

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +..|+++|++.      .-+++++|++.|+.++..||.-|..|.++|.|--+
T Consensus         2 ~~~Il~~l~~~------~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~   47 (57)
T PF08220_consen    2 QQQILELLKEK------GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT   47 (57)
T ss_pred             HHHHHHHHHHc------CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            46799999874      36899999999999999999999999999998654

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

>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=96.39  E-value=0.002  Score=45.64  Aligned_cols=53  Identities=23%  Similarity=0.456  Sum_probs=40.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCcc--CHHHHHHHhCCC-HHHHHHHHHHHHhCCeeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGV--HVNELSEQLKIP-QKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv--~v~~I~~~l~~~-~~~v~~al~~L~~eG~IYs  268 (280)
                      .|++.|++||++|++--   .+.|+  ++.||++.|++. ...|...|..|.+.|+|=.
T Consensus         3 ~LT~rQ~~vL~~I~~~~---~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r   58 (65)
T PF01726_consen    3 ELTERQKEVLEFIREYI---EENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRR   58 (65)
T ss_dssp             ---HHHHHHHHHHHHHH---HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHHHH---HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccC
Confidence            47889999999998731   22344  889999999975 9999999999999999854

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.

>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=96.39  E-value=0.0088  Score=41.13  Aligned_cols=57  Identities=25%  Similarity=0.321  Sum_probs=47.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+-.||.+|...+    +.++++.+|++.++++...|...|..|...|+|..+-|.+
T Consensus         2 glt~~q~~vL~~l~~~~----~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~   58 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHP----GEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPG   58 (62)
T ss_dssp             TSTHHHHHHHHHHHHST----TSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SS
T ss_pred             ccCHHHHHHHHHHHHCC----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCC
Confidence            46778888999998752    3369999999999999999999999999999999887753

...

>PRK07217 replication factor A; Reviewed

Probab=96.38  E-value=0.021  Score=52.38  Aligned_cols=74  Identities=18%  Similarity=0.280  Sum_probs=56.5

Q ss_pred             eeEEEEEEEEEeeecC-CeeEE--EEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEE-eeeCCeeEEEEEEEee
Q 023576           71 TNVTLVGLVYNKEERA-SDVNF--TLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL-KSFQGKKQIVAFSVRP  146 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~-t~~~~--~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l-~~f~~~~~i~~~~ir~  146 (280)
                      .+|.|.|+|..+-+.. ..+.+  .|.|.||+|....|.+.+     ...+++|+.|++.+-. +.|+|+.+|++.+-..
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            5789999999885422 22222  799999999999998743     4569999999998765 5799999999966444


Q ss_pred             CCC
Q 023576          147 VTN  149 (280)
Q Consensus       147 v~d  149 (280)
                      |..
T Consensus       158 I~~  160 (311)
T PRK07217        158 IEE  160 (311)
T ss_pred             EEe
Confidence            443

>PRK14699 replication factor A; Provisional

Probab=96.36  E-value=0.013  Score=57.27  Aligned_cols=77  Identities=14%  Similarity=0.122  Sum_probs=55.0

Q ss_pred             eeEEEEEEEEEeee--------cC--CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEE
Q 023576           71 TNVTLVGLVYNKEE--------RA--SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIV  140 (280)
Q Consensus        71 ~~V~iVG~V~~~~~--------~~--t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~  140 (280)
                      ..|+|.|+|.++..        ..  ...++.|.|.||+|.+.+|.+.... -..-.+++||.|+|.|.++...+.+.|+
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 GPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMADL-IKAGKIKAGQTLQISGYAKQGYSGVEVN  146 (484)
T ss_pred             ceEEEEEEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCccch-hhhcCCCCCCEEEEcceeccCCCCceEE
Confidence            46778888877641        11  3556799999999999999865311 1112599999999999988766667888


Q ss_pred             EE---EEeeCC
Q 023576          141 AF---SVRPVT  148 (280)
Q Consensus       141 ~~---~ir~v~  148 (280)
                      +.   .+++.+
T Consensus       147 ~~~~~~i~~~~  157 (484)
T PRK14699        147 IGNNGVLTESE  157 (484)
T ss_pred             eCCCceeeccC
Confidence            86   455543

>PRK07211 replication factor A; Reviewed

Probab=96.25  E-value=0.026  Score=55.05  Aligned_cols=77  Identities=19%  Similarity=0.287  Sum_probs=58.4

Q ss_pred             eeEEEEEEEEEeee------c-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEE
Q 023576           71 TNVTLVGLVYNKEE------R-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~------~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i  139 (280)
                      ..|.|.|+|.++..      .     ..-..+.|-|.||.|.+.+|.+...  .....|++|+.++|.|+++...+...|
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            46778888876532      1     2567889999999999999987542  235679999999999999765555688


Q ss_pred             EEEEEeeCCC
Q 023576          140 VAFSVRPVTN  149 (280)
Q Consensus       140 ~~~~ir~v~d  149 (280)
                      ++..+.+..|
T Consensus       142 ~i~~ve~~~d  151 (485)
T PRK07211        142 SVDKVEPDPD  151 (485)
T ss_pred             EEeeEEEccc
Confidence            8888777655

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

Probab=96.24  E-value=0.031  Score=60.30  Aligned_cols=78  Identities=18%  Similarity=0.379  Sum_probs=62.5

Q ss_pred             eeEEEEEEEEEeeec-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe--eeCCeeEEEEEE
Q 023576           71 TNVTLVGLVYNKEER-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK--SFQGKKQIVAFS  143 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~--~f~~~~~i~~~~  143 (280)
                      ..|.|.|.|-.++.+     ..-++|.|.|.|.+|.|+.|.....+.+....+++|++|+|.|.+.  .|..+..+.+..
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            678899999777542     3456899999999999999986654444567899999999999988  567788888888


Q ss_pred             EeeCC
Q 023576          144 VRPVT  148 (280)
Q Consensus       144 ir~v~  148 (280)
                      |.++.
T Consensus        88 ~~~~~   92 (1213)
T TIGR01405        88 IEEIP   92 (1213)
T ss_pred             eeecC
Confidence            87664

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

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

Probab=96.19  E-value=0.0055  Score=42.94  Aligned_cols=46  Identities=20%  Similarity=0.379  Sum_probs=39.4

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +++|+++|++.     ..+++..|||+.|+++..++|.-|..|..+|.|-.
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            46799999973     34799999999999999999999999999999975

>PRK00448 polC DNA polymerase III PolC; Validated

Probab=96.17  E-value=0.035  Score=60.78  Aligned_cols=80  Identities=19%  Similarity=0.401  Sum_probs=63.2

Q ss_pred             eeEEEEEEEEEeeecC-----CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee--eCCeeEEEEEE
Q 023576           71 TNVTLVGLVYNKEERA-----SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS--FQGKKQIVAFS  143 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~-----t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~--f~~~~~i~~~~  143 (280)
                      ..|.|-|.|-.++.+.     .-++|.|.|.|.+|.|+.|.....+.+....++.|++|+|.|++..  |.....+.+..
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            5788999997775432     3568999999999999999865544445678999999999999984  77778888888


Q ss_pred             EeeCCCc
Q 023576          144 VRPVTNF  150 (280)
Q Consensus       144 ir~v~d~  150 (280)
                      |.++..+
T Consensus       317 ~~~~~~~  323 (1437)
T PRK00448        317 INEIKHP  323 (1437)
T ss_pred             eeecCCc
Confidence            8776543

>PRK08402 replication factor A; Reviewed

Probab=96.16  E-value=0.027  Score=52.99  Aligned_cols=70  Identities=21%  Similarity=0.324  Sum_probs=53.2

Q ss_pred             eeEEEEEEEEEeee--------cC--CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeee-CCeeE
Q 023576           71 TNVTLVGLVYNKEE--------RA--SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSF-QGKKQ  138 (280)
Q Consensus        71 ~~V~iVG~V~~~~~--------~~--t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f-~~~~~  138 (280)
                      ..|.++|+|.++..        .+  .-...+|.|.||.|.+.+|.+....  ....+.+|+.|+|. +.++.| +|..+
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 RGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVAK--YYNKINVGDVIKVIDAQVRESLSGLPE  150 (355)
T ss_pred             ceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEEEEechhhhh--hcccCCCCCEEEEECCEEeecCCCcEE
Confidence            56888999988742        11  1344799999999999999876421  13468999999986 888875 88889


Q ss_pred             EEEE
Q 023576          139 IVAF  142 (280)
Q Consensus       139 i~~~  142 (280)
                      |++.
T Consensus       151 Lsvg  154 (355)
T PRK08402        151 LHIN  154 (355)
T ss_pred             EEEC
Confidence            9884

>PRK07218 replication factor A; Provisional

Probab=96.16  E-value=0.037  Score=53.23  Aligned_cols=72  Identities=22%  Similarity=0.323  Sum_probs=56.7

Q ss_pred             eeEEEEEEEEEeeec--------CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEEEE
Q 023576           71 TNVTLVGLVYNKEER--------ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQIVA  141 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~--------~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i~~  141 (280)
                      ..|.|.|+|.++.++        .......|-|.||+|...+|.+.        .+++|+.|+|. +.++.|+++.+|++
T Consensus        69 ~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~~~--------~l~~Gdvv~I~na~vre~~g~~el~i  140 (423)
T PRK07218         69 KNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWKDF--------GLSPGDTVTIGNAGVREWDGRPELNI  140 (423)
T ss_pred             ceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEECCC--------CCCCCCEEEEeccEeeccCCceEEec
Confidence            567888888877421        24667799999999999999842        29999999999 57889999999986


Q ss_pred             ---EEEeeCCCc
Q 023576          142 ---FSVRPVTNF  150 (280)
Q Consensus       142 ---~~ir~v~d~  150 (280)
                         ..|..+++.
T Consensus       141 g~~t~I~~~de~  152 (423)
T PRK07218        141 GESTTVSLLDDS  152 (423)
T ss_pred             cCcceEEEcCcc
Confidence               456665553

>PRK12445 lysyl-tRNA synthetase; Reviewed

Probab=96.11  E-value=0.051  Score=53.53  Aligned_cols=101  Identities=17%  Similarity=0.153  Sum_probs=65.8

Q ss_pred             eeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh---hhhccCCCC
Q 023576           45 VTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT---REMEAIQDG  121 (280)
Q Consensus        45 vtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~G  121 (280)
                      .++++|.+....- ....+.-.|   ..|+|.|+|.+++......-+.|.|++|.|.|.+-.+...+.   .....+..|
T Consensus        44 ~~~~~~~~~~~~~-~~~~~~~~~---~~v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~G  119 (505)
T PRK12445         44 HTSDQLHEEFDAK-DNQELESLN---IEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLG  119 (505)
T ss_pred             cCHHHHHHHhhcc-CcchhhcCC---CEEEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCC
Confidence            5578886653211 011111112   249999999999887777777999999999987643321111   123568999


Q ss_pred             CEEEEEEEEee-eCCeeEEEEEEEeeCCC
Q 023576          122 MYVRLIGNLKS-FQGKKQIVAFSVRPVTN  149 (280)
Q Consensus       122 ~yVrV~G~l~~-f~~~~~i~~~~ir~v~d  149 (280)
                      +.|.|.|.+.. -.+...|.+..+..+..
T Consensus       120 d~V~v~G~~~~t~~gelel~~~~~~llsk  148 (505)
T PRK12445        120 DIIGARGTLFKTQTGELSIHCTELRLLTK  148 (505)
T ss_pred             CEEEEEEEEEecCCCcEEEEEeEEEEEec
Confidence            99999999864 34667777766655443

>PRK05672 dnaE2 error-prone DNA polymerase; Validated

Probab=96.11  E-value=0.022  Score=60.64  Aligned_cols=76  Identities=20%  Similarity=0.307  Sum_probs=59.8

Q ss_pred             eEEEEEEEEEeeecCC---eeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCC
Q 023576           72 NVTLVGLVYNKEERAS---DVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVT  148 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t---~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~  148 (280)
                      .|+|+|+|..+....|   ...++|+|.||.++|.+|.+.-.  .....+.++..|.|.|+++.-++..++.+..|.++.
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            4889999988765322   57789999999999999976421  123568999999999999976777899998888775


Q ss_pred             C
Q 023576          149 N  149 (280)
Q Consensus       149 d  149 (280)
                      +
T Consensus      1033 ~ 1033 (1046)
T PRK05672       1033 P 1033 (1046)
T ss_pred             H
Confidence            4

>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type

Probab=96.10  E-value=0.048  Score=52.65  Aligned_cols=79  Identities=18%  Similarity=0.182  Sum_probs=58.2

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh--hhhccCCCCCEEEEEEEEeeeC---CeeEEEEEEEe
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT--REMEAIQDGMYVRLIGNLKSFQ---GKKQIVAFSVR  145 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~--~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~~~ir  145 (280)
                      ..|+|.|+|.+++.....+-+.|.|++|.|.|..-.+...+.  .....+..|+.|.|.|.+..-+   +...|.+.++.
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            458999999999987776777999999999998754321111  1235799999999999998643   45667777666


Q ss_pred             eCCC
Q 023576          146 PVTN  149 (280)
Q Consensus       146 ~v~d  149 (280)
                      .+..
T Consensus        93 vl~~   96 (428)
T TIGR00458        93 VINE   96 (428)
T ss_pred             EEec
Confidence            5543

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).

>PRK12366 replication factor A; Reviewed

Probab=96.04  E-value=0.023  Score=57.49  Aligned_cols=74  Identities=22%  Similarity=0.301  Sum_probs=58.8

Q ss_pred             eEEEEEEEEEeeec----------CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe-eeCCeeEEE
Q 023576           72 NVTLVGLVYNKEER----------ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK-SFQGKKQIV  140 (280)
Q Consensus        72 ~V~iVG~V~~~~~~----------~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~-~f~~~~~i~  140 (280)
                      .|.|+|.|.++...          .....++|.|.||+|.+.+|.+.+.     ..+.+|+.|+|.|..+ .|++...|.
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            78999999886531          2467899999999999999987642     3589999999999855 477888888


Q ss_pred             EEEEeeCCCc
Q 023576          141 AFSVRPVTNF  150 (280)
Q Consensus       141 ~~~ir~v~d~  150 (280)
                      +.+...+...
T Consensus       261 ~~~~~~i~~~  270 (637)
T PRK12366        261 ANNIEILEKL  270 (637)
T ss_pred             eCCceeeccc
Confidence            8777766543

>PRK14699 replication factor A; Provisional

Probab=96.03  E-value=0.03  Score=54.85  Aligned_cols=75  Identities=24%  Similarity=0.322  Sum_probs=55.5

Q ss_pred             eEEEEEEEEEeee-c------C---CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEE-Ee--eeCCeeE
Q 023576           72 NVTLVGLVYNKEE-R------A---SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN-LK--SFQGKKQ  138 (280)
Q Consensus        72 ~V~iVG~V~~~~~-~------~---t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~-l~--~f~~~~~  138 (280)
                      .|.|.|+|.++.. +      .   .-..+.|-|.||+|.+..|.+...   ..+.|++|++|+|.+. ++  .|++...
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            4888888887643 1      1   244579999999999999987531   2457999999998744 43  5888999


Q ss_pred             EEEEEEeeCCC
Q 023576          139 IVAFSVRPVTN  149 (280)
Q Consensus       139 i~~~~ir~v~d  149 (280)
                      |++.....+..
T Consensus       255 l~~~~~s~i~~  265 (484)
T PRK14699        255 LQVGNRSIIRK  265 (484)
T ss_pred             EEecCceEeec
Confidence            99876665554

>PRK06920 dnaE DNA polymerase III DnaE; Reviewed

Probab=96.01  E-value=0.019  Score=61.36  Aligned_cols=76  Identities=12%  Similarity=0.102  Sum_probs=60.2

Q ss_pred             eEEEEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576           72 NVTLVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus        72 ~V~iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~  146 (280)
                      .|+++|.|.+++.     ......++|+|.||.+++.+|.+.-.  .....+.++..|.|.|++..-++..++.+..|.+
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            5889999988753     23467789999999999999976421  2235689999999999998767778999988877


Q ss_pred             CCC
Q 023576          147 VTN  149 (280)
Q Consensus       147 v~d  149 (280)
                      +.+
T Consensus      1023 l~~ 1025 (1107)
T PRK06920       1023 LEE 1025 (1107)
T ss_pred             HHH
Confidence            743

>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=96.00  E-value=0.015  Score=38.92  Aligned_cols=44  Identities=20%  Similarity=0.403  Sum_probs=38.1

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .||++|.+.     +.++++.+|+++++++...+...|..|.+.|.|..
T Consensus         7 ~iL~~l~~~-----~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen    7 RILEALAES-----GGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             HHHHCHHCT-----BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHcC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence            578888774     45789999999999999999999999999999875

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.

>PRK07374 dnaE DNA polymerase III subunit alpha; Validated

Probab=95.99  E-value=0.029  Score=60.37  Aligned_cols=77  Identities=10%  Similarity=0.157  Sum_probs=60.9

Q ss_pred             eeEEEEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEe
Q 023576           71 TNVTLVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVR  145 (280)
Q Consensus        71 ~~V~iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir  145 (280)
                      ..|.++|.|.+++.     +.....++|+|.||.++|.+|.+.-.  .....+.+|..|-|.|++..-.++.+|.+..|.
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            36889999988753     22467789999999999999976421  123568999999999999875577899999998


Q ss_pred             eCCC
Q 023576          146 PVTN  149 (280)
Q Consensus       146 ~v~d  149 (280)
                      ++.+
T Consensus      1079 ~l~~ 1082 (1170)
T PRK07374       1079 EIDD 1082 (1170)
T ss_pred             cHhh
Confidence            8755

>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=95.96  E-value=0.0062  Score=43.08  Aligned_cols=52  Identities=23%  Similarity=0.388  Sum_probs=44.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      +|++...+|+..|-.      ..++++.+|++.++++...|..+|..|.+.|.|...-
T Consensus         5 gLs~~E~~vy~~Ll~------~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~   56 (68)
T PF01978_consen    5 GLSENEAKVYLALLK------NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE   56 (68)
T ss_dssp             CHHHHHHHHHHHHHH------HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHHHHH------cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence            456777889888763      2488999999999999999999999999999997753

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.

>PRK05159 aspC aspartyl-tRNA synthetase; Provisional

Probab=95.90  E-value=0.063  Score=51.96  Aligned_cols=79  Identities=15%  Similarity=0.187  Sum_probs=57.5

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeeeC---CeeEEEEEEEee
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSFQ---GKKQIVAFSVRP  146 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~~~ir~  146 (280)
                      ..|+|-|+|.+++.....+-+.|.|++|.|.|.+=.+...+ ......+..|+.|.|.|.+..-+   +...|.+..|..
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            45889999999988776666799999999999764332111 12346799999999999999754   446677766665


Q ss_pred             CCC
Q 023576          147 VTN  149 (280)
Q Consensus       147 v~d  149 (280)
                      +..
T Consensus        97 ls~   99 (437)
T PRK05159         97 LNK   99 (437)
T ss_pred             EeC
Confidence            543

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=95.81  E-value=0.031  Score=41.43  Aligned_cols=54  Identities=19%  Similarity=0.327  Sum_probs=45.0

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      ..|+++|...     +.++++.+|++.++++...|...|..|.+.|.|...-++..|..
T Consensus         8 ~~Il~~l~~~-----~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l   61 (91)
T smart00346        8 LAVLRALAEE-----PGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRL   61 (91)
T ss_pred             HHHHHHHHhC-----CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceee
Confidence            4578888653     24799999999999999999999999999999998655556754

>PRK06826 dnaE DNA polymerase III DnaE; Reviewed

Probab=95.76  E-value=0.04  Score=59.22  Aligned_cols=77  Identities=13%  Similarity=0.171  Sum_probs=60.2

Q ss_pred             eeEEEEEEEEEeee-----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee-CCeeEEEEEEE
Q 023576           71 TNVTLVGLVYNKEE-----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF-QGKKQIVAFSV  144 (280)
Q Consensus        71 ~~V~iVG~V~~~~~-----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f-~~~~~i~~~~i  144 (280)
                      ..|.++|.|.+++.     +.....++|+|.||.+++.+|.+.-.  .....+..|..|.|.|++... ++..++.+..|
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            36789999988764     22467789999999999999976421  123568999999999999865 56689999999


Q ss_pred             eeCCC
Q 023576          145 RPVTN  149 (280)
Q Consensus       145 r~v~d  149 (280)
                      .++.+
T Consensus      1070 ~~l~~ 1074 (1151)
T PRK06826       1070 EPLVI 1074 (1151)
T ss_pred             ecHhh
Confidence            88764

>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=95.74  E-value=0.11  Score=42.13  Aligned_cols=69  Identities=17%  Similarity=0.275  Sum_probs=52.9

Q ss_pred             eeEEEEEEEEEeee------cCCeeEEEEEcCCce----EEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEE
Q 023576           71 TNVTLVGLVYNKEE------RASDVNFTLDDGTGR----VVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~------~~t~~~~~LdDgTG~----I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i  139 (280)
                      ..|.|+|+|+++..      +.-.++|+|-|.|..    |.|.+|.+..   +..+.+.+||.|.+.+ +|+.|+++.+.
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 GSVNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNE---ESLPIVKVGDIILLRRVKIQSYNGKPQG   91 (138)
T ss_pred             CeEEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCCh---hhCCCCCCCCEEEEEEEEEEEECCceEE
Confidence            56789999988743      234788999998872    9999998864   2356579999999986 56789988766


Q ss_pred             EEE
Q 023576          140 VAF  142 (280)
Q Consensus       140 ~~~  142 (280)
                      ...
T Consensus        92 ~~~   94 (138)
T cd04497          92 ISN   94 (138)
T ss_pred             EEC
Confidence            654

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

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

Probab=95.73  E-value=0.076  Score=51.00  Aligned_cols=91  Identities=19%  Similarity=0.189  Sum_probs=65.5

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEeccccc-ChhhhccCCCC
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVF-DTREMEAIQDG  121 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~-~~~~~~~~~~G  121 (280)
                      +.++|++|.+..     +      +   +.|+|-|+|.+++......-..|-|+||.|.|+.-.+... +......+..+
T Consensus         3 ~~~~i~di~~~~-----~------~---~~V~v~GWV~~~R~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~e   68 (435)
T COG0017           3 KRTYIKDIKPHV-----G------G---QEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLE   68 (435)
T ss_pred             ceeeHHhhhccC-----C------C---cEEEEEEEeeeecccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCc
Confidence            356778876531     1      1   7899999999999888777779999999999998754221 11114578999


Q ss_pred             CEEEEEEEEeeeCC---eeEEEEEEEeeC
Q 023576          122 MYVRLIGNLKSFQG---KKQIVAFSVRPV  147 (280)
Q Consensus       122 ~yVrV~G~l~~f~~---~~~i~~~~ir~v  147 (280)
                      +.|.|.|.|+.-..   .-.|.+.+|..+
T Consensus        69 s~v~V~G~v~~~~~a~~g~El~v~~i~Vl   97 (435)
T COG0017          69 SSVVVTGIVKASPKAPQGFELQVEKIEVL   97 (435)
T ss_pred             cEEEEEEEEEcCCCCCCCEEEEEEEEEEe
Confidence            99999999997652   234666555443

>PRK00484 lysS lysyl-tRNA synthetase; Reviewed

Probab=95.71  E-value=0.083  Score=51.92  Aligned_cols=101  Identities=18%  Similarity=0.162  Sum_probs=66.4

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh--hhhccCCC
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT--REMEAIQD  120 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~--~~~~~~~~  120 (280)
                      +..+|++|......-. .....   ..-..|+|.|+|.+++.....+-+.|.|+||.|.|.+-.+...+.  .....+..
T Consensus        31 ~~~~~~~~~~~~~~~~-~~~~~---~~~~~v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~  106 (491)
T PRK00484         31 RTHTAAELRAKYDDKE-KEELE---ELEIEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDL  106 (491)
T ss_pred             CccCHHHHHHHhcccc-chhhc---ccCcEEEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCC
Confidence            3467899876543210 00110   001569999999999887766777999999999997643321111  12345999


Q ss_pred             CCEEEEEEEEee-eCCeeEEEEEEEeeC
Q 023576          121 GMYVRLIGNLKS-FQGKKQIVAFSVRPV  147 (280)
Q Consensus       121 G~yVrV~G~l~~-f~~~~~i~~~~ir~v  147 (280)
                      |+.|.|.|.+.. -.+...|.+..++.+
T Consensus       107 g~~v~v~G~v~~t~~ge~el~~~~~~vl  134 (491)
T PRK00484        107 GDIIGVEGTLFKTKTGELSVKATELTLL  134 (491)
T ss_pred             CCEEEEEEEEEEcCCCcEEEEEeEEEEE
Confidence            999999999985 346666766666554

>PRK15491 replication factor A; Provisional

Probab=95.70  E-value=0.069  Score=50.68  Aligned_cols=75  Identities=20%  Similarity=0.383  Sum_probs=55.8

Q ss_pred             eEEEEEEEEEeee-------c-C--CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEE-Ee--eeCCeeE
Q 023576           72 NVTLVGLVYNKEE-------R-A--SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN-LK--SFQGKKQ  138 (280)
Q Consensus        72 ~V~iVG~V~~~~~-------~-~--t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~-l~--~f~~~~~  138 (280)
                      .|.|.|+|.++..       . .  ......|.|.||.|.+.+|.+...   ....+++|+.|++... +|  .|+++..
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            4888888877642       1 1  356689999999999999987542   2357999999999663 55  4668888


Q ss_pred             EEEE---EEeeCCC
Q 023576          139 IVAF---SVRPVTN  149 (280)
Q Consensus       139 i~~~---~ir~v~d  149 (280)
                      |++.   .|.++++
T Consensus       255 l~~~~~s~I~~~~~  268 (374)
T PRK15491        255 IQIGNHGSLRKTDR  268 (374)
T ss_pred             EEeCCCceEEECCc
Confidence            8874   5777765

>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type

Probab=95.70  E-value=0.077  Score=53.10  Aligned_cols=75  Identities=20%  Similarity=0.225  Sum_probs=56.1

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee----------eCCeeEEEE
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS----------FQGKKQIVA  141 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~----------f~~~~~i~~  141 (280)
                      .|+|.|+|.+++....-+-+.|.|+||.|.|..-.+ .........+..|+.|.|.|.+..          -.+...|.+
T Consensus        17 ~V~l~GwV~~~R~~Gkl~Fi~LrD~sg~iQvv~~~~-~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~~~tg~iEl~~   95 (583)
T TIGR00459        17 TVTLAGWVNRRRDLGGLIFIDLRDRSGIVQVVCDPD-ADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLDTGEIEILA   95 (583)
T ss_pred             EEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCC-HHHHHHHhcCCCCCEEEEEEEEEeCCccccCccCCCCcEEEEE
Confidence            699999999998877767779999999999876333 111123467999999999999974          235567777


Q ss_pred             EEEeeC
Q 023576          142 FSVRPV  147 (280)
Q Consensus       142 ~~ir~v  147 (280)
                      ..+..+
T Consensus        96 ~~i~iL  101 (583)
T TIGR00459        96 ESITLL  101 (583)
T ss_pred             eEEEEe
Confidence            777654

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.

>PTZ00401 aspartyl-tRNA synthetase; Provisional

Probab=95.65  E-value=0.16  Score=50.64  Aligned_cols=77  Identities=12%  Similarity=0.094  Sum_probs=56.2

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh---hhhccCCCCCEEEEEEEEeee--------CCeeEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT---REMEAIQDGMYVRLIGNLKSF--------QGKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~G~yVrV~G~l~~f--------~~~~~i  139 (280)
                      ..|+|.|+|.+++.....+-+.|-|++|.|.|.+-.....+.   .....+..+++|.|.|.+..-        .+...|
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            359999999999887777777999999999998743321111   123578999999999998862        344567


Q ss_pred             EEEEEeeC
Q 023576          140 VAFSVRPV  147 (280)
Q Consensus       140 ~~~~ir~v  147 (280)
                      .+.+|..+
T Consensus       159 ~v~~i~vl  166 (550)
T PTZ00401        159 KVKKIHTV  166 (550)
T ss_pred             EeeEEEEE
Confidence            66666544

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

Probab=95.60  E-value=0.016  Score=41.25  Aligned_cols=47  Identities=26%  Similarity=0.342  Sum_probs=38.4

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      .+|.++|++.      .-++.++|+.+|+.+++.|+..|+.|+.-|+|-...+
T Consensus         3 ~~i~~~l~~~------~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~   49 (69)
T PF09012_consen    3 QEIRDYLRER------GRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM   49 (69)
T ss_dssp             HHHHHHHHHS-------SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred             HHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence            3688888863      3689999999999999999999999999999987543

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

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

Probab=95.56  E-value=0.12  Score=50.77  Aligned_cols=99  Identities=10%  Similarity=0.095  Sum_probs=63.0

Q ss_pred             eeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh-h-hh-ccCCCC
Q 023576           45 VTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT-R-EM-EAIQDG  121 (280)
Q Consensus        45 vtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~-~-~~-~~~~~G  121 (280)
                      .+++++......-. .....-.|   ..|+|.|+|.+++......-+.|.|+||.|.+.+-.+...+. . .. ..+..|
T Consensus        32 ~~~~~~~~~~~~~~-~~~~~~~~---~~v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~g  107 (496)
T TIGR00499        32 HSSQEFQEEYADLS-NEELEDKN---IEVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLG  107 (496)
T ss_pred             cCHHHHHHHhhccC-ccchhcCC---CEEEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCC
Confidence            67888876543210 11111111   248999999999977766777999999999987643321111 1 11 237999


Q ss_pred             CEEEEEEEEeeeC-CeeEEEEEEEeeC
Q 023576          122 MYVRLIGNLKSFQ-GKKQIVAFSVRPV  147 (280)
Q Consensus       122 ~yVrV~G~l~~f~-~~~~i~~~~ir~v  147 (280)
                      +.|.|.|.+..-+ +...|.+.+|..+
T Consensus       108 d~V~v~G~~~~t~~gelel~~~~i~il  134 (496)
T TIGR00499       108 DIIGVTGYPFKTKTGELSVHVTELQIL  134 (496)
T ss_pred             CEEEEEEEEEECCCCcEEEEeeEEEEE
Confidence            9999999997543 4466666655443

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.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.54  E-value=0.04  Score=36.07  Aligned_cols=46  Identities=35%  Similarity=0.502  Sum_probs=39.8

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +..|+++|.+.      .++++.+|++.++++...+...|..|...|.|...
T Consensus         2 ~~~il~~l~~~------~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~   47 (53)
T smart00420        2 QQQILELLAQQ------GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV   47 (53)
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            45688888652      36999999999999999999999999999999863

>PRK06386 replication factor A; Reviewed

Probab=95.53  E-value=0.065  Score=50.38  Aligned_cols=70  Identities=16%  Similarity=0.263  Sum_probs=52.9

Q ss_pred             eeEEEEEEEEEeeec--------CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEE-eeeCCeeEEEE
Q 023576           71 TNVTLVGLVYNKEER--------ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL-KSFQGKKQIVA  141 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~--------~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l-~~f~~~~~i~~  141 (280)
                      ..|.|.|+|.++.+.        ..-....|.|.||+|....|.+         .+.+|+.|+|.+-. +.|++..+|++
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            356788888776331        2345789999999999999964         37899999998765 47899999998


Q ss_pred             EEEeeCCC
Q 023576          142 FSVRPVTN  149 (280)
Q Consensus       142 ~~ir~v~d  149 (280)
                      .....|..
T Consensus       189 ~~~t~I~~  196 (358)
T PRK06386        189 GNKSVIKE  196 (358)
T ss_pred             CCeEEEEE
Confidence            66554444

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.53  E-value=0.087  Score=53.83  Aligned_cols=66  Identities=21%  Similarity=0.273  Sum_probs=51.4

Q ss_pred             eeEEEEEEEEEeeec---CCeeEEEEEcCCceEEEEEec-ccccChhhhccCCCCCEEEEEEEEeeeCCeeEE
Q 023576           71 TNVTLVGLVYNKEER---ASDVNFTLDDGTGRVVCKRWA-SEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~---~t~~~~~LdDgTG~I~~~~w~-~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i  139 (280)
                      ..|+|+|.|.++...   ...+.+.+.|+||.|.+++|. +..   .-...|++|+.|.|+|+++.+++++++
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            468899998876432   357899999999999998773 221   224679999999999999998877665

>PLN02903 aminoacyl-tRNA ligase

Probab=95.52  E-value=0.11  Score=52.67  Aligned_cols=78  Identities=24%  Similarity=0.278  Sum_probs=56.0

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC-hhhhccCCCCCEEEEEEEEeee----------CCeeEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD-TREMEAIQDGMYVRLIGNLKSF----------QGKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~-~~~~~~~~~G~yVrV~G~l~~f----------~~~~~i  139 (280)
                      ..|+|.|+|.+++....-+-+.|-|+||.|.|++-.+...+ ......+..++.|.|.|.|+.-          .+...|
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            36999999999988776667799999999998764332111 1123579999999999999853          144666


Q ss_pred             EEEEEeeCC
Q 023576          140 VAFSVRPVT  148 (280)
Q Consensus       140 ~~~~ir~v~  148 (280)
                      .+..|..+.
T Consensus       153 ~~~~i~VL~  161 (652)
T PLN02903        153 VAESVDILN  161 (652)
T ss_pred             EEeEEEEEe
Confidence            666665543

>PRK00476 aspS aspartyl-tRNA synthetase; Validated

Probab=95.45  E-value=0.12  Score=51.95  Aligned_cols=77  Identities=17%  Similarity=0.250  Sum_probs=55.2

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee----------CCeeEEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF----------QGKKQIV  140 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f----------~~~~~i~  140 (280)
                      ..|+|.|+|.+++.....+-+.|.|+||.|.|.+-. ....-.....+..|+.|.|.|.+..-          .+...|.
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            359999999999987777777999999999987632 11111234679999999999999863          2345566


Q ss_pred             EEEEeeCC
Q 023576          141 AFSVRPVT  148 (280)
Q Consensus       141 ~~~ir~v~  148 (280)
                      +..|+.+.
T Consensus        97 ~~~i~il~  104 (588)
T PRK00476         97 ASELEVLN  104 (588)
T ss_pred             EeEEEEEe
Confidence            66655443

>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=95.41  E-value=0.045  Score=36.78  Aligned_cols=46  Identities=28%  Similarity=0.421  Sum_probs=36.5

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCC-eeee
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEG-LIYS  268 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG-~IYs  268 (280)
                      +.+|+.+|.+.     ...++.++|++.|+++...|+..|..|.+.| .|.+
T Consensus         2 ~~~il~~L~~~-----~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~~~I~~   48 (55)
T PF08279_consen    2 QKQILKLLLES-----KEPITAKELAEELGVSRRTIRRDIKELREWGIPIES   48 (55)
T ss_dssp             HHHHHHHHHHT-----TTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT-EEEE
T ss_pred             HHHHHHHHHHc-----CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEe
Confidence            45788888542     2349999999999999999999999999999 4433

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 ....

>PLN02502 lysyl-tRNA synthetase

Probab=95.38  E-value=0.16  Score=50.56  Aligned_cols=77  Identities=16%  Similarity=0.191  Sum_probs=55.1

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh----hhh-ccCCCCCEEEEEEEEeee-CCeeEEEEEEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT----REM-EAIQDGMYVRLIGNLKSF-QGKKQIVAFSV  144 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~----~~~-~~~~~G~yVrV~G~l~~f-~~~~~i~~~~i  144 (280)
                      ..|+|.|+|.+++.....+-+.|.|++|.|.|..-.+...+.    ... ..+..|+.|.|.|.+..- .+...|.+..|
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            359999999999988777778999999999987643321111    112 358999999999988753 35566666655


Q ss_pred             eeC
Q 023576          145 RPV  147 (280)
Q Consensus       145 r~v  147 (280)
                      ..+
T Consensus       189 ~vL  191 (553)
T PLN02502        189 EVL  191 (553)
T ss_pred             EEE
Confidence            443

>PRK07279 dnaE DNA polymerase III DnaE; Reviewed

Probab=95.35  E-value=0.065  Score=56.88  Aligned_cols=75  Identities=11%  Similarity=0.220  Sum_probs=57.5

Q ss_pred             EEEEEEEEEee----e--cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576           73 VTLVGLVYNKE----E--RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus        73 V~iVG~V~~~~----~--~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~  146 (280)
                      +.++|+|.++.    .  ......++|+|.||.|+|.+|.+.-.  .....+.++..|.|.|++..-++..++.+..+.+
T Consensus       887 ~~~~~~i~~~~~~~tk~~g~~maf~~leD~~g~ie~~vFp~~y~--~~~~~l~~~~~~~v~G~v~~~~~~~~l~~~~i~~  964 (1034)
T PRK07279        887 ATILVQIQSIRVIRTKTKGQQMAFLSVTDTKKKLDVTLFPETYR--QYKDELKEGKFYYLKGKIQERDGRLQMVLQQIQE  964 (1034)
T ss_pred             ceEEEEEEEEEEEEEcCCCCeEEEEEEeeCCCcEEEEECHHHHH--HHHHHhccCCEEEEEEEEEecCCeeEEEEeeeec
Confidence            56667766543    2  23567889999999999999976421  2235689999999999999767788999999988


Q ss_pred             CCC
Q 023576          147 VTN  149 (280)
Q Consensus       147 v~d  149 (280)
                      +..
T Consensus       965 l~~  967 (1034)
T PRK07279        965 ASS  967 (1034)
T ss_pred             ccc
Confidence            753

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=95.32  E-value=0.038  Score=42.44  Aligned_cols=47  Identities=26%  Similarity=0.492  Sum_probs=42.5

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      .+++++||..|+..      ..++..+|++.+++++..|+..+..|.+.|.|.
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            45788999999874      268999999999999999999999999999987

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

>PRK15491 replication factor A; Provisional

Probab=95.30  E-value=0.11  Score=49.38  Aligned_cols=77  Identities=18%  Similarity=0.200  Sum_probs=55.6

Q ss_pred             eeEEEEEEEEEeee--------c--CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe-eeCCeeEE
Q 023576           71 TNVTLVGLVYNKEE--------R--ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK-SFQGKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~--------~--~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~-~f~~~~~i  139 (280)
                      ..|.|.|+|.++..        .  .....+.|-|-||+|.+.+|.+.... .....+++|+.|+|.|..+ .|++ ..|
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            56888888887621        1  23556699999999999999865421 1114589999999999988 4655 688


Q ss_pred             EEE---EEeeCCC
Q 023576          140 VAF---SVRPVTN  149 (280)
Q Consensus       140 ~~~---~ir~v~d  149 (280)
                      ++.   .|.+.++
T Consensus       146 ~i~~~~~i~~~~~  158 (374)
T PRK15491        146 NIGRYGGISESDE  158 (374)
T ss_pred             EeCCCceeeeccc
Confidence            886   4666654

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

Probab=95.29  E-value=0.12  Score=52.66  Aligned_cols=77  Identities=14%  Similarity=0.145  Sum_probs=56.0

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC--hhhhccCCCCCEEEEEEEEeee----------CCeeE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD--TREMEAIQDGMYVRLIGNLKSF----------QGKKQ  138 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~G~yVrV~G~l~~f----------~~~~~  138 (280)
                      ..|+|.|+|.+++....-+-+.|-|+||.|.|.+-.+...+  ......+..++.|.|.|.++.-          .+...
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            45999999999988777677799999999998764332111  1124579999999999999872          14456


Q ss_pred             EEEEEEeeC
Q 023576          139 IVAFSVRPV  147 (280)
Q Consensus       139 i~~~~ir~v  147 (280)
                      |.+..+..+
T Consensus        99 l~~~~i~iL  107 (706)
T PRK12820         99 VFVRELSIL  107 (706)
T ss_pred             EEeeEEEEE
Confidence            666666554

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=95.27  E-value=0.056  Score=40.21  Aligned_cols=53  Identities=25%  Similarity=0.401  Sum_probs=46.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|..+|..|.+.|.|+.+-|
T Consensus         7 ~l~~~~~~il~~l~~~------~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~   59 (101)
T smart00347        7 GLTPTQFLVLRILYEE------GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS   59 (101)
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCC
Confidence            5677888899999863      2689999999999999999999999999999998755

>PLN02603 asparaginyl-tRNA synthetase

Probab=95.19  E-value=0.16  Score=50.73  Aligned_cols=77  Identities=19%  Similarity=0.247  Sum_probs=54.2

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCc--eEEEEEecccccChhhhc--cCCCCCEEEEEEEEeeeCCe---eEEEEEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTG--RVVCKRWASEVFDTREME--AIQDGMYVRLIGNLKSFQGK---KQIVAFS  143 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG--~I~~~~w~~~~~~~~~~~--~~~~G~yVrV~G~l~~f~~~---~~i~~~~  143 (280)
                      ..|+|.|+|++++......-..|.|+|+  .|.|++=.+ ........  .+..|+.|.|.|.+..-.+.   ..|.+.+
T Consensus       108 ~~V~v~GwV~~iR~~g~~~Fi~l~Dgs~~~~lQ~v~~~~-~~~~~~l~~~~l~~gs~V~V~G~v~~~~~~~~~~EL~v~~  186 (565)
T PLN02603        108 KTLNVMGWVRTLRAQSSVTFIEVNDGSCLSNMQCVMTPD-AEGYDQVESGLITTGASVLVQGTVVSSQGGKQKVELKVSK  186 (565)
T ss_pred             CEEEEEEEEEEEEeCCCeEEEEEECCCCCEeEEEEEECc-HHHHHHHhhcCCCCCCEEEEEEEEEecCCCCccEEEEEeE
Confidence            4699999999999877777779999998  499886322 11111222  38899999999999865432   5666666


Q ss_pred             EeeCC
Q 023576          144 VRPVT  148 (280)
Q Consensus       144 ir~v~  148 (280)
                      |..+.
T Consensus       187 i~vlg  191 (565)
T PLN02603        187 IVVVG  191 (565)
T ss_pred             EEEEE
Confidence            65443

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=95.09  E-value=0.041  Score=45.95  Aligned_cols=51  Identities=27%  Similarity=0.487  Sum_probs=45.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee--eec
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI--YST  269 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I--YsT  269 (280)
                      .+.++..+||++|+.++      -++..+|++++++++..|+..++.|.++|.|  |..
T Consensus        11 ~lD~~D~~IL~~Lq~d~------R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~   63 (164)
T PRK11169         11 DLDRIDRNILNELQKDG------RISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTA   63 (164)
T ss_pred             hHHHHHHHHHHHhccCC------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEE
Confidence            46789999999999753      5799999999999999999999999999998  554

>PRK08402 replication factor A; Reviewed

Probab=95.06  E-value=0.11  Score=49.01  Aligned_cols=75  Identities=21%  Similarity=0.210  Sum_probs=54.5

Q ss_pred             eeEEEEEcCCceEEEEEecccccC-----h---hhh-----------c-----------cCCCCCEEEEEEEEe--eeCC
Q 023576           88 DVNFTLDDGTGRVVCKRWASEVFD-----T---REM-----------E-----------AIQDGMYVRLIGNLK--SFQG  135 (280)
Q Consensus        88 ~~~~~LdDgTG~I~~~~w~~~~~~-----~---~~~-----------~-----------~~~~G~yVrV~G~l~--~f~~  135 (280)
                      .+.+.|+|+||.+.|.+|.+....     .   ...           +           .-..|.+..|+|+++  .|++
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            456789999999999999865421     0   000           0           023488999999998  5777


Q ss_pred             eeEEEEEEEeeCCCchHHHHHHHHHHHHH
Q 023576          136 KKQIVAFSVRPVTNFDEVTCHYIECIYFH  164 (280)
Q Consensus       136 ~~~i~~~~ir~v~d~Nei~~H~Le~i~~~  164 (280)
                      .. +.+..+.|| |+....-|+++-+...
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            65 899999999 5777778888877543

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

Probab=95.06  E-value=0.18  Score=50.79  Aligned_cols=75  Identities=25%  Similarity=0.245  Sum_probs=59.9

Q ss_pred             eeEEEEEEEEEeeec----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576           71 TNVTLVGLVYNKEER----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~  146 (280)
                      ..|+++|.|.++...    ...+.+++.|+||.|.+++|.-..   .-...+++|.-|.|+|+++.|++.+++.--.+..
T Consensus        61 ~~vti~g~V~~~~~~~~~~~~~l~v~~~d~~~~l~l~fFn~~~---~l~~~~~~G~~v~v~Gk~~~~~~~~~~~hpe~~~  137 (677)
T COG1200          61 EIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNFPA---YLKKKLKVGERVIVYGKVKRFKGGLQITHPEYIV  137 (677)
T ss_pred             ceEEEEEEEEeeeccCCCCCceEEEEEecCcEEEEEEEECccH---HHHhhCCCCCEEEEEEEEeeccCceEEEcceEEe
Confidence            578999999887543    468899999999999999887653   2346799999999999999999888876555554


Q ss_pred             CC
Q 023576          147 VT  148 (280)
Q Consensus       147 v~  148 (280)
                      ..
T Consensus       138 ~~  139 (677)
T COG1200         138 ND  139 (677)
T ss_pred             cC
Confidence            43

>PLN02850 aspartate-tRNA ligase

Probab=95.05  E-value=0.21  Score=49.55  Aligned_cols=78  Identities=17%  Similarity=0.163  Sum_probs=56.5

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEeccccc-Ch---hhhccCCCCCEEEEEEEEeee-------CCeeEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVF-DT---REMEAIQDGMYVRLIGNLKSF-------QGKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~-~~---~~~~~~~~G~yVrV~G~l~~f-------~~~~~i  139 (280)
                      ..|+|.|+|.+++.....+-+.|-|++|.|.|.+-..... ..   .....+..|++|.|.|.|+.-       .+...|
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            4699999999998877766779999999999987544321 11   124579999999999999842       123566


Q ss_pred             EEEEEeeCC
Q 023576          140 VAFSVRPVT  148 (280)
Q Consensus       140 ~~~~ir~v~  148 (280)
                      .+.+|..+.
T Consensus       162 ~~~~i~vls  170 (530)
T PLN02850        162 QVRKIYCVS  170 (530)
T ss_pred             EEeEEEEEe
Confidence            666666443

>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=95.04  E-value=0.42  Score=39.06  Aligned_cols=71  Identities=18%  Similarity=0.267  Sum_probs=54.6

Q ss_pred             eeEEEEEEEEEeeec--------CCeeEEEEEcCCc--------eEEEEEecccccChhhhccCCC-CCEEEEE-EEEee
Q 023576           71 TNVTLVGLVYNKEER--------ASDVNFTLDDGTG--------RVVCKRWASEVFDTREMEAIQD-GMYVRLI-GNLKS  132 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~--------~t~~~~~LdDgTG--------~I~~~~w~~~~~~~~~~~~~~~-G~yVrV~-G~l~~  132 (280)
                      ..|.|+|+|+....-        .-.++++|-|.|-        .|.|.+|.+..   +..+.+.. ||.|++. =+|+.
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 KFVNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHK---ESLPNVKSVGDIIRLRRVKVQS   89 (146)
T ss_dssp             EEEEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSH---HHSCTTCSTTHEEEEEEEEEEE
T ss_pred             CEEEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCH---HHCCCCCCCCCEEEEEEEEEEE
Confidence            578899999886432        2367899999883        69999997654   34566776 9999998 78999


Q ss_pred             eCCeeEEEEEEE
Q 023576          133 FQGKKQIVAFSV  144 (280)
Q Consensus       133 f~~~~~i~~~~i  144 (280)
                      |+++.++....-
T Consensus        90 ~~~~~~~~~~~~  101 (146)
T PF02765_consen   90 YNGKPQGLSNST  101 (146)
T ss_dssp             ETTEEEEEEECE
T ss_pred             ECCEEEEEecCC
Confidence            999998776543

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 ....

>PLN02221 asparaginyl-tRNA synthetase

Probab=94.98  E-value=0.24  Score=49.55  Aligned_cols=95  Identities=20%  Similarity=0.177  Sum_probs=62.5

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCC--eeEEEEEcCC--ceEEEEEecccccChhhhccC
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERAS--DVNFTLDDGT--GRVVCKRWASEVFDTREMEAI  118 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t--~~~~~LdDgT--G~I~~~~w~~~~~~~~~~~~~  118 (280)
                      ..++|+.|+...-..     -...|   ..|+|.|||.+++....  .+-+.|.|+|  |.|.|++-.+..   .....+
T Consensus        31 ~~~~~~~~~~~~~~~-----~~~~g---~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~---~~~~~L   99 (572)
T PLN02221         31 DRVLIRSILDRPDGG-----AGLAG---QKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSLY---DLSTLV   99 (572)
T ss_pred             CceEHHHHhccccCC-----hhcCC---CEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCchh---hHHhcC
Confidence            566899998542211     11122   46999999999987763  4556899999  899997632211   111357


Q ss_pred             CCCCEEEEEEEEeeeC------CeeEEEEEEEeeCC
Q 023576          119 QDGMYVRLIGNLKSFQ------GKKQIVAFSVRPVT  148 (280)
Q Consensus       119 ~~G~yVrV~G~l~~f~------~~~~i~~~~ir~v~  148 (280)
                      ..++.|.|.|.|+.-.      +...|.+..|..+.
T Consensus       100 ~~ES~V~V~G~V~~~~~~~~~~~~iEl~v~~i~vl~  135 (572)
T PLN02221        100 ATGTCVTVDGVLKVPPEGKGTKQKIELSVEKVIDVG  135 (572)
T ss_pred             CCceEEEEEEEEEeCCccCCCCccEEEEEeEEEEEe
Confidence            8999999999998642      23456666554443

>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=94.94  E-value=0.047  Score=38.12  Aligned_cols=53  Identities=23%  Similarity=0.327  Sum_probs=41.3

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +.-+-.||.+|..     ....++..+|++.++++...+..+|+.|.+.|.|...-|+
T Consensus         2 t~~q~~vL~~l~~-----~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~   54 (68)
T PF13463_consen    2 TRPQWQVLRALAH-----SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDP   54 (68)
T ss_dssp             -HHHHHHHHHHT-------TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEES
T ss_pred             CHHHHHHHHHHHc-----cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCC
Confidence            3456778999982     2458899999999999999999999999999999877555

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

Probab=94.94  E-value=0.067  Score=56.64  Aligned_cols=79  Identities=20%  Similarity=0.418  Sum_probs=63.2

Q ss_pred             EeeEEEEEEEEEeeec-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee--eCCeeEEEEE
Q 023576           70 ITNVTLVGLVYNKEER-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS--FQGKKQIVAF  142 (280)
Q Consensus        70 i~~V~iVG~V~~~~~~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~--f~~~~~i~~~  142 (280)
                      ..+|.|.|.|-.++..     .+-+.|.+-|.|-++.|+.|.....+......++.|+.|+|.|.|..  |....++.+.
T Consensus       239 ~~~v~v~G~IF~~e~~~~ksGr~l~~i~vTD~t~Sl~~k~f~~~~ed~~~~~~ik~g~wvk~~g~v~~d~f~~~l~m~i~  318 (1444)
T COG2176         239 ETRVKVEGYIFKIEIKELKSGRTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGIKKGMWVKARGNVQLDTFTRDLTMIIN  318 (1444)
T ss_pred             ccceEEEEEEEEEeeeecccCcEEEEEEEecCchheeehhhccccccHHHHhhcccCcEEEEEEEEEecccccceEEEhh
Confidence            3569999999877542     35688999999999999999987766677889999999999999985  4566677766


Q ss_pred             EEeeCC
Q 023576          143 SVRPVT  148 (280)
Q Consensus       143 ~ir~v~  148 (280)
                      .|.+|.
T Consensus       319 ~I~ei~  324 (1444)
T COG2176         319 DINEIE  324 (1444)
T ss_pred             hhhhhh
Confidence            665554

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

Probab=94.94  E-value=0.12  Score=49.34  Aligned_cols=75  Identities=13%  Similarity=0.153  Sum_probs=58.7

Q ss_pred             EEeeEEEEEEEEEe--eecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEee
Q 023576           69 EITNVTLVGLVYNK--EERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus        69 ~i~~V~iVG~V~~~--~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~  146 (280)
                      +-+...++|+|...  .....-+.+.|.|++|.|.|..+............+..||.|.+.|.++...    |++.+++.
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            34568889988764  3345678899999999999999987665545568899999999999999866    66666555


Q ss_pred             C
Q 023576          147 V  147 (280)
Q Consensus       147 v  147 (280)
                      +
T Consensus       341 ~  341 (421)
T COG1571         341 L  341 (421)
T ss_pred             E
Confidence            4

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=94.93  E-value=0.052  Score=44.29  Aligned_cols=48  Identities=33%  Similarity=0.545  Sum_probs=43.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      .+.++..+||++|+..+      -++..+|++++++++..+..-+..|.++|.|
T Consensus         5 ~lD~~D~~IL~~L~~d~------r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI   52 (154)
T COG1522           5 KLDDIDRRILRLLQEDA------RISNAELAERVGLSPSTVLRRIKRLEEEGVI   52 (154)
T ss_pred             cccHHHHHHHHHHHHhC------CCCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence            46789999999999863      2899999999999999999999999999977

>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=94.92  E-value=0.11  Score=34.04  Aligned_cols=46  Identities=26%  Similarity=0.411  Sum_probs=39.3

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +.+.+|+.+|.+       .-.++.+|++.++++.+.|..-|..|.+.|.|.+
T Consensus         2 ~~R~~Il~~L~~-------~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen    2 PTRLRILKLLSE-------GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             HHHHHHHHHHTT-------SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHh-------CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence            456789999876       2479999999999999999999999999999864

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 ....

>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=94.92  E-value=0.11  Score=36.13  Aligned_cols=50  Identities=18%  Similarity=0.256  Sum_probs=37.2

Q ss_pred             hHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          218 DQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      -..|.+.|.... -..++=+ +..+|+++++.+...|++||..|.++|.|+.
T Consensus         6 ~~~l~~~I~~g~-~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~   56 (64)
T PF00392_consen    6 YDQLRQAILSGR-LPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER   56 (64)
T ss_dssp             HHHHHHHHHTTS-S-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHcCC-CCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence            345555555532 2334567 8999999999999999999999999999986

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 ....

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=94.91  E-value=0.055  Score=44.64  Aligned_cols=51  Identities=20%  Similarity=0.330  Sum_probs=45.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee--eec
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI--YST  269 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I--YsT  269 (280)
                      .+.++.++||++|+.++      =.+..+|++++++++..|+..++.|.++|.|  |..
T Consensus         6 ~lD~~D~~Il~~Lq~d~------R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~   58 (153)
T PRK11179          6 QIDNLDRGILEALMENA------RTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTRV   58 (153)
T ss_pred             ccCHHHHHHHHHHHHcC------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEE
Confidence            36789999999999853      4699999999999999999999999999999  554

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

Probab=94.81  E-value=0.44  Score=36.59  Aligned_cols=64  Identities=22%  Similarity=0.258  Sum_probs=46.3

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN  149 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d  149 (280)
                      +.|+|||+|.+.+..    .+++.+.-| .++|++-.+.        ....+.||.|+|++..   ...|.+......-+
T Consensus        16 k~V~ivGkV~~~~~~----~~~~~~~Dg~~v~v~l~~~~--------~~~~~~~vEViG~V~~---~~~I~~~~~~~~g~   80 (101)
T cd04479          16 KTVRIVGKVEKVDGD----SLTLISSDGVNVTVELNRPL--------DLPISGYVEVIGKVSP---DLTIRVLSYIDFGD   80 (101)
T ss_pred             CEEEEEEEEEEecCC----eEEEEcCCCCEEEEEeCCCC--------CcccCCEEEEEEEECC---CCeEEEEEEEECCC
Confidence            689999999998654    355655555 7888855432        3577899999999985   46677777666654

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=94.68  E-value=0.085  Score=42.21  Aligned_cols=51  Identities=25%  Similarity=0.391  Sum_probs=44.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +|+++.-+||..|=+.     +.+.++++|++.|+.+.+.|..+|..|.+-|.|+-
T Consensus        24 GLs~~Dv~v~~~LL~~-----~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~R   74 (126)
T COG3355          24 GLSELDVEVYKALLEE-----NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVER   74 (126)
T ss_pred             CCcHHHHHHHHHHHhh-----cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeee
Confidence            7888998988877642     35889999999999999999999999999999874

>PRK12366 replication factor A; Reviewed

Probab=94.64  E-value=0.12  Score=52.44  Aligned_cols=75  Identities=13%  Similarity=0.322  Sum_probs=56.3

Q ss_pred             eeEEEEEEEEEeee------c----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEE-EeeeCCeeEE
Q 023576           71 TNVTLVGLVYNKEE------R----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN-LKSFQGKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~------~----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~-l~~f~~~~~i  139 (280)
                      ..|.|.|+|.++..      .    .....+.|-|.||+|.+.+|.+...   ....|++|+.++|.+. ++.|++...|
T Consensus        74 ~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG~Ir~t~W~~~~~---~~~~le~G~v~~i~~~~v~~~~~~~el  150 (637)
T PRK12366         74 INVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTIRLTLWNDNAK---LLKGLKEGDVIKIENARSRKWNNDVEL  150 (637)
T ss_pred             cceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCCEEEEEEEchhhh---hhccCCCCCEEEEeccEecccCCceEE
Confidence            45777788766531      1    2357889999999999999987542   2467999999998876 7889999888


Q ss_pred             EEE---EEeeCC
Q 023576          140 VAF---SVRPVT  148 (280)
Q Consensus       140 ~~~---~ir~v~  148 (280)
                      ++.   .|.+++
T Consensus       151 ~~~~~t~I~~~~  162 (637)
T PRK12366        151 NSGSETRIDKLE  162 (637)
T ss_pred             EcCCcceEEEcc
Confidence            763   466665

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=94.59  E-value=0.26  Score=49.96  Aligned_cols=65  Identities=22%  Similarity=0.248  Sum_probs=49.1

Q ss_pred             eEEEEEEEEEeee----cCCeeEEEEEc-CCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEE
Q 023576           72 NVTLVGLVYNKEE----RASDVNFTLDD-GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIV  140 (280)
Q Consensus        72 ~V~iVG~V~~~~~----~~t~~~~~LdD-gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~  140 (280)
                      .+.++|.|.+...    ....+.+.+.| +||.|.+++|...    .....+++|+.|.|+|+++.+++++++.
T Consensus        34 ~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~F~~~----~~~~~~~~g~~~~~~Gk~~~~~~~~~~~  103 (630)
T TIGR00643        34 RATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNRA----FLKKKFKVGSKVVVYGKVKSSKFKAYLI  103 (630)
T ss_pred             EEEEEEEEEEeEeccCCCCceEEEEEEECCCCEEEEEEECCH----HHHhhCCCCCEEEEEEEEEeeCCEEEEE
Confidence            5677777765421    12468899999 9999999888521    2346799999999999999998876643

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

Probab=94.47  E-value=0.047  Score=39.78  Aligned_cols=55  Identities=20%  Similarity=0.312  Sum_probs=40.7

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      .+-.+||++++       +.+.++.+|+...+++...+.+.|.+|.+.|.|  +-++..|+.|+
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            35556777765       247889999999999999999999999999999  44788998874

>PRK05813 single-stranded DNA-binding protein; Provisional

Probab=94.45  E-value=0.36  Score=42.37  Aligned_cols=80  Identities=23%  Similarity=0.240  Sum_probs=57.2

Q ss_pred             EEeeEEEEEEEEEe-----e-ecCCeeEEEEE-----cCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC---
Q 023576           69 EITNVTLVGLVYNK-----E-ERASDVNFTLD-----DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ---  134 (280)
Q Consensus        69 ~i~~V~iVG~V~~~-----~-~~~t~~~~~Ld-----DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~---  134 (280)
                      +-+.|.|+|.+.+=     + ....+.+|+|.     |.|-.|.|..|..-.+    ...+..|+.|.|.|+|++|+   
T Consensus         7 ~~NkV~L~Grl~~d~e~~~~~~G~~~~~f~laV~R~s~~~D~i~v~v~~rlae----~~~l~kG~~v~VeGqlrsy~~~~   82 (219)
T PRK05813          7 ENNKVYLEGKVVSELEFSHEMYGEGFYNFKLEVPRLSDSKDILPVTVSERLLA----GMDLKVGTLVIVEGQLRSYNKFI   82 (219)
T ss_pred             hcCEEEEEEEEcCCceEEEEeCCeEEEEEEEEeeccCCCccEEEEEEEhhhhh----hhcccCCCEEEEEEEEEEeccCC
Confidence            45789999999652     1 23456677665     8888999999977542    22399999999999999884   


Q ss_pred             -Ce----eEEEEEEEeeCCCchH
Q 023576          135 -GK----KQIVAFSVRPVTNFDE  152 (280)
Q Consensus       135 -~~----~~i~~~~ir~v~d~Ne  152 (280)
                       ++    ..|.+..|..+...++
T Consensus        83 ~G~~R~vl~V~a~~i~~l~~~~~  105 (219)
T PRK05813         83 DGKNRLILTVFARNIEYCDERSD  105 (219)
T ss_pred             CCcEEEEEEEEEEEEEEccCCCc
Confidence             33    2356667777777544

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

Probab=94.29  E-value=0.14  Score=35.63  Aligned_cols=50  Identities=28%  Similarity=0.382  Sum_probs=42.9

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ..+..|+.+|...       +++..+|++.++++...|..+|+.|.+.|.|...-+.
T Consensus         7 ~~~~~il~~l~~~-------~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~   56 (78)
T cd00090           7 PTRLRILRLLLEG-------PLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG   56 (78)
T ss_pred             hHHHHHHHHHHHC-------CcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence            4677889888752       2899999999999999999999999999999976544

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=94.18  E-value=0.23  Score=33.20  Aligned_cols=34  Identities=26%  Similarity=0.489  Sum_probs=31.3

Q ss_pred             cc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          236 GV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       236 Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      -+ +..+|++.++++...|+++|..|.++|.|...
T Consensus        19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~   53 (60)
T smart00345       19 KLPSERELAAQLGVSRTTVREALSRLEAEGLVQRR   53 (60)
T ss_pred             cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            56 89999999999999999999999999998753

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

Probab=94.16  E-value=0.31  Score=33.29  Aligned_cols=38  Identities=24%  Similarity=0.336  Sum_probs=32.3

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576          238 HVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK  276 (280)
Q Consensus       238 ~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk  276 (280)
                      ++.+|++.++++...|+++|..|.++|.|... ...+|.
T Consensus        27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~-~~~~~~   64 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELEAEGLVERR-PGRGTF   64 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec-CCCeEE
Confidence            59999999999999999999999999998764 333443

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

>PTZ00385 lysyl-tRNA synthetase; Provisional

Probab=94.16  E-value=0.47  Score=48.12  Aligned_cols=78  Identities=12%  Similarity=0.094  Sum_probs=57.5

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccc-cC-h-hh-hccCCCCCEEEEEEEEeee-CCeeEEEEEEEee
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEV-FD-T-RE-MEAIQDGMYVRLIGNLKSF-QGKKQIVAFSVRP  146 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~-~~-~-~~-~~~~~~G~yVrV~G~l~~f-~~~~~i~~~~ir~  146 (280)
                      .|+|-|+|.+++....-.-+.|-|.||.|.|.+-.+.. .+ . .. ...+..|+.|.|.|.+..- .+...|.+..+..
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            49999999999877766667899999999998865431 11 1 11 2468999999999988865 4777777777665


Q ss_pred             CCC
Q 023576          147 VTN  149 (280)
Q Consensus       147 v~d  149 (280)
                      +..
T Consensus       189 Lsk  191 (659)
T PTZ00385        189 LSP  191 (659)
T ss_pred             ech
Confidence            543

>PRK08486 single-stranded DNA-binding protein; Provisional

Probab=94.06  E-value=0.48  Score=40.41  Aligned_cols=78  Identities=17%  Similarity=0.183  Sum_probs=49.5

Q ss_pred             EeeEEEEEEEEEe-e-----ecCCeeEEEEE-------------cCCceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576           70 ITNVTLVGLVYNK-E-----ERASDVNFTLD-------------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL  130 (280)
Q Consensus        70 i~~V~iVG~V~~~-~-----~~~t~~~~~Ld-------------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l  130 (280)
                      ++.|.|||.|..- +     .....+.|+|-             +.|--|.|.+|...++  .....++.|+.|-|.|+|
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            4678888888541 1     12345566661             2345689999976432  234669999999999999


Q ss_pred             ee--eCCe-------eEEEEEEEeeCCC
Q 023576          131 KS--FQGK-------KQIVAFSVRPVTN  149 (280)
Q Consensus       131 ~~--f~~~-------~~i~~~~ir~v~d  149 (280)
                      +.  |.++       ..|.+..|..+..
T Consensus        80 ~~~~y~dkdG~~r~~~eI~a~~v~~L~~  107 (182)
T PRK08486         80 TFESWMDQNGQKRSKHTITAESMQMLDS  107 (182)
T ss_pred             EeCcEECCCCcEEEEEEEEEeEEEECCC
Confidence            75  5332       3466666666554

>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=93.99  E-value=0.56  Score=36.38  Aligned_cols=69  Identities=22%  Similarity=0.247  Sum_probs=41.1

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCC-ceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGT-GRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN  149 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgT-G~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d  149 (280)
                      ..|+|||+|.++.....  .++|.-.. +.|.+..-.+.        .+..+.||.|+|++..-.+-..|....+.+..+
T Consensus        19 k~VrivGkv~~~~~~g~--~~~l~~~d~~~V~v~l~~~~--------~~~~~~~vEviG~V~~~~~~~~i~~~~~~~~g~   88 (109)
T PF08661_consen   19 KTVRIVGKVESVDPDGG--SATLSTSDGGQVTVSLNPPS--------DEELSKYVEVIGKVNDDGTVLSIRYFSFTDFGD   88 (109)
T ss_dssp             SEEEEEEEEEEE-TTSS--EEEEE-TTS-EEEEEESS----------SS---SEEEEEEEE-TTS-EEEEEEEE---SSS
T ss_pred             CeEEEEEEEeeEcCCCC--EEEEEcCCCCEEEEEeCCCC--------CCCCCCEEEEEEEEcCCCCceEEEEEEeccCCC
Confidence            58999999999875444  44566433 35776654322        345689999999999877666888877777666

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

>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=93.98  E-value=0.48  Score=36.44  Aligned_cols=68  Identities=19%  Similarity=0.287  Sum_probs=42.1

Q ss_pred             cCCeeEEEEEcCCc-eEEEEEecccccChhh-h-ccCCCCCEEEE-E-EEEeeeCCeeEE----EEEEEeeCCCchH
Q 023576           85 RASDVNFTLDDGTG-RVVCKRWASEVFDTRE-M-EAIQDGMYVRL-I-GNLKSFQGKKQI----VAFSVRPVTNFDE  152 (280)
Q Consensus        85 ~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~-~-~~~~~G~yVrV-~-G~l~~f~~~~~i----~~~~ir~v~d~Ne  152 (280)
                      ...+..|+|.|.+| .|+|..|-+.+.+-.. . .....+-.|-| . .+++.|++.+.|    .+.++..=.|..|
T Consensus        21 ~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~ls~~~~~s~v~inp~ipe   97 (106)
T cd04481          21 PSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSLSNSFGASKVYINPDIPE   97 (106)
T ss_pred             cceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEEEcCCCceEEEECCCcHH
Confidence            34589999999998 6999999765422110 1 12345555555 3 699999986665    3444444333333

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.

>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=93.97  E-value=0.13  Score=35.46  Aligned_cols=48  Identities=31%  Similarity=0.391  Sum_probs=41.0

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ++...+||..|..      ..++++.+|++.++++...+..-|..|.+.|.|=.
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            4678889999943      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=93.96  E-value=0.31  Score=33.59  Aligned_cols=44  Identities=20%  Similarity=0.355  Sum_probs=38.0

Q ss_pred             CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      ...++..+|++.++++...|..+|..|.++|.|...- ..+|..+
T Consensus        23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~-~~~~~l~   66 (67)
T cd00092          23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG-RGKYRVN   66 (67)
T ss_pred             cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC-CCeEEeC
Confidence            3568999999999999999999999999999998753 4577654

>PRK06386 replication factor A; Reviewed

Probab=93.88  E-value=0.46  Score=44.77  Aligned_cols=65  Identities=23%  Similarity=0.242  Sum_probs=49.4

Q ss_pred             eeEEEEEEEEEeee--------cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEE-EeeeCCeeEEEE
Q 023576           71 TNVTLVGLVYNKEE--------RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN-LKSFQGKKQIVA  141 (280)
Q Consensus        71 ~~V~iVG~V~~~~~--------~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~-l~~f~~~~~i~~  141 (280)
                      ..|.|.++|+++..        ......-.|-|.||.|....|...       ..+++|+.|++..- ++.|+++.+|++
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 QNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEFP-------DAVKSGDVIEIKYCYSKEYNGKIRIYF   85 (358)
T ss_pred             CcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcceEEEEecCCc-------ccCCCCCEEEEEeEEEeeECCEEEEEE
Confidence            45677777776542        123445589999999999999742       46899999999865 558999999998


Q ss_pred             E
Q 023576          142 F  142 (280)
Q Consensus       142 ~  142 (280)
                      .
T Consensus        86 ~   86 (358)
T PRK06386         86 D   86 (358)
T ss_pred             c
Confidence            5

>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=93.84  E-value=0.1  Score=35.44  Aligned_cols=52  Identities=31%  Similarity=0.379  Sum_probs=43.4

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      ..+-.||.+|.+.      .+++..+|++.++++...+...++.|...|.|-...|.+
T Consensus         3 ~~q~~iL~~l~~~------~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~   54 (59)
T PF01047_consen    3 PSQFRILRILYEN------GGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPD   54 (59)
T ss_dssp             HHHHHHHHHHHHH------SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             HHHHHHHHHHHHc------CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence            3456688888764      379999999999999999999999999999998876654

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 ....

>PRK07275 single-stranded DNA-binding protein; Provisional

Probab=93.60  E-value=0.61  Score=39.05  Aligned_cols=78  Identities=21%  Similarity=0.391  Sum_probs=48.5

Q ss_pred             EeeEEEEEEEEE-ee-----ecCCeeEEEEE------c-----CCceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576           70 ITNVTLVGLVYN-KE-----ERASDVNFTLD------D-----GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS  132 (280)
Q Consensus        70 i~~V~iVG~V~~-~~-----~~~t~~~~~Ld------D-----gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~  132 (280)
                      ++.|.|+|.+.. .+     .....+.|+|-      +     .|--|.|+.|...++  .....++.|+.|-|.|+|+.
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 11     12245566662      2     234599999987542  23467899999999999975


Q ss_pred             --eCC---e----eEEEEEEEeeCCC
Q 023576          133 --FQG---K----KQIVAFSVRPVTN  149 (280)
Q Consensus       133 --f~~---~----~~i~~~~ir~v~d  149 (280)
                        |.+   +    ..|.+..|..+..
T Consensus        80 r~y~dkdG~k~~~~evva~~i~~l~~  105 (162)
T PRK07275         80 RNYENQQGQRVYVTEVVADNFQMLES  105 (162)
T ss_pred             ceEECCCCCEEEEEEEEEeEEEECCC
Confidence              533   2    2355555555443

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

Probab=93.49  E-value=0.29  Score=35.75  Aligned_cols=64  Identities=20%  Similarity=0.200  Sum_probs=41.4

Q ss_pred             EEEEEEEeeecCCeeEEEEEcCCce-----EEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEE
Q 023576           75 LVGLVYNKEERASDVNFTLDDGTGR-----VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFS  143 (280)
Q Consensus        75 iVG~V~~~~~~~t~~~~~LdDgTG~-----I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~  143 (280)
                      +-|+|..+......--|-|.|.++-     -++++-...    . ...+++|+.|+|.|+++.|++..||....
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            4577877765433345568886432     122211111    0 35689999999999999999988887644

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.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=93.48  E-value=0.24  Score=40.16  Aligned_cols=55  Identities=11%  Similarity=0.100  Sum_probs=47.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..|-.||.+|..      +.|++..+|++.++++...|..+|+.|...|.|+...|.+
T Consensus        37 glt~~q~~vL~~l~~------~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~   91 (144)
T PRK11512         37 DITAAQFKVLCSIRC------AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPN   91 (144)
T ss_pred             CCCHHHHHHHHHHHH------cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcc
Confidence            467778889998864      2489999999999999999999999999999999987753

>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=93.45  E-value=0.23  Score=38.23  Aligned_cols=56  Identities=18%  Similarity=0.185  Sum_probs=40.3

Q ss_pred             eeEEEEEEEEEeee---------cCCeeEEEEEcC-CceEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576           71 TNVTLVGLVYNKEE---------RASDVNFTLDDG-TGRVVCKRWASEVFDTREMEAIQDGMYVRLIG  128 (280)
Q Consensus        71 ~~V~iVG~V~~~~~---------~~t~~~~~LdDg-TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G  128 (280)
                      ..++|+|+|+.+..         ....+.+.|-|. +|.|.|.+|.+..+  .....|++|+.+.+.+
T Consensus        10 ~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~--~f~~~l~eG~vy~i~~   75 (104)
T cd04474          10 NKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVD--KFYDLLEVGKVYYISK   75 (104)
T ss_pred             CcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHH--HhhcccccccEEEEec
Confidence            45778888876421         134578999999 88999999986432  2356789998887764

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=93.43  E-value=0.7  Score=49.79  Aligned_cols=73  Identities=19%  Similarity=0.161  Sum_probs=52.8

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh---hhhccCCCCCEEEEEEEEeee-CCeeEEEEEEE
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT---REMEAIQDGMYVRLIGNLKSF-QGKKQIVAFSV  144 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~G~yVrV~G~l~~f-~~~~~i~~~~i  144 (280)
                      .|+|.|+|.+++......-+.|.|+||.|.|..=.+...+.   .....+..|+.|.|.|.+..- .+...|.+..+
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            59999999999887776777999999999997643321111   112358899999999998753 35555655554

>PRK12423 LexA repressor; Provisional

Probab=93.37  E-value=0.1  Score=45.06  Aligned_cols=53  Identities=17%  Similarity=0.307  Sum_probs=44.8

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCcc--CHHHHHHHhC-CCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGV--HVNELSEQLK-IPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv--~v~~I~~~l~-~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      |++-|++||++|++.   ..+.|+  ++.||+++|+ .+...|+++|+.|...|+|-.+
T Consensus         4 lt~~q~~il~~l~~~---i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~   59 (202)
T PRK12423          4 LTPKRAAILAFIRER---IAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVV   59 (202)
T ss_pred             CCHHHHHHHHHHHHH---HHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence            678899999999874   123455  9999999999 5899999999999999999864

>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=93.33  E-value=0.17  Score=32.49  Aligned_cols=41  Identities=29%  Similarity=0.408  Sum_probs=32.6

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      .++..+||+.|+..      .-.+..+|++.+++++..|...+..|.
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            46889999999975      246999999999999999999998873

...

>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=93.26  E-value=0.25  Score=36.24  Aligned_cols=48  Identities=29%  Similarity=0.403  Sum_probs=37.4

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      -.+|-+|....   .+.-++.++|+++++.++..+++.+..|...|.|-++
T Consensus        11 l~~l~~la~~~---~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~   58 (83)
T PF02082_consen   11 LRILLYLARHP---DGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS   58 (83)
T ss_dssp             HHHHHHHHCTT---TSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHhCC---CCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence            44666666542   2223999999999999999999999999999999765

(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.

>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=93.21  E-value=0.65  Score=35.22  Aligned_cols=64  Identities=19%  Similarity=0.284  Sum_probs=42.5

Q ss_pred             EEEEEEEEEeee-----------cCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEE
Q 023576           73 VTLVGLVYNKEE-----------RASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQI  139 (280)
Q Consensus        73 V~iVG~V~~~~~-----------~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i  139 (280)
                      |-|+|.|.++..           ......+.|.|.|+ .|++.+|.+.+..    .....|+.|.+.+ +++.|+ .+.+
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            567787776531           12578899999999 8999999875421    1112277777765 455677 4566


Q ss_pred             EE
Q 023576          140 VA  141 (280)
Q Consensus       140 ~~  141 (280)
                      +.
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

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=93.18  E-value=0.2  Score=32.10  Aligned_cols=41  Identities=22%  Similarity=0.304  Sum_probs=34.7

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      -.++..+|++.++++...+..+|..|.++|.|...  ..+|..
T Consensus         7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~--~~~~~i   47 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE--GGRIVI   47 (48)
T ss_pred             eccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe--CCEEEE
Confidence            35789999999999999999999999999999753  346643

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

Probab=93.07  E-value=0.22  Score=39.69  Aligned_cols=48  Identities=10%  Similarity=0.296  Sum_probs=43.9

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ..|+..|++++++.+      =+++.+++..++.+...++..+.+|+..|+||-
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            468899999999863      469999999999999999999999999999996

>TIGR00498 lexA SOS regulatory protein LexA

Probab=93.02  E-value=0.13  Score=44.13  Aligned_cols=56  Identities=16%  Similarity=0.251  Sum_probs=46.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCC-HHHHHHHHHHHHhCCeeeec
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIP-QKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~-~~~v~~al~~L~~eG~IYsT  269 (280)
                      +|++.|.+||++|++... ......++.+|++.++++ ...|...|..|...|.|-..
T Consensus         3 ~lt~~q~~iL~~l~~~~~-~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~   59 (199)
T TIGR00498         3 PLTARQQEVLDLIRAHIE-STGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERD   59 (199)
T ss_pred             ccCHHHHHHHHHHHHHHH-hcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecC
Confidence            478899999999985311 123457889999999998 99999999999999999874

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.

>PRK06751 single-stranded DNA-binding protein; Provisional

Probab=93.01  E-value=0.81  Score=38.74  Aligned_cols=62  Identities=19%  Similarity=0.354  Sum_probs=40.5

Q ss_pred             EeeEEEEEEEEE-ee-----ecCCeeEEEEE------cC-----CceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576           70 ITNVTLVGLVYN-KE-----ERASDVNFTLD------DG-----TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS  132 (280)
Q Consensus        70 i~~V~iVG~V~~-~~-----~~~t~~~~~Ld------Dg-----TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~  132 (280)
                      ++.|.|+|+|.. .+     .....+.|+|-      +.     |--|.|+.|...++  .....++.|+.|.|.|+|+.
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            356777887754 11     12245666662      22     23589999986532  23466899999999999996


Q ss_pred             e
Q 023576          133 F  133 (280)
Q Consensus       133 f  133 (280)
                      -
T Consensus        80 r   80 (173)
T PRK06751         80 R   80 (173)
T ss_pred             C
Confidence            3

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=92.94  E-value=0.31  Score=42.03  Aligned_cols=61  Identities=20%  Similarity=0.327  Sum_probs=50.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC-CCccccccC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI-DEFHYKFAR  279 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi-Dd~hfk~t~  279 (280)
                      .++..+..||.+|...      .++++.+|++.++++.+.+...|..|.+.|.|...- ....|+.|+
T Consensus       140 ~ls~~~~~IL~~l~~~------g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~  201 (203)
T TIGR01884       140 GLSREELKVLEVLKAE------GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGRKGKRYSLTK  201 (203)
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCCccEEEeCC
Confidence            5677888999999763      268999999999999999999999999999999875 334565554

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.

>PTZ00425 asparagine-tRNA ligase; Provisional

Probab=92.93  E-value=0.6  Score=46.82  Aligned_cols=62  Identities=15%  Similarity=0.119  Sum_probs=45.0

Q ss_pred             eeEEEEEEEEEeeecCC--eeEEEEEcCCc--eEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576           71 TNVTLVGLVYNKEERAS--DVNFTLDDGTG--RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF  133 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t--~~~~~LdDgTG--~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f  133 (280)
                      ..|+|.|||.+++....  .+-..|.|+||  .|.|++- ...........+..|+-|+|.|++..-
T Consensus        82 ~~Vtl~GWv~~iR~~g~~~~~Fv~lrDgsg~~~iQiVv~-~~~~~~~~l~~l~~gs~v~v~G~v~~~  147 (586)
T PTZ00425         82 QIITVCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVD-QSIENYEKLLKCGVGCCFRFTGKLIIS  147 (586)
T ss_pred             CEEEEEEEEeehhhcCCceEEEEEEECCCCCcceEEEEC-CchHHHHHHhcCCCccEEEEEEEEEcC
Confidence            46999999999988653  55668999999  4887652 221111234568899999999999853

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=92.91  E-value=0.25  Score=44.38  Aligned_cols=55  Identities=18%  Similarity=0.360  Sum_probs=46.4

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      -.||++|.+.     +.+++..||++.++++.+.+...|..|.++|.|...-|+..|..+
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            3478888653     346999999999999999999999999999999987677788754

>PRK07459 single-stranded DNA-binding protein; Provisional

Probab=92.79  E-value=0.51  Score=37.48  Aligned_cols=61  Identities=23%  Similarity=0.339  Sum_probs=43.4

Q ss_pred             EeeEEEEEEEEEe---e---ecCCeeEEEEE-------cCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576           70 ITNVTLVGLVYNK---E---ERASDVNFTLD-------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS  132 (280)
Q Consensus        70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld-------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~  132 (280)
                      ++.|.|+|.+..-   .   .....+.|+|-       +.|--+.|..|...++  .....++.|+.|.|.|+|+.
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            4678888888551   1   22346677765       4566799999976432  23456899999999999995

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=92.72  E-value=0.24  Score=43.37  Aligned_cols=47  Identities=30%  Similarity=0.461  Sum_probs=41.2

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .-++.||.+|+..      .+++.++|+++|+++...||.-|+.|..+|.|=.
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            4677899999874      3889999999999999999999999999997643

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=92.71  E-value=0.37  Score=38.96  Aligned_cols=56  Identities=20%  Similarity=0.244  Sum_probs=47.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..|-.||..|...     +.|++..+|++.++++...|...|+.|...|.|..+-|++
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            4566777888888652     2478999999999999999999999999999999998864

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=92.54  E-value=0.32  Score=43.93  Aligned_cols=54  Identities=19%  Similarity=0.354  Sum_probs=45.2

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      -.||++|...     +.++++.||++.++++.+.+...|..|.+.|+|+..-+...|..
T Consensus        28 l~IL~~~~~~-----~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~l   81 (271)
T PRK10163         28 IAILQYLEKS-----GGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHI   81 (271)
T ss_pred             HHHHHHHHhC-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEe
Confidence            3478888652     35799999999999999999999999999999998655666754

>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]

Probab=92.54  E-value=0.98  Score=44.11  Aligned_cols=99  Identities=18%  Similarity=0.232  Sum_probs=67.3

Q ss_pred             eHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC---hhhhccCCCCC
Q 023576           46 TVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD---TREMEAIQDGM  122 (280)
Q Consensus        46 tIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~---~~~~~~~~~G~  122 (280)
                      ++.+|....... ....+  ....+ .|.+.|+|..++......-+.|.|.+|.|.+.+-.+....   ......+..||
T Consensus        41 ~~~~l~~~~~~~-~~~el--~~~~~-~v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGD  116 (502)
T COG1190          41 TSADLREKYADK-TKEEL--EALNI-EVSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGD  116 (502)
T ss_pred             cHHHHHHHHhcc-chhhh--hhccc-eeEEecceeeecccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCC
Confidence            788888776532 11111  11111 2999999999987776667799999999998877554221   11245678999


Q ss_pred             EEEEEEEEeeeC-CeeEEEEEEEeeCC
Q 023576          123 YVRLIGNLKSFQ-GKKQIVAFSVRPVT  148 (280)
Q Consensus       123 yVrV~G~l~~f~-~~~~i~~~~ir~v~  148 (280)
                      +|-|.|.+-.-+ |...|.+..++.++
T Consensus       117 iigv~G~~~~T~~GelSv~v~~~~lLs  143 (502)
T COG1190         117 IIGVEGPLFKTKTGELSVSVEELRLLS  143 (502)
T ss_pred             EEeeeeeeeecCCCceEEEEEEEeeec
Confidence            999999987665 77777776655443

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=92.53  E-value=0.48  Score=36.64  Aligned_cols=58  Identities=22%  Similarity=0.345  Sum_probs=47.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|.-..  ..+.+++..+|+..++++...|..+|+.|...|.|...-|+
T Consensus        22 ~ls~~q~~vL~~l~~~~--~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~   79 (109)
T TIGR01889        22 NLSLEELLILYYLGKLE--NNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSE   79 (109)
T ss_pred             CCCHHHHHHHHHHHhhh--ccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCc
Confidence            46677778998887210  12458999999999999999999999999999999976665

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.

>PRK02801 primosomal replication protein N; Provisional

Probab=92.50  E-value=1.1  Score=34.29  Aligned_cols=33  Identities=12%  Similarity=0.083  Sum_probs=25.7

Q ss_pred             EEEEEecccccChhhhccCCCCCEEEEEEEEeeeC
Q 023576          100 VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ  134 (280)
Q Consensus       100 I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~  134 (280)
                      |+|+.|-..++  .....+..|+.|.|.|.|+.+.
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            89999986542  2234699999999999999853

>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=92.49  E-value=0.21  Score=34.65  Aligned_cols=35  Identities=17%  Similarity=0.382  Sum_probs=31.3

Q ss_pred             CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ...+...+||+.|+++...|.++|..|.++|.|--
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            45899999999999999999999999999999854

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 ....

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

Probab=92.46  E-value=0.28  Score=29.63  Aligned_cols=30  Identities=20%  Similarity=0.473  Sum_probs=26.0

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          237 VHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       237 v~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      ++.+||++.++.+.+.|-.+|..|..+|.|
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 ....

>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family

Probab=92.42  E-value=0.32  Score=43.13  Aligned_cols=51  Identities=10%  Similarity=0.189  Sum_probs=43.2

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      .||++|...     ..++++.||++.++++.+.+...|..|.+.|.+..  |+..|..
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            477777652     45899999999999999999999999999999987  5567764

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.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=92.35  E-value=0.32  Score=32.67  Aligned_cols=44  Identities=30%  Similarity=0.414  Sum_probs=36.8

Q ss_pred             HHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          221 ILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       221 Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      |+++|. .      ..++..+|++.++++...+..+|+.|.+.|.|...-+
T Consensus         2 il~~l~-~------~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~   45 (66)
T smart00418        2 ILKLLA-E------GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE   45 (66)
T ss_pred             HHHHhh-c------CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence            566665 2      3579999999999999999999999999999986543

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=92.32  E-value=0.42  Score=37.28  Aligned_cols=55  Identities=24%  Similarity=0.317  Sum_probs=47.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..|-.||.+|...      .++++.+|++.++++...|...|+.|...|.|-..-|..
T Consensus        25 ~lt~~q~~iL~~l~~~------~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~   79 (118)
T TIGR02337        25 GLTEQQWRILRILAEQ------GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASN   79 (118)
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCC
Confidence            4566777899998753      378999999999999999999999999999999987653

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.

>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function

Probab=92.30  E-value=0.32  Score=36.80  Aligned_cols=49  Identities=27%  Similarity=0.474  Sum_probs=41.2

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ++++...||..|....   .+   +..-|+++++++.++|+.+|+.|.+.|.|=.
T Consensus         5 ~~~l~~~IL~hl~~~~---~D---y~k~ia~~l~~~~~~v~~~l~~Le~~GLler   53 (92)
T PF10007_consen    5 LDPLDLKILQHLKKAG---PD---YAKSIARRLKIPLEEVREALEKLEEMGLLER   53 (92)
T ss_pred             cChhHHHHHHHHHHHC---CC---cHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence            3567888999998752   33   6678999999999999999999999999855

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=92.30  E-value=0.24  Score=44.39  Aligned_cols=48  Identities=27%  Similarity=0.430  Sum_probs=41.5

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +=+++|+++|++.+      -+++.|+++.|+.++..||.-|.+|.++|.|..+
T Consensus         5 eR~~~Il~~L~~~~------~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~   52 (256)
T PRK10434          5 QRQAAILEYLQKQG------KTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT   52 (256)
T ss_pred             HHHHHHHHHHHHcC------CEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence            35678999999742      4899999999999999999999999999987553

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=92.02  E-value=0.28  Score=43.92  Aligned_cols=48  Identities=19%  Similarity=0.321  Sum_probs=42.5

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +-+++|+++|++.      .-+++.+|+++|++++..||.-|.+|.++|.|..+
T Consensus         5 ~R~~~Il~~l~~~------~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~   52 (252)
T PRK10906          5 QRHDAIIELVKQQ------GYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH   52 (252)
T ss_pred             HHHHHHHHHHHHc------CCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            4567899999874      25899999999999999999999999999999775

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=92.02  E-value=0.49  Score=41.41  Aligned_cols=32  Identities=22%  Similarity=0.397  Sum_probs=30.3

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          238 HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       238 ~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +..+++++++.+...||+||+.|.+||.|+.-
T Consensus        34 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~   65 (238)
T TIGR02325        34 AEMQLAERFGVNRHTVRRAIAALVERGLLRAE   65 (238)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            78999999999999999999999999999873

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.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=92.01  E-value=0.17  Score=36.58  Aligned_cols=49  Identities=12%  Similarity=0.220  Sum_probs=41.7

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      ..+.+..++++.+.+.      .+|+++.||++.+++++..|+..+..+.++|.+
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            3567788888888754      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.

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=91.99  E-value=0.48  Score=41.48  Aligned_cols=51  Identities=14%  Similarity=0.151  Sum_probs=37.5

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +.+.|.+-|.+..- ....=+ +-.+++++++.+...||+||+.|.+||.|+.
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            44556666654211 111123 7899999999999999999999999999986

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.

>PTZ00417 lysine-tRNA ligase; Provisional

Probab=91.88  E-value=1  Score=45.27  Aligned_cols=101  Identities=14%  Similarity=0.102  Sum_probs=63.0

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCC-eeEEEEEcCCceEEEEEecccc---cCh-hh-hc
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERAS-DVNFTLDDGTGRVVCKRWASEV---FDT-RE-ME  116 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t-~~~~~LdDgTG~I~~~~w~~~~---~~~-~~-~~  116 (280)
                      +..+|+++.+....-..+ .. ..+   ..|+|-|+|.+++.... -.-+.|.|.+|.|.|..-.+..   .+. .. ..
T Consensus       110 ~~~~~~~~~~~~~~~~~~-~~-~~~---~~v~v~Grv~~~R~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~  184 (585)
T PTZ00417        110 RTITVPEFVEKYQDLASG-EH-LED---TILNVTGRIMRVSASGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYD  184 (585)
T ss_pred             CCcCHHHHHHHhhccCcc-cc-ccC---CeEEEEEEEEeeecCCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHh
Confidence            346788887654321001 11 111   23899999999988764 4455777888899988754321   111 11 24


Q ss_pred             cCCCCCEEEEEEEEeee-CCeeEEEEEEEeeCC
Q 023576          117 AIQDGMYVRLIGNLKSF-QGKKQIVAFSVRPVT  148 (280)
Q Consensus       117 ~~~~G~yVrV~G~l~~f-~~~~~i~~~~ir~v~  148 (280)
                      .+..|+.|.|.|.+..- .+...|.+..|..+.
T Consensus       185 ~l~~Gd~V~V~G~~~~t~~gel~i~~~~i~lls  217 (585)
T PTZ00417        185 KIRRGDIVGIVGFPGKSKKGELSIFPKETIILS  217 (585)
T ss_pred             cCCCCCEEEEEeEEcCCCCceEEEEEEEEEEEe
Confidence            68999999999997654 466777776655443

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=91.86  E-value=0.52  Score=41.58  Aligned_cols=51  Identities=8%  Similarity=0.173  Sum_probs=37.5

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +.+.|.+-|.+..- ....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus        10 i~~~L~~~I~~g~~-~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r   61 (240)
T PRK09764         10 IADRIREQIARGEL-KPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILES   61 (240)
T ss_pred             HHHHHHHHHHcCCC-CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            44555555544211 112234 6799999999999999999999999999985

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=91.78  E-value=0.52  Score=41.22  Aligned_cols=51  Identities=18%  Similarity=0.236  Sum_probs=37.6

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +.+.|.+-|....- ....=+ +..+++++++.+...||+||+.|.+||.||.
T Consensus         6 i~~~l~~~I~~g~~-~~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r   57 (230)
T TIGR02018         6 IKQDILERIRSGEW-PPGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLER   57 (230)
T ss_pred             HHHHHHHHHHhCCC-CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            44555555544211 112224 7899999999999999999999999999986

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.

>PRK06752 single-stranded DNA-binding protein; Validated

Probab=91.72  E-value=1.8  Score=33.72  Aligned_cols=77  Identities=16%  Similarity=0.309  Sum_probs=47.1

Q ss_pred             eeEEEEEEEEEe---e---ecCCeeEEEEE------cC-----CceEEEEEecccccChhhhccCCCCCEEEEEEEEee-
Q 023576           71 TNVTLVGLVYNK---E---ERASDVNFTLD------DG-----TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS-  132 (280)
Q Consensus        71 ~~V~iVG~V~~~---~---~~~t~~~~~Ld------Dg-----TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~-  132 (280)
                      +.|.|+|.+..-   .   ....++.|+|-      |.     |--+.|..|...++  .....+..|+.|.|.|+|+. 
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            566777776441   1   12234555554      21     33588999976432  23456899999999999986 


Q ss_pred             -eCC---e----eEEEEEEEeeCCC
Q 023576          133 -FQG---K----KQIVAFSVRPVTN  149 (280)
Q Consensus       133 -f~~---~----~~i~~~~ir~v~d  149 (280)
                       |.+   +    ..|.+..|..++.
T Consensus        81 ~~~~~~G~~~~~~ei~a~~i~~l~~  105 (112)
T PRK06752         81 NYEDDQGKRIYITEVVIESITFLER  105 (112)
T ss_pred             ccCCCCCcEEEEEEEEEEEEEECCC
Confidence             432   2    2366777776654

>PRK14999 histidine utilization repressor; Provisional

Probab=91.70  E-value=0.56  Score=41.38  Aligned_cols=51  Identities=18%  Similarity=0.193  Sum_probs=38.2

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +...|.+-|.+.. -....=+ +..+++++++.+...||+||+.|.+||.|+.
T Consensus        17 i~~~i~~~I~~g~-~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r   68 (241)
T PRK14999         17 VKQDICKKIAGGV-WQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVR   68 (241)
T ss_pred             HHHHHHHHHHcCC-CCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            4455555555421 1122234 7899999999999999999999999999985

>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=91.67  E-value=0.51  Score=33.29  Aligned_cols=48  Identities=17%  Similarity=0.372  Sum_probs=35.9

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCee
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I  266 (280)
                      +++.|+++|+....  .-.=.=+.|+++.+ ...+.+|++++..|++||.+
T Consensus         2 ~K~~Ile~L~~k~~--~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l   50 (67)
T PF08679_consen    2 AKQKILEFLEAKKK--KKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKL   50 (67)
T ss_dssp             HHHHHHHHHSSCCC--HSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHhccC--CCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeE
Confidence            67889999985421  22345678999977 69999999999999999976

The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.

>PRK06293 single-stranded DNA-binding protein; Provisional

Probab=91.64  E-value=1.7  Score=36.29  Aligned_cols=61  Identities=20%  Similarity=0.229  Sum_probs=41.1

Q ss_pred             eeEEEEEEEEE-ee-----ecCCeeEEEEE--------cCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576           71 TNVTLVGLVYN-KE-----ERASDVNFTLD--------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF  133 (280)
Q Consensus        71 ~~V~iVG~V~~-~~-----~~~t~~~~~Ld--------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f  133 (280)
                      +.|.|+|.+.. .+     ....++.|+|-        +.|--|.|..|...++  .....++.|+.|-|.|+|+.-
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            46778888754 11     12346666665        2455699999976431  224569999999999999964

>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=91.63  E-value=1.5  Score=35.20  Aligned_cols=54  Identities=24%  Similarity=0.311  Sum_probs=39.5

Q ss_pred             eeEEEEEEEE--Eeee--cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576           71 TNVTLVGLVY--NKEE--RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL  130 (280)
Q Consensus        71 ~~V~iVG~V~--~~~~--~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l  130 (280)
                      ..|+|-|.|.  ++..  ....++|.|.|+...|.|.+--.      .++.|++|.-|-|.|++
T Consensus        51 ~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~------~Pd~F~eg~~VVv~G~~  108 (131)
T PF03100_consen   51 RKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGP------LPDLFREGQGVVVEGRL  108 (131)
T ss_dssp             SEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--------CTT--TTSEEEEEEEE
T ss_pred             ceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCC------CCccccCCCeEEEEEEE
Confidence            5788899998  4555  46899999999988898886543      24679999999999998

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.

>PRK06863 single-stranded DNA-binding protein; Provisional

Probab=91.60  E-value=1.6  Score=36.70  Aligned_cols=81  Identities=20%  Similarity=0.197  Sum_probs=50.1

Q ss_pred             EeeEEEEEEEEEe---e---ecCCeeEEEEE------c-C-------CceEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576           70 ITNVTLVGLVYNK---E---ERASDVNFTLD------D-G-------TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN  129 (280)
Q Consensus        70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld------D-g-------TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~  129 (280)
                      +++|.|+|.+..-   +   .....+.|+|-      | .       |--+.|..|....+  .....++.|+.|.|.|+
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            6788888888652   1   12234555543      1 1       22477888875431  23466999999999999


Q ss_pred             Eeee--CC---e----eEEEEEEEeeCCCchH
Q 023576          130 LKSF--QG---K----KQIVAFSVRPVTNFDE  152 (280)
Q Consensus       130 l~~f--~~---~----~~i~~~~ir~v~d~Ne  152 (280)
                      |+.-  .+   +    ..|.+..|..+...++
T Consensus        82 L~~r~w~DkdG~~r~~~eI~a~~i~~L~~r~~  113 (168)
T PRK06863         82 LKTRKWQDQNGQDRYTTEIQGDVLQMLGGRNQ  113 (168)
T ss_pred             EEeCCccCCCCCEEEEEEEEEeEEEECCCCCc
Confidence            9974  32   2    3466666766665443

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=91.44  E-value=0.58  Score=41.26  Aligned_cols=31  Identities=13%  Similarity=0.313  Sum_probs=29.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          238 HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       238 ~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +-.+++++++.+...||+||+.|.+||.||.
T Consensus        37 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r   67 (241)
T PRK10079         37 AEQQLAARYEVNRHTLRRAIDQLVEKGWVQR   67 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            7799999999999999999999999999986

>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea

Probab=91.38  E-value=0.39  Score=33.97  Aligned_cols=48  Identities=19%  Similarity=0.178  Sum_probs=40.1

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      -.|+++|.+.      ..+++.+|.+..+++..++.-||-.|..|+.|+---.+
T Consensus        11 G~Vw~~L~~~------~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~   58 (65)
T PF10771_consen   11 GKVWQLLNEN------GEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEEKN   58 (65)
T ss_dssp             HHHHHHHCCS------SSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEET
T ss_pred             HHHHHHHhhC------CCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeC
Confidence            3689999873      36899999999999999999999999999999865433

The function is not known. ; PDB: 2L02_B 2L01_A.

>PRK06958 single-stranded DNA-binding protein; Provisional

Probab=91.34  E-value=1.8  Score=36.93  Aligned_cols=62  Identities=19%  Similarity=0.176  Sum_probs=40.9

Q ss_pred             EeeEEEEEEEEEe-e-----ecCCeeEEEEE--------------cCCceEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576           70 ITNVTLVGLVYNK-E-----ERASDVNFTLD--------------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN  129 (280)
Q Consensus        70 i~~V~iVG~V~~~-~-----~~~t~~~~~Ld--------------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~  129 (280)
                      ++.|.|+|.|..- +     .....+.|+|-              +.|--+.|.+|...++  .....++.|+.|.|.|+
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            5788888888552 1     12245566662              1244577888865431  23457899999999999


Q ss_pred             Eeee
Q 023576          130 LKSF  133 (280)
Q Consensus       130 l~~f  133 (280)
                      |+..
T Consensus        82 L~~~   85 (182)
T PRK06958         82 IRTR   85 (182)
T ss_pred             EEeC
Confidence            9964

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=91.34  E-value=0.31  Score=43.70  Aligned_cols=46  Identities=30%  Similarity=0.481  Sum_probs=40.9

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      =+++|+++|++.      .=++++++++.|+.++..||.-|.+|.++|.+=.
T Consensus         6 R~~~Il~~l~~~------g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R   51 (253)
T COG1349           6 RHQKILELLKEK------GKVSVEELAELFGVSEMTIRRDLNELEEQGLLLR   51 (253)
T ss_pred             HHHHHHHHHHHc------CcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEE
Confidence            567899999974      2579999999999999999999999999998754

>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=91.29  E-value=1.2  Score=33.56  Aligned_cols=62  Identities=21%  Similarity=0.269  Sum_probs=35.7

Q ss_pred             EeeEEEEEEEEE---eee---cCCeeEEEEE--c-----------CCceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576           70 ITNVTLVGLVYN---KEE---RASDVNFTLD--D-----------GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL  130 (280)
Q Consensus        70 i~~V~iVG~V~~---~~~---~~t~~~~~Ld--D-----------gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l  130 (280)
                      ++.|.|+|.|..   +..   ...++.|.|.  +           .|--+.|..|.+.++  .....++.|+.|.|.|++
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            467888888844   211   1234444432  2           122488888866431  224569999999999999


Q ss_pred             eee
Q 023576          131 KSF  133 (280)
Q Consensus       131 ~~f  133 (280)
                      +..
T Consensus        79 ~~~   81 (104)
T PF00436_consen   79 RTR   81 (104)
T ss_dssp             EEE
T ss_pred             Eee
Confidence            975

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 ....

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=91.24  E-value=0.54  Score=41.92  Aligned_cols=54  Identities=24%  Similarity=0.451  Sum_probs=46.1

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      -+||++|.+.     +.++++.+|+++++++.+.+...|..|.+.|.+...-++.+|..
T Consensus         7 l~iL~~l~~~-----~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~L   60 (246)
T COG1414           7 LAILDLLAEG-----PGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRL   60 (246)
T ss_pred             HHHHHHHHhC-----CCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEee
Confidence            3588888862     35789999999999999999999999999999999755557764

>TIGR00621 ssb single stranded DNA-binding protein (ssb)

Probab=91.24  E-value=2  Score=35.96  Aligned_cols=36  Identities=14%  Similarity=0.057  Sum_probs=27.3

Q ss_pred             CCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576           96 GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF  133 (280)
Q Consensus        96 gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f  133 (280)
                      .|--|.|+.|...+.  .....++.|+.|.|.|+|+.-
T Consensus        49 ~t~~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~L~~~   84 (164)
T TIGR00621        49 ETEWHDIVIFGRLAE--VAAQYLKKGSLVYVEGRLRTR   84 (164)
T ss_pred             cceEEEEEEehHHHH--HHHHhCCCCCEEEEEEEEEec
Confidence            355799999976432  234579999999999999963

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN)

Probab=91.02  E-value=0.25  Score=34.42  Aligned_cols=55  Identities=18%  Similarity=0.379  Sum_probs=39.8

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHH-HHHHHHHHHhCCeeeecCCCccccccC
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKK-IMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~-v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      +.+.|+.-|+-      ..|++++++.++++.+..+ +.+.|+.|.++|.|  ++|+++++.|.
T Consensus         7 ~~e~i~~~LR~------~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll--~~~~~~l~lT~   62 (66)
T PF06969_consen    7 LREYIMLGLRC------NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLL--EIDGGRLRLTE   62 (66)
T ss_dssp             HHHHHHHHHHH------HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSE--EE-SSEEEE-T
T ss_pred             HHHHHHHHHHh------HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCE--EEeCCEEEECc
Confidence            44556666664      2599999999999977555 58889999999999  56788998875

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.

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=90.90  E-value=0.74  Score=40.53  Aligned_cols=31  Identities=26%  Similarity=0.431  Sum_probs=29.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          238 HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       238 ~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +-.+++++++.+...||+||+.|.+||.|+.
T Consensus        35 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r   65 (241)
T PRK11402         35 TENELCTQYNVSRITIRKAISDLVADGVLIR   65 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            7799999999999999999999999999986

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=90.89  E-value=0.62  Score=37.07  Aligned_cols=48  Identities=19%  Similarity=0.274  Sum_probs=39.8

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      -.+|..|...    .+..+++++|+++++++..-+++.|..|...|.|.+.-
T Consensus        12 l~~l~~la~~----~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~   59 (130)
T TIGR02944        12 TLVLTTLAQN----DSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKR   59 (130)
T ss_pred             HHHHHHHHhC----CCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecC
Confidence            3466666542    34579999999999999999999999999999998753

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.

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=90.88  E-value=0.65  Score=41.45  Aligned_cols=52  Identities=17%  Similarity=0.340  Sum_probs=43.5

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      .||++|.+.      .++++.||+++++++.+.+...|..|.+.|.|+..-++..|..
T Consensus        18 ~IL~~l~~~------~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~l   69 (257)
T PRK15090         18 GILQALGEE------REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSL   69 (257)
T ss_pred             HHHHHhhcC------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEe
Confidence            477777541      3689999999999999999999999999999998655667764

>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=90.81  E-value=0.75  Score=37.44  Aligned_cols=65  Identities=17%  Similarity=0.341  Sum_probs=37.0

Q ss_pred             eeEEEEEcCCceEEEEEecccccC----------------hhh----hcc-CCCCCEEEEEEEEeeeCCe--eEEEEEEE
Q 023576           88 DVNFTLDDGTGRVVCKRWASEVFD----------------TRE----MEA-IQDGMYVRLIGNLKSFQGK--KQIVAFSV  144 (280)
Q Consensus        88 ~~~~~LdDgTG~I~~~~w~~~~~~----------------~~~----~~~-~~~G~yVrV~G~l~~f~~~--~~i~~~~i  144 (280)
                      .+.+.|.|+||.+.+..|.+....                ...    ... +-..-.++|.++...|+++  ..+++.+|
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            466789999999999999864320                000    111 1222457899999999865  56888999


Q ss_pred             eeCCCchH
Q 023576          145 RPVTNFDE  152 (280)
Q Consensus       145 r~v~d~Ne  152 (280)
                      .||+-..|
T Consensus       135 ~~vd~~~e  142 (146)
T PF08646_consen  135 EPVDYAEE  142 (146)
T ss_dssp             EE--HHHH
T ss_pred             EeCCHHHH
Confidence            99854333

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.

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=90.78  E-value=0.73  Score=40.72  Aligned_cols=51  Identities=20%  Similarity=0.270  Sum_probs=37.2

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      |...|.+-|.+-.- ....-+ +-.+++++++.+...||+||+.|.++|.|+.
T Consensus        12 I~~~i~~~I~~G~~-~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r   63 (236)
T COG2188          12 IAEDIRQRIESGEL-PPGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVR   63 (236)
T ss_pred             HHHHHHHHHHhCCC-CCCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEE
Confidence            45555555554211 111123 6799999999999999999999999999985

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=90.52  E-value=1.1  Score=31.40  Aligned_cols=50  Identities=20%  Similarity=0.258  Sum_probs=40.3

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK  276 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk  276 (280)
                      .+|++++++.       -++..+|+++++++...|+..+..|.++|...... ...|.
T Consensus         3 ~~il~~L~~~-------~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~-~~g~~   52 (69)
T TIGR00122         3 LRLLALLADN-------PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV-GKGYR   52 (69)
T ss_pred             HHHHHHHHcC-------CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec-CCceE
Confidence            4678887742       36799999999999999999999999999976554 44554

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.

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=90.50  E-value=0.68  Score=39.35  Aligned_cols=51  Identities=18%  Similarity=0.344  Sum_probs=44.8

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +..+.||.+|+..     +.+++.-+|+++|+++-.+|+..|-.|..+|.||.+ |+
T Consensus         4 ~~~~~i~~~l~~~-----~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~-~~   54 (183)
T PHA02701          4 DCASLILTLLSSS-----GDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCE-DG   54 (183)
T ss_pred             hHHHHHHHHHHhc-----CCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecC-CC
Confidence            4678899999974     335999999999999999999999999999999987 44

>PRK09954 putative kinase; Provisional

Probab=90.41  E-value=0.5  Score=44.22  Aligned_cols=46  Identities=24%  Similarity=0.427  Sum_probs=40.7

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      ++...+||++|++++      =++..+|+++|+++...|+..|..|.++|.|
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            456778999999752      4799999999999999999999999999876

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=90.37  E-value=0.75  Score=35.61  Aligned_cols=49  Identities=22%  Similarity=0.343  Sum_probs=41.0

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecC
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      .+..||++|.+.     +.-++.++|.+++     +++...|-.+|+.|.+.|.|=...
T Consensus         2 qR~~Il~~l~~~-----~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~   55 (116)
T cd07153           2 QRLAILEVLLES-----DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIE   55 (116)
T ss_pred             HHHHHHHHHHhC-----CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEE
Confidence            356799999863     3578999999998     489999999999999999987643

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.

>PRK05813 single-stranded DNA-binding protein; Provisional

Probab=90.35  E-value=3.3  Score=36.42  Aligned_cols=81  Identities=14%  Similarity=0.203  Sum_probs=56.3

Q ss_pred             EEEeeEEEEEEEEEe---e---ecCCeeEEEEEc-----CCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee--C
Q 023576           68 LEITNVTLVGLVYNK---E---ERASDVNFTLDD-----GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF--Q  134 (280)
Q Consensus        68 ~~i~~V~iVG~V~~~---~---~~~t~~~~~LdD-----gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f--~  134 (280)
                      ..++.|.|+|.+..-   .   .....+.|+|-=     .|--|.|..|...+.   .+..++.|+.|.|.|+|+..  .
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            457899999999652   1   123466666652     255799999987542   24469999999999999974  3


Q ss_pred             C--------e---eEEEEEEEeeCCCch
Q 023576          135 G--------K---KQIVAFSVRPVTNFD  151 (280)
Q Consensus       135 ~--------~---~~i~~~~ir~v~d~N  151 (280)
                      +        +   -.|.+.+|..+...+
T Consensus       184 ~k~g~~~g~kr~~~eV~v~~i~~l~~~~  211 (219)
T PRK05813        184 KKLSEGEVVTKVAYEVSISKMEKVEKEE  211 (219)
T ss_pred             cCCCCccceEEEEEEEEEEEEEEcCChh
Confidence            2        2   247778887776644

>PRK11569 transcriptional repressor IclR; Provisional

Probab=90.34  E-value=0.69  Score=41.76  Aligned_cols=53  Identities=15%  Similarity=0.396  Sum_probs=44.2

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      .||++|.+.     +.++++.||++.++++.+.+...|..|.++|.+...-+...|..
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            478887652     45799999999999999999999999999999987555566753

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=90.22  E-value=1.2  Score=35.30  Aligned_cols=45  Identities=27%  Similarity=0.355  Sum_probs=38.0

Q ss_pred             CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC-CCcccccc
Q 023576          234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI-DEFHYKFA  278 (280)
Q Consensus       234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi-Dd~hfk~t  278 (280)
                      +..++.++|++.++++...|++.|+.|...|.|-++- .+..|+.+
T Consensus        23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~   68 (132)
T TIGR00738        23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLA   68 (132)
T ss_pred             CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCC
Confidence            3489999999999999999999999999999998753 33467654

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.

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=90.20  E-value=0.84  Score=38.50  Aligned_cols=56  Identities=25%  Similarity=0.240  Sum_probs=43.5

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHh--CCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQL--KIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l--~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      ....|++++.-.+      |. ...+|+++|  +++.++|+++|++|..-|.|=-.-| ..|+.|+
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 YHPAIRELLPLMP------FAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD-GKYVQTD   83 (171)
T ss_pred             HHHHHHHHhhcCC------CCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC-CcEEEec
Confidence            3445666665432      33 899999999  7999999999999999999987544 4777665

>PRK08763 single-stranded DNA-binding protein; Provisional

Probab=90.08  E-value=3.1  Score=34.85  Aligned_cols=61  Identities=21%  Similarity=0.164  Sum_probs=41.1

Q ss_pred             EeeEEEEEEEEE---ee---ecCCeeEEEEE------cC-------CceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576           70 ITNVTLVGLVYN---KE---ERASDVNFTLD------DG-------TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL  130 (280)
Q Consensus        70 i~~V~iVG~V~~---~~---~~~t~~~~~Ld------Dg-------TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l  130 (280)
                      ++.|.|+|.|.+   +.   .....+.|+|-      |.       |--+.|.+|...++  .....++.|+.|.|.|+|
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            788899998866   21   12345666664      22       22388889965321  234568999999999999


Q ss_pred             ee
Q 023576          131 KS  132 (280)
Q Consensus       131 ~~  132 (280)
                      +.
T Consensus        83 ~~   84 (164)
T PRK08763         83 RY   84 (164)
T ss_pred             Ee
Confidence            86

>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=90.07  E-value=0.49  Score=34.62  Aligned_cols=54  Identities=28%  Similarity=0.318  Sum_probs=41.9

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      |++-|++||..|=+.= ....+-|.=.+|++.++.++..||..+..|.+.|+|.+
T Consensus         2 Lt~rq~~IL~alV~~Y-~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~   55 (78)
T PF03444_consen    2 LTERQREILKALVELY-IETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVES   55 (78)
T ss_pred             CCHHHHHHHHHHHHHH-HhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence            5667777777553321 12345677799999999999999999999999999985

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

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=89.76  E-value=0.37  Score=41.09  Aligned_cols=47  Identities=13%  Similarity=0.113  Sum_probs=41.2

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      -++.|+++|++.+      =+++.++++.|+.++..||.-|.+|..+|++=.|
T Consensus         8 R~~~Il~~l~~~~------~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~   54 (185)
T PRK04424          8 RQKALQELIEENP------FITDEELAEKFGVSIQTIRLDRMELGIPELRERI   54 (185)
T ss_pred             HHHHHHHHHHHCC------CEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHH
Confidence            5677999998742      4799999999999999999999999999988655

>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=89.69  E-value=1.8  Score=35.92  Aligned_cols=72  Identities=14%  Similarity=0.230  Sum_probs=45.5

Q ss_pred             eeEEEEEcCCceEEEEEecccccC-----h--------h-------hhccCCCCC--EEEEEEEEeeeCC--eeEEEEEE
Q 023576           88 DVNFTLDDGTGRVVCKRWASEVFD-----T--------R-------EMEAIQDGM--YVRLIGNLKSFQG--KKQIVAFS  143 (280)
Q Consensus        88 ~~~~~LdDgTG~I~~~~w~~~~~~-----~--------~-------~~~~~~~G~--yVrV~G~l~~f~~--~~~i~~~~  143 (280)
                      .+.+.|.|+||.+.+..|.+....     .        .       ....+ .|.  .++|..+...|++  +...++.+
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 ILSLNVADHTGEAWLTLFDEVAEQIFGKSAEELLELKEEDPDAFPDAIQDL-VGKTFLFRVSVKEETYNDEGRIRYTVVK  147 (166)
T ss_pred             EEEEEEEeCCCCEEEEEehHHHHHHhCCCHHHHHHHhhcCHHHHHHHHHHh-hCceEEEEEEEEehhcCCcceEEEEEEE
Confidence            467899999999999999754320     0        0       01111 233  4566666778887  66677777


Q ss_pred             EeeCCCchHHHHHHHHHH
Q 023576          144 VRPVTNFDEVTCHYIECI  161 (280)
Q Consensus       144 ir~v~d~Nei~~H~Le~i  161 (280)
                      |.|+.- .+...++|+-+
T Consensus       148 i~~~~~-~~~~~~l~~~i  164 (166)
T cd04476         148 VAPVDY-KKESKRLIQSI  164 (166)
T ss_pred             cccCCH-HHHHHHHHHHh
Confidence            777743 45566666654

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

>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB)

Probab=89.66  E-value=2.7  Score=31.23  Aligned_cols=36  Identities=14%  Similarity=0.152  Sum_probs=27.5

Q ss_pred             CCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576           96 GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF  133 (280)
Q Consensus        96 gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f  133 (280)
                      .+--+.|..|.+.+.  .....++.|+.|.|.|+++..
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            445699999987432  234569999999999999975

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

>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3

Probab=89.42  E-value=0.64  Score=32.89  Aligned_cols=49  Identities=22%  Similarity=0.392  Sum_probs=38.6

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +++++||++|++.+    ......-+++..|+.+..+|+..|-.|..+|.|+.
T Consensus         4 ~~ee~Il~~L~~~g----~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k   52 (66)
T PF02295_consen    4 DLEEKILDFLKELG----GSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCK   52 (66)
T ss_dssp             HHHHHHHHHHHHHT----SSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             hHHHHHHHHHHhcC----CccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEee
Confidence            57889999999852    33555555666677889999999999999999985

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 ....

>PHA02943 hypothetical protein; Provisional

Probab=89.28  E-value=1.1  Score=36.96  Aligned_cols=46  Identities=13%  Similarity=0.225  Sum_probs=38.6

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +-..+||++|+.       -..+..+||+.++++-.+++-+|--|..||.|-+
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            345678888832       1467999999999999999999999999999865

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=89.12  E-value=0.73  Score=41.66  Aligned_cols=47  Identities=28%  Similarity=0.429  Sum_probs=41.1

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +-+.+|+++|++.+      -+++.+|++.|+.++..||.-|.+|.++|.+..
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            45677999998742      399999999999999999999999999999865

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

Probab=89.08  E-value=0.66  Score=34.06  Aligned_cols=39  Identities=15%  Similarity=0.334  Sum_probs=36.2

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      .=+++++|++.++++.++++..|-.|+.+|.|.-.||..
T Consensus        23 ~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~   61 (88)
T smart00088       23 SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV   61 (88)
T ss_pred             ceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence            468999999999999999999999999999999999863

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.

>smart00753 PAM PCI/PINT associated module

Probab=89.08  E-value=0.66  Score=34.06  Aligned_cols=39  Identities=15%  Similarity=0.334  Sum_probs=36.2

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      .=+++++|++.++++.++++..|-.|+.+|.|.-.||..
T Consensus        23 ~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~   61 (88)
T smart00753       23 SSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV   61 (88)
T ss_pred             ceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence            468999999999999999999999999999999999863

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=88.98  E-value=1.7  Score=34.86  Aligned_cols=34  Identities=24%  Similarity=0.403  Sum_probs=31.8

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       237 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      -|+.++|..+++++..|..|..+|..+|.||+--
T Consensus        36 PSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~r   69 (125)
T COG1725          36 PSVRELAKDLGVNPNTVQRAYQELEREGIVETKR   69 (125)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            4999999999999999999999999999999853

>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=88.75  E-value=3.1  Score=34.27  Aligned_cols=55  Identities=24%  Similarity=0.257  Sum_probs=42.8

Q ss_pred             eeEEEEEEEEE--eee-cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe
Q 023576           71 TNVTLVGLVYN--KEE-RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK  131 (280)
Q Consensus        71 ~~V~iVG~V~~--~~~-~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~  131 (280)
                      ..|++-|.|..  +.. ....++|.|.|+...|.|.+--.      .++.|++|.-|-|.|++.
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            56788888864  444 56789999999987888776432      256799999999999985

>PRK07772 single-stranded DNA-binding protein; Provisional

Probab=88.74  E-value=4.3  Score=34.75  Aligned_cols=35  Identities=26%  Similarity=0.383  Sum_probs=26.5

Q ss_pred             CceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576           97 TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF  133 (280)
Q Consensus        97 TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f  133 (280)
                      |--|+|..|...++  .....|+.|+.|.|.|+|+.-
T Consensus        52 t~fi~V~~Wg~~Ae--~va~~L~KGd~V~V~GrL~~r   86 (186)
T PRK07772         52 ALFLRCSIWRQAAE--NVAESLTKGMRVIVTGRLKQR   86 (186)
T ss_pred             ceEEEEEEecHHHH--HHHHhcCCCCEEEEEEEEEcC
Confidence            33589999976432  234569999999999999963

>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]

Probab=88.48  E-value=1.4  Score=36.05  Aligned_cols=55  Identities=24%  Similarity=0.268  Sum_probs=46.5

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++.+..||++|.+..    + .++.++|.+.+     +++...|-.+|+.|.+.|.|...-.++
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            5778899999999752    3 49999999988     399999999999999999998766544

>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=88.47  E-value=1.3  Score=32.57  Aligned_cols=54  Identities=17%  Similarity=0.216  Sum_probs=42.8

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----C---CCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----K---IPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~---~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +.+|-+.|..+|.+..  ..+..++.+.|.+.|     +   =+.+-|+.+|..|+.|+.||-|
T Consensus         9 fiPL~EvlC~~I~dln--~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY~t   70 (80)
T PF10264_consen    9 FIPLPEVLCWVISDLN--AAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIYHT   70 (80)
T ss_pred             ceeHHHHHHHHHHHHh--ccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCceeeC
Confidence            4667888888887753  346678999999888     2   2455599999999999999998

This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=88.45  E-value=0.98  Score=40.35  Aligned_cols=48  Identities=25%  Similarity=0.327  Sum_probs=41.9

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +-+++|+++|++.      .-+++.+|++.|+.++..||.-|..|.++|.|-.+
T Consensus         5 ~R~~~Il~~l~~~------~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~   52 (251)
T PRK13509          5 QRHQILLELLAQL------GFVTVEKVIERLGISPATARRDINKLDESGKLKKV   52 (251)
T ss_pred             HHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            3567899999874      36899999999999999999999999999998653

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=88.33  E-value=0.9  Score=40.37  Aligned_cols=46  Identities=26%  Similarity=0.433  Sum_probs=40.2

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +-+++|+++|++.      ..+++++|++.|++++..||.-|.+|.++|.|-
T Consensus         4 ~R~~~Il~~l~~~------~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~   49 (240)
T PRK10411          4 ARQQAIVDLLLNH------TSLTTEALAEQLNVSKETIRRDLNELQTQGKIL   49 (240)
T ss_pred             HHHHHHHHHHHHc------CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            3567899999863      378999999999999999999999999998773

>PRK09010 single-stranded DNA-binding protein; Provisional

Probab=88.25  E-value=2.2  Score=36.27  Aligned_cols=63  Identities=24%  Similarity=0.243  Sum_probs=40.5

Q ss_pred             EEeeEEEEEEEEEe---e---ecCCeeEEEEE------c-CCc-------eEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576           69 EITNVTLVGLVYNK---E---ERASDVNFTLD------D-GTG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIG  128 (280)
Q Consensus        69 ~i~~V~iVG~V~~~---~---~~~t~~~~~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G  128 (280)
                      -++.|.|||.|..-   +   .....+.|+|-      | .+|       -+.|.+|...++  .....|+.|+.|.|.|
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            36788888888552   1   12244555553      2 123       378888875431  2346799999999999


Q ss_pred             EEeee
Q 023576          129 NLKSF  133 (280)
Q Consensus       129 ~l~~f  133 (280)
                      +|+.-
T Consensus        83 rL~~~   87 (177)
T PRK09010         83 QLRTR   87 (177)
T ss_pred             EEEec
Confidence            99863

>PRK10870 transcriptional repressor MprA; Provisional

Probab=88.07  E-value=2.2  Score=36.00  Aligned_cols=57  Identities=21%  Similarity=0.225  Sum_probs=48.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..|-.||..|...    .+.+++..+|++.++++...|...|+.|...|.|...-|.+
T Consensus        52 gLt~~q~~iL~~L~~~----~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~  108 (176)
T PRK10870         52 GINETLFMALITLESQ----ENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDN  108 (176)
T ss_pred             CCCHHHHHHHHHHhcC----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence            4666777899988753    24578999999999999999999999999999999877654

>PRK09462 fur ferric uptake regulator; Provisional

Probab=88.03  E-value=1.4  Score=35.94  Aligned_cols=51  Identities=20%  Similarity=0.367  Sum_probs=42.9

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ++..+..||++|.+.    .+.-++.++|.++|     +++...|-.+|+.|.+.|.|-.
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            577888999999863    23478999999988     2789999999999999999954

>KOG0554 consensus Asparaginyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis]

Probab=87.94  E-value=1.1  Score=42.41  Aligned_cols=87  Identities=15%  Similarity=0.155  Sum_probs=62.3

Q ss_pred             eeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCc--eEEEEEecccccChhhhccCC
Q 023576           42 LVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTG--RVVCKRWASEVFDTREMEAIQ  119 (280)
Q Consensus        42 ~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG--~I~~~~w~~~~~~~~~~~~~~  119 (280)
                      +.+|.++.+......             -..+.|-|+|++++......-+.|+|||-  .+.|+.=.      .....+.
T Consensus         5 ~~~v~~~~~~~~~~~-------------g~~~~i~GWvKsvr~~~~~~Fl~i~DGs~~~~lQvVv~~------~~~q~la   65 (446)
T KOG0554|consen    5 SLSVLSGRILGHPRA-------------GDTISIGGWVKSVRKLKKVTFLDINDGSCPSPLQVVVDS------EQSQLLA   65 (446)
T ss_pred             eeeeeccccccCCCC-------------CCceeecchhhhcccccceEEEEecCCCCCcceEEEech------HHhhhcc
Confidence            456666666554433             25678889999999888888889999996  47777544      2356789


Q ss_pred             CCCEEEEEEEEeeeCCe---eEEEEEEEeeC
Q 023576          120 DGMYVRLIGNLKSFQGK---KQIVAFSVRPV  147 (280)
Q Consensus       120 ~G~yVrV~G~l~~f~~~---~~i~~~~ir~v  147 (280)
                      .|+-|.|.|.++.-++-   ..+++.+|..|
T Consensus        66 ~Gt~i~~~g~l~~~~~~~q~iel~~eki~~v   96 (446)
T KOG0554|consen   66 TGTCISAEGVLKVSKGAKQQIELNAEKIKVV   96 (446)
T ss_pred             ccceEEEEeeEEeccchheeeeeeeeEEEEE
Confidence            99999999999987632   33555555443

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=87.83  E-value=0.46  Score=37.22  Aligned_cols=51  Identities=22%  Similarity=0.356  Sum_probs=41.2

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      +..+..||++|.+.     +.-++.++|.+.+     +++...|-.+|+.|.+.|.|-...
T Consensus         7 T~~R~~Il~~l~~~-----~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~   62 (120)
T PF01475_consen    7 TPQRLAILELLKES-----PEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIE   62 (120)
T ss_dssp             HHHHHHHHHHHHHH-----SSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHHHHcC-----CCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEE
Confidence            55778899999985     2379999999988     388899999999999999986643

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 ....

>PRK08182 single-stranded DNA-binding protein; Provisional

Probab=87.81  E-value=5.2  Score=32.90  Aligned_cols=61  Identities=15%  Similarity=0.156  Sum_probs=39.2

Q ss_pred             eeEEEEEEEEEe---e--ecCC-----eeEEEEE------cCCc--------eEEEEEecccccChhhhccCCCCCEEEE
Q 023576           71 TNVTLVGLVYNK---E--ERAS-----DVNFTLD------DGTG--------RVVCKRWASEVFDTREMEAIQDGMYVRL  126 (280)
Q Consensus        71 ~~V~iVG~V~~~---~--~~~t-----~~~~~Ld------DgTG--------~I~~~~w~~~~~~~~~~~~~~~G~yVrV  126 (280)
                      +.|.|+|.+..-   .  ....     .+.|+|-      +.+|        -+.|..|...++  .....++.|+.|-|
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            567788877541   1  1122     5677772      2222        488999975432  23456899999999


Q ss_pred             EEEEeee
Q 023576          127 IGNLKSF  133 (280)
Q Consensus       127 ~G~l~~f  133 (280)
                      .|+|+.-
T Consensus        81 ~GrL~~~   87 (148)
T PRK08182         81 EGRMERD   87 (148)
T ss_pred             EEEEEec
Confidence            9999753

>PRK07274 single-stranded DNA-binding protein; Provisional

Probab=87.79  E-value=2.7  Score=33.78  Aligned_cols=62  Identities=18%  Similarity=0.233  Sum_probs=39.4

Q ss_pred             EeeEEEEEEEEEe---e---ecCCeeEEEEE------cCCc-----eEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576           70 ITNVTLVGLVYNK---E---ERASDVNFTLD------DGTG-----RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS  132 (280)
Q Consensus        70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld------DgTG-----~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~  132 (280)
                      ++.|.|+|.+..-   .   ....++.|+|-      |..|     -+.|..|...++  .-...++.|+.|.|.|+|+.
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            3567777777542   1   12245566654      3223     488888965321  23456999999999999986


Q ss_pred             e
Q 023576          133 F  133 (280)
Q Consensus       133 f  133 (280)
                      -
T Consensus        80 ~   80 (131)
T PRK07274         80 R   80 (131)
T ss_pred             c
Confidence            3

>TIGR03337 phnR transcriptional regulator protein

Probab=87.79  E-value=1.8  Score=37.56  Aligned_cols=52  Identities=19%  Similarity=0.308  Sum_probs=38.7

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +.+.+.+.|++..-. ...=+ +..+++++|+.+.-.|++||..|.++|.||..
T Consensus         6 i~~~l~~~I~~g~~~-~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~   58 (231)
T TIGR03337         6 IKDHLSYQIRAGALL-PGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYRE   58 (231)
T ss_pred             HHHHHHHHHHcCCCC-CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEe
Confidence            455666666553211 11123 67999999999999999999999999999974

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.

>PRK13732 single-stranded DNA-binding protein; Provisional

Probab=87.78  E-value=2.3  Score=36.00  Aligned_cols=62  Identities=21%  Similarity=0.220  Sum_probs=41.8

Q ss_pred             EeeEEEEEEEEEe---e---ecCCeeEEEEEc-------CCc-------eEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576           70 ITNVTLVGLVYNK---E---ERASDVNFTLDD-------GTG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIGN  129 (280)
Q Consensus        70 i~~V~iVG~V~~~---~---~~~t~~~~~LdD-------gTG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~  129 (280)
                      ++.|.|+|.|..-   .   .....+.|+|--       .+|       -+.|..|...++  .....++.|+.|.|.|+
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            6889999998652   1   223466666642       233       468888875431  23456899999999999


Q ss_pred             Eeee
Q 023576          130 LKSF  133 (280)
Q Consensus       130 l~~f  133 (280)
                      |+.-
T Consensus        84 L~~r   87 (175)
T PRK13732         84 LRTR   87 (175)
T ss_pred             EEee
Confidence            9864

>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A

Probab=87.71  E-value=0.73  Score=33.80  Aligned_cols=45  Identities=22%  Similarity=0.333  Sum_probs=36.9

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +-.|+.+|...      ..+++.+|.+.++++...+...|..|.++|.|=.
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            45678888752      4799999999999999999999999999999854

>PRK05733 single-stranded DNA-binding protein; Provisional

Probab=87.55  E-value=2.7  Score=35.57  Aligned_cols=62  Identities=21%  Similarity=0.247  Sum_probs=40.6

Q ss_pred             EeeEEEEEEEEEe---e---ecCCeeEEEEE------c-CCc-------eEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576           70 ITNVTLVGLVYNK---E---ERASDVNFTLD------D-GTG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIGN  129 (280)
Q Consensus        70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~  129 (280)
                      ++.|.|+|.|..-   .   .....+.|+|-      | .+|       -+.|.+|...++  .....++.|+.|.|.|+
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            6788888888552   1   12234555543      1 133       388889975432  23467899999999999


Q ss_pred             Eeee
Q 023576          130 LKSF  133 (280)
Q Consensus       130 l~~f  133 (280)
                      |+.-
T Consensus        83 Lr~~   86 (172)
T PRK05733         83 LQTR   86 (172)
T ss_pred             EEeC
Confidence            9974

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=87.45  E-value=0.99  Score=36.56  Aligned_cols=34  Identities=15%  Similarity=0.342  Sum_probs=32.1

Q ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      =++.++|+++++++..-|++++..|..+|.|.++
T Consensus        25 ~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~   58 (141)
T PRK11014         25 MTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAV   58 (141)
T ss_pred             ccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEe
Confidence            4799999999999999999999999999999875

>PRK00215 LexA repressor; Validated

Probab=87.37  E-value=0.77  Score=39.48  Aligned_cols=56  Identities=21%  Similarity=0.360  Sum_probs=45.0

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCC-CHHHHHHHHHHHHhCCeeeecC
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKI-PQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~-~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      +++.|.+||++|++.- .......++.+|++.+++ +...+...|..|.+.|.|-...
T Consensus         2 lt~~q~~il~~i~~~~-~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~   58 (205)
T PRK00215          2 LTKRQQEILDFIRDHI-EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDP   58 (205)
T ss_pred             CCHHHHHHHHHHHHHH-HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCC
Confidence            4678899999997521 012356799999999999 9999999999999999996543

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=87.32  E-value=1.3  Score=40.90  Aligned_cols=45  Identities=31%  Similarity=0.369  Sum_probs=39.3

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCe-eee
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGL-IYS  268 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~-IYs  268 (280)
                      ..+||++|++      +..++.++|+++|+++...|..+|..|.++|. |++
T Consensus         6 ~~~il~~L~~------~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~   51 (319)
T PRK11886          6 MLQLLSLLAD------GDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFS   51 (319)
T ss_pred             HHHHHHHHHc------CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEE
Confidence            4578888875      24789999999999999999999999999999 766

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=86.93  E-value=2.1  Score=36.65  Aligned_cols=55  Identities=16%  Similarity=0.148  Sum_probs=47.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..|-.||.+|...      .|++..+|++.+.++...|...|+.|...|.|.-..|.+
T Consensus        42 gLt~~q~~iL~~L~~~------~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~   96 (185)
T PRK13777         42 DLNINEHHILWIAYHL------KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKED   96 (185)
T ss_pred             CCCHHHHHHHHHHHhC------CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCC
Confidence            5677788899998763      389999999999999999999999999999999876653

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=86.86  E-value=1.7  Score=38.01  Aligned_cols=35  Identities=17%  Similarity=0.283  Sum_probs=31.6

Q ss_pred             CCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          234 ERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       234 e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ..=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus        28 G~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~   63 (239)
T PRK04984         28 GSILPAERELSELIGVTRTTLREVLQRLARDGWLTI   63 (239)
T ss_pred             CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            3456 6889999999999999999999999999985

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=86.78  E-value=1.5  Score=37.97  Aligned_cols=36  Identities=14%  Similarity=0.183  Sum_probs=32.5

Q ss_pred             CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +..=++..+|+++|+++..-||+||..|..+|.|..
T Consensus        31 pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~   66 (221)
T PRK11414         31 PGARLITKNLAEQLGMSITPVREALLRLVSVNALSV   66 (221)
T ss_pred             CCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEe
Confidence            445678899999999999999999999999999975

>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=86.77  E-value=1.7  Score=31.28  Aligned_cols=49  Identities=29%  Similarity=0.483  Sum_probs=43.8

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +++-.||+.|...    .+.|+...++.+.++++...+--.+..|.+.|.|.-
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            5678899999874    578999999999999999999999999999999864

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.

>PF14502 HTH_41: Helix-turn-helix domain

Probab=86.75  E-value=1.4  Score=29.21  Aligned_cols=32  Identities=25%  Similarity=0.399  Sum_probs=29.6

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          237 VHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       237 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      -+++|.+++|+.+.-.|..||.+|.++|-|..
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            47899999999999999999999999998864

>KOG0555 consensus Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=86.65  E-value=1  Score=42.83  Aligned_cols=65  Identities=20%  Similarity=0.221  Sum_probs=48.2

Q ss_pred             EEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576           68 LEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF  133 (280)
Q Consensus        68 ~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f  133 (280)
                      ..=++|++-|||-+.+.+.+-+-..|-||||.+.|++-..-.. +.+.-.+..-.-|.|+|.|+..
T Consensus       121 ~r~qrVkv~gWVhrlR~qk~l~FivLrdg~gflqCVl~~kl~~-~yd~~~Ls~essv~vYG~i~~~  185 (545)
T KOG0555|consen  121 NRGQRVKVFGWVHRLRRQKSLIFIVLRDGTGFLQCVLSDKLCQ-SYDALTLSTESSVTVYGTIKKL  185 (545)
T ss_pred             ccCceEEeehhhHhhhhcCceEEEEEecCCceEEEEEcchhhh-hhccccccccceEEEEEEEecC
Confidence            3346899999998888777777779999999999997654321 1122345566789999999876

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=86.46  E-value=1.6  Score=37.66  Aligned_cols=47  Identities=13%  Similarity=0.218  Sum_probs=40.6

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      ++|+.++.+.     ..|.+.++|+++|++++..|+.-+.+|...|.+=..+
T Consensus       165 r~Vl~~~~~g-----~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~  211 (225)
T PRK10046        165 NAVRKLFKEP-----GVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEI  211 (225)
T ss_pred             HHHHHHHHcC-----CCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEe
Confidence            4789888752     3489999999999999999999999999999987654

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=86.41  E-value=1.6  Score=37.41  Aligned_cols=36  Identities=14%  Similarity=0.380  Sum_probs=31.8

Q ss_pred             CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +..=++..+++++|+++..-||+||..|..+|.|-.
T Consensus        31 pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~   66 (212)
T TIGR03338        31 PGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRN   66 (212)
T ss_pred             CCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE
Confidence            345668899999999999999999999999999853

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.

>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=86.09  E-value=1.7  Score=34.17  Aligned_cols=49  Identities=22%  Similarity=0.396  Sum_probs=43.8

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ..+..-++.|+++.+.        -.|+.||+..++++..-++--+..|.+.|+|-.
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            4678889999998764        569999999999999999999999999999864

The function of these proteins is unknown.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=85.88  E-value=2.9  Score=27.18  Aligned_cols=41  Identities=22%  Similarity=0.435  Sum_probs=32.4

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN  262 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~  262 (280)
                      +++.+..|+.++.        .|.+..+|++.++++...|+..+..+..
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            5566667776653        3789999999999999999998887643

lux regulon (activates the bioluminescence operon

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=85.87  E-value=3  Score=31.46  Aligned_cols=35  Identities=20%  Similarity=0.380  Sum_probs=32.9

Q ss_pred             CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ...++..+|++.++++...|..+|..|...|.|..
T Consensus        45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r   79 (95)
T TIGR01610        45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR   79 (95)
T ss_pred             CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            46899999999999999999999999999999985

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=85.69  E-value=2.1  Score=38.09  Aligned_cols=46  Identities=22%  Similarity=0.391  Sum_probs=39.1

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +.||+.|+..     +.-++..+|+++++++..-|++|+..|...|.|.+-
T Consensus       186 ~~IL~~L~~~-----egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r  231 (251)
T TIGR02787       186 EHIFEELDGN-----EGLLVASKIADRVGITRSVIVNALRKLESAGVIESR  231 (251)
T ss_pred             HHHHHHhccc-----cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            4577777652     345789999999999999999999999999999874

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.

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=85.67  E-value=2.3  Score=34.30  Aligned_cols=57  Identities=11%  Similarity=0.178  Sum_probs=42.8

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      +.-+.|+.++...      ..+++.+|++.++++...|..+|..|...|.|... ....|..|+
T Consensus         8 dyL~~I~~l~~~~------~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~-~~~~i~LT~   64 (142)
T PRK03902          8 DYIEQIYLLIEEK------GYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE-KYRGLVLTP   64 (142)
T ss_pred             HHHHHHHHHHhcC------CCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe-cCceEEECH
Confidence            3445566666542      36799999999999999999999999999999643 234555553

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=85.66  E-value=1.8  Score=36.74  Aligned_cols=46  Identities=20%  Similarity=0.162  Sum_probs=39.5

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      .....||.+|...+      -++.++|+..|+++..+||+.|..|.++|.|-
T Consensus        22 ~~~~~Vl~~L~~~g------~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~   67 (178)
T PRK06266         22 EEGFEVLKALIKKG------EVTDEEIAEQTGIKLNTVRKILYKLYDARLAD   67 (178)
T ss_pred             ccHhHHHHHHHHcC------CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence            34567888887632      37999999999999999999999999999987

>PRK03837 transcriptional regulator NanR; Provisional

Probab=85.52  E-value=2.3  Score=37.14  Aligned_cols=35  Identities=14%  Similarity=0.289  Sum_probs=31.8

Q ss_pred             CCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          234 ERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       234 e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .+=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus        34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~   69 (241)
T PRK03837         34 GDQLPSERELMAFFGVGRPAVREALQALKRKGLVQI   69 (241)
T ss_pred             CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            3456 7899999999999999999999999999976

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=85.51  E-value=1.9  Score=37.40  Aligned_cols=36  Identities=11%  Similarity=0.239  Sum_probs=31.7

Q ss_pred             CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +..=++..+++++|+++..-||+||..|..+|.|-.
T Consensus        27 pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~   62 (224)
T PRK11534         27 PDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTV   62 (224)
T ss_pred             CCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEE
Confidence            344678899999999999999999999999999853

>PRK07217 replication factor A; Reviewed

Probab=85.35  E-value=2.8  Score=38.68  Aligned_cols=58  Identities=24%  Similarity=0.254  Sum_probs=41.6

Q ss_pred             CeeEEEEEcCCceEEEEEecccccC--------h--------------hhhccCCCCCEEEEEEEEeeeCCeeEEEEEEE
Q 023576           87 SDVNFTLDDGTGRVVCKRWASEVFD--------T--------------REMEAIQDGMYVRLIGNLKSFQGKKQIVAFSV  144 (280)
Q Consensus        87 t~~~~~LdDgTG~I~~~~w~~~~~~--------~--------------~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~i  144 (280)
                      -++.+.||||||.++|++..+.-..        .              ......-.|.|++|+|.+  |  -++|.+..+
T Consensus       217 Lrik~vlDDGt~~~~~~~~~e~te~l~G~~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~~--~--g~~l~~~~~  292 (311)
T PRK07217        217 LRIKGVLDDGEEVQEVIFNREATEELTGITLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGPT--L--GRYLLADSV  292 (311)
T ss_pred             eEEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEecc--C--CcEEEeeEe
Confidence            3889999999999999998653210        0              011224689999999976  3  368888888


Q ss_pred             eeCC
Q 023576          145 RPVT  148 (280)
Q Consensus       145 r~v~  148 (280)
                      .+.+
T Consensus       293 ~~~~  296 (311)
T PRK07217        293 EPLT  296 (311)
T ss_pred             eccc
Confidence            7774

>PRK06642 single-stranded DNA-binding protein; Provisional

Probab=85.27  E-value=4  Score=33.70  Aligned_cols=62  Identities=21%  Similarity=0.208  Sum_probs=42.5

Q ss_pred             EeeEEEEEEEEE---ee---ecCCeeEEEEE------c---C-----CceEEEEEecc-cccChhhhccCCCCCEEEEEE
Q 023576           70 ITNVTLVGLVYN---KE---ERASDVNFTLD------D---G-----TGRVVCKRWAS-EVFDTREMEAIQDGMYVRLIG  128 (280)
Q Consensus        70 i~~V~iVG~V~~---~~---~~~t~~~~~Ld------D---g-----TG~I~~~~w~~-~~~~~~~~~~~~~G~yVrV~G  128 (280)
                      ++.|.|+|.+..   +.   .....+.|+|-      |   +     |--+.|..|.. .+.  .....++.|+.|.|.|
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   22   22357777776      2   1     33488888874 221  2345689999999999


Q ss_pred             EEeee
Q 023576          129 NLKSF  133 (280)
Q Consensus       129 ~l~~f  133 (280)
                      +|+..
T Consensus        83 rL~~~   87 (152)
T PRK06642         83 SLQTR   87 (152)
T ss_pred             EEEeC
Confidence            99864

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=85.24  E-value=2.2  Score=37.72  Aligned_cols=37  Identities=16%  Similarity=0.357  Sum_probs=32.4

Q ss_pred             CCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          232 ERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       232 ~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .+..-+ +..+|+++|+++..-||+||..|..+|.|-.
T Consensus        26 ~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~   63 (251)
T PRK09990         26 KVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIET   63 (251)
T ss_pred             CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            344567 6899999999999999999999999999854

>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=85.08  E-value=3.6  Score=26.79  Aligned_cols=41  Identities=15%  Similarity=0.277  Sum_probs=31.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL  260 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L  260 (280)
                      .|++-++.|+...-.       +|.+..+|++.++++...|+.....-
T Consensus         4 ~L~~~er~vi~~~y~-------~~~t~~eIa~~lg~s~~~V~~~~~~a   44 (50)
T PF04545_consen    4 QLPPREREVIRLRYF-------EGLTLEEIAERLGISRSTVRRILKRA   44 (50)
T ss_dssp             TS-HHHHHHHHHHHT-------ST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhc-------CCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence            477888888886542       48899999999999999988776543

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 ....

>PF15072 DUF4539: Domain of unknown function (DUF4539)

Probab=85.05  E-value=2.6  Score=31.49  Aligned_cols=65  Identities=15%  Similarity=0.150  Sum_probs=44.7

Q ss_pred             EEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC---CeeEEEE
Q 023576           74 TLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ---GKKQIVA  141 (280)
Q Consensus        74 ~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~  141 (280)
                      ++++.|+++.........+|.|.||+|.|.+-.+--.  +....+..|..+-+. .+..|.   .+.+|++
T Consensus         6 ~l~v~Iks~~~~~~D~~v~l~DpTG~i~~tiH~~v~~--~y~~~l~~GavLlLk-~V~Vf~ps~~~~yLnI   73 (86)
T PF15072_consen    6 CLVVIIKSIVPSSEDAFVVLKDPTGEIRGTIHRKVLE--EYGDELSPGAVLLLK-DVTVFSPSPRSHYLNI   73 (86)
T ss_pred             EEEEEEEEeeccCCCeEEEEECCCCcEEEEEeHHHHh--hcCCccccCEEEEEe-eeeEEecCCCccEEEE
Confidence            5788999998777788999999999999998754321  134567888755544 444443   3344544

>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=85.01  E-value=2.3  Score=28.14  Aligned_cols=40  Identities=18%  Similarity=0.239  Sum_probs=28.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS  259 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~  259 (280)
                      .|++.++.|+.+..-       .|.+..+|++.++++++.|+..+..
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            467788888887654       4999999999999999999887653

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.

>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional

Probab=84.79  E-value=1.8  Score=38.65  Aligned_cols=46  Identities=11%  Similarity=0.214  Sum_probs=39.3

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +-+.+|+++|++.      .-+++.++++.|+.++..||.-|.+|...+.+|
T Consensus         7 eR~~~I~~~l~~~------~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~~~~   52 (252)
T PRK10681          7 ERIGQLLQALKRS------DKLHLKDAAALLGVSEMTIRRDLNAHSAPVVLL   52 (252)
T ss_pred             HHHHHHHHHHHHc------CCCcHHHHHHHhCCCHHHHHHHHHHhhcCeEEE
Confidence            3567899999874      358999999999999999999999999877643

>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=84.56  E-value=7.4  Score=32.49  Aligned_cols=55  Identities=22%  Similarity=0.274  Sum_probs=42.2

Q ss_pred             eeEEEEEEEE--EeeecC--CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe
Q 023576           71 TNVTLVGLVY--NKEERA--SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK  131 (280)
Q Consensus        71 ~~V~iVG~V~--~~~~~~--t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~  131 (280)
                      ..+++=|.|.  ++....  ..+.|+|-|+...|.+.+=-.      -++.|++|.=|-|.|++.
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            5677778887  455433  378999999999988875432      246799999999999986

>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=84.40  E-value=2.3  Score=28.70  Aligned_cols=41  Identities=24%  Similarity=0.397  Sum_probs=33.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      .|++.+.+|+.++..        |.+..+|++.+++++..|+.-+..+.
T Consensus         3 ~LT~~E~~vl~~l~~--------G~~~~eIA~~l~is~~tV~~~~~~i~   43 (58)
T PF00196_consen    3 SLTERELEVLRLLAQ--------GMSNKEIAEELGISEKTVKSHRRRIM   43 (58)
T ss_dssp             SS-HHHHHHHHHHHT--------TS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHh--------cCCcchhHHhcCcchhhHHHHHHHHH
Confidence            367888899999864        89999999999999999988877664

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 ....

>PRK07135 dnaE DNA polymerase III DnaE; Validated

Probab=84.12  E-value=3.7  Score=43.71  Aligned_cols=59  Identities=12%  Similarity=0.028  Sum_probs=44.0

Q ss_pred             eEEEEEEEEEeee----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576           72 NVTLVGLVYNKEE----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF  133 (280)
Q Consensus        72 ~V~iVG~V~~~~~----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f  133 (280)
                      .|+++|.|.+++.    +.+...++|+|.||.|+|.+|.+.-   .....+.+++++.|.|+...-
T Consensus       899 ~~~v~g~i~~~~~~~K~g~~maf~~~eD~~~~~e~~~F~~~~---~~~~~l~~~~~~~~~~~~~~~  961 (973)
T PRK07135        899 EYRLAIEVKNVKRLRKANKEYKKVILSDDSVEITIFVNDNDY---LLFETLKKGDIYEFLISKSKN  961 (973)
T ss_pred             eEEEEEEEEEEEEEeeCCCeEEEEEEEECCCcEEEEEcHHHH---HHHHHhhcCCEEEEEEEEcCC
Confidence            4677888876532    3467778999999999999997642   123358889999999887763

>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=84.09  E-value=2  Score=30.40  Aligned_cols=34  Identities=18%  Similarity=0.374  Sum_probs=31.0

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ..++.++|+..++.+...|...|..|.++|.|=.
T Consensus        27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~   60 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSRETVSRILKRLKDEGIIEV   60 (76)
T ss_dssp             EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            4578999999999999999999999999998853

...

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=84.07  E-value=2.1  Score=37.55  Aligned_cols=40  Identities=23%  Similarity=0.282  Sum_probs=36.3

Q ss_pred             CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ...+++..+|++.++++...+...|..|.++|.|.-..|.
T Consensus        18 ~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~   57 (217)
T PRK14165         18 NTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVP   57 (217)
T ss_pred             CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcC
Confidence            3458999999999999999999999999999999987764

>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function

Probab=84.01  E-value=5.9  Score=32.99  Aligned_cols=41  Identities=17%  Similarity=0.259  Sum_probs=26.0

Q ss_pred             eeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE
Q 023576           82 KEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI  127 (280)
Q Consensus        82 ~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~  127 (280)
                      ......++.|.|.|.||.++|...-.-.     .-..++||-+|++
T Consensus       125 K~v~~~~~~YeI~DnTG~MeVvv~G~~~-----ni~CEeGDKLrL~  165 (170)
T PF02760_consen  125 KTVNKKNTIYEIQDNTGKMEVVVYGKWH-----NIKCEEGDKLRLF  165 (170)
T ss_dssp             EEEESSEEEEEEEETTEEEEEEEEGGGC-----GCC--TT-EEEEE
T ss_pred             EEEcCCeEEEEEecCCCcEEEEEeccCc-----ccccCCCCeEEEE
Confidence            3445678999999999999999754321     2346777755543

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.

>COG3888 Predicted transcriptional regulator [Transcription]

Probab=83.80  E-value=2.3  Score=38.32  Aligned_cols=46  Identities=15%  Similarity=0.463  Sum_probs=42.0

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      ++++|+..|+..    .+.|+..-||-+..+++.+.+-+||..|.++|.|
T Consensus         5 ~reklir~Lk~a----~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv   50 (321)
T COG3888           5 LREKLIRELKRA----GPEGIDQTEIEELMGLSKSTVSEALSELEKQGIV   50 (321)
T ss_pred             HHHHHHHHHHhc----CCCCccHHHHHHHhCcchhHHHHHHHHHHhcCee
Confidence            678899999985    4679999999999999999999999999999987

>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=83.78  E-value=0.94  Score=34.72  Aligned_cols=44  Identities=23%  Similarity=0.336  Sum_probs=33.5

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      -.-.|+++|-..      ..++-++|++.++++..+||.+|..|.++|.|
T Consensus        14 ~~~~Il~~L~~~------~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv   57 (105)
T PF02002_consen   14 EAVRILDALLRK------GELTDEDLAKKLGLKPKEVRKILYKLYEDGLV   57 (105)
T ss_dssp             TTHHHHHHHHHH--------B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-
T ss_pred             hHHHHHHHHHHc------CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence            445788888753      25788999999999999999999999999998

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.

>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=83.67  E-value=2.2  Score=27.44  Aligned_cols=33  Identities=12%  Similarity=0.340  Sum_probs=23.9

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA  258 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~  258 (280)
                      .+.|++++++        |+++.+||+.++++...|...|.
T Consensus        11 ~~~i~~l~~~--------G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   11 IEEIKELYAE--------GMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHHHT--------T--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHHHC--------CCCHHHHHHHHCcCHHHHHHHHh
Confidence            4567777653        89999999999999999887663

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 ....

>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed

Probab=83.55  E-value=8.6  Score=32.06  Aligned_cols=55  Identities=24%  Similarity=0.325  Sum_probs=42.5

Q ss_pred             eeEEEEEEEE--Eeeec--CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe
Q 023576           71 TNVTLVGLVY--NKEER--ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK  131 (280)
Q Consensus        71 ~~V~iVG~V~--~~~~~--~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~  131 (280)
                      ..+++=|.|.  ++...  ...+.|.|.|+...|.+.+=-.      -++.|++|.=|-|.|++.
T Consensus        58 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~Gi------lPDlFrEG~gVVveG~~~  116 (159)
T PRK13150         58 QRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGI------LPDLFREGQGVVVQGTLE  116 (159)
T ss_pred             CEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEecc------CCccccCCCeEEEEEEEC
Confidence            5677888887  45543  3579999999999998875432      246799999999999985

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=83.54  E-value=2.9  Score=37.02  Aligned_cols=35  Identities=23%  Similarity=0.452  Sum_probs=31.1

Q ss_pred             CCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          234 ERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       234 e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .+=+ +..+|+++|+++..-||+||..|..+|.|-.
T Consensus        31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~   66 (254)
T PRK09464         31 GEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLR   66 (254)
T ss_pred             CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            3455 6899999999999999999999999999864

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=83.54  E-value=3.1  Score=36.92  Aligned_cols=36  Identities=19%  Similarity=0.338  Sum_probs=31.8

Q ss_pred             CCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          233 RERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       233 ~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +.+=+ +..+++++|+++..-||+||..|..+|.|..
T Consensus        29 pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~   65 (257)
T PRK10225         29 PGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEV   65 (257)
T ss_pred             CCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            44567 5889999999999999999999999999964

>TIGR00617 rpa1 replication factor-a protein 1 (rpa1)

Probab=83.47  E-value=4.6  Score=40.90  Aligned_cols=73  Identities=18%  Similarity=0.285  Sum_probs=49.9

Q ss_pred             eEEEEEcCCceEEEEEecccccC----------------hhhh-ccCC----CCCEEEEEEEEeeeCCee--EEEEEEEe
Q 023576           89 VNFTLDDGTGRVVCKRWASEVFD----------------TREM-EAIQ----DGMYVRLIGNLKSFQGKK--QIVAFSVR  145 (280)
Q Consensus        89 ~~~~LdDgTG~I~~~~w~~~~~~----------------~~~~-~~~~----~G~yVrV~G~l~~f~~~~--~i~~~~ir  145 (280)
                      +.+.|.|.||.+.+..|.+....                .... ..|.    .--.+||.-+...|+++.  ..++.++.
T Consensus       512 l~~~i~D~Tg~~~~t~F~~~ae~llG~sA~eL~~l~~~~~~~~~~i~~~~~~~~~~f~~~~k~e~yn~e~r~~~~v~~~~  591 (608)
T TIGR00617       512 LQISISDETGQLWVTAFNDQAEQILGKSAAELGELKEEDPDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVD  591 (608)
T ss_pred             EEEEEEeCCCCEEEEEEhHHHHHHcCCCHHHHHHHHhcCHHHHHHHHHHhhCcEEEEEEEEEEcccCCEeeEEEEEEEee
Confidence            56789999999999999864320                0000 1111    223567777788898774  46777888


Q ss_pred             eCCCchHHHHHHHHHHH
Q 023576          146 PVTNFDEVTCHYIECIY  162 (280)
Q Consensus       146 ~v~d~Nei~~H~Le~i~  162 (280)
                      || |+.+...++|+.|.
T Consensus       592 ~v-d~~~e~~~L~~~i~  607 (608)
T TIGR00617       592 PV-NYRAEAKYLLQEIE  607 (608)
T ss_pred             eC-CHHHHHHHHHHHhc
Confidence            88 57888999998763

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=83.42  E-value=2.4  Score=35.61  Aligned_cols=51  Identities=12%  Similarity=0.208  Sum_probs=43.1

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+..+..||++|.+.     +.-++.++|.++|     +++...|-..|+.|.+.|.|-.-
T Consensus        24 ~T~qR~~IL~~l~~~-----~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~   79 (169)
T PRK11639         24 LTPQRLEVLRLMSLQ-----PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKV   79 (169)
T ss_pred             CCHHHHHHHHHHHhc-----CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEE
Confidence            466788899999873     3578999999988     37899999999999999998653

>TIGR00617 rpa1 replication factor-a protein 1 (rpa1)

Probab=83.33  E-value=6.5  Score=39.84  Aligned_cols=65  Identities=20%  Similarity=0.360  Sum_probs=45.6

Q ss_pred             eEEEEEEEEEeee------c-----CCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeE
Q 023576           72 NVTLVGLVYNKEE------R-----ASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQ  138 (280)
Q Consensus        72 ~V~iVG~V~~~~~------~-----~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~  138 (280)
                      .|.|+|+|.++..      +     .....++|.|.|| .|++.+|.+.+..   . ....+..|.+. .+++.|++ +.
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---F-DVSVQPVIAIKGVRVSDFGG-KS  386 (608)
T ss_pred             CccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhh---c-CCCCCCEEEEEeEEEEecCC-ce
Confidence            5778888877632      1     1357899999999 5999999876421   1 25677888777 56778865 46


Q ss_pred             EEE
Q 023576          139 IVA  141 (280)
Q Consensus       139 i~~  141 (280)
                      |..
T Consensus       387 Ls~  389 (608)
T TIGR00617       387 LST  389 (608)
T ss_pred             Eec
Confidence            653

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=83.17  E-value=4  Score=26.55  Aligned_cols=40  Identities=18%  Similarity=0.334  Sum_probs=31.3

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN  262 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~  262 (280)
                      ++.+..|+.++.        .|++..+|++.++++...|+..+..+..
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        3789999999999999999998887643

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

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=83.14  E-value=2.2  Score=27.43  Aligned_cols=38  Identities=13%  Similarity=0.331  Sum_probs=20.3

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA  258 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~  258 (280)
                      |+.-++..+..+.+       .|.++.+||+.|+.+.+.|...|.
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            45555555555543       499999999999999999988764

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=83.03  E-value=2.7  Score=44.21  Aligned_cols=42  Identities=17%  Similarity=0.188  Sum_probs=35.9

Q ss_pred             CCccCHHHHHHHh------------CCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576          234 ERGVHVNELSEQL------------KIPQKKIMDSIASLENEGLIYSTIDEFHYK  276 (280)
Q Consensus       234 e~Gv~v~~I~~~l------------~~~~~~v~~al~~L~~eG~IYsTiDd~hfk  276 (280)
                      ..++++++|.+.+            ++++++++++|+.|..+|.||.+-+. +||
T Consensus       857 ~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~~~l~~L~~~g~i~~~~~g-~y~  910 (915)
T PTZ00111        857 NKSLDLNEVLSLCHKTFKDNRDHKDGEIYKLISEVLNKMVQEGTAVRENNS-YYL  910 (915)
T ss_pred             CCceeHHHHHHHHHhhccccchhccCCCHHHHHHHHHHHHhCCeEeeeCCC-chh
Confidence            3589999998664            59999999999999999999998555 776

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=82.79  E-value=2.3  Score=38.37  Aligned_cols=49  Identities=27%  Similarity=0.477  Sum_probs=44.1

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCc-cCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERG-VHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~G-v~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      ..|++-.+.|+++|++.+      | +...||.+.+++|...|-.+|..|...|.|
T Consensus       191 ~~L~~~e~~il~~i~~~G------Gri~Q~eL~r~lglsktTvsR~L~~LEk~GlI  240 (258)
T COG2512         191 YDLNEDEKEILDLIRERG------GRITQAELRRALGLSKTTVSRILRRLEKRGLI  240 (258)
T ss_pred             CCCCHHHHHHHHHHHHhC------CEEeHHHHHHhhCCChHHHHHHHHHHHhCCce
Confidence            367888899999999853      5 789999999999999999999999999987

>COG4742 Predicted transcriptional regulator [Transcription]

Probab=82.75  E-value=2.8  Score=37.73  Aligned_cols=57  Identities=19%  Similarity=0.385  Sum_probs=50.2

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      +++.++.||-+|++.       -.+++||...++.+...|.-.|..|.+.|.|-..  ++.|+.|+
T Consensus        11 ~SekRk~lLllL~eg-------Pkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~~--~~~Y~LS~   67 (260)
T COG4742          11 LSEKRKDLLLLLKEG-------PKTIEEIKNELNVSSSAILPQIKKLKDKGLVVQE--GDRYSLSS   67 (260)
T ss_pred             ccHHHHHHHHHHHhC-------CCCHHHHHHHhCCCcHHHHHHHHHHhhCCCEEec--CCEEEecc
Confidence            467888999999873       3589999999999999999999999999999995  77998875

>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=82.29  E-value=2  Score=29.39  Aligned_cols=37  Identities=24%  Similarity=0.365  Sum_probs=31.8

Q ss_pred             CCCccCHHHHHHHh---CCCHHHHHHHHHHHHhCCeeeec
Q 023576          233 RERGVHVNELSEQL---KIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       233 ~e~Gv~v~~I~~~l---~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      ...|++.+++.+++   +++...+...|+.|+.+|.|-.+
T Consensus        14 lr~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~~   53 (59)
T PF09106_consen   14 LRPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKVE   53 (59)
T ss_dssp             TSS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEEE
T ss_pred             CccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeeeE
Confidence            56799999999998   68999999999999999999875

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.

>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=82.18  E-value=2.6  Score=35.18  Aligned_cols=45  Identities=22%  Similarity=0.493  Sum_probs=39.1

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhC--CCHHHHHHHHHHHHhCCeee
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLK--IPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~--~~~~~v~~al~~L~~eG~IY  267 (280)
                      ...|+++|+..     ..-.++.+|...|+  ++-..|.++|+.|..+|.|-
T Consensus         3 e~~Il~y~~~q-----NRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~   49 (169)
T PF07106_consen    3 EDAILEYMKEQ-----NRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIV   49 (169)
T ss_pred             HHHHHHHHHHc-----CCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCee
Confidence            45799999974     35789999999994  99999999999999999863

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 [].

>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold []

Probab=82.10  E-value=5.6  Score=31.88  Aligned_cols=87  Identities=13%  Similarity=0.204  Sum_probs=42.2

Q ss_pred             eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecC-CeeEEEEEcCCc--eEEEEEecccccChhhhccCCC
Q 023576           44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERA-SDVNFTLDDGTG--RVVCKRWASEVFDTREMEAIQD  120 (280)
Q Consensus        44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~-t~~~~~LdDgTG--~I~~~~w~~~~~~~~~~~~~~~  120 (280)
                      .++..+|.+.....+....=.+.|   ..|.|-|.|.++.... .+......+..+  .|.|.+-.+.. .......++.
T Consensus        44 ~~sa~~L~~~y~~N~~~A~~kY~g---K~i~vtG~V~~I~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~-~~~~~~~l~~  119 (144)
T PF12869_consen   44 SVSAEELYKDYKDNEVAADKKYKG---KIIEVTGTVSSIDKGFGDNYVVLLGTENGFAGVQCYFSNDQE-KRASVAKLKK  119 (144)
T ss_dssp             EEEHHHHHHHHHH-HHHHHHHHTT----EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGG-GHHHHHH--T
T ss_pred             eecHHHHHHHHHhCHHHHHhhcCC---CEEEEEEEEEEEEEcCCCcEEEEccCCCCceeEEEEEccchh-hhhhHhcCCC
Confidence            899999988764431111122344   4567789999987633 333223333233  35544433331 1112345999


Q ss_pred             CCEEEEEEEEeeeC
Q 023576          121 GMYVRLIGNLKSFQ  134 (280)
Q Consensus       121 G~yVrV~G~l~~f~  134 (280)
                      |+.|.|.|++..|.
T Consensus       120 G~~Vti~G~~~g~~  133 (144)
T PF12869_consen  120 GQKVTIKGICTGYS  133 (144)
T ss_dssp             TSEEEEEEE-----
T ss_pred             CCEEEEEEEEEeee
Confidence            99999999999985

; PDB: 3F1Z_I.

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=82.09  E-value=4  Score=36.13  Aligned_cols=36  Identities=14%  Similarity=0.219  Sum_probs=31.4

Q ss_pred             CCCccC-HHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          233 RERGVH-VNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       233 ~e~Gv~-v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +..=++ ..+|+++|+++..-||+||..|..+|.|-.
T Consensus        28 pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~   64 (253)
T PRK11523         28 VGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEV   64 (253)
T ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            445664 789999999999999999999999999964

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=82.07  E-value=3.7  Score=32.47  Aligned_cols=49  Identities=24%  Similarity=0.316  Sum_probs=41.8

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+...+||.+|...      ..+++.+|++.++++.+.|..-|..|.+-|.|-..
T Consensus        15 dptRl~IL~~L~~~------~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~   63 (117)
T PRK10141         15 DETRLGIVLLLRES------GELCVCDLCTALDQSQPKISRHLALLRESGLLLDR   63 (117)
T ss_pred             CHHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence            45777899998742      25899999999999999999999999999999544

>PRK04036 DNA polymerase II small subunit; Validated

Probab=81.91  E-value=5.4  Score=39.42  Aligned_cols=61  Identities=16%  Similarity=0.218  Sum_probs=42.8

Q ss_pred             eeEEEEEEEEEeeec-CCeeEEEEEcCCceEEEEEecccccCh-hhhccCCCCCEEEEEEEEee
Q 023576           71 TNVTLVGLVYNKEER-ASDVNFTLDDGTGRVVCKRWASEVFDT-REMEAIQDGMYVRLIGNLKS  132 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~-~t~~~~~LdDgTG~I~~~~w~~~~~~~-~~~~~~~~G~yVrV~G~l~~  132 (280)
                      ..|.|||.|.++... .....+.|+|.||+|.+..-.+.. +- .....+..|..|-|.|++..
T Consensus       154 ~~~~viG~v~~~~~~~~g~~~~~LED~sgrv~l~~~~~~~-~~~~~~~~lvtg~vv~v~G~~~~  216 (504)
T PRK04036        154 EEVSIIGMVSDIRSTKNGHKIVELEDTTGTFPVLIMKDRE-DLAELADELLLDEVIGVEGTLSG  216 (504)
T ss_pred             ceEEEEEEEEEeecccCCceEEEEECCCCeEEEEeecchh-hhhhhhhcccCceEEEEEEEEcC
Confidence            458999999887543 334578999999999987632210 11 11346889999999998753

>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=81.90  E-value=1.8  Score=40.40  Aligned_cols=53  Identities=21%  Similarity=0.496  Sum_probs=44.5

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .+|++-++.||.+|++.    ...||-..+|.++.+++...|.++|..|.+.++|=+
T Consensus        80 ~~l~~~e~lvy~~I~~a----g~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~  132 (327)
T PF05158_consen   80 KGLSDEERLVYQLIEEA----GNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKS  132 (327)
T ss_dssp             -SSSCCHHHHHHHHHHH----TTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEE
T ss_pred             cCCCHHHHHHHHHHHHh----CCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE
Confidence            46788889999999985    467999999999999999999999999999998865

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.

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=81.88  E-value=4.1  Score=32.69  Aligned_cols=47  Identities=21%  Similarity=0.231  Sum_probs=37.4

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .++-+|....   .+.-++.++|++++++|..-+++.|..|...|.|-++
T Consensus        12 ~~l~~La~~~---~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~   58 (135)
T TIGR02010        12 TAMLDLALNA---ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSV   58 (135)
T ss_pred             HHHHHHHhCC---CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence            3455554321   2346899999999999999999999999999999774

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=81.83  E-value=3.2  Score=30.24  Aligned_cols=55  Identities=27%  Similarity=0.289  Sum_probs=43.1

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH-HHHhCCeeeec
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA-SLENEGLIYST  269 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~-~L~~eG~IYsT  269 (280)
                      .+|..+++++|++|.+.-   ...-|.++-||..++.+.+.|++.++ +|+..|.|--|
T Consensus         4 ~GLd~~D~~yL~~l~~~f---~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT   59 (76)
T PF05491_consen    4 LGLDELDRRYLKTLIENF---KGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRT   59 (76)
T ss_dssp             TS-BHHHHHHHHHHHHCS---TTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEE
T ss_pred             ccCCHHHHHHHHHHHHHc---CCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhC
Confidence            468899999999998752   23457899999999999999998887 89999998766

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=81.82  E-value=3  Score=34.64  Aligned_cols=42  Identities=21%  Similarity=0.249  Sum_probs=35.5

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      -.|++.|-..      .-++.++||..|+++..+||.+|..|.+.|.|
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.

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=81.80  E-value=7.3  Score=28.57  Aligned_cols=57  Identities=25%  Similarity=0.289  Sum_probs=43.4

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      ....++.++...    ...-+|=++|++.|+++...|.+.++.|-++|.=-.+.-..-|+.
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            445566666553    345789999999999999999999999999998666555545553

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=81.76  E-value=4.4  Score=36.81  Aligned_cols=43  Identities=26%  Similarity=0.284  Sum_probs=36.0

Q ss_pred             cc-CHHHHHHHhC--CCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          236 GV-HVNELSEQLK--IPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       236 Gv-~v~~I~~~l~--~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      |- ...+|+++|+  ++.++|+++|++|..-|.|=-.- +-.|+.|+
T Consensus       136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~-~g~y~~t~  181 (271)
T TIGR02147       136 FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE-DGFYKQTD  181 (271)
T ss_pred             CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC-CCcEEeec
Confidence            44 7889999996  99999999999999999998753 33677765

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.

>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins

Probab=81.53  E-value=3  Score=28.27  Aligned_cols=33  Identities=27%  Similarity=0.393  Sum_probs=23.7

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhC-CCHHHHHHHHHH
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLK-IPQKKIMDSIAS  259 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~-~~~~~v~~al~~  259 (280)
                      ..|++.++        .|.+.++|++.+. ++.++|+.||.+
T Consensus        22 ~~i~~~~~--------~G~s~eeI~~~yp~Lt~~~i~aAl~y   55 (56)
T PF04255_consen   22 RDILDLLA--------AGESPEEIAEDYPSLTLEDIRAALAY   55 (56)
T ss_dssp             HHHHHHHH--------TT--HHHHHHHSTT--HHHHHHHHHH
T ss_pred             HHHHHHHH--------cCCCHHHHHHHCCCCCHHHHHHHHHh
Confidence            34667663        3899999999996 999999999986

; PDB: 2GA1_B.

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=81.27  E-value=3.7  Score=36.35  Aligned_cols=36  Identities=22%  Similarity=0.387  Sum_probs=31.6

Q ss_pred             CCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          233 RERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       233 ~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +..=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus        22 pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~   58 (253)
T PRK10421         22 AGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLS   58 (253)
T ss_pred             CCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            34456 5889999999999999999999999999964

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=81.20  E-value=4.2  Score=35.49  Aligned_cols=36  Identities=17%  Similarity=0.267  Sum_probs=32.1

Q ss_pred             CCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          233 RERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       233 ~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +..=+ +..+|+++|+++..-||+||..|..+|.|..
T Consensus        26 pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~   62 (235)
T TIGR02812        26 PGSILPAERELSELIGVTRTTLREVLQRLARDGWLTI   62 (235)
T ss_pred             CCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            34457 6899999999999999999999999999975

Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=81.08  E-value=4.6  Score=36.52  Aligned_cols=61  Identities=21%  Similarity=0.264  Sum_probs=48.6

Q ss_pred             CCchhHHHHHHhcCCCCC-CCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576          214 LKDCDQMILDYLQQPSSS-ERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK  276 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~-~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk  276 (280)
                      +.+.-+.||.+|++.... .-..=-+-++|-+.|+++-.+.+.||-.|.-.|.||.  |-+.|+
T Consensus       223 l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q--~g~~t~  284 (287)
T COG2996         223 LDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQ--DGDGTE  284 (287)
T ss_pred             hhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEE--cCceEE
Confidence            566778999999886422 1123347899999999999999999999999999999  555554

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=81.07  E-value=3.8  Score=36.43  Aligned_cols=57  Identities=23%  Similarity=0.318  Sum_probs=44.2

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      ..-+||..|...     ..-++..||++.++++...|-+-+.+|++||+|=+ ----||+.|.
T Consensus        11 t~fqIL~ei~~~-----qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~-~gR~~Y~iTk   67 (260)
T COG1497          11 TRFQILSEIAVR-----QPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK-EGRGEYEITK   67 (260)
T ss_pred             hHHHHHHHHHHh-----CCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee-cCCeeEEEeh
Confidence            345677766542     12578999999999999999999999999999987 3334777764

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=80.86  E-value=4.9  Score=30.46  Aligned_cols=55  Identities=27%  Similarity=0.366  Sum_probs=45.5

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcc
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFH  274 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~h  274 (280)
                      ++..+-.||.+|...+      +++..+|++.++++...|...|+.|...|+|....|.+-
T Consensus        20 lt~~q~~~L~~l~~~~------~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~D   74 (126)
T COG1846          20 LTPPQYQVLLALYEAG------GITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPED   74 (126)
T ss_pred             CCHHHHHHHHHHHHhC------CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccc
Confidence            6677888888887642      322299999999999999999999999999999888643

>PRK15481 transcriptional regulatory protein PtsJ; Provisional

Probab=80.73  E-value=3.9  Score=39.10  Aligned_cols=34  Identities=24%  Similarity=0.368  Sum_probs=31.0

Q ss_pred             Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .=+ ++.+++++|+.+...|++|++.|..||.|+.
T Consensus        27 ~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~   61 (431)
T PRK15481         27 DSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQS   61 (431)
T ss_pred             CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            345 6899999999999999999999999999985

>PHA00738 putative HTH transcription regulator

Probab=80.67  E-value=4.5  Score=31.47  Aligned_cols=49  Identities=16%  Similarity=0.217  Sum_probs=42.9

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+.+++||++|...      ..+.+.+|+..++++-+.|-.-|.-|.+-|.|-+.
T Consensus        11 dptRr~IL~lL~~~------e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~sr   59 (108)
T PHA00738         11 KILRRKILELIAEN------YILSASLISHTLLLSYTTVLRHLKILNEQGYIELY   59 (108)
T ss_pred             CHHHHHHHHHHHHc------CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEE
Confidence            56889999999762      25899999999999999999999999999988554

>PRK11050 manganese transport regulator MntR; Provisional

Probab=80.52  E-value=4.2  Score=33.40  Aligned_cols=35  Identities=14%  Similarity=0.306  Sum_probs=32.6

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+++..+|++.++++...|..+|..|...|.|...
T Consensus        50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~   84 (152)
T PRK11050         50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR   84 (152)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            47899999999999999999999999999999864

>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO

Probab=80.07  E-value=5.6  Score=30.50  Aligned_cols=56  Identities=13%  Similarity=0.243  Sum_probs=42.7

Q ss_pred             CCCchhHHHHH-HhcCC-CCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          213 GLKDCDQMILD-YLQQP-SSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       213 ~l~~~~~~Vl~-~i~~~-~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +++.-+-+|+. ++|.. +......-|+..+|+...+++.+.|.+++.+|++.|.|..
T Consensus        29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~   86 (100)
T PF04492_consen   29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIR   86 (100)
T ss_pred             cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            45666655544 45543 2334556899999999999999999999999999999954

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	280
2pi2_A	270	Full-Length Replication Protein A Subunits Rpa14 An		2e-22
4gop_B	136	Structure And Conformational Change Of A Replicatio		4e-18
2pqa_A	131	Crystal Structure Of Full-Length Human Rpa 1432 HET		6e-14
1quq_A	129	Complex Of Replication Protein A Subunits Rpa14 And		9e-14
1l1o_B	128	Structure Of The Human Replication Protein A (Rpa)		1e-13
3kdf_D	132	X-Ray Crystal Structure Of The Human Replication Pr		2e-13

>pdb|2PI2|A Chain A, Full-Length Replication Protein A Subunits Rpa14 And Rpa32 Length = 270

Iteration: 1
 Score =  103 bits (256), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 131/269 (48%), Gaps = 32/269 (11%)
Query: 14  SGGGFMPSQPPQSADYPSSTARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNV 73
           S GGF    P Q+       +R+R +Q +VP T+  +  A+   +    F I  +EI+ V
Sbjct: 23  SPGGFGSPAPSQA----EKKSRAR-AQHIVPCTISQLLSATLVDEV---FRIGNVEISQV 74
Query: 74  TLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKS 132
           T+VG++ + E+  +++ + +DD T   +  ++W      + E   +    YV++ G+L+S
Sbjct: 75  TIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRS 134
Query: 133 FQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQG----FPSSQPQMVDSSLN 188
           FQ KK +VAF + P+ + +E T H +E I  H+  SK+  Q      P S P M ++   
Sbjct: 135 FQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAG-- 192
Query: 189 TSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK- 247
                   G    P N        GL      +L+ ++   +  R  G++  +L  QLK 
Sbjct: 193 -----NFGGNSFMPAN--------GLTVAQNQVLNLIK---ACPRPEGLNFQDLKNQLKH 236
Query: 248 IPQKKIMDSIASLENEGLIYSTIDEFHYK 276
           +    I  ++  L NEG IYST+D+ H+K
Sbjct: 237 MSVSSIKQAVDFLSNEGHIYSTVDDDHFK 265

>pdb|4GOP|B Chain B, Structure And Conformational Change Of A Replication Protein A Heterotrimer Bound To Ssdna Length = 136

Iteration: 1
 Score = 88.2 bits (217), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 44/129 (34%), Positives = 82/129 (63%), Gaps = 2/129 (1%)
Query: 42  LVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVV 101
           L PVT++ I  A     D + F+++G E+  +T V +V N    A++V ++++DGTG++ 
Sbjct: 9   LRPVTIRQILNAEQPHPD-AEFILDGAELGQLTFVAVVRNISRNATNVAYSVEDGTGQIE 67
Query: 102 CKRW-ASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIEC 160
            ++W  S   D+ +   I++ +YVR++G LKSFQ ++ I +  +RPV +++EV  H +E 
Sbjct: 68  VRQWLDSSSDDSSKASEIRNNVYVRVLGTLKSFQNRRSISSGHMRPVIDYNEVMFHRLEA 127
Query: 161 IYFHLQNSK 169
           ++ HLQ ++
Sbjct: 128 VHAHLQVTR 136

>pdb|2PQA|A Chain A, Crystal Structure Of Full-Length Human Rpa 1432 HETERODIMER Length = 131

Iteration: 1
 Score = 74.7 bits (182), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 75/133 (56%), Gaps = 4/133 (3%)
Query: 39  SQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTG 98
           +Q +VP T+  +  A+   +    F I  +EI+ VT+VG++ + E+  +++ + +DD T 
Sbjct: 2   AQHIVPCTISQLLSATLVDE---VFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTA 58
Query: 99  RVV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHY 157
             +  ++W      + E   +    YV++ G+L+SFQ KK +VAF + P+ + +E T H 
Sbjct: 59  APMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHI 118
Query: 158 IECIYFHLQNSKS 170
           +E I  H+  SK+
Sbjct: 119 LEVINAHMVLSKA 131

>pdb|1QUQ|A Chain A, Complex Of Replication Protein A Subunits Rpa14 And Rpa32 Length = 129

Iteration: 1
 Score = 73.9 bits (180), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 40/132 (30%), Positives = 74/132 (56%), Gaps = 4/132 (3%)
Query: 39  SQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTG 98
           +Q +VP T+  +  A+   +    F I  +EI+ VT+VG++ + E+  +++ + +DD T 
Sbjct: 1   AQHIVPCTISQLLSATLVDE---VFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTA 57
Query: 99  RVV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHY 157
             +  ++W      + E   +    YV++ G+L+SFQ KK +VAF + P+ + +E T H 
Sbjct: 58  APMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHI 117
Query: 158 IECIYFHLQNSK 169
           +E I  H+  SK
Sbjct: 118 LEVINAHMVLSK 129

>pdb|1L1O|B Chain B, Structure Of The Human Replication Protein A (Rpa) Trimerization Core Length = 128

Iteration: 1
 Score = 73.2 bits (178), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 73/131 (55%), Gaps = 4/131 (3%)
Query: 40  QGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGR 99
           Q +VP T+  +  A+   +    F I  +EI+ VT+VG++ + E+  +++ + +DD T  
Sbjct: 1   QHIVPCTISQLLSATLVDE---VFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAA 57
Query: 100 VV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYI 158
            +  ++W      + E   +    YV++ G+L+SFQ KK +VAF + P+ + +E T H +
Sbjct: 58  PMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHIL 117
Query: 159 ECIYFHLQNSK 169
           E I  H+  SK
Sbjct: 118 EVINAHMVLSK 128

>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 = 72.4 bits (176), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 73/133 (54%), Gaps = 4/133 (3%)
Query: 39  SQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTG 98
           +Q +VP T+  +  A+   +    F I  +EI+ VT+VG++ + E+  +++ + +DD T 
Sbjct: 3   AQHIVPCTISQLLSATLVDE---VFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDXTA 59
Query: 99  RVV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHY 157
                ++W      + E   +    YV++ G+L+SFQ KK +VAF + P+ + +E T H 
Sbjct: 60  APXDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIXPLEDXNEFTTHI 119
Query: 158 IECIYFHLQNSKS 170
           +E I  H   SK+
Sbjct: 120 LEVINAHXVLSKA 132

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	280
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	1e-63
3kdf_D	132	Replication protein A 32 kDa subunit; wheat GERM c	2e-50
3kf6_A	159	Protein STN1; OB fold, chromosomal protein, DNA-bi	1e-15
3f2b_A	1041	DNA-directed DNA polymerase III alpha chain; DNA p	1e-04

>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 =  200 bits (508), Expect = 1e-63
 Identities = 73/282 (25%), Positives = 131/282 (46%), Gaps = 23/282 (8%)

Query: 1   MFSSS--QFDASNAFSGGGFMPSQPPQSADYPSSTARSRDS--QGLVPVTVKMISEASHS 56
           M++S    + +S+    GG+  S     +  PS   +   +  Q +VP T+  +  A+  
Sbjct: 1   MWNSGFESYGSSSYGGAGGYTQSPGGFGSPAPSQAEKKSRARAQHIVPCTISQLLSATLV 60

Query: 57  GDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVV-CKRWASEVFDTREM 115
            +    F I  +EI+ VT+VG++ + E+  +++ + +DD T   +  ++W      + E 
Sbjct: 61  DEV---FRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSEN 117

Query: 116 EAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKSQVQGF 175
             +    YV++ G+L+SFQ KK +VAF + P+ + +E T H +E I  H+  SK+  Q  
Sbjct: 118 TVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPS 177

Query: 176 PSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERER 235
               P             G           +S    +GL      +L+ ++     E   
Sbjct: 178 AGRAPISNPGMSEAGNFGG-----------NSFMPANGLTVAQNQVLNLIKACPRPE--- 223

Query: 236 GVHVNELSEQLK-IPQKKIMDSIASLENEGLIYSTIDEFHYK 276
           G++  +L  QLK +    I  ++  L NEG IYST+D+ H+K
Sbjct: 224 GLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFK 265

>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 =  161 bits (409), Expect = 2e-50
 Identities = 40/133 (30%), Positives = 75/133 (56%), Gaps = 4/133 (3%)

Query: 39  SQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTG 98
           +Q +VP T+  +  A+   +    F I  +EI+ VT+VG++ + E+  +++ + +DD T 
Sbjct: 3   AQHIVPCTISQLLSATLVDEV---FRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTA 59

Query: 99  RVV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHY 157
             +  ++W      + E   +    YV++ G+L+SFQ KK +VAF + P+ + +E T H 
Sbjct: 60  APMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHI 119

Query: 158 IECIYFHLQNSKS 170
           +E I  H+  SK+
Sbjct: 120 LEVINAHMVLSKA 132

>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe} Length = 159

 Score = 71.9 bits (176), Expect = 1e-15
 Identities = 19/127 (14%), Positives = 52/127 (40%), Gaps = 3/127 (2%)

Query: 43  VPVTVKMISE-ASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVV 101
            P+ +  + + + H    +      G  I  + +VG +   +        T+DD +G V+
Sbjct: 19  NPMFISDVHKISFHPHLQRYIGFWMGFPIRWIQIVGYIAAIDIYEGKHVLTVDDCSGMVL 78

Query: 102 -CKRWASEVFD-TREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIE 159
                  + F  ++   ++  G  V + G + SF+ + +++A S   + + ++    + +
Sbjct: 79  RVVFIIQDDFSMSKRAISMSPGNVVCVFGKINSFRSEVELIAQSFEELRDPNDEWKAWQK 138

Query: 160 CIYFHLQ 166
            + +   
Sbjct: 139 RMRYKKN 145

>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* Length = 1041

 Score = 42.3 bits (100), Expect = 1e-04
 Identities = 15/79 (18%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 69  EITNVTLVGLVYNKEERASD-----VNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMY 123
           E   V + G V++ E          +   + D T  ++ K ++ +  D   M  ++ GM+
Sbjct: 16  EERRVVVQGYVFDAEVSELKSGRTLLTMKITDYTNSILVKMFSRDKEDAELMSGVKKGMW 75

Query: 124 VRLIGNLKSFQGKKQIVAF 142
           V++ G++++    + +V  
Sbjct: 76  VKVRGSVQNDTFVRDLVII 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	280
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	99.91
3kf8_A	220	Protein STN1; OB fold; 2.40A {Candida tropicalis m	99.37
3mxn_B	150	RECQ-mediated genome instability protein 2; bloom	99.02
2k50_A	115	Replication factor A related protein; uncharacteri	98.71
1o7i_A	119	SSB, SSO2364, single stranded DNA binding protein;	98.67
2kbn_A	109	Conserved protein; nucleic acid binding protein, b	98.66
2k75_A	106	Uncharacterized protein TA0387; closed beta barrel	98.65
3e0e_A	97	Replication protein A; structural genomics, PSI-2,	98.34
3dm3_A	105	Replication factor A; probably plays AN essential	98.02
1nnx_A	109	Protein YGIW; structural genomics, hypothetical pr	97.81
1wjj_A	145	Hypothetical protein F20O9.120; DNA-binding protei	97.46
3au7_A	402	TIAS, putative uncharacterized protein; ATP hydrol	97.28
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.1
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	97.03
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.0
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	96.99
3f2b_A	1041	DNA-directed DNA polymerase III alpha chain; DNA p	96.74
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.68
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.49
1wyd_A	429	Hypothetical aspartyl-tRNA synthetase; archaea, LI	96.47
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	96.37
3m4p_A	456	Ehasnrs, asparaginyl-tRNA synthetase, putative; am	96.35
1l0w_A	580	Aspartyl-tRNA synthetase; space-grown crystal, dim	96.28
1e1o_A	504	Lysyl-tRNA synthetase, heat inducible; ligase, ami	96.25
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.23
3nem_A	438	Aspartyl-tRNA synthetase; rossmann fold, OB fold,	96.22
1c0a_A	585	Aspartyl tRNA synthetase; protein-RNA complex, lig	96.2
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.17
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	96.17
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	96.16
1eov_A	487	ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy	96.12
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	96.09
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	96.04
4ex5_A	529	Lysine--tRNA ligase; structural genomics, niaid, n	95.99
1n9w_A	422	Aspartyl-tRNA synthetase 2; biosynthetic protein;	95.91
1x54_A	434	Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthe	95.9
3a74_A	493	Lysyl-tRNA synthetase; aminoacyl tRNA synthetase,	95.78
2xgt_A	435	Asparaginyl-tRNA synthetase, cytoplasmic; ligase,	95.77
1qzg_A	187	Protection of telomeres protein 1; protrein-DNA co	95.76
3i7f_A	548	Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-bi	95.61
3bju_A	521	Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase,	95.52
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	95.5
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	95.48
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	95.26
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	95.21
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	95.04
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	95.03
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	94.93
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	94.93
3r0a_A	123	Putative transcriptional regulator; structural gen	94.91
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	94.87
4gs3_A	107	Single-stranded DNA-binding protein; primosome, ol	94.86
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	94.8
1l1o_C	181	Replication protein A 70 kDa DNA-binding subunit;	94.79
1sfx_A	109	Conserved hypothetical protein AF2008; structural	94.78
1y0u_A	96	Arsenical resistance operon repressor, putative; s	94.77
2w25_A	150	Probable transcriptional regulatory protein; trans	94.71
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	94.69
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	94.53
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	94.5
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	94.47
2hpi_A	1220	DNA polymerase III alpha subunit; POL-beta-like nu	94.44
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	94.33
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	94.32
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	94.31
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	94.25
1txy_A	104	Primosomal replication protein N; OB fold, dimer,	94.17
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	94.11
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	94.09
2dk8_A	81	DNA-directed RNA polymerase III 39 kDa polypeptide	93.99
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	93.98
4dka_C	105	RNA-editing complex protein MP81; krepa1, VHH, sin	93.91
2kko_A	108	Possible transcriptional regulatory protein (possi	93.74
1p6r_A	82	Penicillinase repressor; transcription regulation,	93.74
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	93.68
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	93.54
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	93.51
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	93.5
3by6_A	126	Predicted transcriptional regulator; structural ge	93.42
3kdf_A	121	Replication protein A 14 kDa subunit; wheat GERM c	93.37
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	93.34
1xjv_A	294	Protection of telomeres 1; protein-DNA complex, si	93.33
1ynx_A	114	Replication factor-A protein 1; canonical OB fold,	93.27
3koj_A	108	Uncharacterized protein YCF41; single-strand bindi	93.25
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	93.25
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	93.22
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	93.22
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	93.18
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	93.15
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	93.12
2gxg_A	146	146AA long hypothetical transcriptional regulator;	93.11
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	93.06
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	93.03
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	93.01
4gop_A	114	Putative uncharacterized protein; OB fold, ssDNA b	92.96
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	92.92
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	92.91
2nnn_A	140	Probable transcriptional regulator; structural gen	92.88
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	92.83
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	92.81
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	92.79
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	92.75
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	92.75
3s2w_A	159	Transcriptional regulator, MARR family; structural	92.7
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	92.68
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	92.63
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	92.63
2vn2_A	128	DNAD, chromosome replication initiation protein; D	92.62
1ku9_A	152	Hypothetical protein MJ223; putative transcription	92.55
4ah6_A	617	Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo	92.54
2pex_A	153	Transcriptional regulator OHRR; transcription regu	92.47
2pi2_E	142	Replication protein A 14 kDa subunit; FULL-length	92.46
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	92.36
3jth_A	98	Transcription activator HLYU; transcription factor	92.32
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	92.29
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	92.28
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	92.12
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	92.11
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	92.09
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	92.06
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	92.05
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	92.03
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	92.01
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	92.0
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	91.99
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	91.98
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	91.98
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	91.84
3fhw_A	115	Primosomal replication protein N; PRIB BPR162 X-RA	91.79
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	91.69
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	91.61
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	91.6
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	91.59
3f3x_A	144	Transcriptional regulator, MARR family, putative;	91.55
1ucr_A	78	Protein DSVD; dissimilatory sulfite reductase D, D	91.53
2eth_A	154	Transcriptional regulator, putative, MAR family; M	91.5
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	91.5
1mkm_A	249	ICLR transcriptional regulator; structural genomic	91.49
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	91.42
3tqy_A	158	Single-stranded DNA-binding protein; DNA replicati	91.28
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	91.21
3nqo_A	189	MARR-family transcriptional regulator; structural	91.19
3bja_A	139	Transcriptional regulator, MARR family, putative;	91.16
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	91.1
2vw9_A	134	Single-stranded DNA binding protein; DNA replicati	91.1
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	91.0
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	90.98
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	90.96
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	90.92
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	90.9
3eiv_A	199	Single-stranded DNA-binding protein 2; DNA damage,	90.84
3vdy_A	116	SSB, single-stranded DNA-binding protein SSBB; OB	90.84
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	90.74
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	90.72
4gop_C	444	Putative uncharacterized protein; OB fold, ssDNA b	90.7
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	90.58
3k8a_A	103	Putative primosomal replication protein; beta-barr	90.57
1z9f_A	153	Single-strand binding protein; TM0604, single stra	90.56
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	90.55
1qvc_A	145	Single stranded DNA binding protein monomer; beta-	90.55
4fx0_A	148	Probable transcriptional repressor protein; helix-	90.44
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	90.41
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	90.31
1z91_A	147	Organic hydroperoxide resistance transcriptional;	90.3
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	90.13
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	90.04
1sr3_A	136	APO-CCME; OB fold, beta barrel, flexible C-termina	89.89
1se8_A	301	Single-strand binding protein; DNA binding protein	89.84
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	89.82
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	89.76
1v1q_A	134	Primosomal replication protein N; primosome, DNA r	89.73
1bia_A	321	BIRA bifunctional protein; transcription regulatio	89.61
2g7u_A	257	Transcriptional regulator; ICLR family, structural	89.58
1okr_A	123	MECI, methicillin resistance regulatory protein ME	89.56
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	89.53
3en2_A	101	Probable primosomal replication protein N; PRIB RS	89.4
2w57_A	150	Ferric uptake regulation protein; gene regulation,	89.37
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	89.3
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	89.26
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	89.14
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	89.09
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	89.09
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	88.98
3stb_C	148	RNA-editing complex protein MP42; editosome, nanob	88.97
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	88.95
2fxa_A	207	Protease production regulatory protein HPR; protea	88.95
3rn5_A	208	Interferon-inducible protein AIM2; OB fold, DNA bi	88.78
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	88.65
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	88.63
1z05_A	429	Transcriptional regulator, ROK family; structural	88.57
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	88.56
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	88.55
2l02_A	82	Uncharacterized protein; structural genomics, nort	88.55
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	88.5
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	88.44
1jmc_A	246	Protein (replication protein A (RPA)); human ssDNA	88.43
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	88.34
3afp_A	168	Single-stranded DNA-binding protein; OB-fold, quat	88.3
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	88.23
2kct_A	94	Cytochrome C-type biogenesis protein CCME; solutio	88.2
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	88.17
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	88.13
2l01_A	77	Uncharacterized protein; structural genomics, nort	88.05
3eet_A	272	Putative GNTR-family transcriptional regulator; st	87.92
2pg4_A	95	Uncharacterized protein; structural genomics, join	87.9
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	87.89
1se8_A	301	Single-strand binding protein; DNA binding protein	87.83
1j6q_A	136	Cytochrome C maturation protein E; all-beta protei	87.8
2obp_A	96	Putative DNA-binding protein; structural genomics,	87.75
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	87.73
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	87.68
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	87.57
1jmc_A	246	Protein (replication protein A (RPA)); human ssDNA	87.53
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	87.35
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	87.27
2fxq_A	264	Single-strand binding protein; strand beta-sheet e	87.19
4dam_A	128	Single-stranded DNA-binding protein 1; OB-fold; 1.	87.17
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	87.05
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	86.98
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	86.56
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	86.24
3ulp_A	124	Single-strand binding protein; OB-fold, DNA bindin	86.21
2h09_A	155	Transcriptional regulator MNTR; transcription regu	86.19
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	86.12
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	85.87
3k7u_C	148	MP18 RNA editing complex protein; OB-fold, RNA-edi	85.84
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	85.8
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	85.66
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	85.65
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	85.58
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	85.4
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	85.39
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	85.38
3c7j_A	237	Transcriptional regulator, GNTR family; structural	85.04
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	84.97
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	84.9
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	84.86
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	84.82
3lgj_A	169	Single-stranded DNA-binding protein; niaid, CAT sc	84.82
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	84.74
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	84.7
3c57_A	95	Two component transcriptional regulatory protein;	84.69
3ull_A	132	DNA binding protein; DNA replication, mitochondrio	84.68
1hsj_A	487	Fusion protein consisting of staphylococcus access	84.61
4ets_A	162	Ferric uptake regulation protein; metal binding pr	84.53
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	84.39
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	84.31
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	84.19
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	83.96
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	83.76
1yyv_A	131	Putative transcriptional regulator; reductive meth	83.59
3pgz_A	193	Single-stranded DNA-binding protein; ssgcid, singl	83.55
1ylf_A	149	RRF2 family protein; structural genomics, transcri	83.55
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	83.52
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	83.36
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	83.19
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	83.15
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	82.7
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	82.61
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	82.46
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	82.34
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	82.34
4hik_A	143	Protection of telomeres protein 1; specificity, pl	82.14
1eqq_A	178	Single stranded DNA binding protein; beta barrel,	81.99
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	81.98
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	81.92
2fxq_A	264	Single-strand binding protein; strand beta-sheet e	81.71
3df8_A	111	Possible HXLR family transcriptional factor; APC89	81.69
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	81.65
3k69_A	162	Putative transcription regulator; putative transcr	81.59
3rlo_A	204	Gamma-interferon-inducible protein 16; HIN200/OB f	81.56
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	81.52
1jb7_A	495	Telomere-binding protein alpha subunit; DNA-protei	81.51
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	80.85
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	80.44

>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=1.7e-61  Score=435.10  Aligned_cols=256  Identities=27%  Similarity=0.450  Sum_probs=120.5

Q ss_pred             CCCCCCcCccccCCCCCCC-CCCCCCC-cccCCCCCceeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeee
Q 023576            7 FDASNAFSGGGFMPSQPPQ-SADYPSS-TARSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEE   84 (280)
Q Consensus         7 ~~~~~~~~ggGf~~~~~~~-~~~~~~~-~~k~~~~~~~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~   84 (280)
                      |++++.+++||||++++++ ++.++++ +++.++.++|+|||||||+++.++   ++.|+|+|++|++|+|||+|++++.
T Consensus         9 ~~~~~~~~~ggf~~~~~~~~~~~~~~~~~~~~~~~~~l~PvtIkqil~a~~~---d~~f~i~g~~i~~V~ivG~V~~i~~   85 (270)
T 2pi2_A            9 YGSSSYGGAGGYTQSPGGFGSPAPSQAEKKSRARAQHIVPCTISQLLSATLV---DEVFRIGNVEISQVTIVGIIRHAEK   85 (270)
T ss_dssp             --------------------------------CCCCCCEECCHHHHHHCEEE---TTEEEETTEEESEEEEEEEEEEEEE
T ss_pred             cCCcCCCCCCCcccCCCCCCCCCCCCCccccCCCCCceEEEEHHHHhcCccC---CCcEEECCEEEEEEEEEEEEEEEEe
Confidence            7777778899999876643 2222222 333568899999999999999864   4689999999999999999999999


Q ss_pred             cCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHHHH
Q 023576           85 RASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYF  163 (280)
Q Consensus        85 ~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i~~  163 (280)
                      ..+++.|+|+|+|| +|+|++|.+.+.+......|++|+||||+|+|+.|++++||++++||||+|+||+++|+|||+++
T Consensus        86 ~~~~~~~~L~D~TG~~I~~k~W~~~~~~~~~~~~~~~G~yVrV~G~v~~f~g~~qi~i~~ir~v~d~nEi~~H~Le~i~~  165 (270)
T 2pi2_A           86 APTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINA  165 (270)
T ss_dssp             CSSEEEEEEECSSSSCEEEEEECC-------CCCCCTTCEEEEEEEEEEETTEEEEEEEEEEECSCTHHHHHHHHHHHHH
T ss_pred             ccceEEEEEECCCCCEEEEEEEcCcCcccchhhcCCCCCEEEEEEEEEecCCeeEEEEEEEEecCCHhHHHHHHHHHHHH
Confidence            99999999999999 89999998764322235789999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCchhHHHHHHhcCCCCCCCCCccCHHHHH
Q 023576          164 HLQNSKSQVQGFPSSQPQMVDSSLNTSARTGLSGYQTAPTNLSSQFGVDGLKDCDQMILDYLQQPSSSERERGVHVNELS  243 (280)
Q Consensus       164 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~  243 (280)
                      ||+++++.+..   +....   +.+.........+..    + .....+++++++++||++||++.   .++|+|+++|+
T Consensus       166 hl~~~~~~~~~---~~~~~---~~~~~~~~~~~~~~~----~-~~~~~~~~~~~~~~Vl~~i~~~~---~~~Gi~~~~I~  231 (270)
T 2pi2_A          166 HMVLSKANSQP---SAGRA---PISNPGMSEAGNFGG----N-SFMPANGLTVAQNQVLNLIKACP---RPEGLNFQDLK  231 (270)
T ss_dssp             HHHHHHHTCCC---------------------------------------------------------------------
T ss_pred             HHHHccCCccc---cccCC---CcCCCCcccccccCc----c-cccCCCCCCHHHHHHHHHHHhCC---CccCCCHHHHH
Confidence            99999887641   10000   000000000001110    0 00112357889999999999864   47899999999


Q ss_pred             HHh-CCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          244 EQL-KIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       244 ~~l-~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      ++| ++++++|++||++|++|||||+|+||+|||+||
T Consensus       232 ~~l~~~~~~~v~~al~~L~~eG~IYsTiDd~h~k~t~  268 (270)
T 2pi2_A          232 NQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFKSTD  268 (270)
T ss_dssp             -------------------------------------
T ss_pred             HHhcCCCHHHHHHHHHHHHhCCEEeccccccceeecc
Confidence            999 699999999999999999999999999999997

>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=8.2e-40  Score=264.19  Aligned_cols=130  Identities=31%  Similarity=0.550  Sum_probs=113.8

Q ss_pred             CCCceeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCc-eEEEEEecccccChhhhc
Q 023576           38 DSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTG-RVVCKRWASEVFDTREME  116 (280)
Q Consensus        38 ~~~~~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~  116 (280)
                      +.++|+|||||||++|.++   ++.|+++|+++++|+|||+|++++..++++.|+|+|+|| .|+|++|.+.+.+.....
T Consensus         2 r~~~l~PvtIkqil~a~~~---~~~f~i~g~~i~~V~iVG~V~~~~~~~~~~~~~ldD~TG~~I~~~~W~~~~~~~~~~~   78 (132)
T 3kdf_D            2 RAQHIVPCTISQLLSATLV---DEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENT   78 (132)
T ss_dssp             ---CCEECCHHHHHTCEES---SSCEEETTEECCEEEEEEEEEEEEECSSEEEEEEECSSSSCEEEEEEC---------C
T ss_pred             CCCceeeEEHHHHhhCccC---CCcEEECCEEEEEEEEEEEEEEEEEcCCeEEEEEECCCCCEEEEEEEccCCCcccccc
Confidence            5789999999999999875   468999999999999999999999999999999999999 999999988764434467


Q ss_pred             cCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHhcCC
Q 023576          117 AIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSKS  170 (280)
Q Consensus       117 ~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~~~~  170 (280)
                      .+++|+||||+|+++.|+++++|+++.|||++|+||+++|+|||+++||+++|.
T Consensus        79 ~~~~g~yVrV~G~l~~f~g~~qi~~~~ir~v~d~Nei~~H~Le~i~~hl~~~k~  132 (132)
T 3kdf_D           79 VVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKA  132 (132)
T ss_dssp             CCCTTCEEEEEEEEEEETTEEEEEEEEEEECSSTHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccCCCEEEEEEEEEeECCEEEEEEEEEEEcCCccHHHHHHHHHHHHHHeecCC
Confidence            899999999999999999999999999999999999999999999999999863

>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=1.7e-39  Score=263.65  Aligned_cols=134  Identities=31%  Similarity=0.632  Sum_probs=117.0

Q ss_pred             cCCCCCceeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEeccccc-Chh
Q 023576           35 RSRDSQGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVF-DTR  113 (280)
Q Consensus        35 k~~~~~~~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~-~~~  113 (280)
                      |++..++|+|||||||++|.++. +++.|+++|++|++|+|||+|++++..++++.|+|+|+||.|+|++|.+.+. +..
T Consensus         2 ~~~~~~~l~PvtIkqil~a~~~~-~~~~f~i~g~~i~~V~iVG~V~~~~~~~~~~~~~ldD~TG~I~~~~W~~~~~~~~~   80 (136)
T 4gop_B            2 KKAGNNTLRPVTIRQILNAEQPH-PDAEFILDGAELGQLTFVAVVRNISRNATNVAYSVEDGTGQIEVRQWLDSSSDDSS   80 (136)
T ss_dssp             -----CCEEECCHHHHHHCBCCS-SSCCCBSSSSBCCEEEEEEEEEEEEECSSEEEEEEECSSCEEEEEEECC-------
T ss_pred             CCCCCCcEEeEEHHHHhhccccC-CCCcEEECCEEEEEEEEEEEEEEEEecCCeEEEEEECCCCCEEEEEecccCCcccc
Confidence            45578999999999999998875 3578999999999999999999999999999999999999999999987543 222


Q ss_pred             hhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHhcC
Q 023576          114 EMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSK  169 (280)
Q Consensus       114 ~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~~~  169 (280)
                      ..+.+++|+||||.|+++.|++++||+++.|||++|+||+++|+|||+++||+++|
T Consensus        81 ~~~~~~~g~yVrV~G~v~~f~g~~qi~~~~ir~v~d~Nei~~H~Le~i~~hl~~t~  136 (136)
T 4gop_B           81 KASEIRNNVYVRVLGTLKSFQNRRSISSGHMRPVIDYNEVMFHRLEAVHAHLQVTR  136 (136)
T ss_dssp             -CCSCCTTCEEEEEEEEEEETTEEEEEESEEEECSSHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccCCCCEEEEEEEEEEeCCEEEEEEEEEEECCCccHHHHHHHHHHHHHHhhcC
Confidence            46789999999999999999999999999999999999999999999999999975

>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe}

Probab=99.91  E-value=1.6e-23  Score=173.04  Aligned_cols=130  Identities=14%  Similarity=0.178  Sum_probs=110.4

Q ss_pred             CCCceeeeeHHHHhhcccCCCC-CCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCc-eEEEEEecccccCh-hh
Q 023576           38 DSQGLVPVTVKMISEASHSGDD-KSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTG-RVVCKRWASEVFDT-RE  114 (280)
Q Consensus        38 ~~~~~~PvtIkqi~~a~~~~~~-~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG-~I~~~~w~~~~~~~-~~  114 (280)
                      .-...+|+.|++|+...+...- ...+.+.|+||++|+|||+|+++++.++++.|+|||+|| .|+|++|.+...+. ..
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            3467899999999998665421 224478999999999999999999999999999999999 59999998864221 12


Q ss_pred             hccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHh
Q 023576          115 MEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQN  167 (280)
Q Consensus       115 ~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~  167 (280)
                      ...+.+|+||||.|+|+.|++++||.+++++++.|+|++..||.+++....++
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            34589999999999999999999999999999999999999999999987664

>3kf8_A Protein STN1; OB fold; 2.40A {Candida tropicalis mya-3404}

Probab=99.37  E-value=1.5e-11  Score=105.38  Aligned_cols=126  Identities=10%  Similarity=0.185  Sum_probs=96.6

Q ss_pred             CceeeeeHHHHhhcccCC--------CCCCCeEECCEEEeeEEEEEEEEEeeecC--------CeeEEEEEcCCce---E
Q 023576           40 QGLVPVTVKMISEASHSG--------DDKSNFMINGLEITNVTLVGLVYNKEERA--------SDVNFTLDDGTGR---V  100 (280)
Q Consensus        40 ~~~~PvtIkqi~~a~~~~--------~~~~~~~i~g~~i~~V~iVG~V~~~~~~~--------t~~~~~LdDgTG~---I  100 (280)
                      ..++|+.|++|+......        ...+.|.+.++||.+|+|+|+|+.++...        .++.|+|||+||.   |
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            579999999999764321        01347899999999999999999997655        4699999999995   7


Q ss_pred             EEEEecccccCh-hhhccCCCCCEEEEEEEEeeeCC--------eeEEEEEEEeeC----CCchHHHHHHHHHHHHHH
Q 023576          101 VCKRWASEVFDT-REMEAIQDGMYVRLIGNLKSFQG--------KKQIVAFSVRPV----TNFDEVTCHYIECIYFHL  165 (280)
Q Consensus       101 ~~~~w~~~~~~~-~~~~~~~~G~yVrV~G~l~~f~~--------~~~i~~~~ir~v----~d~Nei~~H~Le~i~~~l  165 (280)
                      .|+.-....... -.......|..|+|.|.++.|++        .++|.+.+|+.+    .|+..+.-||-+++...-
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            776543211000 00122457999999999999998        899999999999    566788889988887765

>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=99.02  E-value=1.6e-08  Score=80.64  Aligned_cols=118  Identities=15%  Similarity=0.222  Sum_probs=93.4

Q ss_pred             CCceeeeeHHHHhhcccCCCCCCCeEEC-------CEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC
Q 023576           39 SQGLVPVTVKMISEASHSGDDKSNFMIN-------GLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD  111 (280)
Q Consensus        39 ~~~~~PvtIkqi~~a~~~~~~~~~~~i~-------g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~  111 (280)
                      ....+.|.++||.++.+..  ...+.+.       ..+++.|++-|+|+.. ++.   .++|+|+||.+.+..-.+..  
T Consensus        22 ~~PpvK~l~~QLr~~~~~~--~~~w~l~r~~~g~~~l~~s~VWmQG~VV~~-~~g---~~~LdDgTG~~~v~g~~~vp--   93 (150)
T 3mxn_B           22 RSPPLKVLAEQLRRDAEGG--PGAWRLSRAAAGRGPLDLAAVWMQGRVVMA-DRG---EARLRDPSGDFSVRGLERVP--   93 (150)
T ss_dssp             SSCCEECCHHHHHHHEESC--TTCCEECCTTTTCCCEECSEEEEEEEEEEE-ETT---EEEEEETTEEEEEECGGGSC--
T ss_pred             CCCcHHHHHHHHHHHhhCC--CceEEEEecccCCccceeEEEEEEeEEEEe-CCC---eEEEECCCceEEEeeccccC--
Confidence            4556788999999987642  4456554       3789999999999996 333   48999999999876543321  


Q ss_pred             hhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC-chHHHHHHHHHHHHHH
Q 023576          112 TREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN-FDEVTCHYIECIYFHL  165 (280)
Q Consensus       112 ~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d-~Nei~~H~Le~i~~~l  165 (280)
                       .-..-++.|+||.|.|.+..-.....|.+.+|.-+++ ++...+|.|||+.+|-
T Consensus        94 -~g~p~l~~G~YVMV~G~v~~~s~eP~i~AvKm~DLS~~p~~E~mW~lEV~el~r  147 (150)
T 3mxn_B           94 -RGRPCLVPGKYVMVMGVVQACSPEPCLQAVKMTDLSDNPIHESMWELEVEDLHR  147 (150)
T ss_dssp             -CCSCCCSTTCEEEEEEEEEECSSSCEEEEEEEEECCSCHHHHHHHHHHHHHHHT
T ss_pred             -CCCcccCCCCEEEEEEEEEecCCCceEEEEEeeeCCCCcchHHHHHHHHHHHHh
Confidence             1123478999999999999988899999999999988 5788999999999873

>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str}

Probab=98.71  E-value=1.4e-08  Score=78.98  Aligned_cols=81  Identities=17%  Similarity=0.300  Sum_probs=62.6

Q ss_pred             eeEEEEEEEEEe-ee-------c--CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEE--eeeCCeeE
Q 023576           71 TNVTLVGLVYNK-EE-------R--ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL--KSFQGKKQ  138 (280)
Q Consensus        71 ~~V~iVG~V~~~-~~-------~--~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l--~~f~~~~~  138 (280)
                      ..|.++|+|.++ ..       .  ..+..++|.|.||.|++++|.+...   ....+++|++|.|.|.+  ..|++++|
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            356888888877 21       1  3688999999999999999976532   23579999999999999  66999999


Q ss_pred             EEEEEEeeCCCchHHH
Q 023576          139 IVAFSVRPVTNFDEVT  154 (280)
Q Consensus       139 i~~~~ir~v~d~Nei~  154 (280)
                      |.+...+.|....++-
T Consensus        94 L~~~~~~~i~~~~~~~  109 (115)
T 2k50_A           94 AHLMPRSTVEVLDPLE  109 (115)
T ss_dssp             EEECTTCCEEEESSCC
T ss_pred             EEECCCceEEECCccc
Confidence            9997766655444443

>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3

Probab=98.67  E-value=1.2e-07  Score=74.27  Aligned_cols=73  Identities=23%  Similarity=0.314  Sum_probs=59.0

Q ss_pred             eEEEEEEEEEeee--------c-CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEEEE
Q 023576           72 NVTLVGLVYNKEE--------R-ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQIVA  141 (280)
Q Consensus        72 ~V~iVG~V~~~~~--------~-~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i~~  141 (280)
                      .|.++++|.++..        + ..+..++|.|.||+|++++|.+.+      +.+++|++|+|. |+++.|+++.+|++
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            4666777766531        1 269999999999999999998753      358999999999 99999999999999


Q ss_pred             EE---EeeCCCc
Q 023576          142 FS---VRPVTNF  150 (280)
Q Consensus       142 ~~---ir~v~d~  150 (280)
                      .+   |.++.++
T Consensus        88 ~~~~~i~~~~~~   99 (119)
T 1o7i_A           88 GSKTKIAEASED   99 (119)
T ss_dssp             CTTCEEEECCCT
T ss_pred             CCCEEEEEcCCc
Confidence            76   7776653

>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Methanosarcina mazei} PDB: 2ken_A

Probab=98.66  E-value=1e-07  Score=73.54  Aligned_cols=73  Identities=15%  Similarity=0.115  Sum_probs=60.2

Q ss_pred             eeEEEEEEEEEeeec---CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEEEEEEEee
Q 023576           71 TNVTLVGLVYNKEER---ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQIVAFSVRP  146 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~---~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i~~~~ir~  146 (280)
                      ..|.++++|+++...   ..+...+|.|.||+|.++.|.+..     ...+++|+.|+|. |.++.|+++.+|++.+...
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            467888999887642   357788999999999999998543     4579999999999 8999999999999976554


Q ss_pred             CC
Q 023576          147 VT  148 (280)
Q Consensus       147 v~  148 (280)
                      |+
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=98.65  E-value=9.2e-08  Score=73.43  Aligned_cols=76  Identities=18%  Similarity=0.253  Sum_probs=60.4

Q ss_pred             eEEEEEEEEEeee-----cC---CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEEEEE
Q 023576           72 NVTLVGLVYNKEE-----RA---SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQIVAF  142 (280)
Q Consensus        72 ~V~iVG~V~~~~~-----~~---t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i~~~  142 (280)
                      .|.+++.|.++.+     ..   .+..++|.|.||+|.+++|.+.         +++|+.|+|. |.++.|+++.+|++.
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            3555666655432     22   2889999999999999999763         9999999999 999999999999985


Q ss_pred             ---EEeeCCCchHHHHH
Q 023576          143 ---SVRPVTNFDEVTCH  156 (280)
Q Consensus       143 ---~ir~v~d~Nei~~H  156 (280)
                         .|.++.++.++-+|
T Consensus        86 ~~~~I~~~~~~~~~~~~  102 (106)
T 2k75_A           86 DSSRIESVNVNIPLEHH  102 (106)
T ss_dssp             TTSEEEECCSCCCCSCC
T ss_pred             CcEEEEECCCCCccccc
Confidence               48888887776544

>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=98.34  E-value=3.2e-06  Score=63.66  Aligned_cols=72  Identities=17%  Similarity=0.157  Sum_probs=56.0

Q ss_pred             eeEEEEEEEEEeee-----c-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEE
Q 023576           71 TNVTLVGLVYNKEE-----R-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIV  140 (280)
Q Consensus        71 ~~V~iVG~V~~~~~-----~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~  140 (280)
                      ..|.|+|+|.++..     +     .....++|.|.||+|.+..|.+...    . .+++|++|+|.|.++.|.+..+|+
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            46788888888641     1     1377899999999999999987642    1 699999999999999999999998


Q ss_pred             EEEEeeC
Q 023576          141 AFSVRPV  147 (280)
Q Consensus       141 ~~~ir~v  147 (280)
                      +-+--.|
T Consensus        87 ~g~~~~i   93 (97)
T 3e0e_A           87 VDNIGII   93 (97)
T ss_dssp             EEEEEEE
T ss_pred             ECCCcEE
Confidence            8765443

>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii}

Probab=98.02  E-value=4.5e-05  Score=58.18  Aligned_cols=72  Identities=24%  Similarity=0.304  Sum_probs=56.4

Q ss_pred             eeEEEEEEEEEeee-----c-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC-CeeEE
Q 023576           71 TNVTLVGLVYNKEE-----R-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ-GKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~-----~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~-~~~~i  139 (280)
                      ..|.|+|+|.++..     +     .....++|.|.||+|.+.+|.+...    . .+++|+.|+|.|.++.+. +.++|
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            57888888877642     1     1356799999999999999987652    1 799999999999999984 58899


Q ss_pred             EEEEEeeC
Q 023576          140 VAFSVRPV  147 (280)
Q Consensus       140 ~~~~ir~v  147 (280)
                      ++-+--.|
T Consensus        90 ~~g~~~~i   97 (105)
T 3dm3_A           90 TANYVEIL   97 (105)
T ss_dssp             EEEEEEEE
T ss_pred             EeCCceEE
Confidence            88664444

>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=97.81  E-value=0.00052  Score=52.52  Aligned_cols=83  Identities=18%  Similarity=0.158  Sum_probs=62.5

Q ss_pred             eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCE
Q 023576           44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMY  123 (280)
Q Consensus        44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~y  123 (280)
                      ..|++|++++.    ++          ..|.|-|.|+..-...   .|...|+||+|.+.+=.+.    ..-..+.+++.
T Consensus        25 ~~TV~~a~~~~----Dd----------~~V~L~G~Iv~~~~~d---~Y~F~D~TG~I~VeId~~~----w~g~~v~p~~~   83 (109)
T 1nnx_A           25 VTTVESAKSLR----DD----------TWVTLRGNIVERISDD---LYVFKDASGTINVDIDHKR----WNGVTVTPKDT   83 (109)
T ss_dssp             CCCHHHHTTSC----SS----------EEEEEEEEEEEEEETT---EEEEEETTEEEEEECCGGG----STTCCCCTTSC
T ss_pred             eEeHHHHhhCc----CC----------CeEEEEEEEEEEeCCC---eEEEECCCccEEEEEChhh----cCCcccCCCCE
Confidence            47899998752    22          6788999998876555   5789999999998852111    11246788999


Q ss_pred             EEEEEEEeeeCCeeEEEEEEEeeC
Q 023576          124 VRLIGNLKSFQGKKQIVAFSVRPV  147 (280)
Q Consensus       124 VrV~G~l~~f~~~~~i~~~~ir~v  147 (280)
                      |||.|.+..--....|-+.+|..+
T Consensus        84 Vri~GevDkd~~~~eIdV~~i~~~  107 (109)
T 1nnx_A           84 VEIQGEVDKDWNSVEIDVKQIRKV  107 (109)
T ss_dssp             EEEEEEEEEETTEEEEEEEEEEEC
T ss_pred             EEEEEEECCCCCceEEEEEEEEEc
Confidence            999999998556778888888776

>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=97.46  E-value=0.00092  Score=53.77  Aligned_cols=55  Identities=16%  Similarity=0.247  Sum_probs=44.9

Q ss_pred             CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEEEEEEEeeC
Q 023576           87 SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQIVAFSVRPV  147 (280)
Q Consensus        87 t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i~~~~ir~v  147 (280)
                      .-....|-|.||+|....|.+.      .+.+++|+.|++.+ .++.|++...|.+-+--.|
T Consensus        62 ~V~~~lVgDeTG~I~ftlW~e~------~~~l~~Gd~v~i~na~v~~~~G~~~L~vgk~g~I  117 (145)
T 1wjj_A           62 RIVECLIGDETGCILFTARNDQ------VDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRI  117 (145)
T ss_dssp             CCEEEEEECSSCEEEEEECTTH------HHHTCTTCEEEEEEEEEEEETTEEEEEECTTCCB
T ss_pred             eEEEEEEEcCCcEEEEEEecCC------cCcCCCCCEEEEeccEEEeECCEEEEEECCCEEE
Confidence            3567899999999999999763      34588999999987 6889999999988653333

>3au7_A TIAS, putative uncharacterized protein; ATP hydrolysis, RNA binding protein; 2.60A {Archaeoglobus fulgidus} PDB: 3amt_A* 3amu_A*

Probab=97.28  E-value=0.001  Score=62.01  Aligned_cols=78  Identities=19%  Similarity=0.212  Sum_probs=63.2

Q ss_pred             EEEeeEEEEEEEEEe-e-ecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEe
Q 023576           68 LEITNVTLVGLVYNK-E-ERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVR  145 (280)
Q Consensus        68 ~~i~~V~iVG~V~~~-~-~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir  145 (280)
                      .+...+++.|.|.+. . .....+.|+|+|+++.|+|..|.....-......+.+||.|.|.|.++.  +  +|++.+++
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            455789999999988 4 3556899999999999999999865422233567899999999999888  3  99999988


Q ss_pred             eCCC
Q 023576          146 PVTN  149 (280)
Q Consensus       146 ~v~d  149 (280)
                      ++.-
T Consensus       358 v~~l  361 (402)
T 3au7_A          358 IVEL  361 (402)
T ss_dssp             EEEC
T ss_pred             Eccc
Confidence            8754

>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=97.10  E-value=0.00071  Score=49.02  Aligned_cols=52  Identities=27%  Similarity=0.454  Sum_probs=45.5

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+++++||++|++.+   ....++..+|+++|+++...|+.+|..|..+|.|...
T Consensus         9 ~~~~~~IL~~L~~~~---pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~   60 (81)
T 1qbj_A            9 QDQEQRILKFLEELG---EGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKE   60 (81)
T ss_dssp             HHHHHHHHHHHHHHC---TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             hHHHHHHHHHHHHcC---CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            357889999999753   3457999999999999999999999999999999864

>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=97.03  E-value=0.00061  Score=48.80  Aligned_cols=52  Identities=27%  Similarity=0.440  Sum_probs=46.0

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      +++.+||++|++.+   .+.+++..+|+++|+++...|+..|..|..+|.|+..-
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   34589999999999999999999999999999998864

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=97.00  E-value=0.00076  Score=46.87  Aligned_cols=58  Identities=19%  Similarity=0.256  Sum_probs=47.4

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      +.+.+++||++|++.     ...++..+|+++|+++.+.|...|..|.++|.|-++-. -+|..
T Consensus         8 m~~~~~~IL~~L~~~-----~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~~~~-G~y~l   65 (67)
T 2heo_A            8 GDNLEQKILQVLSDD-----GGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSSPSP-KYWSI   65 (67)
T ss_dssp             -CHHHHHHHHHHHHH-----CSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEEEET-TEEEE
T ss_pred             ccHHHHHHHHHHHHc-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEecCCC-ceEee
Confidence            556788999999853     24699999999999999999999999999999987533 35544

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=96.99  E-value=0.00053  Score=48.73  Aligned_cols=52  Identities=17%  Similarity=0.249  Sum_probs=46.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+.++.++||++|++.     ..-+.-.+|++.++++..+|.++|..|-.||.|+++
T Consensus        16 ~~~d~eekVLe~Lkea-----G~PlkageIae~~GvdKKeVdKaik~LKkEgkI~SP   67 (80)
T 2lnb_A           16 REGHLEQRILQVLTEA-----GSPVKLAQLVKECQAPKRELNQVLYRMKKELKVSLT   67 (80)
T ss_dssp             HHHHHHHHHHHHHHHH-----TSCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccchHHHHHHHHHHHc-----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCccCC
Confidence            3466899999999985     347889999999999999999999999999999987

>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=96.74  E-value=0.0054  Score=63.50  Aligned_cols=79  Identities=20%  Similarity=0.398  Sum_probs=62.2

Q ss_pred             EeeEEEEEEEEEeeec-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe--eeCCeeEEEEE
Q 023576           70 ITNVTLVGLVYNKEER-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK--SFQGKKQIVAF  142 (280)
Q Consensus        70 i~~V~iVG~V~~~~~~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~--~f~~~~~i~~~  142 (280)
                      ...|.|-|.|-.++.+     ..-++|.|.|.|++|.|+.|.+...+.+....+++|++|+|.|.+.  .|.....+.+.
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            4678999999876542     3567899999999999999977654334456799999999999987  46677788887


Q ss_pred             EEeeCC
Q 023576          143 SVRPVT  148 (280)
Q Consensus       143 ~ir~v~  148 (280)
                      .|.++.
T Consensus        97 ~~~~~~  102 (1041)
T 3f2b_A           97 DLNEIA  102 (1041)
T ss_dssp             EEEEEC
T ss_pred             eeEEec
Confidence            776655

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=96.68  E-value=0.0023  Score=46.41  Aligned_cols=48  Identities=15%  Similarity=0.351  Sum_probs=43.4

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .....+||++|+..       |++..+|+++|+++...|+..|..|..+|.|...
T Consensus        16 ~~~~~~IL~lL~~~-------g~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           16 AEIVCEAIKTIGIE-------GATAAQLTRQLNMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             HHHHHHHHHHHSSS-------TEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHHHHHHHHHHHHc-------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            46888999999852       4999999999999999999999999999999875

>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=96.49  E-value=0.0022  Score=46.18  Aligned_cols=49  Identities=18%  Similarity=0.354  Sum_probs=44.0

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHH-HHHHHHHHHHhCCeeeec
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQK-KIMDSIASLENEGLIYST  269 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~-~v~~al~~L~~eG~IYsT  269 (280)
                      .+.+++||.+|+..      .+.+..+|++.|+++.. .|+..|..|..+|.|...
T Consensus        10 ~~~~~~IL~~Lk~~------g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~   59 (79)
T 1xmk_A           10 AEIKEKICDYLFNV------SDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQ   59 (79)
T ss_dssp             HHHHHHHHHHHHHT------CCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             hhHHHHHHHHHHHc------CCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEec
Confidence            46889999999975      27899999999999999 999999999999999843

>1wyd_A Hypothetical aspartyl-tRNA synthetase; archaea, LIGA; HET: EPE; 2.30A {Sulfolobus tokodaii}

Probab=96.47  E-value=0.023  Score=53.55  Aligned_cols=74  Identities=14%  Similarity=0.022  Sum_probs=56.7

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCC---eeEEEEEEEee
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQG---KKQIVAFSVRP  146 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~---~~~i~~~~ir~  146 (280)
                      .|+|.|+|.+++....-+-+.|.|+||.|.|.+-.+. ..-.....+..|+.|.|.|.+..-..   ...|.+..+..
T Consensus        18 ~V~v~Gwv~~~R~~g~~~F~~lrD~~g~iQ~v~~~~~-~~~~~~~~l~~~~~v~v~G~v~~~~~~~~~~el~~~~~~v   94 (429)
T 1wyd_A           18 EVIWAGWVHLLRDLGGKKFIILRDKTGLGQVVVDKNS-SAFGISQELTQESVIQVRGIVKADKRAPRGIELHAEEITL   94 (429)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEECTTS-TTHHHHTTCCTTCEEEEEEEEEECSSSGGGEEEEEEEEEE
T ss_pred             EEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEeCCh-HHHHHHHhCCCCCEEEEEEEEEecCCCCccEEEEEeEEEE
Confidence            5999999999988777677799999999999975432 11123467999999999999987653   46676666543

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=96.37  E-value=0.0046  Score=44.36  Aligned_cols=45  Identities=22%  Similarity=0.268  Sum_probs=40.4

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+|+++|++.      .-+++++|++.|+.++..||.-|+.|.+.|.|-.+
T Consensus         5 ~~Il~~L~~~------g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            5 IQVRDLLALR------GRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHHS------CSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHc------CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            4689999874      36899999999999999999999999999999775

>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=96.35  E-value=0.028  Score=53.35  Aligned_cols=77  Identities=16%  Similarity=0.314  Sum_probs=55.6

Q ss_pred             eeEEEEEEEEEeeecCC-eeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC-----------CeeE
Q 023576           71 TNVTLVGLVYNKEERAS-DVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ-----------GKKQ  138 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t-~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~-----------~~~~  138 (280)
                      ..|+|.|+|.+++.... -+-+.|.|+||.|.|.+-.+...+......+..|+.|.|.|.|..-.           +...
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            46899999999988754 55568999999999987542211112234689999999999997432           4567


Q ss_pred             EEEEEEeeC
Q 023576          139 IVAFSVRPV  147 (280)
Q Consensus       139 i~~~~ir~v  147 (280)
                      |.+..+..+
T Consensus       111 l~~~~i~vl  119 (456)
T 3m4p_A          111 MQVTEWKVI  119 (456)
T ss_dssp             EEEEEEEEE
T ss_pred             EEEeEEEEE
Confidence            777776654

>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=96.28  E-value=0.028  Score=54.89  Aligned_cols=75  Identities=17%  Similarity=0.196  Sum_probs=57.3

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee--------CCeeEEEEEE
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF--------QGKKQIVAFS  143 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f--------~~~~~i~~~~  143 (280)
                      .|+|.|+|.+++.....+-+.|-|+||.|.|.+-.+.. .-.....+..|+.|.|.|.|..-        .+...|.+..
T Consensus        18 ~V~l~GwV~~~R~~G~~~Fi~LrD~~g~iQvv~~~~~~-~~~~~~~l~~e~~V~V~G~v~~~~~~~~~~~~ge~Ei~~~~   96 (580)
T 1l0w_A           18 EVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASP-AYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSA   96 (580)
T ss_dssp             EEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECTTST-THHHHTTCCTTCEEEEEEEEEECSSCCTTSTTTTEEEEEEE
T ss_pred             EEEEEEEEEEEecCCCeEEEEEEECCeeEEEEEeCChh-HHHHHhcCCCCcEEEEEEEEEcCCCcCccCCCccEEEEEeE
Confidence            69999999999887777777999999999998754321 11234679999999999999874        3556777776


Q ss_pred             EeeC
Q 023576          144 VRPV  147 (280)
Q Consensus       144 ir~v  147 (280)
                      |..+
T Consensus        97 i~vl  100 (580)
T 1l0w_A           97 LEVL  100 (580)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            6433

>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=96.25  E-value=0.041  Score=52.82  Aligned_cols=101  Identities=16%  Similarity=0.132  Sum_probs=67.7

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEeccccc-Ch-h-hhccCC
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVF-DT-R-EMEAIQ  119 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~-~~-~-~~~~~~  119 (280)
                      +-.++++|......-+ ...+.-.|   ..|+|.|+|.+++......-+.|.|+||.|.|.+-.+... +. . ....+.
T Consensus        41 ~~~~~~~~~~~~~~~~-~~~~~~~~---~~V~v~Gwv~~~R~~gk~~F~~LrD~sg~iQvv~~~~~~~~~~~~~~~~~l~  116 (504)
T 1e1o_A           41 RDHTSDQLHEEFDAKD-NQELESLN---IEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWD  116 (504)
T ss_dssp             CSCCHHHHHHHHTTCC-HHHHHHHC---CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSSTTHHHHTGGGCC
T ss_pred             CceEHHHHHHHhhccC-ccccccCC---CEEEEEEEEEEEecCCCcEEEEEEECCeeEEEEEECCcCCHHHHHHHHhcCC
Confidence            4456888876543210 00000001   3699999999998877777779999999999997644211 11 1 345799


Q ss_pred             CCCEEEEEEEEeee-CCeeEEEEEEEeeC
Q 023576          120 DGMYVRLIGNLKSF-QGKKQIVAFSVRPV  147 (280)
Q Consensus       120 ~G~yVrV~G~l~~f-~~~~~i~~~~ir~v  147 (280)
                      .|+.|.|.|.|..- .+...|.+..+..+
T Consensus       117 ~g~~V~V~G~v~~~~~ge~ei~~~~i~vl  145 (504)
T 1e1o_A          117 LGDIIGARGTLFKTQTGELSIHCTELRLL  145 (504)
T ss_dssp             TTCEEEEEEEEEECTTCCEEEEEEEEEEE
T ss_pred             CCCEEEEEEEEEecCCceEEEEEEEEEEe
Confidence            99999999999864 46677777776544

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=96.23  E-value=0.0047  Score=44.17  Aligned_cols=54  Identities=9%  Similarity=0.185  Sum_probs=42.8

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      ..+++||++|++.-......-+++.||++.|++++..|+.-|..|...|.|-.+
T Consensus         4 ~r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~   57 (77)
T 2jt1_A            4 SIVTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKV   57 (77)
T ss_dssp             THHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence            367889999987400000135799999999999999999999999999999765

>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=96.22  E-value=0.029  Score=52.95  Aligned_cols=77  Identities=13%  Similarity=0.069  Sum_probs=57.2

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC--hhhhccCCCCCEEEEEEEEeeeC---CeeEEEEEEEe
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD--TREMEAIQDGMYVRLIGNLKSFQ---GKKQIVAFSVR  145 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~~~ir  145 (280)
                      ..|+|.|+|.+++....-+-+.|.|+||.|.|.+-.+....  -.....+..|+.|.|.|.+..-.   +...|.+..+.
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            46899999999988776555699999999998875432110  12245799999999999998754   46677777665


Q ss_pred             eC
Q 023576          146 PV  147 (280)
Q Consensus       146 ~v  147 (280)
                      .+
T Consensus        97 vl   98 (438)
T 3nem_A           97 VL   98 (438)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>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=96.20  E-value=0.023  Score=55.57  Aligned_cols=77  Identities=17%  Similarity=0.244  Sum_probs=57.6

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee----------CCeeEEEE
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF----------QGKKQIVA  141 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f----------~~~~~i~~  141 (280)
                      .|+|.|+|.+++....-+-+.|-|+||.|.|.+-.+....-.....+..|+.|.|.|.|..-          .+...|.+
T Consensus        17 ~V~l~GwV~~~R~~G~~~Fi~LrD~~g~iQvv~~~~~~~~~~~~~~l~~e~~V~V~G~v~~~~~~~~n~~~~~geiEl~~   96 (585)
T 1c0a_A           17 QVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNEFCIQVTGTVRARDEKNINRDMATGEIEVLA   96 (585)
T ss_dssp             EEEEEEEEEEEEECSSCEEEEEEETTEEEEEEECGGGHHHHHHHTTCCTTCEEEEEEEEEECCTTTCCTTSTTTTEEEEE
T ss_pred             EEEEEEEEEEEecCCCcEEEEEEECCeeEEEEEeCCchHHHHHHhcCCCCCEEEEEeEEEccCcccccccCCCccEEEEE
Confidence            59999999999887777777999999999998743221101123578999999999999864          35577777


Q ss_pred             EEEeeCC
Q 023576          142 FSVRPVT  148 (280)
Q Consensus       142 ~~ir~v~  148 (280)
                      ..+..+.
T Consensus        97 ~~i~vl~  103 (585)
T 1c0a_A           97 SSLTIIN  103 (585)
T ss_dssp             EEEEEEE
T ss_pred             eEEEEEe
Confidence            7765543

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=96.17  E-value=0.0055  Score=43.69  Aligned_cols=45  Identities=22%  Similarity=0.396  Sum_probs=40.0

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +++||++|.+.      ..+++.+|++.++++...|+..|..|.++|.|..
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            56899999763      2589999999999999999999999999999974

>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=96.17  E-value=0.0083  Score=44.26  Aligned_cols=54  Identities=15%  Similarity=0.393  Sum_probs=48.6

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+|+.-|..||.+|.+.    .+.|+...+|+++++++...|..+|+.|...|+|...
T Consensus        16 ~~Lt~~q~~Vl~~I~~~----g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr~   69 (91)
T 2dk5_A           16 KGSDNQEKLVYQIIEDA----GNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAV   69 (91)
T ss_dssp             CCSCSSHHHHHHHHHHH----CTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCHHHHHHHHHHHHc----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            47888999999999974    2469999999999999999999999999999999943

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=96.16  E-value=0.0059  Score=44.71  Aligned_cols=46  Identities=22%  Similarity=0.271  Sum_probs=41.1

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      .+|+++|++.      .-+++++|++.|++++..||.-|+.|...|.|.-+-
T Consensus         5 ~~Il~~L~~~------g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            5 MEVRDMLALQ------GRMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHHS------CSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHHc------CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            4689999864      368999999999999999999999999999998874

>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=96.12  E-value=0.029  Score=53.71  Aligned_cols=78  Identities=13%  Similarity=0.093  Sum_probs=57.7

Q ss_pred             eeEEEEEEEEEeeecCCe-eEEEEEcCCceEEEEEecccc--cC---hhhhccCCCCCEEEEEEEEeeeC--------Ce
Q 023576           71 TNVTLVGLVYNKEERASD-VNFTLDDGTGRVVCKRWASEV--FD---TREMEAIQDGMYVRLIGNLKSFQ--------GK  136 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~-~~~~LdDgTG~I~~~~w~~~~--~~---~~~~~~~~~G~yVrV~G~l~~f~--------~~  136 (280)
                      ..|+|.|+|.+++..... +-+.|.|++|.|.|.+-.+.+  ..   ......+..|+.|.|.|.+..-.        +.
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            369999999999887766 677999999999998754311  11   11235789999999999998765        35


Q ss_pred             eEEEEEEEeeCC
Q 023576          137 KQIVAFSVRPVT  148 (280)
Q Consensus       137 ~~i~~~~ir~v~  148 (280)
                      ..|.+..+..+.
T Consensus       117 ~El~~~~i~vl~  128 (487)
T 1eov_A          117 LEIHITKIYTIS  128 (487)
T ss_dssp             EEEEEEEEEEEE
T ss_pred             EEEEEEEEEEee
Confidence            667777665543

>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=96.09  E-value=0.015  Score=41.24  Aligned_cols=51  Identities=20%  Similarity=0.201  Sum_probs=45.3

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +++..|+++|...+   .++..+..+||++|+++-.+|+.+|-.|...|.|+..
T Consensus        12 ~~~~~v~~~i~~L~---~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~   62 (75)
T 1sfu_A           12 EIFSLVKKEVLSLN---TNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMV   62 (75)
T ss_dssp             HHHHHHHHHHHTSC---TTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhCC---CCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecC
Confidence            58889999998874   3445999999999999999999999999999999875

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=96.04  E-value=0.0096  Score=39.68  Aligned_cols=45  Identities=22%  Similarity=0.543  Sum_probs=39.7

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      ..++||++|++.+      |+ .++.+++.++.+.++|..+|..|.+.|+|=
T Consensus        11 ~e~~lL~yIr~sG------GildI~~~a~kygV~kdeV~~~LrrLe~KGLI~   56 (59)
T 2xvc_A           11 TERELLDYIVNNG------GFLDIEHFSKVYGVEKQEVVKLLEALKNKGLIA   56 (59)
T ss_dssp             CHHHHHHHHHHTT------SEEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEE
T ss_pred             cHHHHHHHHHHcC------CEEeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence            3568999999842      54 999999999999999999999999999984

>4ex5_A Lysine--tRNA ligase; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: LYS; 2.40A {Burkholderia thailandensis}

Probab=95.99  E-value=0.027  Score=54.39  Aligned_cols=77  Identities=18%  Similarity=0.157  Sum_probs=57.2

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC--hhhhccCCCCCEEEEEEEEeeeC-CeeEEEEEEEeeC
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD--TREMEAIQDGMYVRLIGNLKSFQ-GKKQIVAFSVRPV  147 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~G~yVrV~G~l~~f~-~~~~i~~~~ir~v  147 (280)
                      ..|+|.|+|.+++....-+-+.|.|+||.|.|.+-.+...+  -.....+..|+.|.|.|.+..-. +...|.+..|+.+
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            46999999999987776666799999999998865432110  12235699999999999998643 6777877776543

>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=95.91  E-value=0.06  Score=50.53  Aligned_cols=68  Identities=16%  Similarity=0.126  Sum_probs=54.9

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCC-CCCEEEEEEEEeeeCC---eeEEEEEEEeeC
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQ-DGMYVRLIGNLKSFQG---KKQIVAFSVRPV  147 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~-~G~yVrV~G~l~~f~~---~~~i~~~~ir~v  147 (280)
                      .|+|.|+|.+++.....+-+.|.|+||.|.|..-.         ..+. .|+.|.|.|.+..-..   ...|.+..+..+
T Consensus        15 ~V~v~Gwv~~~R~~g~~~F~~lrD~~g~iQ~v~~~---------~~l~~~~~~v~v~G~v~~~~~~~~~~el~~~~~~vl   85 (422)
T 1n9w_A           15 EVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGG---------LKLPLPESALRVRGLVVENAKAPGGLEVQAKEVEVL   85 (422)
T ss_dssp             EEEEEEEEEEEEECSSEEEEEEEETTEEEEEEEES---------CCCCCTTCEEEEEEEEEECTTSTTSEEEEEEEEEEE
T ss_pred             EEEEEEEEEEEecCCCeEEEEEEECCEEEEEEEEc---------cccCCCCCEEEEEEEEEecCCCCccEEEEEeEEEEe
Confidence            69999999999988776677999999999988642         4588 9999999999987653   577777776554


Q ss_pred             C
Q 023576          148 T  148 (280)
Q Consensus       148 ~  148 (280)
                      .
T Consensus        86 ~   86 (422)
T 1n9w_A           86 S   86 (422)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=95.90  E-value=0.032  Score=52.62  Aligned_cols=77  Identities=17%  Similarity=0.156  Sum_probs=57.7

Q ss_pred             eEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEeccccc-C-hhhhccCCCCCEEEEEEEEeeeCC---eeEEEEEEEee
Q 023576           72 NVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVF-D-TREMEAIQDGMYVRLIGNLKSFQG---KKQIVAFSVRP  146 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~-~-~~~~~~~~~G~yVrV~G~l~~f~~---~~~i~~~~ir~  146 (280)
                      .|+|.|+|.+++....-+-+.|.|+||.|.|.+-.+... + -.....+..|+.|.|.|.+..-..   ...|.+..+..
T Consensus        18 ~V~v~G~v~~~R~~g~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~~~~v~v~G~v~~~~~~~~~~el~~~~~~v   97 (434)
T 1x54_A           18 KVRLAGWVYTNMRVGKKIFLWIRDSTGIVQAVVAKNVVGEETFEKAKKLGRESSVIVEGIVKADERAPGGAEVHVEKLEV   97 (434)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEECHHHHCHHHHHHHHTCCTTCEEEEEEEEEECTTSGGGEEEEEEEEEE
T ss_pred             EEEEEEEEEEEecCCCeEEEEEEECCEEEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEecCCCCccEEEEEeEEEE
Confidence            599999999998877766779999999999987532210 1 122357999999999999987653   57777777654


Q ss_pred             CC
Q 023576          147 VT  148 (280)
Q Consensus       147 v~  148 (280)
                      +.
T Consensus        98 l~   99 (434)
T 1x54_A           98 IQ   99 (434)
T ss_dssp             EE
T ss_pred             ee
Confidence            43

>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=95.78  E-value=0.037  Score=53.03  Aligned_cols=102  Identities=16%  Similarity=0.072  Sum_probs=67.3

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC--hhhhccCCC
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD--TREMEAIQD  120 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~  120 (280)
                      +-.++++|......-+ ...+.-.|   ..|+|.|+|.+++.....+-+.|.|+||.|.|.+-.+...+  -.....+..
T Consensus        33 ~~~~~~~~~~~~~~~~-~~~~~~~~---~~V~v~Gwv~~~R~~gk~~F~~LrD~sg~iQvv~~~~~~~~~~~~~~~~l~~  108 (493)
T 3a74_A           33 RTHKAEELFELYGDLS-KEELEEQQ---IEVAVAGRIMTKRGMGKAGFAHIQDVTGQIQIYVRQDDVGEQQYELFKISDL  108 (493)
T ss_dssp             CSCCHHHHHHHHTTSC-HHHHHHHC---CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEEHHHHHHHHHHHHHHCCT
T ss_pred             CceehHHHHHhhcccc-chhhccCC---CEEEEEEEEEEEecCCCcEEEEEEECCEeEEEEEECCcCCHHHHHHHhcCCC
Confidence            3456888877543210 00000001   36999999999988777777799999999999875432100  112356899


Q ss_pred             CCEEEEEEEEeee-CCeeEEEEEEEeeCC
Q 023576          121 GMYVRLIGNLKSF-QGKKQIVAFSVRPVT  148 (280)
Q Consensus       121 G~yVrV~G~l~~f-~~~~~i~~~~ir~v~  148 (280)
                      |+.|.|.|.+..- .+...|.+..+..+.
T Consensus       109 g~~v~V~G~v~~~~~ge~ei~~~~i~vl~  137 (493)
T 3a74_A          109 GDIVGVRGTMFKTKVGELSIKVSSYEFLT  137 (493)
T ss_dssp             TCEEEEEEEEEECTTCCEEEEEEEEEEEE
T ss_pred             CCEEEEEEEEEeCCCCcEEEEEEEEEEcc
Confidence            9999999999864 466777777765443

>2xgt_A Asparaginyl-tRNA synthetase, cytoplasmic; ligase, ATP-binding, protein biosynthesis; HET: NSS; 1.90A {Brugia malayi} PDB: 2xti_A*

Probab=95.77  E-value=0.074  Score=50.11  Aligned_cols=76  Identities=18%  Similarity=0.225  Sum_probs=55.6

Q ss_pred             eEEEEEEEEEeeecC-CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC------CeeEEEEEEE
Q 023576           72 NVTLVGLVYNKEERA-SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ------GKKQIVAFSV  144 (280)
Q Consensus        72 ~V~iVG~V~~~~~~~-t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~------~~~~i~~~~i  144 (280)
                      .|+|.|+|.+++... .-+-+.|.|+||.|.|.+-.+.. +......+..|+.|.|.|.|+.-.      +...|.+..+
T Consensus        13 ~V~v~Gwv~~~R~~Gk~~~Fi~LrD~~g~iQvv~~~~~~-~~~~~~~l~~~~~v~v~G~v~~~~~~~~~~g~~El~~~~~   91 (435)
T 2xgt_A           13 RVCIKGWIHRMRRQGKSLMFFILRDGTGFLQVLLMDKLC-QTYDALTVNTECTVEIYGAIKEVPEGKEAPNGHELIADFW   91 (435)
T ss_dssp             EEEEEEEEEEEEECTTSEEEEEEECSSCEEEEEEEGGGG-SSHHHHHCCTTCEEEEEEEEEECC------TTEEEEEEEE
T ss_pred             EEEEEEEEEEecccCCCcEEEEEEECCceEEEEECCcch-hHHHHhcCCCCCEEEEEEEEEecCCCcCCCCcEEEEEEEE
Confidence            599999999998874 45667999999999998742211 111123689999999999998632      4467777777


Q ss_pred             eeCC
Q 023576          145 RPVT  148 (280)
Q Consensus       145 r~v~  148 (280)
                      ..+.
T Consensus        92 ~vl~   95 (435)
T 2xgt_A           92 KIIG   95 (435)
T ss_dssp             EEEE
T ss_pred             EEee
Confidence            6655

>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=95.76  E-value=0.22  Score=41.43  Aligned_cols=88  Identities=19%  Similarity=0.196  Sum_probs=62.1

Q ss_pred             CceeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEee----e-cCC---eeEEEEEcCC----c-eEEEEEec
Q 023576           40 QGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKE----E-RAS---DVNFTLDDGT----G-RVVCKRWA  106 (280)
Q Consensus        40 ~~~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~----~-~~t---~~~~~LdDgT----G-~I~~~~w~  106 (280)
                      ....-.+|++++...+..             ..|.++|+|+.+.    . +.+   .++|+|-|.+    + .|.|++|.
T Consensus        25 ~~~~~~~~r~~l~~~~~g-------------~~VNviGVVvd~~~P~~S~rGtkD~~~TltI~D~S~~~~~~gL~v~iF~   91 (187)
T 1qzg_A           25 GELTFQSIRSSQELQKKN-------------TIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTCDTSSIGLQIHLFS   91 (187)
T ss_dssp             TTEEEECHHHHTSCCSSC-------------EEEEEEEEEEEEEEEEECSSTTCCEEEEEEEECTTSCTTSCCEEEEEEE
T ss_pred             cceeEEEHHHHHhhccCC-------------CEEEEEEEEEEccCceecCCCCccEEEEEEEEeCCCCCCCCceEEEEEC
Confidence            345556777777532221             4688999998863    1 223   6789999977    3 49999998


Q ss_pred             ccccChhhhccC-CCCCEEEEEE-EEeeeCCeeEEEEEE
Q 023576          107 SEVFDTREMEAI-QDGMYVRLIG-NLKSFQGKKQIVAFS  143 (280)
Q Consensus       107 ~~~~~~~~~~~~-~~G~yVrV~G-~l~~f~~~~~i~~~~  143 (280)
                      +..+   ..+.+ .+||.|++.. +++.|+++.++...+
T Consensus        92 ~~~e---~LP~V~~~GDIIlL~rvkiq~~~g~~~~v~~~  127 (187)
T 1qzg_A           92 KQGN---DLPVIKQVGQPLLLHQITLRSYRDRTQGLSKD  127 (187)
T ss_dssp             SSSS---CSCCCCSTTCEEEEEEEEEEEETTEEEEEEEE
T ss_pred             CChh---hCCCCCCCCCEEEEEEEEEEEECCeEEEEEcC
Confidence            7542   35666 8999999975 677899998886544

>3i7f_A Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-binding, aminoacyl-tRNA synthetase, LI nucleotide-binding, protein biosynthesis; 2.80A {Entamoeba histolytica}

Probab=95.61  E-value=0.097  Score=50.69  Aligned_cols=77  Identities=18%  Similarity=0.138  Sum_probs=57.7

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh---hhhccCCCCCEEEEEEEEeeeC--------CeeEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT---REMEAIQDGMYVRLIGNLKSFQ--------GKKQI  139 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~G~yVrV~G~l~~f~--------~~~~i  139 (280)
                      ..|+|.|+|.+++....-+-+.|-|++|.|.|.+-.+...+.   .....+..|+.|.|.|.|..-.        +...|
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            468999999999887765566899999999999865322111   1245799999999999999753        45677


Q ss_pred             EEEEEeeC
Q 023576          140 VAFSVRPV  147 (280)
Q Consensus       140 ~~~~ir~v  147 (280)
                      .+..|..+
T Consensus       143 ~~~~i~vl  150 (548)
T 3i7f_A          143 HVTSIAVV  150 (548)
T ss_dssp             EEEEEEEE
T ss_pred             EEeEEEEE
Confidence            77776654

>3bju_A Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP- binding, cytoplasm, ligase, nucleotide-binding, phosphoprotein, polymorphism; HET: LYS ATP; 2.31A {Homo sapiens}

Probab=95.52  E-value=0.1  Score=50.35  Aligned_cols=101  Identities=9%  Similarity=0.152  Sum_probs=67.7

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecC-CeeEEEEEcCCceEEEEEecccc-c-Ch-h-hhcc
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERA-SDVNFTLDDGTGRVVCKRWASEV-F-DT-R-EMEA  117 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~-t~~~~~LdDgTG~I~~~~w~~~~-~-~~-~-~~~~  117 (280)
                      +..++++|......-..+..  ..|   ..|+|.|+|.+++... .-.-+.|.|+||.|.|.+-.+.. . +. . ....
T Consensus        33 ~~~~~~~~~~~~~~~~~~~~--~~~---~~V~v~Grv~~~R~~gkk~~F~~LrD~sg~iQvv~~~~~~~~~~~~~~~~~~  107 (521)
T 3bju_A           33 VDISLTDFIQKYSHLQPGDH--LTD---ITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNK  107 (521)
T ss_dssp             CCSCHHHHHHHHTTCCTTCB--CSS---CCEEEEEEEEEEEESSSSEEEEEEEETTEEEEEEEEGGGSSCHHHHHHHHHH
T ss_pred             CccchHHHHHHhhhhccccc--cCC---cEEEEEEEEEEEecCCCCcEEEEEEECCEEEEEEEECCccCCHHHHHHHHhc
Confidence            44678898765432111001  112   4699999999998877 55667999999999999865432 1 11 1 1245


Q ss_pred             CCCCCEEEEEEEEeee-CCeeEEEEEEEeeCC
Q 023576          118 IQDGMYVRLIGNLKSF-QGKKQIVAFSVRPVT  148 (280)
Q Consensus       118 ~~~G~yVrV~G~l~~f-~~~~~i~~~~ir~v~  148 (280)
                      +..|+.|.|.|.+..- .+...|.+..+..+.
T Consensus       108 l~~gd~V~V~G~v~~t~~ge~ei~~~~i~~l~  139 (521)
T 3bju_A          108 LRRGDIIGVQGNPGKTKKGELSIIPYEITLLS  139 (521)
T ss_dssp             CCTTCEEEEEEEEEECTTCCEEEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEecCCCCEEEEEeEEEEee
Confidence            8999999999999764 466777777765443

>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=95.50  E-value=0.02  Score=42.59  Aligned_cols=57  Identities=14%  Similarity=0.352  Sum_probs=51.4

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      .+|++.+..||.+|++.    .+.||...+|..+++++...|..+|..|++.|+|.+--+.
T Consensus        33 ~~Lt~~E~lVy~~I~~a----Gn~GIw~kdL~~~tnL~~~~vtkiLK~LE~k~lIK~Vksv   89 (95)
T 2yu3_A           33 KGSDNQEKLVYQIIEDA----GNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSV   89 (95)
T ss_dssp             CSCSHHHHHHHHHHHHH----TTSCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEECCS
T ss_pred             cCCCHHHHHHHHHHHHh----CCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEecCc
Confidence            57889999999999985    3679999999999999999999999999999999886554

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=95.48  E-value=0.022  Score=46.02  Aligned_cols=48  Identities=23%  Similarity=0.415  Sum_probs=42.7

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      |.++.++||+.|++.      .-++..+|++++++++..|+..|..|.++|.|-
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      257999999999999999999999999999984

>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=95.26  E-value=0.025  Score=44.71  Aligned_cols=48  Identities=23%  Similarity=0.436  Sum_probs=43.4

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +.+++.+||++|++.      ..++..+|+++++++...|...|..|.+.|.|-
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            567899999999863      358999999999999999999999999999995

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=95.21  E-value=0.018  Score=43.98  Aligned_cols=59  Identities=15%  Similarity=0.285  Sum_probs=49.8

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh--CCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL--KIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      +...+++||++|+..      .-+++.+|++.+  +++...|++.|..|.+.|.|-..-.- .|..|+
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------GNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPLANG-VYVITE   71 (111)
T ss_dssp             CCHHHHHHHHHHHHH------SCBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEECSTT-CEEECH
T ss_pred             cCHHHHHHHHHHHHc------CCCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEecCCc-eEEECc
Confidence            577899999999864      257999999999  99999999999999999999875333 677663

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=95.04  E-value=0.039  Score=39.16  Aligned_cols=54  Identities=19%  Similarity=0.300  Sum_probs=45.6

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +++-+..||++|.+.    ....+++++|++.+     +++...|...|+.|.+.|.|-..-.
T Consensus        15 ~t~~r~~IL~~l~~~----~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~   73 (83)
T 2fu4_A           15 VTLPRLKILEVLQEP----DNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNF   73 (83)
T ss_dssp             CCHHHHHHHHHHTSG----GGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             cCHHHHHHHHHHHhC----CCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEee
Confidence            466788899999863    11478999999999     7999999999999999999987644

>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=95.03  E-value=0.039  Score=43.67  Aligned_cols=48  Identities=27%  Similarity=0.475  Sum_probs=42.8

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .+.+.+||.+|+..      ..++..+|++.++++...|...|..|.+.|.|-.
T Consensus         2 d~~~~~il~~L~~~------~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   49 (150)
T 2pn6_A            2 DEIDLRILKILQYN------AKYSLDEIAREIRIPKATLSYRIKKLEKDGVIKG   49 (150)
T ss_dssp             CHHHHHHHHHHTTC------TTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCC
T ss_pred             ChHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence            56788999999863      2689999999999999999999999999999954

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=94.93  E-value=0.029  Score=44.56  Aligned_cols=48  Identities=23%  Similarity=0.395  Sum_probs=43.6

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +.+++.+||++|+..      ..++..+|++.++++...|+..|..|.++|.|-
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

>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=94.93  E-value=0.027  Score=44.04  Aligned_cols=48  Identities=23%  Similarity=0.499  Sum_probs=42.5

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +++++..||..|+..      ..++..+|+++++++...|+..|..|.++|.|-
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      257999999999999999999999999999994

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=94.91  E-value=0.033  Score=43.00  Aligned_cols=53  Identities=17%  Similarity=0.343  Sum_probs=45.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +++..+..||.+|.+.+    +..+++.+|++.++++...|..+|+.|.+.|.|...
T Consensus        23 gLt~~e~~il~~L~~~~----~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~   75 (123)
T 3r0a_A           23 NLTKADLNVMKSFLNEP----DRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRS   75 (123)
T ss_dssp             TCCHHHHHHHHHHHHST----TCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHHCC----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            67889999999998631    112999999999999999999999999999999764

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=94.87  E-value=0.07  Score=38.64  Aligned_cols=52  Identities=25%  Similarity=0.315  Sum_probs=44.5

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      .+.+..||.+|..      ..++++.+|++.++++...|...|..|.+.|.|-..-|.
T Consensus        23 ~~~~~~il~~l~~------~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~~   74 (99)
T 3cuo_A           23 HPKRLLILCMLSG------SPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRDA   74 (99)
T ss_dssp             SHHHHHHHHHHTT------CCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             ChHHHHHHHHHHh------CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecC
Confidence            3577889999865      237899999999999999999999999999999876554

>4gs3_A Single-stranded DNA-binding protein; primosome, oligonucleotide/oligosaccharide binding domain, D binding protein; 1.09A {Thermoanaerobacter tengcongensis}

Probab=94.86  E-value=0.33  Score=36.68  Aligned_cols=60  Identities=25%  Similarity=0.283  Sum_probs=42.4

Q ss_pred             EeeEEEEEEEEEe-----e-ecCCeeEEEEE-----cCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576           70 ITNVTLVGLVYNK-----E-ERASDVNFTLD-----DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF  133 (280)
Q Consensus        70 i~~V~iVG~V~~~-----~-~~~t~~~~~Ld-----DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f  133 (280)
                      .++|.|+|.+..=     + ....+.+|+|.     |.+--|.|..|...++    ...+..|+.|.|.|++++|
T Consensus        11 ~N~V~LiGrl~~dpelr~t~~G~~v~~f~lAV~R~~~~~Dfi~ivvw~klAe----~~~~~kG~~v~v~G~lrsy   81 (107)
T 4gs3_A           11 NNTVTLVGKVFTPLEFSHELYGEKFFNFILEVPRLSETKDYLPITISNRLFE----GMNLEVGTRVKIEGQLRSY   81 (107)
T ss_dssp             CSCEEEEEEECSCCEEEEEETTEEEEEEEEEEECTTSCEEEEEEEEEGGGST----TCCCCTTCEEEEEEEEEEE
T ss_pred             CCEEEEEEEECCCceEEEecCCcEEEEEEEEeCCCCCCCcEEEEEEEhHHhh----HHhhcCCCEEEEEEEEEec
Confidence            3778888888541     1 23346666664     5566799999987653    2335689999999999986

>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=94.80  E-value=0.034  Score=44.19  Aligned_cols=49  Identities=20%  Similarity=0.342  Sum_probs=44.0

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +.+++.+||++|+..      ..++..+|++++++++..|+..|..|.++|.|-.
T Consensus         6 ld~~d~~il~~L~~~------~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   54 (152)
T 2cg4_A            6 IDNLDRGILEALMGN------ARTAYAELAKQFGVSPETIHVRVEKMKQAGIITG   54 (152)
T ss_dssp             CCHHHHHHHHHHHHC------TTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             cCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcce
Confidence            677899999999864      3689999999999999999999999999999953

>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=94.79  E-value=0.1  Score=43.18  Aligned_cols=76  Identities=11%  Similarity=0.141  Sum_probs=50.0

Q ss_pred             eeEEEEEcCCceEEEEEecccccC-----hhhh------------ccC--CCCC--EEEEEEEEeeeCCe--eEEEEEEE
Q 023576           88 DVNFTLDDGTGRVVCKRWASEVFD-----TREM------------EAI--QDGM--YVRLIGNLKSFQGK--KQIVAFSV  144 (280)
Q Consensus        88 ~~~~~LdDgTG~I~~~~w~~~~~~-----~~~~------------~~~--~~G~--yVrV~G~l~~f~~~--~~i~~~~i  144 (280)
                      .+.+.|.|.||.+.|..|.+....     ....            ..+  ..+.  .++|..+...|+++  ...++.++
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            567889999999999999864320     0000            000  1122  45666667778766  56888999


Q ss_pred             eeCCCchHHHHHHHHHHHHH
Q 023576          145 RPVTNFDEVTCHYIECIYFH  164 (280)
Q Consensus       145 r~v~d~Nei~~H~Le~i~~~  164 (280)
                      .|| |+.+...|+|+.|...
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            999 6788889999998654

>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=94.78  E-value=0.038  Score=40.43  Aligned_cols=53  Identities=23%  Similarity=0.399  Sum_probs=46.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +++..+..||.+|...      .++++.+|++.++++...|...|..|.+.|.|...-+
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            4677888999999753      3689999999999999999999999999999987654

>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=94.77  E-value=0.06  Score=39.30  Aligned_cols=55  Identities=20%  Similarity=0.245  Sum_probs=45.8

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      .+.+..||.+| .       ..+++.+|++.++++...|...|..|.+.|.|...- . +|..+.
T Consensus        30 ~~~r~~Il~~L-~-------~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~-g-~y~l~~   84 (96)
T 1y0u_A           30 NPVRRKILRML-D-------KGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG-E-RWVVTD   84 (96)
T ss_dssp             CHHHHHHHHHH-H-------TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET-T-EEEECT
T ss_pred             CHHHHHHHHHH-c-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC-C-EEEECC
Confidence            34677899998 3       148999999999999999999999999999998765 3 776553

>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=94.71  E-value=0.042  Score=43.56  Aligned_cols=48  Identities=19%  Similarity=0.379  Sum_probs=43.4

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +++.+.+||.+|+..      ..++..+|+++++++...|...|..|.+.|.|-
T Consensus         5 ld~~~~~iL~~L~~~------~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   52 (150)
T 2w25_A            5 LDDIDRILVRELAAD------GRATLSELATRAGLSVSAVQSRVRRLESRGVVQ   52 (150)
T ss_dssp             CCHHHHHHHHHHHHC------TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            678899999999863      368999999999999999999999999999994

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=94.69  E-value=0.041  Score=45.00  Aligned_cols=49  Identities=39%  Similarity=0.527  Sum_probs=44.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      .+.+++.+||.+|+..      ..++..+|+++++++...|+..|..|.++|.|-
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            4678999999999864      258999999999999999999999999999993

>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=94.53  E-value=0.068  Score=41.06  Aligned_cols=56  Identities=20%  Similarity=0.386  Sum_probs=47.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...    .+.+++..+|++.++++...|..+|+.|.+.|.|...-|.
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            4667788899999864    2348999999999999999999999999999999987653

>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=94.50  E-value=0.039  Score=43.83  Aligned_cols=49  Identities=24%  Similarity=0.386  Sum_probs=43.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      .+++.+.+||++|+..      ..++..+|++.++++...|...|..|.+.|.|-
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            3678899999999864      268999999999999999999999999999994

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=94.47  E-value=0.05  Score=43.73  Aligned_cols=49  Identities=27%  Similarity=0.398  Sum_probs=43.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      .+++.+.+||++|+..      ..++..+|++.++++...|...|..|.+.|.|-
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            3678899999999864      247999999999999999999999999999994

>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=94.44  E-value=0.046  Score=57.56  Aligned_cols=75  Identities=16%  Similarity=0.228  Sum_probs=43.9

Q ss_pred             eeEEEEEEEEEeeec-----CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEe
Q 023576           71 TNVTLVGLVYNKEER-----ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVR  145 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~-----~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir  145 (280)
                      ..|.+.|.|.+++..     .....++|+|.||.+++++|.+.-.  .....+..+..|.|.|+++.-. ..+|.+..|.
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            357799999887532     2356789999999999999987532  2245689999999999997544 5788888887


Q ss_pred             eCC
Q 023576          146 PVT  148 (280)
Q Consensus       146 ~v~  148 (280)
                      +++
T Consensus      1120 ~l~ 1122 (1220)
T 2hpi_A         1120 TLE 1122 (1220)
T ss_dssp             EHH
T ss_pred             cHH
Confidence            653

>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=94.33  E-value=0.072  Score=40.96  Aligned_cols=56  Identities=21%  Similarity=0.418  Sum_probs=48.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...    .+.+++..+|++.++++...|...|+.|...|.|...-|.
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            4677888999999764    2459999999999999999999999999999999987654

>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=94.32  E-value=0.019  Score=47.89  Aligned_cols=56  Identities=16%  Similarity=0.309  Sum_probs=45.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .|+.-|++||++|.+.-. ......++.||++.|+++...|...|..|...|+|...
T Consensus         2 ~lt~~q~~il~~I~~~~~-~~g~~~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~~   57 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIE-KNGYPPSVREIARRFRITPRGALLHLIALEKKGYIERK   57 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHH-HHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECC
T ss_pred             CcCHHHHHHHHHHHHHHH-HhCCCCCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEec
Confidence            367899999999876310 11235799999999999999999999999999999764

>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=94.25  E-value=0.046  Score=40.96  Aligned_cols=34  Identities=24%  Similarity=0.518  Sum_probs=31.5

Q ss_pred             cc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          236 GV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       236 Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      -+ +..+|+++|+++...|++||..|.++|.|+..
T Consensus        42 ~lps~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~   76 (102)
T 2b0l_A           42 GLLVASKIADRVGITRSVIVNALRKLESAGVIESR   76 (102)
T ss_dssp             EEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            45 99999999999999999999999999999864

>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=94.17  E-value=0.65  Score=34.58  Aligned_cols=77  Identities=17%  Similarity=0.189  Sum_probs=48.7

Q ss_pred             EeeEEEEEEEEEee---e---cCCeeEEEE-----EcCCce-------EEEEEecccccChhhhccCCCCCEEEEEEEEe
Q 023576           70 ITNVTLVGLVYNKE---E---RASDVNFTL-----DDGTGR-------VVCKRWASEVFDTREMEAIQDGMYVRLIGNLK  131 (280)
Q Consensus        70 i~~V~iVG~V~~~~---~---~~t~~~~~L-----dDgTG~-------I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~  131 (280)
                      ++.|.|+|.+..--   .   ......|+|     .+.|+-       |.|..|...++  .....+..|+.|.|.|+|+
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            36788888886531   1   223455655     244677       99999976542  2235699999999999999


Q ss_pred             eeC---C--eeEEEEEEEeeCC
Q 023576          132 SFQ---G--KKQIVAFSVRPVT  148 (280)
Q Consensus       132 ~f~---~--~~~i~~~~ir~v~  148 (280)
                      .-.   |  +..|.+..|..+.
T Consensus        80 ~~~~~~G~~r~~v~~~~i~~l~  101 (104)
T 1txy_A           80 CHKAKNGLSKMVLHAEQIELID  101 (104)
T ss_dssp             C--------CCEEEEEEEEEC-
T ss_pred             eccCCCCCEEEEEEEEEEEECc
Confidence            742   1  1336666676654

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=94.11  E-value=0.12  Score=39.73  Aligned_cols=54  Identities=19%  Similarity=0.294  Sum_probs=46.3

Q ss_pred             CCCchhHHHHHHh-cCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYL-QQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i-~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+| ...      .+++..+|++.++++...|..+|+.|.+.|.|....|.
T Consensus        34 ~l~~~~~~iL~~l~~~~------~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~~~~   88 (146)
T 2fbh_A           34 GLSQARWLVLLHLARHR------DSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVA   88 (146)
T ss_dssp             CCTTTHHHHHHHHHHCS------SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCB
T ss_pred             CCCHHHHHHHHHHHHcC------CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeecCCC
Confidence            3566777899999 542      47999999999999999999999999999999987653

>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=94.09  E-value=0.073  Score=41.57  Aligned_cols=53  Identities=9%  Similarity=0.264  Sum_probs=40.0

Q ss_pred             chhHHHHHHhcCC---CCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          216 DCDQMILDYLQQP---SSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       216 ~~~~~Vl~~i~~~---~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ++-.+|.+.|+..   +.-...+=+ +..+++++|+++...||+|+..|..+|.|+.
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            4666666665541   111233346 7899999999999999999999999999986

>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=93.99  E-value=0.059  Score=38.74  Aligned_cols=47  Identities=15%  Similarity=0.263  Sum_probs=41.9

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I  266 (280)
                      ..+..+||++++..     .+||+-++|...+ +++.++.-++|..|..+|.|
T Consensus        13 ~~ie~~IL~l~~~~-----P~GItd~~L~~~~p~~~~~~r~~aIN~LL~~gki   60 (81)
T 2dk8_A           13 VEIENRIIELCHQF-----PHGITDQVIQNEMPHIEAQQRAVAINRLLSMGQL   60 (81)
T ss_dssp             HHHHHHHHHHHHHC-----SSCEEHHHHHHHCTTSCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHHHhC-----CCCCCHHHHHHHCCCCCHHHHHHHHHHHHHcCCe
Confidence            45888999999974     4699999999999 58999999999999999876

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=93.98  E-value=0.12  Score=39.08  Aligned_cols=35  Identities=14%  Similarity=0.264  Sum_probs=31.7

Q ss_pred             Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .-+ +..+|+++|+++...|++||..|.++|.|+..
T Consensus        31 ~~lPs~~~La~~~~vSr~tvr~al~~L~~~Gli~~~   66 (113)
T 3tqn_A           31 EMIPSIRKISTEYQINPLTVSKAYQSLLDDNVIEKR   66 (113)
T ss_dssp             CEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            345 89999999999999999999999999999864

>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=93.91  E-value=0.43  Score=35.61  Aligned_cols=64  Identities=16%  Similarity=0.270  Sum_probs=40.2

Q ss_pred             eeEEEEEEEEEeee----cCCeeEEEEE-cCCc-----eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC
Q 023576           71 TNVTLVGLVYNKEE----RASDVNFTLD-DGTG-----RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ  134 (280)
Q Consensus        71 ~~V~iVG~V~~~~~----~~t~~~~~Ld-DgTG-----~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~  134 (280)
                      +++.+||.|.+++.    ...-..|+|. |+.+     .+.++.+-+......-.+.+++|..|+|.|+||...
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    3344455543 4443     467777765432112246799999999999999864

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=93.74  E-value=0.089  Score=39.42  Aligned_cols=50  Identities=18%  Similarity=0.229  Sum_probs=42.4

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +.+..||.+|..       .++++.+|++.++++...|...|..|.+.|.|...-|.
T Consensus        25 ~~r~~IL~~L~~-------~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~~g   74 (108)
T 2kko_A           25 GRRLQILDLLAQ-------GERAVEAIATATGMNLTTASANLQALKSGGLVEARREG   74 (108)
T ss_dssp             STTHHHHHHHTT-------CCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEET
T ss_pred             HHHHHHHHHHHc-------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            456778888863       26899999999999999999999999999999766544

>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=93.74  E-value=0.092  Score=37.07  Aligned_cols=54  Identities=15%  Similarity=0.279  Sum_probs=46.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhC----CCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK----IPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~----~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+..||.+|...      .++++.+|++.++    ++...|...|+.|.+.|.|-..-|.
T Consensus         6 ~lt~~e~~vL~~L~~~------~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~g   63 (82)
T 1p6r_A            6 QISDAELEVMKVIWKH------SSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKEG   63 (82)
T ss_dssp             CCCHHHHHHHHHHHTS------SSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHcC------CCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEecC
Confidence            5788999999999762      3799999999995    7899999999999999999765444

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=93.68  E-value=0.17  Score=39.62  Aligned_cols=54  Identities=17%  Similarity=0.315  Sum_probs=46.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|....|.
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            4677888899999753      37999999999999999999999999999999987654

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=93.54  E-value=0.08  Score=41.01  Aligned_cols=55  Identities=20%  Similarity=0.419  Sum_probs=43.0

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +++..+..+|.+|....  ....++++.+|++.++++...|..+|..|.++|.|...
T Consensus        10 ~lt~~~~~~L~~l~~l~--~~~~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~   64 (139)
T 2x4h_A           10 NLSRREFSYLLTIKRYN--DSGEGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKK   64 (139)
T ss_dssp             -CCHHHHHHHHHHHHHH--TTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             hcCHHHHHHHHHHHHHH--hcCCCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEec
Confidence            35666777777664321  12357999999999999999999999999999999864

>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=93.51  E-value=0.078  Score=40.69  Aligned_cols=56  Identities=14%  Similarity=0.310  Sum_probs=48.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...    .+.+++..+|++.++++...|...|+.|...|+|....|.
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            4677888899999763    2358999999999999999999999999999999986654

>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=93.50  E-value=0.14  Score=39.51  Aligned_cols=54  Identities=15%  Similarity=0.278  Sum_probs=46.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|....|.
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            4677888899999752      48999999999999999999999999999999987664

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=93.42  E-value=0.15  Score=39.40  Aligned_cols=35  Identities=23%  Similarity=0.263  Sum_probs=32.0

Q ss_pred             Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .=+ +..+|+++|+++...|++||..|..+|.|+..
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            446 89999999999999999999999999999864

>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=93.37  E-value=1.3  Score=34.17  Aligned_cols=66  Identities=21%  Similarity=0.246  Sum_probs=46.1

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN  149 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d  149 (280)
                      +.|+|||+|.+++....  +++|+++-| .|.+++-...+      +  ..+.||.|+|++..   +..|.+.......+
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            68999999999875433  557777665 68888643211      1  22569999999984   45777777777665

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=93.34  E-value=0.19  Score=38.82  Aligned_cols=52  Identities=27%  Similarity=0.455  Sum_probs=44.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +++..+-.||.+|...       |++..+|++.++++...|...|+.|...|.|...-|
T Consensus        35 ~lt~~~~~iL~~l~~~-------~~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~~   86 (146)
T 3tgn_A           35 ALTNTQEHILMLLSEE-------SLTNSELARRLNVSQAAVTKAIKSLVKEGMLETSKD   86 (146)
T ss_dssp             CCCHHHHHHHHHHTTC-------CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---
T ss_pred             CCCHHHHHHHHHHHhC-------CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeccC
Confidence            5788999999999752       299999999999999999999999999999988765

>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=93.33  E-value=0.94  Score=40.09  Aligned_cols=68  Identities=19%  Similarity=0.280  Sum_probs=50.4

Q ss_pred             eeEEEEEEEEEeee----c--CCeeEEEEEcCCc-eEEEEEecccccChhhhccC-CCCCEEEEE-EEEeeeCCeeEEEE
Q 023576           71 TNVTLVGLVYNKEE----R--ASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAI-QDGMYVRLI-GNLKSFQGKKQIVA  141 (280)
Q Consensus        71 ~~V~iVG~V~~~~~----~--~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~-~~G~yVrV~-G~l~~f~~~~~i~~  141 (280)
                      ..|.|+|+|+.+..    +  .-.++|+|-|.+- .|.|.+|.+..   +..+.+ .+||.|++. -+++.|+++.++..
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            45788888887643    2  2378899999553 39999998653   235656 999999998 56788999988744

>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=93.27  E-value=0.1  Score=39.74  Aligned_cols=40  Identities=15%  Similarity=0.146  Sum_probs=32.1

Q ss_pred             CeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576           87 SDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG  128 (280)
Q Consensus        87 t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G  128 (280)
                      ..+.+.|-|.||.|.|.+|.+...  .....|++|+.+.|.+
T Consensus        40 ~~~~~~L~De~G~I~at~~~~~~~--~f~~~l~eG~vy~Is~   79 (114)
T 1ynx_A           40 KLFNVNFLDTSGEIRATAFNDFAT--KFNEILQEGKVYYVSK   79 (114)
T ss_dssp             EEEEEEEEETTEEEEEEECHHHHH--HHHHHSCSSSEEEEES
T ss_pred             eEEEEEEECCCCeEEEEECHHHHH--HHHhhcccCcEEEECC
Confidence            467889999999999999986532  2346799999888875

>3koj_A Uncharacterized protein YCF41; single-strand binding protein family, PF00436, SNR59A, NESG, structural genomics, PSI-2; 1.90A {Synechococcus elongatus pcc 6301}

Probab=93.25  E-value=1.1  Score=33.75  Aligned_cols=76  Identities=13%  Similarity=0.168  Sum_probs=48.7

Q ss_pred             EEeeEEEEEEEEEe---e--e-c-CCeeEEEEE-------cCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeee-
Q 023576           69 EITNVTLVGLVYNK---E--E-R-ASDVNFTLD-------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF-  133 (280)
Q Consensus        69 ~i~~V~iVG~V~~~---~--~-~-~t~~~~~Ld-------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f-  133 (280)
                      ..+.|.|+|.+..-   +  . . .....|+|.       |.|--|.|..|...++  .....+..|+.|.|.|+|+.- 
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            35788999998652   1  1 2 234555553       4566799999986542  223568999999999999964 


Q ss_pred             -CC---e----eEEEEEEEee
Q 023576          134 -QG---K----KQIVAFSVRP  146 (280)
Q Consensus       134 -~~---~----~~i~~~~ir~  146 (280)
                       .+   +    ..|.+..|.|
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             22   1    3466666655

>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=93.25  E-value=0.1  Score=38.07  Aligned_cols=55  Identities=24%  Similarity=0.369  Sum_probs=43.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+..++..+...     ..++++.+|++.++++...|...|..|.+.|.|...-+.
T Consensus        18 ~l~~~~~~~l~~l~~~-----~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~~~   72 (109)
T 2d1h_A           18 KITDTDVAVLLKMVEI-----EKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKTE   72 (109)
T ss_dssp             TCCHHHHHHHHHHHHH-----CSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-
T ss_pred             cCCHHHHHHHHHHHHc-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeeccc
Confidence            4566676666554331     247999999999999999999999999999999887553

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=93.22  E-value=0.13  Score=39.32  Aligned_cols=54  Identities=22%  Similarity=0.367  Sum_probs=46.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|...-|.
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            4677888899999763      47899999999999999999999999999999886543

>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=93.22  E-value=0.13  Score=39.56  Aligned_cols=54  Identities=22%  Similarity=0.380  Sum_probs=46.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .++++.+|++.++++...|..+|+.|.+.|.|....|.
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            3566777899998753      38999999999999999999999999999999987654

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=93.18  E-value=0.19  Score=39.03  Aligned_cols=35  Identities=23%  Similarity=0.397  Sum_probs=31.8

Q ss_pred             Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .=+ +..+|+++|+++...|++||..|..+|.|+..
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 89999999999999999999999999999864

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=93.15  E-value=0.16  Score=39.35  Aligned_cols=54  Identities=19%  Similarity=0.207  Sum_probs=47.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|+|....|.
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            4677888899999763      26999999999999999999999999999999987664

>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=93.12  E-value=0.14  Score=37.26  Aligned_cols=54  Identities=17%  Similarity=0.322  Sum_probs=46.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHH----HHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNEL----SEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I----~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|    ++.++++...|...|+.|.+.|.|....|.
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            4677888999999753      37899999    788899999999999999999999876554

>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=93.11  E-value=0.23  Score=38.27  Aligned_cols=53  Identities=23%  Similarity=0.263  Sum_probs=46.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|. .      .+++..+|++.++++...|..+|+.|.+.|.|...-|.
T Consensus        34 ~l~~~~~~iL~~l~-~------~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   86 (146)
T 2gxg_A           34 NLSYLDFLVLRATS-D------GPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDR   86 (146)
T ss_dssp             TCCHHHHHHHHHHT-T------SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHh-c------CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeecCC
Confidence            35678888999987 3      37899999999999999999999999999999876553

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=93.06  E-value=0.13  Score=44.50  Aligned_cols=60  Identities=18%  Similarity=0.347  Sum_probs=50.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      +++..+..||.+|.+.      .++++.+|++.++++.+.|...|..|.+.|.|-..-....|..|
T Consensus       149 ~L~~~~~~IL~~L~~~------~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~~r~~~~~LT  208 (244)
T 2wte_A          149 DYSREEMKLLNVLYET------KGTGITELAKMLDKSEKTLINKIAELKKFGILTQKGKDRKVELN  208 (244)
T ss_dssp             CCCHHHHHHHHHHHHH------TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTTEEEEC
T ss_pred             CCCHHHHHHHHHHHHc------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCccEEEEC
Confidence            6788899999998753      37999999999999999999999999999999876444456554

>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=93.03  E-value=0.17  Score=39.40  Aligned_cols=54  Identities=20%  Similarity=0.330  Sum_probs=47.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|..+|+.|...|.|....|.
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            4677888899999753      27999999999999999999999999999999987654

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=93.01  E-value=0.14  Score=39.25  Aligned_cols=53  Identities=25%  Similarity=0.330  Sum_probs=46.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|...-|
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            3566788899999753      3799999999999999999999999999999988765

>4gop_A Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=92.96  E-value=0.29  Score=37.36  Aligned_cols=67  Identities=15%  Similarity=0.203  Sum_probs=46.3

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCe---eEEEEEEEee
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGK---KQIVAFSVRP  146 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~---~~i~~~~ir~  146 (280)
                      ..|+|||+|.+...    -+++|...+| .|.|+.-.+        ..++.+.+|.|+|++..-.+.   ..|.+....+
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    3678887765 688775432        224578999999999965443   6677766555


Q ss_pred             CCC
Q 023576          147 VTN  149 (280)
Q Consensus       147 v~d  149 (280)
                      .-+
T Consensus        87 ~g~   89 (114)
T 4gop_A           87 CGH   89 (114)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=92.92  E-value=0.17  Score=39.28  Aligned_cols=54  Identities=17%  Similarity=0.259  Sum_probs=45.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|...-|.
T Consensus        37 ~l~~~~~~iL~~l~~~------~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   90 (148)
T 3nrv_A           37 GIGMTEWRIISVLSSA------SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS   90 (148)
T ss_dssp             TCCHHHHHHHHHHHHS------SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----
T ss_pred             CCCHHHHHHHHHHHcC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCC
Confidence            4677888999999763      28999999999999999999999999999999887553

>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=92.91  E-value=0.1  Score=40.29  Aligned_cols=54  Identities=22%  Similarity=0.359  Sum_probs=42.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|....|.
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            4677888999999863      37999999999999999999999999999999987664

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=92.88  E-value=0.13  Score=39.32  Aligned_cols=54  Identities=22%  Similarity=0.270  Sum_probs=46.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|....|.
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            4667788899999753      28999999999999999999999999999999886543

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=92.83  E-value=0.17  Score=39.44  Aligned_cols=50  Identities=20%  Similarity=0.355  Sum_probs=44.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +++..+-.||.+|...      .++++.+|++.++++...|...|+.|...|.|..
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            3667888899999763      3799999999999999999999999999999988

>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=92.81  E-value=0.16  Score=37.67  Aligned_cols=51  Identities=18%  Similarity=0.239  Sum_probs=43.2

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      .+.+..||.+|..       .++++.+|++.++++.+.|...|..|.+.|.|...-+.
T Consensus        25 ~~~r~~IL~~L~~-------~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~~g   75 (106)
T 1r1u_A           25 DYNRIRIMELLSV-------SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQG   75 (106)
T ss_dssp             SHHHHHHHHHHHH-------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CHHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            4567789998862       25899999999999999999999999999999765444

>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=92.79  E-value=0.13  Score=40.04  Aligned_cols=55  Identities=22%  Similarity=0.382  Sum_probs=44.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...     +.+++..+|++.++++...|...|+.|...|+|....|.
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            4667788899998642     246899999999999999999999999999999987665

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=92.75  E-value=0.29  Score=37.71  Aligned_cols=35  Identities=23%  Similarity=0.440  Sum_probs=31.7

Q ss_pred             Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .=+ +..+|+++|+++...|++||..|.++|.|+..
T Consensus        35 ~~Lps~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   70 (125)
T 3neu_A           35 DKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAK   70 (125)
T ss_dssp             CBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEe
Confidence            345 59999999999999999999999999999874

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=92.75  E-value=0.13  Score=39.72  Aligned_cols=54  Identities=13%  Similarity=0.122  Sum_probs=46.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|...-|.
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            4667888899999763      48999999999999999999999999999999987654

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=92.70  E-value=0.16  Score=40.09  Aligned_cols=54  Identities=28%  Similarity=0.411  Sum_probs=46.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|+|...-|.
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            4566777899999753      48999999999999999999999999999999987664

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=92.68  E-value=0.23  Score=33.11  Aligned_cols=44  Identities=18%  Similarity=0.347  Sum_probs=38.1

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .+|..|.+.     ..|++..|++.+++.+.++-+.+|+.|..+|.+--
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            577777664     36999999999999999999999999999998743

>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=92.63  E-value=0.1  Score=38.97  Aligned_cols=49  Identities=20%  Similarity=0.270  Sum_probs=40.9

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +...+|+..+..+     ...++..+|++.++++...|+++|..|.++|.|...
T Consensus        18 ~~~l~Il~~l~~~-----g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           18 DDVIDVLRILLDK-----GTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             STTHHHHHHHHHH-----CSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             hHHHHHHHHHHHc-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4667788877543     224899999999999999999999999999999764

>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=92.63  E-value=0.17  Score=40.52  Aligned_cols=55  Identities=20%  Similarity=0.279  Sum_probs=46.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...     ..++++.+|++.++++...|...|+.|...|+|....|.
T Consensus        50 glt~~q~~vL~~L~~~-----~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~~~  104 (166)
T 3deu_A           50 ELTQTHWVTLHNIHQL-----PPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCA  104 (166)
T ss_dssp             TCCHHHHHHHHHHHHS-----CSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             CCCHHHHHHHHHHHHc-----CCCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEeeCCC
Confidence            6788888999999752     247999999999999999999999999999999988764

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=92.62  E-value=0.13  Score=39.83  Aligned_cols=58  Identities=21%  Similarity=0.229  Sum_probs=44.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +++.-+-.||-+|.... .....+.+..+|++++++++.+|..+|+.|+..|.|--..|
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            45666666766664321 12345689999999999999999999999999999988655

>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=92.55  E-value=0.22  Score=38.30  Aligned_cols=54  Identities=20%  Similarity=0.345  Sum_probs=45.5

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +++..+..||.+|...     +.++++.+|++.++++...|...|+.|.+.|.|....|
T Consensus        23 gl~~~~~~il~~L~~~-----~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~~~   76 (152)
T 1ku9_A           23 GLNKSVGAVYAILYLS-----DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWI   76 (152)
T ss_dssp             TCCHHHHHHHHHHHHC-----SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             CCChhHHHHHHHHHHc-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec
Confidence            4667788899988421     24799999999999999999999999999999988653

>4ah6_A Aspartate--tRNA ligase, mitochondrial; 3.70A {Homo sapiens}

Probab=92.54  E-value=0.23  Score=48.80  Aligned_cols=74  Identities=19%  Similarity=0.148  Sum_probs=52.5

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC--hhhhccCCCCCEEEEEEEEeee----------CCeeE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD--TREMEAIQDGMYVRLIGNLKSF----------QGKKQ  138 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~G~yVrV~G~l~~f----------~~~~~  138 (280)
                      ..|+|.|+|..++..   .-+.|-|+||.|.|.+=.+....  ......+..|+.|.|.|.|+.-          .+...
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            369999999987643   35689999999999864332110  1224579999999999999752          24577


Q ss_pred             EEEEEEeeC
Q 023576          139 IVAFSVRPV  147 (280)
Q Consensus       139 i~~~~ir~v  147 (280)
                      |.+..|..+
T Consensus       102 l~~~~i~vL  110 (617)
T 4ah6_A          102 IKVKTAELL  110 (617)
T ss_dssp             EEEEEEEEE
T ss_pred             EEEeEEEEe
Confidence            777776643

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=92.47  E-value=0.19  Score=39.18  Aligned_cols=54  Identities=19%  Similarity=0.245  Sum_probs=46.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|....|.
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            4677888899999753      37999999999999999999999999999999987654

>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=92.46  E-value=1.3  Score=35.16  Aligned_cols=66  Identities=20%  Similarity=0.218  Sum_probs=45.8

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeCCC
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTN  149 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d  149 (280)
                      ..|+|||+|.++....  -+++|....| .|.|+.-..-        .-..+.||.|+|++..   +..|.+..+.+..|
T Consensus        44 k~VriVGkV~~~~~~G--~~~~l~s~Dg~~VtV~l~~pL--------~~~~~~~VEViG~V~~---~~tI~~~~~~~fGd  110 (142)
T 2pi2_E           44 KPVCFVGRLEKIHPTG--KMFILSDGEGKNGTIELMEPL--------DEEISGIVEVVGRVTA---KATILCTSYVQFKE  110 (142)
T ss_dssp             CEEEEEEEEEEECTTS--SEEEEECTTSCEEEEECSSCC--------SSCCCSEEEEEEEECT---TSCEEEEEEEECCC
T ss_pred             CEEEEEEEEeEEcCCC--CEEEEEeCCCcEEEEEeCCCC--------CccCCCEEEEEEEECC---CCcEEEEEEEecCC
Confidence            6899999999985433  3557777655 6888753210        1134789999999966   45677777777765

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=92.36  E-value=0.19  Score=38.97  Aligned_cols=54  Identities=22%  Similarity=0.348  Sum_probs=46.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|....|.
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            4567888899999763      37999999999999999999999999999999887553

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=92.32  E-value=0.35  Score=35.05  Aligned_cols=51  Identities=24%  Similarity=0.396  Sum_probs=43.3

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      .+.+..||.+|.+       ..+++.+|++.++++...|...|..|.+.|.|-..-+.
T Consensus        22 ~~~r~~Il~~L~~-------~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g   72 (98)
T 3jth_A           22 NERRLQILCMLHN-------QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKEA   72 (98)
T ss_dssp             SHHHHHHHHHTTT-------SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             CHHHHHHHHHHhc-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            3467788988864       36899999999999999999999999999999766544

>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=92.29  E-value=0.2  Score=38.28  Aligned_cols=54  Identities=11%  Similarity=0.123  Sum_probs=46.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|....|.
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            4667788899998753      37899999999999999999999999999999986554

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=92.28  E-value=0.22  Score=39.19  Aligned_cols=54  Identities=17%  Similarity=0.257  Sum_probs=44.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|..+|+.|...|.|....|.
T Consensus        46 ~lt~~~~~iL~~l~~~------~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~~~~   99 (162)
T 2fa5_A           46 GMAIPEWRVITILALY------PGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRETHG   99 (162)
T ss_dssp             CCCHHHHHHHHHHHHS------TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----
T ss_pred             CCCHHHHHHHHHHHhC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeecCC
Confidence            4677888899999752      37999999999999999999999999999999876543

>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=92.12  E-value=0.16  Score=45.79  Aligned_cols=58  Identities=17%  Similarity=0.233  Sum_probs=46.6

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK  276 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk  276 (280)
                      .+.+++||++|++.    ...-++-++|+++|+++...|.++|..|.++|+.-..+...-|+
T Consensus         2 ~~~~~~iL~~L~~~----~g~~~Sg~eLa~~lgvSr~aV~k~i~~L~~~G~~i~~~~~~GY~   59 (323)
T 3rkx_A            2 SKYSQDVLQLLYKN----KPNYISGQSIAESLNISRTAVKKVIDQLKLEGCKIDSVNHKGHL   59 (323)
T ss_dssp             -CHHHHHHHHHHHH----TTSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEEETTTEEE
T ss_pred             chHHHHHHHHHHhC----CCCccCHHHHHHHHCCCHHHHHHHHHHHHhcCCeEEEeCCCeEE
Confidence            35788999999753    23468999999999999999999999999999965555555555

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=92.11  E-value=0.21  Score=39.43  Aligned_cols=54  Identities=20%  Similarity=0.369  Sum_probs=46.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|....|.
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            4677888899999753      37999999999999999999999999999999886553

>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=92.09  E-value=0.16  Score=40.29  Aligned_cols=54  Identities=17%  Similarity=0.112  Sum_probs=48.0

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .++++.+|++.++++...|...|+.|...|+|....|.
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            5677888999999763      38999999999999999999999999999999987764

>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=92.06  E-value=0.099  Score=37.79  Aligned_cols=40  Identities=25%  Similarity=0.362  Sum_probs=37.1

Q ss_pred             CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      -.=++++.|++.|+++++++++.|..|+.+|.|+-.||.-
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            3578999999999999999999999999999999999873

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=92.05  E-value=0.17  Score=40.43  Aligned_cols=54  Identities=13%  Similarity=0.051  Sum_probs=47.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .++++.+|++.++++...|...|+.|...|.|....|.
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            4677888899999763      37999999999999999999999999999999886654

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=92.03  E-value=0.18  Score=39.41  Aligned_cols=54  Identities=13%  Similarity=0.281  Sum_probs=45.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|....|.
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            4677888899999753      48999999999999999999999999999999987654

>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=92.01  E-value=0.33  Score=35.68  Aligned_cols=42  Identities=12%  Similarity=0.055  Sum_probs=36.8

Q ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      |+...+|+..+++++..++..+++|.+.|.|-.+-  ..|..|+
T Consensus        20 ~~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~~--~~~~LT~   61 (95)
T 1r7j_A           20 GSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEG--KQYMLTK   61 (95)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET--TEEEECH
T ss_pred             CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEC--CeeEECh
Confidence            38999999999999999999999999999998863  3477764

>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=92.00  E-value=0.24  Score=37.88  Aligned_cols=51  Identities=14%  Similarity=0.163  Sum_probs=41.4

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +.+..||.+|...      .++++.+|++.++++.+.|...|..|.+.|.|-..-+.
T Consensus        42 ~~rl~IL~~L~~~------~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~~g   92 (122)
T 1u2w_A           42 ENRAKITYALCQD------EELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEG   92 (122)
T ss_dssp             HHHHHHHHHHHHS------SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             HHHHHHHHHHHHC------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEC
Confidence            4566788888742      36899999999999999999999999999999775443

>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=91.99  E-value=0.17  Score=39.55  Aligned_cols=54  Identities=20%  Similarity=0.362  Sum_probs=46.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .++++.+|++.++++...|...|+.|.+.|+|....|.
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            4667788899999752      37999999999999999999999999999999887553

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=91.98  E-value=0.16  Score=38.86  Aligned_cols=54  Identities=20%  Similarity=0.298  Sum_probs=46.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|.|....|.
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            4677888899999763      37999999999999999999999999999999876553

>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=91.98  E-value=0.19  Score=38.68  Aligned_cols=54  Identities=22%  Similarity=0.267  Sum_probs=46.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|.+.|.|....|.
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            3667888899999753      37999999999999999999999999999999886543

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=91.84  E-value=0.27  Score=37.79  Aligned_cols=56  Identities=16%  Similarity=0.221  Sum_probs=41.8

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC-ccccc
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE-FHYKF  277 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd-~hfk~  277 (280)
                      -.||.+|....   .+..++..+|+++++++...|+++|..|...|.|.++-.. -.|..
T Consensus        12 l~iL~~la~~~---~~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~~g~~ggy~L   68 (129)
T 2y75_A           12 LTIMIELAKKH---GEGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIRGAYGGYVL   68 (129)
T ss_dssp             HHHHHHHHHTT---TSCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC----CCEEE
T ss_pred             HHHHHHHHhCC---CCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEecCCCCCceEe
Confidence            34666665431   2346899999999999999999999999999999886432 24543

>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=91.79  E-value=1.9  Score=32.85  Aligned_cols=47  Identities=11%  Similarity=0.114  Sum_probs=35.6

Q ss_pred             EEEEEecccccChhhhccCCCCCEEEEEEEEeee--CC-eeEEEEEEEeeCCC
Q 023576          100 VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF--QG-KKQIVAFSVRPVTN  149 (280)
Q Consensus       100 I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f--~~-~~~i~~~~ir~v~d  149 (280)
                      |.|+.|-..++   ....+..|+.|.|.|+|+.-  ++ +..|.|..|..+..
T Consensus        49 i~vv~~Gk~AE---~~~~l~kGs~V~VeGrL~trs~~G~kl~l~a~~Ie~l~~   98 (115)
T 3fhw_A           49 ISAVALGDLAL---LLADTPLGTEMQVQGFLAPARKDSVKVKLHLQQARRIAG   98 (115)
T ss_dssp             EEEEEETHHHH---HHTTCCTTCEEEEEEEEEESSTTCSSEEEEEEEEEECCC
T ss_pred             EEEEEEhHHHH---hhhccCCCCEEEEEEEEEECCCCCCEEEEEEEEEEEcCC
Confidence            88999976542   24679999999999999973  23 34688888887754

>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=91.69  E-value=0.1  Score=40.69  Aligned_cols=56  Identities=23%  Similarity=0.401  Sum_probs=41.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...    .+.+++..+|++.++++...|...|+.|...|.|....|.
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            4677888999999763    2358999999999999999999999999999999887664

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=91.61  E-value=0.2  Score=39.60  Aligned_cols=54  Identities=20%  Similarity=0.226  Sum_probs=46.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|+|...-|.
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      38999999999999999999999999999999987664

>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=91.60  E-value=0.16  Score=36.58  Aligned_cols=50  Identities=18%  Similarity=0.264  Sum_probs=42.7

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      ++.+..||.+|...      .++++.+|++.++++...|...|..|.+.|.|...-
T Consensus        15 ~~~~~~iL~~L~~~------~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~~   64 (100)
T 1ub9_A           15 NPVRLGIMIFLLPR------RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYK   64 (100)
T ss_dssp             SHHHHHHHHHHHHH------SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             ChHHHHHHHHHHhc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            34677899988642      368999999999999999999999999999998654

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=91.59  E-value=0.25  Score=36.69  Aligned_cols=50  Identities=20%  Similarity=0.270  Sum_probs=42.6

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      .+.+..||.+|..       .++++.+|++.++++...|...|..|.+.|.|...-+
T Consensus        20 ~~~r~~IL~~L~~-------~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~   69 (114)
T 2oqg_A           20 DETRWEILTELGR-------ADQSASSLATRLPVSRQAIAKHLNALQACGLVESVKV   69 (114)
T ss_dssp             CHHHHHHHHHHHH-------SCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             ChHHHHHHHHHHc-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEec
Confidence            3577889999832       2589999999999999999999999999999976544

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=91.55  E-value=0.19  Score=38.83  Aligned_cols=54  Identities=22%  Similarity=0.234  Sum_probs=46.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+-.||.+|...      .+ +..+|++.++++...|...|+.|.+.|.|....|..
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            4667788899999763      24 999999999999999999999999999999876653

>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=91.53  E-value=0.17  Score=35.77  Aligned_cols=50  Identities=16%  Similarity=0.434  Sum_probs=40.0

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I  266 (280)
                      .++++.|+++|+..+.  .-.=.=+.++++.+ .....+|.+++..|++||.+
T Consensus         2 ee~K~~Ile~l~~k~~--~KskfYf~D~~k~~P~~k~r~vKK~~~~LV~Eg~l   52 (78)
T 1ucr_A            2 EEAKQKVVDFLNSKSG--SKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVL   52 (78)
T ss_dssp             CHHHHHHHHHHSSHHH--HSSCEEHHHHHHHCTTSCHHHHHHHHHHHHHTTSE
T ss_pred             hHHHHHHHHHHHhccc--ccccchHHHHHHHccccCHHHHHHHHHHHHhcCce
Confidence            4688999999987421  11134578999999 79999999999999999976

>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=91.50  E-value=0.19  Score=39.35  Aligned_cols=54  Identities=20%  Similarity=0.356  Sum_probs=46.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .++++.+|++.++++...|...|+.|.+.|.|...-|.
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            4677888899999763      27999999999999999999999999999999886553

>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=91.50  E-value=0.38  Score=35.18  Aligned_cols=51  Identities=20%  Similarity=0.295  Sum_probs=43.4

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      .+.+..||.+|.+       ..+++.+|++.++++...|...|..|.+.|.|-..-+.
T Consensus        22 ~~~r~~Il~~L~~-------~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g   72 (102)
T 3pqk_A           22 HPVRLMLVCTLVE-------GEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNI   72 (102)
T ss_dssp             SHHHHHHHHHHHT-------CCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECSS
T ss_pred             CHHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            4567789998864       14899999999999999999999999999999876554

>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=91.49  E-value=0.28  Score=42.20  Aligned_cols=54  Identities=20%  Similarity=0.388  Sum_probs=45.1

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      -.||++|.+.     ..++++.||+++++++.+.+...|..|.+.|.|... ++..|..+
T Consensus        11 l~iL~~l~~~-----~~~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~-~~~~Y~lg   64 (249)
T 1mkm_A           11 FEILDFIVKN-----PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK-KDKRYVPG   64 (249)
T ss_dssp             HHHHHHHHHC-----SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC-TTSCEEEC
T ss_pred             HHHHHHHHhC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC-CCCcEEEC
Confidence            3578888652     347999999999999999999999999999999986 56677653

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=91.42  E-value=0.51  Score=44.28  Aligned_cols=76  Identities=12%  Similarity=0.200  Sum_probs=53.2

Q ss_pred             eeEEEEEcCCceEEEEEeccccc----------------Chhh----hccCC-CCCEEEEEEEEeeeCCe--eEEEEEEE
Q 023576           88 DVNFTLDDGTGRVVCKRWASEVF----------------DTRE----MEAIQ-DGMYVRLIGNLKSFQGK--KQIVAFSV  144 (280)
Q Consensus        88 ~~~~~LdDgTG~I~~~~w~~~~~----------------~~~~----~~~~~-~G~yVrV~G~l~~f~~~--~~i~~~~i  144 (280)
                      .+.+.|.|+||.+.|..|.+.+.                +...    ...+. .--.+||..+...|+++  ...++..+
T Consensus       345 ~l~~~v~D~Tg~~~~~~F~~~a~~llG~sa~el~~~~~~d~~~~~~~~~~~~~k~~~f~~~~k~~~y~~~~r~~~~v~~~  424 (444)
T 4gop_C          345 ILSTNVADATGQMWLSGFNEDATQLIGMSAGELHKLREESESEFSAALHRAANRMYMFNCRAKMDTFNDTARVRYTISRA  424 (444)
T ss_dssp             CEEEEEEETTEEEEEEECHHHHHHHTTSCHHHHHHHHTTCHHHHHHHHHTTSSCEEEEEEEEEEEEETTEEEEEEEEEEE
T ss_pred             EEEEEEEeCCCCEEEEEehHHHHHHcCCCHHHHHHHHhcChHHHHHHHHHhhCcEEEEEEEEEeeeeCCeeEEEEEEEEe
Confidence            46679999999999999975432                0000    11111 11356777777799987  55778888


Q ss_pred             eeCCCchHHHHHHHHHHHHH
Q 023576          145 RPVTNFDEVTCHYIECIYFH  164 (280)
Q Consensus       145 r~v~d~Nei~~H~Le~i~~~  164 (280)
                      .|+ |+.+...++|+.|..+
T Consensus       425 ~~~-d~~~~~~~l~~~i~~~  443 (444)
T 4gop_C          425 APV-DFAKAGMELVDAIRAY  443 (444)
T ss_dssp             EEC-CHHHHHHHHHHHHHHH
T ss_pred             eeC-CHHHHHHHHHHHHHhh
Confidence            888 6888899999988765

>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase; 2.60A {Coxiella burnetii}

Probab=91.28  E-value=1.1  Score=36.05  Aligned_cols=79  Identities=23%  Similarity=0.260  Sum_probs=49.9

Q ss_pred             EEeeEEEEEEEEE---eee---cCCeeEEEEE------cC-Cc-------eEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576           69 EITNVTLVGLVYN---KEE---RASDVNFTLD------DG-TG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIG  128 (280)
Q Consensus        69 ~i~~V~iVG~V~~---~~~---~~t~~~~~Ld------Dg-TG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G  128 (280)
                      .++.|.|+|.|..   ++.   ....+.|+|-      |. +|       -|.|..|...++  .....++.|+.|.|.|
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            3788999999855   221   2245566552      22 34       378888976431  1234599999999999


Q ss_pred             EEee--eC---Ce----eEEEEEEEeeCCC
Q 023576          129 NLKS--FQ---GK----KQIVAFSVRPVTN  149 (280)
Q Consensus       129 ~l~~--f~---~~----~~i~~~~ir~v~d  149 (280)
                      +|+.  |.   |+    ..|.+..|..+..
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            9986  42   32    3466777776654

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=91.21  E-value=0.29  Score=38.40  Aligned_cols=57  Identities=16%  Similarity=0.247  Sum_probs=47.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++.-|-.||.+|...    .+.+++..+|++.++++...|...|+.|...|+|...-|.+
T Consensus        32 gLt~~q~~vL~~L~~~----~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~~~~   88 (147)
T 4b8x_A           32 GLTFARYEALVLLTFS----KSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNPN   88 (147)
T ss_dssp             TCCHHHHHHHHHHHTS----GGGEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC-
T ss_pred             CCCHHHHHHHHHHHHC----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEeecCC
Confidence            4677777899988653    23479999999999999999999999999999999887753

>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=91.19  E-value=0.28  Score=40.13  Aligned_cols=56  Identities=16%  Similarity=0.211  Sum_probs=48.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...    ...++++.+|++.++++...|...|..|...|+|....|.
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            3677888999999763    2358999999999999999999999999999999987664

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=91.16  E-value=0.16  Score=38.74  Aligned_cols=54  Identities=11%  Similarity=0.241  Sum_probs=46.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .++++.+|++.++++...|...|+.|.+.|.|....|.
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            4667888899999753      37999999999999999999999999999999876543

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=91.10  E-value=0.38  Score=37.52  Aligned_cols=53  Identities=15%  Similarity=0.259  Sum_probs=44.5

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecC
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      +++.+..||++|.+.    .+.-++.++|.+.+     +++...|-..|+.|.+.|.|-...
T Consensus        16 ~T~qR~~Il~~L~~~----~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~   73 (136)
T 1mzb_A           16 VTLPRVKILQMLDSA----EQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHN   73 (136)
T ss_dssp             CCHHHHHHHHHHHCC-----CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             CCHHHHHHHHHHHhC----CCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEEE
Confidence            577888999999863    21478999999998     599999999999999999997643

>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=91.10  E-value=0.98  Score=35.26  Aligned_cols=50  Identities=18%  Similarity=0.183  Sum_probs=34.3

Q ss_pred             ceEEEEEecccccChhhhccCCCCCEEEEEEEEee--eC---Ce----eEEEEEEEeeCCC
Q 023576           98 GRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS--FQ---GK----KQIVAFSVRPVTN  149 (280)
Q Consensus        98 G~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~--f~---~~----~~i~~~~ir~v~d  149 (280)
                      --|.|..|...++  .....++.|+.|.|.|+|+.  |.   ++    ..|.+..|..+..
T Consensus        49 ~~~~v~~wg~~Ae--~~~~~l~KG~~V~V~G~L~~~~~~dkdG~~r~~~ev~a~~i~~l~~  107 (134)
T 2vw9_A           49 CFIDARLFGRTAE--IANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMDK  107 (134)
T ss_dssp             EEEEEEEEHHHHH--HHHHHCCTTCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEEECCC
T ss_pred             EEEEEEEEcHHHH--HHHHhCCCCCEEEEEEEEEeeeEECCCCCEEEEEEEEEEEEEEccC
Confidence            3588999975431  12345999999999999986  43   22    2367777777654

>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=90.98  E-value=0.27  Score=42.14  Aligned_cols=54  Identities=17%  Similarity=0.285  Sum_probs=44.5

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      .||++|.+.     +.++++.||++.++++.+.+...|..|.+.|.|...-++..|..+
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            478888652     347999999999999999999999999999999885444567653

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=90.96  E-value=0.42  Score=37.72  Aligned_cols=55  Identities=18%  Similarity=0.256  Sum_probs=46.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..|-.||.+|...     +.+++..+|++.++++...|...|+.|...|+|....|.
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            4677777899988642     347888999999999999999999999999999977665

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=90.92  E-value=0.35  Score=41.96  Aligned_cols=51  Identities=20%  Similarity=0.398  Sum_probs=41.5

Q ss_pred             HHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          221 ILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       221 Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      ||++|..     .+.++++.||+++++++.+.+...|..|.+.|.|...-+. +|..
T Consensus        28 iL~~l~~-----~~~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~~~~-~Y~l   78 (260)
T 2o0y_A           28 LLELFDA-----AHPTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSRADG-SYSL   78 (260)
T ss_dssp             HHTTCBT-----TBSSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEECTTS-CEEE
T ss_pred             HHHHHhh-----CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCC-eEEe
Confidence            5555543     2358999999999999999999999999999999885444 7764

>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=90.90  E-value=0.27  Score=42.74  Aligned_cols=54  Identities=11%  Similarity=0.325  Sum_probs=44.1

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      .||++|.+     .+.++++.||+++++++.+.+...|..|.+.|.|...-+...|...
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            36666654     2458999999999999999999999999999999986554677643

>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA replication, phosphoprotein; 2.14A {Streptomyces coelicolor}

Probab=90.84  E-value=1.6  Score=36.59  Aligned_cols=75  Identities=23%  Similarity=0.287  Sum_probs=45.8

Q ss_pred             EeeEEEEEEEEE---eee---cCCeeEEEEEc---------------CCceEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576           70 ITNVTLVGLVYN---KEE---RASDVNFTLDD---------------GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG  128 (280)
Q Consensus        70 i~~V~iVG~V~~---~~~---~~t~~~~~LdD---------------gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G  128 (280)
                      ++.|.|+|.|..   ++.   ....+.|+|-=               .|--|.|+.|...++  .....|+.|+.|.|.|
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            467888888754   111   12355555531               234589999976432  2234699999999999


Q ss_pred             EEeee--CCe-------eEEEEEEEee
Q 023576          129 NLKSF--QGK-------KQIVAFSVRP  146 (280)
Q Consensus       129 ~l~~f--~~~-------~~i~~~~ir~  146 (280)
                      +|+.-  .++       ..|.+..|.+
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            99964  321       3466666654

>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis}

Probab=90.84  E-value=1.3  Score=33.49  Aligned_cols=79  Identities=23%  Similarity=0.318  Sum_probs=50.1

Q ss_pred             EeeEEEEEEEEE---eee---cCCeeEEEEE--c---------CCceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576           70 ITNVTLVGLVYN---KEE---RASDVNFTLD--D---------GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS  132 (280)
Q Consensus        70 i~~V~iVG~V~~---~~~---~~t~~~~~Ld--D---------gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~  132 (280)
                      ++.|.|+|.|..   +..   ....+.|+|-  .         .|--|.|..|...++  .....++.|+.|.|.|+|+.
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            577888888854   111   2245666652  1         122499999976432  12345899999999999995


Q ss_pred             --eC---Ce----eEEEEEEEeeCCCc
Q 023576          133 --FQ---GK----KQIVAFSVRPVTNF  150 (280)
Q Consensus       133 --f~---~~----~~i~~~~ir~v~d~  150 (280)
                        |.   |+    ..|.+..|..+...
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              44   22    35788888887654

>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=90.74  E-value=0.19  Score=38.61  Aligned_cols=53  Identities=17%  Similarity=0.211  Sum_probs=46.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +++..+-.||.+|...      .++++.+|++.++++...|..+|+.|.+.|.|-..-|
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            3566788899999753      3799999999999999999999999999999988765

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=90.72  E-value=0.51  Score=37.20  Aligned_cols=54  Identities=13%  Similarity=0.284  Sum_probs=45.6

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++.+..||++|.+.     +.-++.++|.+.+     +++...|-..|+.|.+.|.|-....+
T Consensus        20 ~T~qR~~Il~~L~~~-----~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~   78 (145)
T 2fe3_A           20 ITPQRHAILEYLVNS-----MAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYG   78 (145)
T ss_dssp             CCHHHHHHHHHHHHC-----SSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             CCHHHHHHHHHHHhC-----CCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeC
Confidence            567888999999863     3478999999999     59999999999999999999765443

>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis}

Probab=90.70  E-value=0.31  Score=45.76  Aligned_cols=69  Identities=14%  Similarity=0.286  Sum_probs=46.1

Q ss_pred             eEEEEEEEEEeee------c-----CCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeE
Q 023576           72 NVTLVGLVYNKEE------R-----ASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQ  138 (280)
Q Consensus        72 ~V~iVG~V~~~~~------~-----~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~  138 (280)
                      .|.|+|.|.++..      +     .....++|.|.|| .|.|.+|.+.+..-........|..|.+.| +++.|+|+ .
T Consensus       135 ~vDViG~V~~v~~~~~i~~k~~g~~~~kr~i~L~D~sg~~i~~tLWg~~A~~f~~~~~~~~~~VV~i~~~kV~~f~G~-~  213 (444)
T 4gop_C          135 QCDVIGILDSYGELSEIVSKASQRPVQKRELTLVDQGNRSVKLTLWGKTAETFPTNAGVDEKPVLAFKGVKVGDFGGR-S  213 (444)
T ss_dssp             CCBEEEEEEEECCCEEECCTTTCSCEEEEEEEEECTTCBEEEEEEEHHHHHTSTTSTTSSSCCEEEEESCEEECTTSS-E
T ss_pred             ceEEEEEEEEcCCcEEEEEccCCceeeEEEEEEEeCCCCEEEEEEEhhhhhhhhhhhccCCCCEEEEEeEEEeecCCe-E
Confidence            4567777777632      1     2467899999999 799999987542211011256788877765 67789885 6


Q ss_pred             EEE
Q 023576          139 IVA  141 (280)
Q Consensus       139 i~~  141 (280)
                      |++
T Consensus       214 ls~  216 (444)
T 4gop_C          214 LSM  216 (444)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            654

>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=90.58  E-value=0.33  Score=44.64  Aligned_cols=47  Identities=13%  Similarity=0.123  Sum_probs=41.5

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      ++.||++|+..      ..++..+|++.++++...|...+++|.++|.|.++-
T Consensus        18 ~~~il~~l~~~------~~~sr~~la~~~~ls~~tv~~~v~~L~~~g~i~~~~   64 (406)
T 1z6r_A           18 AGAVYRLIDQL------GPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQELE   64 (406)
T ss_dssp             HHHHHHHHHSS------CSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC-
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEeec
Confidence            35699999974      368999999999999999999999999999998853

>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold, DNA binding protein; 2.70A {Neisseria gonorrhoeae fa 1090}

Probab=90.57  E-value=3.1  Score=30.92  Aligned_cols=44  Identities=7%  Similarity=0.015  Sum_probs=31.5

Q ss_pred             EEEEEecccccChhhhccCCCCCEEEEEEEEee--eCCe-eEEEEEEEeeC
Q 023576          100 VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS--FQGK-KQIVAFSVRPV  147 (280)
Q Consensus       100 I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~--f~~~-~~i~~~~ir~v  147 (280)
                      |.|+.|-..++    ...+..|+.|.|.|+|+.  |+++ .-|.|..|..+
T Consensus        55 i~vv~~gk~Ae----~~~l~KG~~v~veGrL~~rs~~~~~lvlhi~~i~~i  101 (103)
T 3k8a_A           55 IPARILGRQAE----EWQYRQGDCATVEGFLAQKSRRSLMPMLRIQNIKEY  101 (103)
T ss_dssp             EEEEEEHHHHH----HSTTCTTCEEEEEEEEEESSSSCCCEEEEEEEEEEC
T ss_pred             EEEEEEhHHhh----hhccCCCCEEEEEEEEEECccCCccEEEEEEEEEEc
Confidence            78888876542    455999999999999985  5544 33555666554

>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=90.56  E-value=1.6  Score=34.93  Aligned_cols=78  Identities=17%  Similarity=0.253  Sum_probs=47.7

Q ss_pred             EeeEEEEEEEEE---ee---ecCCeeEEEEE--c-----C------CceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576           70 ITNVTLVGLVYN---KE---ERASDVNFTLD--D-----G------TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL  130 (280)
Q Consensus        70 i~~V~iVG~V~~---~~---~~~t~~~~~Ld--D-----g------TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l  130 (280)
                      ++.|.|+|.|..   ++   .....+.|+|-  .     .      |--|.|..|...++  .....++.|+.|.|.|+|
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            577888888854   11   12345566553  1     1      33488999975431  223459999999999999


Q ss_pred             ee--eC---Ce----eEEEEEEEeeCCC
Q 023576          131 KS--FQ---GK----KQIVAFSVRPVTN  149 (280)
Q Consensus       131 ~~--f~---~~----~~i~~~~ir~v~d  149 (280)
                      +.  |.   |+    ..|.+..|..+..
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            97  43   22    3577788877754

>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=90.55  E-value=0.37  Score=40.06  Aligned_cols=48  Identities=27%  Similarity=0.441  Sum_probs=42.6

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+.+..||.+|+.       ..+++.+|++.++++...|...|..|.+.|.|-..
T Consensus        19 d~~~~~IL~~L~~-------~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           19 EDTRRKILKLLRN-------KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             SHHHHHHHHHHTT-------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHc-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            5678889999973       25899999999999999999999999999999764

>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=90.55  E-value=0.87  Score=36.07  Aligned_cols=61  Identities=21%  Similarity=0.233  Sum_probs=42.8

Q ss_pred             EeeEEEEEEEEEe---e---ecCCeeEEEEE--------------cCCceEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576           70 ITNVTLVGLVYNK---E---ERASDVNFTLD--------------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN  129 (280)
Q Consensus        70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld--------------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~  129 (280)
                      ++.|.|+|.|..-   +   .....+.|+|-              |.|--|.|..|...++  .....++.|+.|.|.|+
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            6889999999552   2   22357778773              1233599999976432  12345999999999999


Q ss_pred             Eee
Q 023576          130 LKS  132 (280)
Q Consensus       130 l~~  132 (280)
                      |+.
T Consensus        83 L~~   85 (145)
T 1qvc_A           83 LRT   85 (145)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            986

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=90.44  E-value=0.44  Score=37.47  Aligned_cols=58  Identities=12%  Similarity=0.324  Sum_probs=41.0

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++.-|-.||.+|..... ....+++..+|++.++++...|...|+.|...|.| ...|+
T Consensus        30 gLt~~q~~vL~~l~~~~~-~~~~~~t~~eLa~~l~~~~~tvsr~v~~Le~~glV-r~~~~   87 (148)
T 4fx0_A           30 GLTNTQFSTLAVISLSEG-SAGIDLTMSELAARIGVERTTLTRNLEVMRRDGLV-RVMAG   87 (148)
T ss_dssp             TCCHHHHHHHHHHHC----------CHHHHHHHHTCCHHHHHHHHHHHHHTTSB-C----
T ss_pred             CCCHHHHHHHHHHHHhcC-CCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCE-EeeCC
Confidence            466777789999876531 12346999999999999999999999999999999 55554

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=90.41  E-value=0.54  Score=36.48  Aligned_cols=57  Identities=19%  Similarity=0.313  Sum_probs=47.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhC----CCHHHHHHHHHHHHhCCeeeecCCCcc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK----IPQKKIMDSIASLENEGLIYSTIDEFH  274 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~----~~~~~v~~al~~L~~eG~IYsTiDd~h  274 (280)
                      +++..+-.||.+|-..     ..+++..+|++.++    ++...|...|+.|...|.|-..-|...
T Consensus         6 ~lt~~e~~vL~~L~~~-----~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~~r~   66 (138)
T 2g9w_A            6 RLGDLERAVMDHLWSR-----TEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDDRA   66 (138)
T ss_dssp             GCCHHHHHHHHHHHTC-----SSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC---C
T ss_pred             cCCHHHHHHHHHHHhc-----CCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEecCCe
Confidence            5788899999999762     24799999999996    799999999999999999988766543

>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=90.31  E-value=0.24  Score=38.26  Aligned_cols=54  Identities=19%  Similarity=0.279  Sum_probs=45.0

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ++..+-.||.+|...     ..+++..+|++.++++...|..+|+.|...|.|....|.
T Consensus        33 l~~~~~~iL~~l~~~-----~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~~~~   86 (147)
T 2hr3_A           33 VQFSQLVVLGAIDRL-----GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP   86 (147)
T ss_dssp             HHHHHHHHHHHHHHT-----TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCHHHHHHHHHHHHc-----CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeCCCC
Confidence            456777899988751     247999999999999999999999999999999887654

>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=90.30  E-value=0.26  Score=38.02  Aligned_cols=54  Identities=20%  Similarity=0.278  Sum_probs=47.0

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|..+|+.|...|.|....|.
T Consensus        37 ~l~~~~~~iL~~l~~~------~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~~~~   90 (147)
T 1z91_A           37 NITYPQYLALLLLWEH------ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSE   90 (147)
T ss_dssp             CCCHHHHHHHHHHHHH------SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCS
T ss_pred             CCCHHHHHHHHHHHHC------CCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEeccCC
Confidence            4667788899999753      28999999999999999999999999999999887653

>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=90.13  E-value=0.17  Score=43.15  Aligned_cols=61  Identities=23%  Similarity=0.388  Sum_probs=48.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCH--HHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHV--NELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v--~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      +++..+..+|.+|....    +.|++.  .+|+++++++...|..+|+.|...|+|...-| ..+..|
T Consensus         3 ~lt~~~e~~L~~L~~l~----~~~~~~~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r~~~-~~v~LT   65 (230)
T 1fx7_A            3 ELVDTTEMYLRTIYDLE----EEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGD-RHLELT   65 (230)
T ss_dssp             TTSSHHHHHHHHHHHHH----HHTSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT-SCEEEC
T ss_pred             CCCHHHHHHHHHHHHHh----hcCCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC-ccEEEC
Confidence            46778888888886542    236766  99999999999999999999999999998765 344444

>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=90.04  E-value=0.64  Score=39.72  Aligned_cols=52  Identities=17%  Similarity=0.190  Sum_probs=37.3

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +.+.|.+.|.... -....-+ +..+++++++.+...||+||..|.++|.|+..
T Consensus        14 i~~~l~~~I~~g~-~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   66 (236)
T 3edp_A           14 IASKIKDSINRDE-YKTGMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVRK   66 (236)
T ss_dssp             HHHHHHHHHHTTS-SCCCC--CCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhCC-CCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3344445454421 1223456 79999999999999999999999999999873

>1sr3_A APO-CCME; OB fold, beta barrel, flexible C-terminal domain, chaperone; NMR {Escherichia coli} SCOP: b.40.9.1

Probab=89.89  E-value=1.3  Score=34.82  Aligned_cols=56  Identities=21%  Similarity=0.285  Sum_probs=43.4

Q ss_pred             eeEEEEEEEEE--eee--cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576           71 TNVTLVGLVYN--KEE--RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS  132 (280)
Q Consensus        71 ~~V~iVG~V~~--~~~--~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~  132 (280)
                      .+|+|-|.|..  +..  ....++|.|.|+...|.|.+--.      .++.|++|.=|-|.|++..
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  443  35689999999988898885432      2467999999999999863

>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3

Probab=89.84  E-value=1.7  Score=38.71  Aligned_cols=77  Identities=17%  Similarity=0.271  Sum_probs=51.4

Q ss_pred             EeeEEEEEEEEE---eee---cCCeeEEEEE------cC-------CceEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576           70 ITNVTLVGLVYN---KEE---RASDVNFTLD------DG-------TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNL  130 (280)
Q Consensus        70 i~~V~iVG~V~~---~~~---~~t~~~~~Ld------Dg-------TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l  130 (280)
                      ++.|.|+|.|..   +..   ....+.|+|-      |.       |--|.|..|...++  .... ++.|+.|.|.|+|
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   221   2346666663      22       22488999976432  1234 9999999999999


Q ss_pred             ee--eCCe-------eEEEEEEEeeCCC
Q 023576          131 KS--FQGK-------KQIVAFSVRPVTN  149 (280)
Q Consensus       131 ~~--f~~~-------~~i~~~~ir~v~d  149 (280)
                      +.  |.++       ..|.+..|..+..
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       3577788877765

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=89.82  E-value=0.17  Score=40.29  Aligned_cols=56  Identities=20%  Similarity=0.273  Sum_probs=45.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...    .+.++++.+|++.++++...|...|+.|...|+|....|.
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            4677888899999763    1358999999999999999999999999999999987654

>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=89.76  E-value=0.37  Score=39.65  Aligned_cols=47  Identities=26%  Similarity=0.367  Sum_probs=39.9

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCe-eee
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGL-IYS  268 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~-IYs  268 (280)
                      -+.+||++|++.     ...++..+|+++|+++...|+.-|..|.+.|. |..
T Consensus        22 R~~~Il~~L~~~-----~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~~I~~   69 (187)
T 1j5y_A           22 RLKSIVRILERS-----KEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVA   69 (187)
T ss_dssp             HHHHHHHHHHHC-----SSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEE
T ss_pred             HHHHHHHHHHHc-----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            456789999753     23599999999999999999999999999998 754

>1v1q_A Primosomal replication protein N; primosome, DNA replication, DNA binding; 2.1A {Escherichia coli} SCOP: b.40.4.3 PDB: 2ccz_A

Probab=89.73  E-value=6  Score=30.86  Aligned_cols=47  Identities=13%  Similarity=0.076  Sum_probs=31.6

Q ss_pred             EEEEEecccccChhhhccCCCCCEEEEEEEEeeeCC----ee-EEEEEEEeeCC
Q 023576          100 VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQG----KK-QIVAFSVRPVT  148 (280)
Q Consensus       100 I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~----~~-~i~~~~ir~v~  148 (280)
                      |.|+.|-..++  .....+..|+.|.|.|+|+.-.+    ++ .+.+..|..++
T Consensus        67 i~vv~wGk~AE--~~~~yl~KGs~V~VeGrL~tr~~k~G~kr~~~~a~~i~~l~  118 (134)
T 1v1q_A           67 MPVIVSGHENQ--AITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELID  118 (134)
T ss_dssp             EEEEEESTGGG--GGGTTCCTTCEEEEEEEEEEECTTTTSCEEEEEEEEEEETT
T ss_pred             EEEEEEhHHHH--HHHHhcCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEEECc
Confidence            89999976542  12345899999999999998632    22 23445555553

>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=89.61  E-value=0.68  Score=41.49  Aligned_cols=57  Identities=18%  Similarity=0.193  Sum_probs=45.1

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      .+.+.+||++|+.      ..-++.++|+++|++++..|+..|..|.+.|.+-.......|..
T Consensus         4 ~~r~~~Il~~L~~------~~~~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~i~~~~g~GY~l   60 (321)
T 1bia_A            4 NTVPLKLIALLAN------GEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGYSL   60 (321)
T ss_dssp             CHHHHHHHHHHTT------SSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEEETTTEEEC
T ss_pred             chHHHHHHHHHHc------CCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCcEEEecCCCcEE
Confidence            3467789999964      23689999999999999999999999999998854444334443

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=89.58  E-value=0.47  Score=40.97  Aligned_cols=52  Identities=10%  Similarity=0.209  Sum_probs=42.2

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      +||++|..     .+.++++.||+++++++.+.+...|..|.+.|.|...  +..|..+
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            36666653     2358999999999999999999999999999999874  4677643

>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=89.56  E-value=0.23  Score=37.40  Aligned_cols=55  Identities=16%  Similarity=0.247  Sum_probs=47.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhC----CCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK----IPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~----~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+..||.+|...      .+++..+|++.++    ++...|...|+.|.+.|.|...-|+.
T Consensus         7 ~lt~~~~~vL~~l~~~------~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~~r   65 (123)
T 1okr_A            7 EISSAEWEVMNIIWMK------KYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNK   65 (123)
T ss_dssp             CCCHHHHHHHHHHHHH------SSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEETT
T ss_pred             cCCHHHHHHHHHHHhC------CCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEecCC
Confidence            5788889999999752      3799999999997    88999999999999999998876654

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=89.53  E-value=0.23  Score=38.96  Aligned_cols=54  Identities=19%  Similarity=0.354  Sum_probs=45.0

Q ss_pred             CCCchhHHHHHHh-cCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYL-QQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i-~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+| ..      ..+++..+|++.++++...|...|+.|...|.|....|.
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            4677888899999 44      248999999999999999999999999999999987654

>3en2_A Probable primosomal replication protein N; PRIB RSR213C NESG X-RAY Q8XZT7 Q8XZT7_ralso, structural genomics, PSI-2; 2.30A {Ralstonia solanacearum}

Probab=89.40  E-value=1.7  Score=32.39  Aligned_cols=31  Identities=13%  Similarity=0.130  Sum_probs=24.4

Q ss_pred             EEEEEecccccChhhhccCCCCCEEEEEEEEeee
Q 023576          100 VVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSF  133 (280)
Q Consensus       100 I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f  133 (280)
                      |.|+.|-..+   +....+..|+.|.|.|+|+.-
T Consensus        50 i~vv~wGk~A---E~~~~~~kGs~V~VeGrL~tr   80 (101)
T 3en2_A           50 IEALGAGKMA---SVLDRIAPGTVLECVGFLARK   80 (101)
T ss_dssp             EEEEEETHHH---HHHTTSCTTCEEEEEEEEEEC
T ss_pred             EEEEEEhHHH---HHHhhcCCCCEEEEEEEEEeC
Confidence            8889997644   234568899999999999953

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=89.37  E-value=0.53  Score=37.38  Aligned_cols=52  Identities=21%  Similarity=0.353  Sum_probs=43.9

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +++.+..||++|.+.    .+.-++.++|.+.+     +++...|-..|+.|.+.|.|-..
T Consensus        15 ~T~qR~~Il~~L~~~----~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~   71 (150)
T 2w57_A           15 VTLPRLKILEVLQQP----ECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRH   71 (150)
T ss_dssp             CCHHHHHHHHHHTSG----GGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhC----CCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEE
Confidence            577888999999863    11468999999998     58999999999999999999764

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=89.30  E-value=0.47  Score=36.70  Aligned_cols=52  Identities=17%  Similarity=0.236  Sum_probs=43.8

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      ++.+..||++|.+.     +.-++.++|.+.+     +++...|-..|+.|.+.|.|-....
T Consensus        10 T~qR~~Il~~l~~~-----~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~   66 (131)
T 2o03_A           10 TRQRAAISTLLETL-----DDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHT   66 (131)
T ss_dssp             HHHHHHHHHHHHHC-----CSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEEC
T ss_pred             CHHHHHHHHHHHhC-----CCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEe
Confidence            55678899999753     3478999999999     5999999999999999999976543

>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=89.26  E-value=0.31  Score=37.97  Aligned_cols=49  Identities=16%  Similarity=0.310  Sum_probs=43.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +++..+-.||.+| ..      .+++..+|++.++++...|...|+.|...|.|..
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            4667888899999 42      4899999999999999999999999999999996

>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=89.14  E-value=0.87  Score=33.69  Aligned_cols=49  Identities=24%  Similarity=0.383  Sum_probs=41.5

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ..-.||..|..       ..+++.+|++.+ +++...+...|+.|.+.|.|....|.
T Consensus        15 ~~~~IL~~L~~-------~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~~~   64 (107)
T 2hzt_A           15 WKXVILXHLTH-------GKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYN   64 (107)
T ss_dssp             THHHHHHHHTT-------CCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred             cHHHHHHHHHh-------CCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecC
Confidence            45568877752       258999999999 99999999999999999999887664

>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=89.09  E-value=0.73  Score=38.92  Aligned_cols=36  Identities=17%  Similarity=0.267  Sum_probs=32.4

Q ss_pred             CCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          233 RERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       233 ~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ...=+ +..+++++|+++..-||+||..|..+|.|..
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            34567 6899999999999999999999999999975

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=89.09  E-value=0.21  Score=37.08  Aligned_cols=55  Identities=7%  Similarity=0.180  Sum_probs=46.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhC----CCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK----IPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~----~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+..||++|.+.      .+++..+|++.++    ++...|...|+.|++.|.|-..-|..
T Consensus        32 ~LT~~e~~VL~~L~~~------~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~~gR   90 (99)
T 2k4b_A           32 NVSNAELIVMRVIWSL------GEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKEGR   90 (99)
T ss_dssp             CCCCSCSHHHHHHHHH------SCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEEETT
T ss_pred             CCCHHHHHHHHHHHhC------CCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEeCCC
Confidence            5778888999999863      3799999999996    57899999999999999998765543

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=88.98  E-value=0.71  Score=36.90  Aligned_cols=47  Identities=19%  Similarity=0.153  Sum_probs=41.3

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .+.+++||++|+ .+      .+++.+|++.+++|-.++.-+|-.|..||.|.+
T Consensus        10 ~erk~~ILE~Lk-~G------~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~   56 (165)
T 2vxz_A           10 LVRLRDILALLA-DG------CKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTR   56 (165)
T ss_dssp             HHHHHHHHHHHT-TC------CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEE
T ss_pred             HHHHHHHHHHHH-hC------CccHHHHHHHhCCcHHHHHHHHHHHHhcCceEE
Confidence            346788999999 32      579999999999999999999999999999865

>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=88.97  E-value=0.71  Score=36.84  Aligned_cols=72  Identities=19%  Similarity=0.312  Sum_probs=46.2

Q ss_pred             CCeEECCEEEeeEEEEEEEEEeeec----CCeeEEE--EEcCC---c-----eEEEEEecccccChhhhccCCCCCEEEE
Q 023576           61 SNFMINGLEITNVTLVGLVYNKEER----ASDVNFT--LDDGT---G-----RVVCKRWASEVFDTREMEAIQDGMYVRL  126 (280)
Q Consensus        61 ~~~~i~g~~i~~V~iVG~V~~~~~~----~t~~~~~--LdDgT---G-----~I~~~~w~~~~~~~~~~~~~~~G~yVrV  126 (280)
                      ..+...-+.++.|.|+|+|.+...+    ..-..|+  ++...   |     -+.++.|- ......-...++.|+.|.|
T Consensus        35 ~~~~~h~r~vN~VvLmGRvtdpq~ry~~~~~Va~FtLAV~~~~~r~ge~~tdf~~V~vfG-g~lAE~i~~ylkkG~rVlV  113 (148)
T 3stb_C           35 GEVAAHWRCVNHCVMLGVVQNIQEGFVFEDKVLQFTLITDFEGPSPGDPDKDFHTVRVFD-SDYSSRVKEQLRDGEWFLV  113 (148)
T ss_dssp             ---CCCCSCSEEEEEEEEEEEEEEEEETTEEEEEEEEEEECSSCCTTSCSEEEEEEEECS-HHHHHHHHHHCCTTCEEEE
T ss_pred             hhhhhhheecceEEEEEEecCccccccCCCcEEEEEEEEecCCCCCCCCccceEEEEEEC-ChHHHHHHHHhcCCCEEEE
Confidence            3455556889999999999877654    1233444  43321   2     38888886 2111123467999999999


Q ss_pred             EEEEeee
Q 023576          127 IGNLKSF  133 (280)
Q Consensus       127 ~G~l~~f  133 (280)
                      .|+|+.-
T Consensus       114 eGRLrmn  120 (148)
T 3stb_C          114 TGRLRMV  120 (148)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEcc
Confidence            9999974

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=88.95  E-value=0.62  Score=40.11  Aligned_cols=34  Identities=15%  Similarity=0.301  Sum_probs=31.5

Q ss_pred             Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .=+ +..+++++++.+...||+||..|.++|.|+.
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            345 8899999999999999999999999999986

>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=88.95  E-value=0.42  Score=39.93  Aligned_cols=54  Identities=17%  Similarity=0.129  Sum_probs=47.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .+++..+|++.++++...|...|+.|...|+|....|.
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            4677888899999753      37999999999999999999999999999999988764

>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=88.78  E-value=3.7  Score=34.18  Aligned_cols=55  Identities=25%  Similarity=0.274  Sum_probs=35.5

Q ss_pred             EeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEEE
Q 023576           81 NKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQIV  140 (280)
Q Consensus        81 ~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i~  140 (280)
                      .......++.|.|.|.||.++|...-.-.     .-..++||-+|++. .|+...++++|.
T Consensus       133 KK~v~~~~~~YeI~DnTG~MeVvv~G~~~-----~i~CEeGDKLrL~cFeL~~~~~~~qL~  188 (208)
T 3rn5_A          133 KVTEKKKNILFDLSDNTGKMEVLGVRNED-----TMKCKEGDKVRLTFFTLSKNGEKLQLT  188 (208)
T ss_dssp             EEEECSSEEEEEEEETTEEEEEEEECSTG-----GGSCCTTCEEEEEEEEEEECSSSEEEE
T ss_pred             EEEeccceEEEEEecCCCcEEEEEeccCc-----ccccCCCCeeEEEEEEEeccCCeeeEE
Confidence            34455678999999999999999764421     23467887665543 334444555543

>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=88.65  E-value=0.87  Score=34.75  Aligned_cols=50  Identities=16%  Similarity=0.254  Sum_probs=41.5

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +.+..||.+|.+       .++++.+|++.++++...|...|..|.+.|.|-..-+.
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            456678888753       25799999999999999999999999999999765443

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=88.63  E-value=0.8  Score=36.06  Aligned_cols=51  Identities=16%  Similarity=0.247  Sum_probs=40.7

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      --.+|-+|....   .+.-++.++|+++++++..-|+++|..|...|.|-++-.
T Consensus        13 Al~~L~~La~~~---~~~~~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~rG   63 (143)
T 3t8r_A           13 GLTLMISLAKKE---GQGCISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSVRG   63 (143)
T ss_dssp             HHHHHHHHHTTT---TSCCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECSS
T ss_pred             HHHHHHHHHhCC---CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEecCC
Confidence            345666666531   233689999999999999999999999999999988643

>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=88.57  E-value=0.42  Score=44.38  Aligned_cols=46  Identities=17%  Similarity=0.198  Sum_probs=41.2

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      ++.||++|+..      ..++..+|++.++++...|...+++|.++|.|.++
T Consensus        41 ~~~il~~l~~~------~~~sr~ela~~~gls~~tv~~~v~~L~~~gli~~~   86 (429)
T 1z05_A           41 AGRVYKLIDQK------GPISRIDLSKESELAPASITKITRELIDAHLIHET   86 (429)
T ss_dssp             HHHHHHHHHHH------CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            35699999874      36899999999999999999999999999999875

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=88.56  E-value=0.55  Score=37.29  Aligned_cols=51  Identities=12%  Similarity=0.174  Sum_probs=43.2

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +++.+..||++|.+.     +.-++.++|.+.+     +++...|-..|+.|.+.|.|-..
T Consensus        25 ~T~qR~~IL~~l~~~-----~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~   80 (150)
T 2xig_A           25 NSKQREEVVSVLYRS-----GTHLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVL   80 (150)
T ss_dssp             CHHHHHHHHHHHHHC-----SSCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhC-----CCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEE
Confidence            466788899999863     3478999999998     59999999999999999999654

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=88.55  E-value=0.54  Score=40.84  Aligned_cols=51  Identities=6%  Similarity=0.198  Sum_probs=42.0

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      .||++|..     ...++++.||+++++++.+.+...|..|.+.|.|...  +..|..
T Consensus        25 ~iL~~l~~-----~~~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~~~--~~~Y~L   75 (265)
T 2ia2_A           25 AVIRCFDH-----RNQRRTLSDVARATDLTRATARRFLLTLVELGYVATD--GSAFWL   75 (265)
T ss_dssp             HHHHTCCS-----SCSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEES--SSEEEE
T ss_pred             HHHHHHHh-----CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec--CCEEEE
Confidence            36666653     2358999999999999999999999999999999884  467764

>2l02_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=88.55  E-value=0.73  Score=32.97  Aligned_cols=46  Identities=13%  Similarity=0.237  Sum_probs=39.9

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      -.|..+|.+.      ...++.+|++..+++.+++.-||-.|..|+.|.---
T Consensus        11 G~VW~~L~~~------~~~s~~el~k~t~l~d~el~lAIGWLaREdKI~~~~   56 (82)
T 2l02_A           11 GKVWHALNEA------DGISIPELARKVNLSVESTALAVGWLARENKVVIER   56 (82)
T ss_dssp             HHHHHHHHHC------CSBCHHHHHHHHTCCHHHHHHHHHHHHTTTSEEEEE
T ss_pred             HHHHHHHhcc------CCCCHHHHHHHhCCCHHHHHHHHHHHhccCceeEEe
Confidence            3688898863      278999999999999999999999999999987643

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=88.50  E-value=0.16  Score=41.11  Aligned_cols=57  Identities=28%  Similarity=0.310  Sum_probs=47.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...+   ...|+++.+|++.++++...|...|+.|...|+|....|.
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            57778889999998642   2247999999999999999999999999999999887653

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=88.44  E-value=1.2  Score=30.12  Aligned_cols=42  Identities=17%  Similarity=0.287  Sum_probs=35.3

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      ..|++.+.+|+.++.        .|.+..+|++.++++...|+..+..+.
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            358889999999873        378999999999999999988887654

>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=88.43  E-value=0.61  Score=39.89  Aligned_cols=55  Identities=16%  Similarity=0.162  Sum_probs=39.5

Q ss_pred             eEEEEEEEEEeee---------cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576           72 NVTLVGLVYNKEE---------RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG  128 (280)
Q Consensus        72 ~V~iVG~V~~~~~---------~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G  128 (280)
                      .++|.++|.++.+         ....+.+.|-|.+|.|.|..|.+...  ...+.|++|+.+.+.+
T Consensus        20 ~w~I~~rV~~k~~~r~~~~~~~~g~~~~~~L~De~G~I~at~~~~~~~--~~~~~l~~G~vy~i~~   83 (246)
T 1jmc_A           20 KWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRATAFNEQVD--KFFPLIEVNKVYYFSK   83 (246)
T ss_dssp             CCEEEEEEEEECCCEEEECSSCEEEEEEEEEECSSCEEEEEEEHHHHH--HHGGGCCTTCEEEEEC
T ss_pred             ceEEEEEEEEecccceeeCCCCCceEEEEEEECCCCeEEEEEChHHHH--HhhhhcccCCEEEECC
Confidence            4566777765421         12457889999999999999976431  2346799999998876

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=88.34  E-value=0.48  Score=37.13  Aligned_cols=51  Identities=18%  Similarity=0.180  Sum_probs=43.1

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +++.+..||++|.+.     ..-++.++|.+.+     +++...|-..|+.|.+.|.|-..
T Consensus        12 ~T~qR~~Il~~L~~~-----~~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~   67 (139)
T 3mwm_A           12 ATRQRAAVSAALQEV-----EEFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVL   67 (139)
T ss_dssp             HHHHHHHHHHHHTTC-----SSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEE
T ss_pred             cCHHHHHHHHHHHhC-----CCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEE
Confidence            356778899999874     2478999999988     48999999999999999998654

>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=88.30  E-value=1.1  Score=36.45  Aligned_cols=61  Identities=30%  Similarity=0.412  Sum_probs=40.3

Q ss_pred             EeeEEEEEEEEEe---e---ecCCeeEEEEE------c---------CCceEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576           70 ITNVTLVGLVYNK---E---ERASDVNFTLD------D---------GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG  128 (280)
Q Consensus        70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld------D---------gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G  128 (280)
                      ++.|.|+|.|..-   +   .....+.|+|-      |         .|--|.|..|...++  .....|+.|+.|.|.|
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            4678888888541   1   12235566664      1         233599999976432  2235699999999999


Q ss_pred             EEee
Q 023576          129 NLKS  132 (280)
Q Consensus       129 ~l~~  132 (280)
                      +|+.
T Consensus        82 rL~~   85 (168)
T 3afp_A           82 RLKQ   85 (168)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            9986

>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=0.84  Score=35.96  Aligned_cols=50  Identities=12%  Similarity=0.188  Sum_probs=42.1

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      ....||..|..       ..+++.+|++.++++...+...|..|.+.|.|-...+.+
T Consensus        25 w~l~IL~~L~~-------g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~~~~~   74 (146)
T 2f2e_A           25 WSMLIVRDAFE-------GLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAES   74 (146)
T ss_dssp             SHHHHHHHHHT-------TCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             hHHHHHHHHHh-------CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEEecCC
Confidence            55567777752       257999999999999999999999999999999877643

>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=88.20  E-value=2.8  Score=30.80  Aligned_cols=66  Identities=23%  Similarity=0.225  Sum_probs=46.8

Q ss_pred             eeEEEEEEEEE--eee--cCCeeEEEEEcC---CceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEE
Q 023576           71 TNVTLVGLVYN--KEE--RASDVNFTLDDG---TGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFS  143 (280)
Q Consensus        71 ~~V~iVG~V~~--~~~--~~t~~~~~LdDg---TG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~  143 (280)
                      .+++|-|.|..  +..  ....++|.|.|+   ...|.|.+--.      .++.|++|.-|-+.|++..-  .-.+.|..
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            57888899864  433  357899999998   67888885432      24679999999999998631  22455555


Q ss_pred             E
Q 023576          144 V  144 (280)
Q Consensus       144 i  144 (280)
                      |
T Consensus        81 v   81 (94)
T 2kct_A           81 L   81 (94)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=88.17  E-value=0.49  Score=36.55  Aligned_cols=43  Identities=9%  Similarity=0.166  Sum_probs=36.2

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      .++++.+|++.++++...|..+|..|...|.|...-+ -.|..|
T Consensus        21 ~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~~~-~~~~LT   63 (142)
T 1on2_A           21 GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKY-RGLVLT   63 (142)
T ss_dssp             SSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT-TEEEEC
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeeC-ceEEEc
Confidence            3789999999999999999999999999999987533 344444

>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=88.13  E-value=0.5  Score=35.62  Aligned_cols=56  Identities=16%  Similarity=0.229  Sum_probs=48.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhC----CCHHHHHHHHHHHHhCCeeeecCCCcc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK----IPQKKIMDSIASLENEGLIYSTIDEFH  274 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~----~~~~~v~~al~~L~~eG~IYsTiDd~h  274 (280)
                      +++..+-.||.+|-+.      .+++..+|++.++    ++...|...|+.|...|.|...-|...
T Consensus         7 ~Lt~~q~~vL~~L~~~------~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~~r~   66 (126)
T 1sd4_A            7 EISMAEWDVMNIIWDK------KSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSENI   66 (126)
T ss_dssp             CCCHHHHHHHHHHHHS------SSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             CCCHHHHHHHHHHHhc------CCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeCCCe
Confidence            5788999999999863      3799999999995    589999999999999999988766543

>2l01_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides vulgatus}

Probab=88.05  E-value=1.1  Score=31.63  Aligned_cols=47  Identities=15%  Similarity=0.215  Sum_probs=40.3

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCC-CHHHHHHHHHHHHhCCeeeecCC
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKI-PQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~-~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      -.|..+|.+.      ...++.+|.+..++ +.+++.-||-.|..|+.|..--.
T Consensus        13 G~VW~~L~~~------~~~s~~el~k~t~l~~d~el~lAiGWLaREdKI~~~~~   60 (77)
T 2l01_A           13 GQIWEALNGT------EGLTQKQIKKATKLKADKDFFLGLGWLLREDKVVTSEV   60 (77)
T ss_dssp             HHHHHHHTTS------SCEEHHHHHHHHTCSCHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             HHHHHHHhcC------CCCCHHHHHHHHCCCCHHHHHHHHHHHhhcCceEEEee
Confidence            4689999863      37899999999999 99999999999999998876433

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=87.92  E-value=0.8  Score=40.04  Aligned_cols=35  Identities=14%  Similarity=0.260  Sum_probs=32.0

Q ss_pred             Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .-+ +..+++++++.+...||+||..|.++|.|+.-
T Consensus        51 ~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   86 (272)
T 3eet_A           51 TRLPSQARIREEYGVSDTVALEARKVLMAEGLVEGR   86 (272)
T ss_dssp             SBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            456 79999999999999999999999999999863

>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=87.90  E-value=0.54  Score=33.90  Aligned_cols=42  Identities=17%  Similarity=0.184  Sum_probs=35.7

Q ss_pred             HHHHhcCCCCCCCCCccCHHHHHHHhCCCHHH-HHHHHHHHHhCCeee
Q 023576          221 ILDYLQQPSSSERERGVHVNELSEQLKIPQKK-IMDSIASLENEGLIY  267 (280)
Q Consensus       221 Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~-v~~al~~L~~eG~IY  267 (280)
                      +|.+|...     +.++++.+|++.++++... |...|+.|.+.|+|.
T Consensus        20 ~L~~l~~~-----~~~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~   62 (95)
T 2pg4_A           20 TLLEFEKK-----GYEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVK   62 (95)
T ss_dssp             HHHHHHHT-----TCCCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEE
T ss_pred             HHHHHHhc-----CCCCCHHHHHHHHCCCchHHHHHHHHHHHHCCCee
Confidence            45555442     2379999999999999999 999999999999998

>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=87.89  E-value=1  Score=32.49  Aligned_cols=43  Identities=26%  Similarity=0.426  Sum_probs=36.6

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN  262 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~  262 (280)
                      ..|++-+++||.++.        +|.+..+|++.|++++..|+.-+..+..
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            468999999999986        3899999999999999999988877653

>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3

Probab=87.83  E-value=2  Score=38.20  Aligned_cols=78  Identities=14%  Similarity=0.197  Sum_probs=47.8

Q ss_pred             EeeEEEEEEEEEe---e---ecCCeeEEEEE------cCCc-------eEEEEEecccccChhhhcc-CCCCCEEEEEEE
Q 023576           70 ITNVTLVGLVYNK---E---ERASDVNFTLD------DGTG-------RVVCKRWASEVFDTREMEA-IQDGMYVRLIGN  129 (280)
Q Consensus        70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld------DgTG-------~I~~~~w~~~~~~~~~~~~-~~~G~yVrV~G~  129 (280)
                      ++.|.|+|.|..-   .   .....+.|+|-      |.+|       -|.|..|...++  ..... ++.|+.|.|.|+
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            6789999998542   2   12345666662      1123       488888965431  12345 899999999999


Q ss_pred             Eee--eCCe-------eEEEEEEEeeCCC
Q 023576          130 LKS--FQGK-------KQIVAFSVRPVTN  149 (280)
Q Consensus       130 l~~--f~~~-------~~i~~~~ir~v~d  149 (280)
                      |+.  |.++       ..|.+..|..+..
T Consensus        83 L~~r~~~dkdG~~r~~~ev~a~~i~~l~~  111 (301)
T 1se8_A           83 LEYRQWEAPEGGKRSAVNVKALRMEQLGT  111 (301)
T ss_dssp             EEEEEEC-----CEEEEEEEEEEEEECSS
T ss_pred             EEeeeEECCCCCEEEEEEEEEeEEEEeec
Confidence            994  6532       2366777776654

>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=87.80  E-value=2.5  Score=33.22  Aligned_cols=56  Identities=16%  Similarity=0.189  Sum_probs=43.0

Q ss_pred             eeEEEEEEEEE--eee--cCCeeEEEEEc-CCceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576           71 TNVTLVGLVYN--KEE--RASDVNFTLDD-GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS  132 (280)
Q Consensus        71 ~~V~iVG~V~~--~~~--~~t~~~~~LdD-gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~  132 (280)
                      .+|+|-|.|..  +..  ....++|.|.| +...|.|.+--.      .++.|++|.-|-|.|++..
T Consensus        33 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~~v~V~Y~Gi------lPDlFrEGqgVVa~G~l~~   93 (136)
T 1j6q_A           33 QRIRVGGMVTVGSMVRDPNSLHVQFAVHDSLGGEILVTYDDL------LPDLFREGQGIVAQGVLGE   93 (136)
T ss_dssp             CEEEEEEEECTTCCEECTTSSCEEEEEECTTCCCEEEEECSC------CTTSCCSSSEEEEEEEECS
T ss_pred             CEEEEeEEEeCCcEEecCCCCEEEEEEEcCCCCEEEEEECCC------CCccccCCCeEEEEEEECC
Confidence            57889999963  443  35689999999 777898875432      2467999999999999863

>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=87.75  E-value=1.3  Score=32.64  Aligned_cols=61  Identities=11%  Similarity=0.223  Sum_probs=48.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+=.||..|.+.....++..++..+|++++.++...+...|+.|...|+|=.+.++|
T Consensus        13 gl~~~q~~vL~~L~~~~~~~~g~~~s~~eLa~~l~l~~stLsR~l~rLe~~GLV~r~~~~D   73 (96)
T 2obp_A           13 GIDPAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVSVEAD   73 (96)
T ss_dssp             CCCHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTT
T ss_pred             CCCHHHHHHHHHHHHHHhhCCCCCcCHHHHHHHhCCchhhHHHHHHHHHHCCCEEeecCCC
Confidence            5777777788877654222234458999999999999999999999999999998776643

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=87.73  E-value=0.69  Score=34.87  Aligned_cols=51  Identities=22%  Similarity=0.319  Sum_probs=43.7

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      .+.+..||.+|..       ..+++.+|++.++++...|...|..|.+.|.|-..-+.
T Consensus        17 ~~~R~~Il~~L~~-------~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~g   67 (118)
T 3f6o_A           17 DPTRRAVLGRLSR-------GPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQG   67 (118)
T ss_dssp             SHHHHHHHHHHHT-------CCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CHHHHHHHHHHHh-------CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEecC
Confidence            4577889999973       25799999999999999999999999999999776543

>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=87.68  E-value=0.69  Score=41.93  Aligned_cols=50  Identities=24%  Similarity=0.419  Sum_probs=43.4

Q ss_pred             CCchhHHHHH-----HhcCCCCCCCCCccCHHHHHHHh--CCCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILD-----YLQQPSSSERERGVHVNELSEQL--KIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~-----~i~~~~~~~~e~Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +++=+++||+     +|+.      ..-|.+.+|++++  +.++..||..|..|.++|.|..+
T Consensus        15 l~eR~~~IL~~i~~~yl~~------~~pV~s~~La~~~~l~VS~aTIRrDL~~LE~~GlL~r~   71 (338)
T 1stz_A           15 LNDRQRKVLYCIVREYIEN------KKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQP   71 (338)
T ss_dssp             CCHHHHHHHHHHHHHHHHH------CSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHHHHHHHHHHHHc------CCCccHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEc
Confidence            4567888999     6665      2468999999999  89999999999999999999876

>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=87.57  E-value=1.1  Score=31.45  Aligned_cols=42  Identities=14%  Similarity=0.299  Sum_probs=35.3

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      ..|++.+++|+.++.        +|.+..+|++.+++++..|+..+..+.
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            358889999999862        389999999999999999988776654

>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=87.53  E-value=1.8  Score=36.89  Aligned_cols=66  Identities=20%  Similarity=0.353  Sum_probs=45.2

Q ss_pred             eeEEEEEEEEEeee------c-----CCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCee
Q 023576           71 TNVTLVGLVYNKEE------R-----ASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKK  137 (280)
Q Consensus        71 ~~V~iVG~V~~~~~------~-----~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~  137 (280)
                      ..|.|+|.|.++..      +     .....+.|.|.|| .|.|.+|.+.+.   . .....|..|.+.| +++.|++ +
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 SLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDAD---K-FDGSRQPVLAIKGARVSDFGG-R  213 (246)
T ss_dssp             CEEEEEEEEEEECCCEEEEETTTTEEEEEEEEEEECTTCCEEEEEEEHHHHH---H-CCCTTCCEEEEEEEEEECTTS-S
T ss_pred             CceeEEEEEEEecCeEEEEEecCCCccEEEEEEEECCCCCEEEEEEEchhhh---h-cccCCCCEEEEEEEEEEecCC-e
Confidence            35778888877642      1     1467889999999 599999987542   1 1246677777665 5667854 6


Q ss_pred             EEEE
Q 023576          138 QIVA  141 (280)
Q Consensus       138 ~i~~  141 (280)
                      .|++
T Consensus       214 ~ls~  217 (246)
T 1jmc_A          214 SLSV  217 (246)
T ss_dssp             EEEC
T ss_pred             EEEe
Confidence            7765

>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=87.35  E-value=0.69  Score=28.21  Aligned_cols=39  Identities=13%  Similarity=0.059  Sum_probs=30.5

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCC
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEG  264 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG  264 (280)
                      +..|+.++.        .|++..+|++.|+++...|...+......|
T Consensus        11 ~~~i~~~~~--------~g~s~~~IA~~lgis~~Tv~~~~~~~~~~g   49 (51)
T 1tc3_C           11 RAQLDVMKL--------LNVSLHEMSRKISRSRHCIRVYLKDPVSYG   49 (51)
T ss_dssp             HHHHHHHHH--------TTCCHHHHHHHHTCCHHHHHHHHHCSTTTT
T ss_pred             HHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHhhHHhcC
Confidence            345666553        388999999999999999999887766555

>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=87.27  E-value=1  Score=38.46  Aligned_cols=52  Identities=19%  Similarity=0.366  Sum_probs=38.1

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +.+.|.+.|.... -....=+ +..+++++++.+...||+||..|.++|.|+..
T Consensus        10 i~~~l~~~I~~g~-~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~g~i~~~   62 (239)
T 3bwg_A           10 IATEIETYIEEHQ-LQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQV   62 (239)
T ss_dssp             HHHHHHHHHHHTT-CCTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhCC-CCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEe
Confidence            4444555444321 1123356 79999999999999999999999999999863

>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=87.19  E-value=3.1  Score=36.12  Aligned_cols=78  Identities=18%  Similarity=0.301  Sum_probs=52.6

Q ss_pred             EEeeEEEEEEEEEe---e---ecCCeeEEEEE----------cCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee
Q 023576           69 EITNVTLVGLVYNK---E---ERASDVNFTLD----------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS  132 (280)
Q Consensus        69 ~i~~V~iVG~V~~~---~---~~~t~~~~~Ld----------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~  132 (280)
                      .++.|.|+|.|..-   .   .....+.|+|-          |.|--|.|..|...+.  ... .++.|+.|.|.|+|+.
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            36899999999652   2   12346677763          2344699999975431  224 8999999999999986


Q ss_pred             --eC---Ce----eEEEEEEEeeCCC
Q 023576          133 --FQ---GK----KQIVAFSVRPVTN  149 (280)
Q Consensus       133 --f~---~~----~~i~~~~ir~v~d  149 (280)
                        |.   |+    ..|.+..|..+..
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    2477778877765

>4dam_A Single-stranded DNA-binding protein 1; OB-fold; 1.70A {Streptomyces coelicolor}

Probab=87.17  E-value=1  Score=34.93  Aligned_cols=62  Identities=21%  Similarity=0.149  Sum_probs=42.0

Q ss_pred             EEEeeEEEEEEEEEe------eecCCeeEEEEE------c---------CCceEEEEEecccccChhhhccCCCCCEEEE
Q 023576           68 LEITNVTLVGLVYNK------EERASDVNFTLD------D---------GTGRVVCKRWASEVFDTREMEAIQDGMYVRL  126 (280)
Q Consensus        68 ~~i~~V~iVG~V~~~------~~~~t~~~~~Ld------D---------gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV  126 (280)
                      ..|+.|.|+|.|..-      ... ..+.|+|-      |         .|--+.|..|...++  .....++.|+.|.|
T Consensus        13 ~~~N~V~LiGrL~~dPelr~t~~G-~v~~fslAv~~~~~d~~~Ge~~d~~t~w~~v~~wg~~Ae--~~~~~l~KG~~V~V   89 (128)
T 4dam_A           13 MNEIMICAVGNVATTPVFRDLANG-PSVRFRLAVTARYWDREKNAWTDGHTNFFTVWANRQLAT--NASGSLAVGDPVVV   89 (128)
T ss_dssp             BCCCEEEEEEEECSCCEEEEETTE-EEEEEEEEEEEEEEETTTTEEEEEEEEEEEEEEEHHHHH--HHHHHCCTTCEEEE
T ss_pred             cceeEEEEEEEECCCCEEEEcCCC-CEEEEEEEEcCceecccCCceecCCcEEEEEEEEcHHHH--HHHHhcCCCCEEEE
Confidence            567889999998541      123 56667662      2         223488888865432  22356999999999


Q ss_pred             EEEEee
Q 023576          127 IGNLKS  132 (280)
Q Consensus       127 ~G~l~~  132 (280)
                      .|+|+.
T Consensus        90 eGrL~~   95 (128)
T 4dam_A           90 QGRLKV   95 (128)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            999985

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=87.05  E-value=0.49  Score=34.74  Aligned_cols=35  Identities=26%  Similarity=0.467  Sum_probs=31.9

Q ss_pred             Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .-+ ++.+|++.|+++...|+++|..|.++|.|...
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 89999999999999999999999999999864

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=86.98  E-value=1  Score=38.55  Aligned_cols=35  Identities=29%  Similarity=0.483  Sum_probs=31.8

Q ss_pred             Ccc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          235 RGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       235 ~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .=+ +..+++++++.+...||+||..|.++|.|+..
T Consensus        32 ~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   67 (243)
T 2wv0_A           32 MPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRL   67 (243)
T ss_dssp             CBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence            345 78999999999999999999999999999863

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=86.56  E-value=0.47  Score=37.25  Aligned_cols=59  Identities=15%  Similarity=0.275  Sum_probs=42.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee--cCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS--TIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs--TiDd  272 (280)
                      ++++-+-.|+=.|.... .....+.+.++|++++++++.+|...|+.|++.|.|--  ..|+
T Consensus        29 gLs~~E~~lLl~L~~~~-~~g~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~~~~d~   89 (135)
T 2v79_A           29 GLNETELILLLKIKMHL-EKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIEECEDQ   89 (135)
T ss_dssp             TCCHHHHHHHHHHHHHH-TTTCCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEEEEEECT
T ss_pred             CCCHHHHHHHHHHHHHH-hcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeEecC
Confidence            45555544433332210 12346899999999999999999999999999999877  4454

>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=86.24  E-value=0.43  Score=34.51  Aligned_cols=51  Identities=16%  Similarity=0.185  Sum_probs=38.8

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      ++.-+-.||.+|-...  .....++..+|++.++++...|...|+.|...|+|
T Consensus        10 l~~~~~~iL~~l~~~~--~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv   60 (95)
T 2qvo_A           10 FKEKALEILMTIYYES--LGGNDVYIQYIASKVNSPHSYVWLIIKKFEEAKMV   60 (95)
T ss_dssp             SCHHHHHHHHHHHHHH--HTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHTTSE
T ss_pred             CchhHHHHHHHHHHcc--CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCc
Confidence            4555556666653311  11123999999999999999999999999999999

>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=86.21  E-value=1.6  Score=33.44  Aligned_cols=65  Identities=18%  Similarity=0.189  Sum_probs=42.6

Q ss_pred             EEeeEEEEEEEEE---ee---ecCCeeEEEEE------cC-Cc-------eEEEEEec-ccccChhhhccCCCCCEEEEE
Q 023576           69 EITNVTLVGLVYN---KE---ERASDVNFTLD------DG-TG-------RVVCKRWA-SEVFDTREMEAIQDGMYVRLI  127 (280)
Q Consensus        69 ~i~~V~iVG~V~~---~~---~~~t~~~~~Ld------Dg-TG-------~I~~~~w~-~~~~~~~~~~~~~~G~yVrV~  127 (280)
                      -++.|.|+|.|..   +.   .....+.|+|-      |. +|       -+.|..|. ..++  .....++.|+.|.|.
T Consensus         5 ~~N~v~l~Grl~~dpelr~t~~G~~v~~f~lA~~~~~~~~~~G~~~~~t~~~~v~~wg~~~Ae--~~~~~l~KG~~V~V~   82 (124)
T 3ulp_A            5 SLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVD--LIDKYLRKGRRVYVQ   82 (124)
T ss_dssp             CEEEEEEEEEECSCCEEEECTTSCEEEEEEEEEEEEEECTTTCCEEEEEEEEEEEECCHHHHH--HHHHHCCTTCEEEEE
T ss_pred             cceEEEEEEEECCCcEEEECCCCCEEEEEEEEEccceecccCCcEecccEEEEEEEEEchHHH--HHHhhcCCCCEEEEE
Confidence            4788999999864   22   12245666652      21 23       48899997 4331  123459999999999


Q ss_pred             EEEe--eeCC
Q 023576          128 GNLK--SFQG  135 (280)
Q Consensus       128 G~l~--~f~~  135 (280)
                      |+|+  .|.+
T Consensus        83 G~L~~~~~~d   92 (124)
T 3ulp_A           83 GSLHTRKWHT   92 (124)
T ss_dssp             EEEEEEEECC
T ss_pred             EEEEeEEEeC
Confidence            9998  4654

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=86.19  E-value=0.93  Score=35.52  Aligned_cols=37  Identities=16%  Similarity=0.184  Sum_probs=33.4

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      .++++.+|++.++++...|..+|..|...|.|...-+
T Consensus        53 ~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~~~   89 (155)
T 2h09_A           53 GEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMIPW   89 (155)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEETT
T ss_pred             CCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEecC
Confidence            3689999999999999999999999999999987643

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=86.12  E-value=0.61  Score=40.82  Aligned_cols=52  Identities=19%  Similarity=0.310  Sum_probs=41.7

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccc
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKF  277 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~  277 (280)
                      .||++|...     ..++++.||+++++++.+.+...|..|.+.|.|...- +..|..
T Consensus        34 ~IL~~l~~~-----~~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~~-~~~Y~L   85 (275)
T 3mq0_A           34 RILDLVAGS-----PRDLTAAELTRFLDLPKSSAHGLLAVMTELDLLARSA-DGTLRI   85 (275)
T ss_dssp             HHHHHHHHC-----SSCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEECT-TSEEEE
T ss_pred             HHHHHHhhC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC-CCcEEe
Confidence            478888753     3589999999999999999999999999999999853 346764

>3sxy_A Transcriptional regulator, GNTR family; transcription factor, metal-binding, structur genomics, PSI-2, protein structure initiative; 1.65A {Thermotoga maritima} PDB: 3dbw_A 3fms_A*

Probab=85.87  E-value=0.83  Score=38.17  Aligned_cols=36  Identities=33%  Similarity=0.462  Sum_probs=32.5

Q ss_pred             CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +..=++..+|+++|+++..-||+||..|..+|.|-.
T Consensus        32 pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~   67 (218)
T 3sxy_A           32 LGEKLNVRELSEKLGISFTPVRDALLQLATEGLVKV   67 (218)
T ss_dssp             TTCEECHHHHHHHHTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCCEeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            445679999999999999999999999999999964

>3k7u_C MP18 RNA editing complex protein; OB-fold, RNA-editing proteins, kinetoplastids, system, RNA binding protein; 2.10A {Trypanosoma brucei} PDB: 3k80_D 3stb_D

Probab=85.84  E-value=2.2  Score=33.95  Aligned_cols=61  Identities=21%  Similarity=0.296  Sum_probs=41.0

Q ss_pred             EeeEEEEEEEEEeeec----CCeeEEEEE--------------cCCceEEEEEeccc-ccChhhhccCCCCCEEEEEEEE
Q 023576           70 ITNVTLVGLVYNKEER----ASDVNFTLD--------------DGTGRVVCKRWASE-VFDTREMEAIQDGMYVRLIGNL  130 (280)
Q Consensus        70 i~~V~iVG~V~~~~~~----~t~~~~~Ld--------------DgTG~I~~~~w~~~-~~~~~~~~~~~~G~yVrV~G~l  130 (280)
                      ++.|.|+|.|..--++    ...+.|+|-              +.|--+.|..|... ++  .....++.|+.|.|.|+|
T Consensus         6 ~NkV~LiGrLg~DPer~t~G~~va~FslAv~~~~~~~~Ge~~~~~t~w~~vv~wgk~lAe--~~~~yl~KG~~V~VeGrL   83 (148)
T 3k7u_C            6 VNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGELFSA--EVKQKVKEGNVVCVNGRL   83 (148)
T ss_dssp             CCCEEEEEEEEEEEEEESSSSEEEEEEEEEECC-----------CEEEEEEEEESHHHHH--HHHHHCCTTCEEEEEEEE
T ss_pred             CcEEEEEEEeccCCEeeeCCcEEEEEEEEECCceecCCCCEEccccEEEEEEEECcHHHH--HHHhhCCCCCEEEEEEEE
Confidence            6788888888653222    235555552              23445999999764 31  223569999999999999


Q ss_pred             ee
Q 023576          131 KS  132 (280)
Q Consensus       131 ~~  132 (280)
                      +.
T Consensus        84 ~~   85 (148)
T 3k7u_C           84 RL   85 (148)
T ss_dssp             EE
T ss_pred             Ee
Confidence            96

>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=85.80  E-value=0.69  Score=46.69  Aligned_cols=65  Identities=25%  Similarity=0.266  Sum_probs=47.5

Q ss_pred             eEEEEEEEEEeee----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCC--CCEEEEEEEEeee--CCeeEEE
Q 023576           72 NVTLVGLVYNKEE----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQD--GMYVRLIGNLKSF--QGKKQIV  140 (280)
Q Consensus        72 ~V~iVG~V~~~~~----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~--G~yVrV~G~l~~f--~~~~~i~  140 (280)
                      .|.|.|.|.+...    ....+..++.|+||.|.+++|...    .....+++  |..|.|.|+++.+  .+..++.
T Consensus       167 ~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~f~~~----~~~~~~~~~~g~~~~~~G~~~~~~~~~~~~~~  239 (780)
T 1gm5_A          167 KVTTQGKIVSVETKKFQNMNILTAVLSDGLVHVPLKWFNQD----YLQTYLKQLTGKEVFVTGTVKSNAYTGQYEIH  239 (780)
T ss_dssp             CCEEEECCCCCEEEECSSCEEEEEEECCSSCCEEEEECSCC----TTHHHHHTTCSSCEEEEEEECSCCTTSSCCEE
T ss_pred             EEEEEEEEEEEEeecCCCCeEEEEEEEECCceEEEEEECcH----HHHhhCccCCCCEEEEEEEEEEccCCCcEEEE
Confidence            7888998877532    234677889999999998877522    22345777  9999999999985  4554443

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=85.66  E-value=1.2  Score=35.74  Aligned_cols=50  Identities=14%  Similarity=0.213  Sum_probs=39.3

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      -.+|-+|....   .+.-++.++|++++++++.-++++|..|...|.|-++-.
T Consensus        30 lr~L~~LA~~~---~~~~~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s~rG   79 (159)
T 3lwf_A           30 LTITLELAKRI---GDGPISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIRG   79 (159)
T ss_dssp             HHHHHHHHHTT---TSCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECS
T ss_pred             HHHHHHHHhcC---CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecC
Confidence            34555554321   233589999999999999999999999999999998743

>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=85.65  E-value=1.2  Score=32.91  Aligned_cols=49  Identities=22%  Similarity=0.320  Sum_probs=41.0

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhC-CCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLK-IPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~-~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ....||..|..       .++++.+|++.++ ++...|...|..|.+.|.|-...|.
T Consensus        26 ~~~~IL~~L~~-------~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~~   75 (107)
T 2fsw_A           26 WTLLIIFQINR-------RIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQYP   75 (107)
T ss_dssp             SHHHHHHHHTT-------SCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred             cHHHHHHHHHh-------CCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEeecC
Confidence            44567777752       2689999999995 9999999999999999999887765

>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=85.58  E-value=1.2  Score=37.76  Aligned_cols=50  Identities=8%  Similarity=0.099  Sum_probs=44.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .++..+..|+++++..      .++++.++++.++.+..-.+++|+.|+.+|.+.-
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            4567889999999753      4999999999999999999999999999999985

>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=85.40  E-value=0.82  Score=36.05  Aligned_cols=50  Identities=18%  Similarity=0.306  Sum_probs=42.6

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      ++..+..||++|.+.     + -++.++|.+.+     +++...|-.+|+.|.+.|.|-..
T Consensus        17 ~T~qR~~Il~~l~~~-----~-h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i   71 (145)
T 3eyy_A           17 LTPQRQLVLEAVDTL-----E-HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHA   71 (145)
T ss_dssp             CCHHHHHHHHHHHHH-----S-SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             cCHHHHHHHHHHHhc-----C-CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEE
Confidence            577888899999863     3 68999999988     48999999999999999998553

>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=85.39  E-value=1.1  Score=38.65  Aligned_cols=56  Identities=14%  Similarity=0.223  Sum_probs=49.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++.-|-.||.+|...    .+.+++..+|++.++++...|..+|+.|...|.|.-.-|+
T Consensus       155 gLt~~q~~vL~~L~~~----~~~~~t~~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~~~~  210 (250)
T 1p4x_A          155 TLSFVEFTILAIITSQ----NKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERST  210 (250)
T ss_dssp             SSCHHHHHHHHHHHTT----TTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECS
T ss_pred             CCCHHHHHHHHHHHhC----CCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCCC
Confidence            6888888999999764    2236999999999999999999999999999999987765

>1u5t_A Appears to BE functionally related to SNF7; SNF8P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 PDB: 1w7p_A

Probab=85.38  E-value=1.2  Score=38.17  Aligned_cols=51  Identities=14%  Similarity=0.174  Sum_probs=45.2

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ..++.-+..||+++...      ..++++++.+.++.+....+++|+.|+.+|.++-
T Consensus       163 ~el~~D~~~vLe~a~~~------g~vt~~~L~~~lgW~~~Ra~~~L~~l~~~G~lwv  213 (233)
T 1u5t_A          163 NELTSDQTKILEICSIL------GYSSISLLKANLGWEAVRSKSALDEMVANGLLWI  213 (233)
T ss_dssp             SCCCTTHHHHHHTTTTT------SCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEE
T ss_pred             CccchHHHHHHHHHHhc------CcCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            35788899999988642      4899999999999999999999999999999985

>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=85.04  E-value=1.4  Score=37.47  Aligned_cols=37  Identities=14%  Similarity=0.296  Sum_probs=33.1

Q ss_pred             CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +..=++..+|+++|+++..-||+||..|..+|.|...
T Consensus        46 pG~~L~e~~La~~lgVSr~~VReAL~~L~~~Glv~~~   82 (237)
T 3c7j_A           46 SGTALRQQELATLFGVSRMPVREALRQLEAQSLLRVE   82 (237)
T ss_dssp             TTCBCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCeeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3456799999999999999999999999999999753

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=84.97  E-value=1.6  Score=33.15  Aligned_cols=52  Identities=13%  Similarity=0.131  Sum_probs=41.4

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccc
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYK  276 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk  276 (280)
                      +..+|++.++.       .+..+.++++.++++++.+++.|..|..+|.|.. +++++|-
T Consensus         8 l~~~i~~~~~~-------~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~-i~~~~~~   59 (121)
T 2pjp_A            8 IWQKAEPLFGD-------EPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITA-IVKDRYY   59 (121)
T ss_dssp             HHHHHGGGCSS-------SCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE-EETTEEE
T ss_pred             HHHHHHHHHHh-------CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE-ecCCceE
Confidence            44556666642       4679999999999999999999999999999988 4555553

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=84.90  E-value=1.5  Score=36.85  Aligned_cols=44  Identities=11%  Similarity=0.260  Sum_probs=36.9

Q ss_pred             CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      ..+++..+|+++|+++...|..+|..|..+|+|...-| ..+..|
T Consensus        18 ~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~~-~~i~LT   61 (214)
T 3hrs_A           18 HNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDKK-AGYLLT   61 (214)
T ss_dssp             CSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT-TEEEEC
T ss_pred             CCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEecC-CCeEEC
Confidence            35899999999999999999999999999999987644 234443

>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=84.86  E-value=1.1  Score=38.19  Aligned_cols=52  Identities=8%  Similarity=0.180  Sum_probs=39.1

Q ss_pred             hhHHHHHHhcCC---CCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          217 CDQMILDYLQQP---SSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       217 ~~~~Vl~~i~~~---~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +...|++.|++.   +.-.+..=++..+|+++|+++..-||+||..|..+|.|..
T Consensus        29 ~~~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~   83 (239)
T 2hs5_A           29 RTTRVAGILRDAIIDGTFRPGARLSEPDICAALDVSRNTVREAFQILIEDRLVAH   83 (239)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHHHcCCCCCcCEeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            455555555431   1123345679999999999999999999999999999965

>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=84.82  E-value=1.5  Score=30.60  Aligned_cols=50  Identities=20%  Similarity=0.403  Sum_probs=43.2

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +-+...++|+..      .=+.++++|..|++..+++.+.|+.|.++|.|-=-+||
T Consensus         8 ll~~Fi~yIk~~------Kvv~LedLA~~F~l~t~~~i~RI~~Le~~g~ltGViDD   57 (72)
T 1wi9_A            8 FLTEFINYIKKS------KVVLLEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDD   57 (72)
T ss_dssp             HHHHHHHHHHHC------SEECHHHHHHHHCSCHHHHHHHHHHHHHHSSSCEEECT
T ss_pred             HHHHHHHHHHHc------CeeeHHHHHHHhCCChHHHHHHHHHHHHCCCeEEEEeC
Confidence            556778888874      36799999999999999999999999999988777776

>3lgj_A Single-stranded DNA-binding protein; niaid, CAT scratch fever, rochalimaea, LYME disease, ALS collaborative crystallography, DNA replication; 2.50A {Bartonella henselae}

Probab=84.82  E-value=2.3  Score=34.64  Aligned_cols=63  Identities=19%  Similarity=0.248  Sum_probs=41.7

Q ss_pred             EEeeEEEEEEEEE---eee---cCCeeEEEEE------c--------CCceEEEEEecc-cccChhhhccCCCCCEEEEE
Q 023576           69 EITNVTLVGLVYN---KEE---RASDVNFTLD------D--------GTGRVVCKRWAS-EVFDTREMEAIQDGMYVRLI  127 (280)
Q Consensus        69 ~i~~V~iVG~V~~---~~~---~~t~~~~~Ld------D--------gTG~I~~~~w~~-~~~~~~~~~~~~~G~yVrV~  127 (280)
                      -++.|.|+|.|..   ++.   ....+.|+|-      |        .|--|.|..|.. .++  .....++.|+.|.|.
T Consensus        22 ~mNkV~LiGrL~~DPelr~t~~G~~v~~FslAv~~~~~~~~~Ge~~~~t~~i~vv~wg~~lAe--~~~~~l~KG~~V~Ve   99 (169)
T 3lgj_A           22 MLNKVMLIGYLGDDPESKTMTSGAEVVNFRMATFESYMNKNTHQKVEKTEWHSVVVFNPHFAK--IALQYLHKGSKVYIE   99 (169)
T ss_dssp             CEEEEEEEEEESSCCEEEECTTSCEEEEEEEEEEC------------CEEEEEEEECCHHHHH--HHHHHCCTTCEEEEE
T ss_pred             ceeEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecccCCccccccEEEEEEEeCHHHHH--HHHHhCCCCCEEEEE
Confidence            3789999999954   221   2245556552      1        233588999976 331  223459999999999


Q ss_pred             EEEeee
Q 023576          128 GNLKSF  133 (280)
Q Consensus       128 G~l~~f  133 (280)
                      |+|+.-
T Consensus       100 GrL~~r  105 (169)
T 3lgj_A          100 GKLQTR  105 (169)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            999864

>3ihu_A Transcriptional regulator, GNTR family; YP_298823.1, DNA binding protein, structural genomics, joint for structural genomics, JCSG; HET: MSE; 1.92A {Ralstonia eutropha}

Probab=84.74  E-value=1.1  Score=37.45  Aligned_cols=52  Identities=8%  Similarity=0.174  Sum_probs=39.5

Q ss_pred             hhHHHHHHhcCC---CCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          217 CDQMILDYLQQP---SSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       217 ~~~~Vl~~i~~~---~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +...|++.|++.   +.-....=++..+|+++|+++..-||+||..|..+|.|-.
T Consensus        17 ~~~~v~~~l~~~I~~g~l~pG~~L~E~~La~~lgVSRtpVREAl~~L~~eGlv~~   71 (222)
T 3ihu_A           17 ASDTVFFGIMSGLELGTFVPGQRLVETDLVAHFGVGRNSVREALQRLAAEGIVDL   71 (222)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            455555555431   1123455788999999999999999999999999999965

>3cuq_A Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_A

Probab=84.70  E-value=1.5  Score=37.66  Aligned_cols=51  Identities=22%  Similarity=0.288  Sum_probs=45.3

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ..++.-|..||+++...      ..++++++++.++.+....+++|+.|+.+|.++-
T Consensus       150 ~el~~D~~~vLela~~~------g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gllwv  200 (234)
T 3cuq_A          150 AELNMDHTVVLQLAEKN------GYVTVSEIKASLKWETERARQVLEHLLKEGLAWL  200 (234)
T ss_dssp             CCCCHHHHHHHHHHTTT------SEECHHHHHHHHTCCHHHHHHHHHHHHHHTSCEE
T ss_pred             CccchHHHHHHHHHHhc------CcCcHHHHHHHhCCCHHHHHHHHHHHHhCCCEEE
Confidence            35788999999998642      4899999999999999999999999999999985

>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=84.69  E-value=1.9  Score=31.22  Aligned_cols=42  Identities=19%  Similarity=0.476  Sum_probs=34.7

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      ..|++.+++|+.++.        +|.+..+|++.|++++..|+..+..+.
T Consensus        26 ~~Lt~~e~~vl~l~~--------~g~s~~eIA~~l~is~~tV~~~l~r~~   67 (95)
T 3c57_A           26 SGLTDQERTLLGLLS--------EGLTNKQIADRMFLAEKTVKNYVSRLL   67 (95)
T ss_dssp             -CCCHHHHHHHHHHH--------TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            468899999999872        389999999999999999887776554

>3ull_A DNA binding protein; DNA replication, mitochondrion, transit peptide; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 PDB: 1s3o_A* 2dud_A

Probab=84.68  E-value=5.2  Score=30.87  Aligned_cols=80  Identities=15%  Similarity=0.190  Sum_probs=47.8

Q ss_pred             EEeeEEEEEEEEEe---ee---cCCeeEEEEE------c------CCc-------eEEEEEecc-cccChhhhccCCCCC
Q 023576           69 EITNVTLVGLVYNK---EE---RASDVNFTLD------D------GTG-------RVVCKRWAS-EVFDTREMEAIQDGM  122 (280)
Q Consensus        69 ~i~~V~iVG~V~~~---~~---~~t~~~~~Ld------D------gTG-------~I~~~~w~~-~~~~~~~~~~~~~G~  122 (280)
                      .++.|.|+|.|..-   ..   ....+.|+|-      |      .+|       -+.|..|.+ .+.  .....+..|+
T Consensus        13 ~mN~V~L~GrL~~dPelr~t~~G~~v~~f~lA~~~~~~~~~g~~~~~g~~~~~t~w~~v~~wg~~~Ae--~~~~~l~KG~   90 (132)
T 3ull_A           13 SLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVYQLGDVSQKTTWHRISVFRPGLRD--VAYQYVKKGS   90 (132)
T ss_dssp             CEEEEEEEEEECSCCEEECCTTSCCEEEEEEEEEEEECC---------CCEEEEEEEEEEECSTTHHH--HHHHHCCTTC
T ss_pred             cCcEEEEEEEECCCCEEEECCCCCEEEEEEEEEecceeccccccccCCceecceEEEEEEEEchHHHH--HHHhhCCCCC
Confidence            47899999999652   11   2245556553      1      123       366666653 221  1234599999


Q ss_pred             EEEEEEEEee--eC---Ce----eEEEEEEEeeCCCc
Q 023576          123 YVRLIGNLKS--FQ---GK----KQIVAFSVRPVTNF  150 (280)
Q Consensus       123 yVrV~G~l~~--f~---~~----~~i~~~~ir~v~d~  150 (280)
                      .|.|.|+|+.  |.   |+    ..|.+..|..+...
T Consensus        91 ~V~V~G~L~~~~~~d~dG~~r~~~ev~a~~i~~l~~~  127 (132)
T 3ull_A           91 RIYLEGKIDYGEYMDKNNVRRQATTIIADNIIFLSDQ  127 (132)
T ss_dssp             EEEEEEEEECCCEESSSSEECCCEEEEEEEEECC---
T ss_pred             EEEEEEEEEeeEEECCCCCEEEEEEEEEEEEEEccCC
Confidence            9999999985  42   32    35888888777654

>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=84.61  E-value=0.93  Score=42.33  Aligned_cols=56  Identities=11%  Similarity=0.155  Sum_probs=49.3

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +|+.-|-.||.+|.+.    .+.+++..+|+++++++...|...|+.|...|+|...-|+
T Consensus       401 ~lt~~q~~vl~~l~~~----~~~~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~~~~  456 (487)
T 1hsj_A          401 NLNYEEIYILNHILRS----ESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSL  456 (487)
T ss_dssp             CCCHHHHHHHHHHHTC----SCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECC
T ss_pred             CCCHHHHHHHHHHHhC----CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCC
Confidence            6888888899999763    2358999999999999999999999999999999987665

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=84.53  E-value=1.5  Score=35.23  Aligned_cols=51  Identities=12%  Similarity=0.211  Sum_probs=43.0

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-------CCCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-------KIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-------~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +++.+..||++|.+.     +.-++.++|.+.+       +++...|-.+|+.|.+.|.|-..
T Consensus        31 ~T~qR~~IL~~L~~~-----~~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~~i   88 (162)
T 4ets_A           31 YTKQREVLLKTLYHS-----DTHYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVTSI   88 (162)
T ss_dssp             CCHHHHHHHHHHHSC-----CSCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHHHHHhC-----CCCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEEEE
Confidence            467888899999874     3578999998766       38899999999999999999765

>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=84.39  E-value=0.32  Score=41.27  Aligned_cols=60  Identities=22%  Similarity=0.372  Sum_probs=45.4

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCH--HHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHV--NELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v--~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      ++..+..+|++|-...    +.|++.  .+|+++++++...|..+|+.|...|+|...-| ..+..|
T Consensus         4 lt~~~e~yL~~i~~l~----~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~GlV~r~~~-~~v~LT   65 (226)
T 2qq9_A            4 LVATTEMYLRTIYELE----EEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASD-RSLQMT   65 (226)
T ss_dssp             HHHHHHHHHHHHHHHH----HHTCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT-SBEEEC
T ss_pred             CCHHHHHHHHHHHHHh----hcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC-CCeEEC
Confidence            5567777888775531    235655  99999999999999999999999999987544 334444

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=84.31  E-value=0.96  Score=40.22  Aligned_cols=33  Identities=12%  Similarity=0.263  Sum_probs=31.8

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      .++++++|+++|++++..||.-|++|.++|.|-
T Consensus        20 ~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~   52 (315)
T 2w48_A           20 QDMTQAQIARELGIYRTTISRLLKRGREQGIVT   52 (315)
T ss_dssp             SCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence            489999999999999999999999999999996

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=84.19  E-value=2  Score=33.34  Aligned_cols=51  Identities=14%  Similarity=0.219  Sum_probs=42.5

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      .....||..|..       ..+.+.+|++.+ +++...+...|..|.++|.|-.+.+.+
T Consensus        26 kW~l~IL~~L~~-------g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~~~   77 (131)
T 4a5n_A           26 KWKGILFYHMID-------GKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQ   77 (131)
T ss_dssp             SSHHHHHHHHTT-------SCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECS
T ss_pred             cCHHHHHHHHhc-------CCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEecCC
Confidence            355667777752       267999999999 999999999999999999999887654

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=83.96  E-value=1.6  Score=32.07  Aligned_cols=42  Identities=21%  Similarity=0.263  Sum_probs=34.8

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      ..|++-+++||.++.        +|.+..||++.|++++..|+..+..+.
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            468899999998874        389999999999999999887766543

>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=83.76  E-value=1.3  Score=32.91  Aligned_cols=50  Identities=24%  Similarity=0.306  Sum_probs=42.4

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ..+-.||..|..       .++++.+|++.+ +++...|...|+.|.+.|.|-...|.
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            355678887753       268999999999 99999999999999999999887664

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=83.59  E-value=1.3  Score=34.15  Aligned_cols=49  Identities=16%  Similarity=0.297  Sum_probs=40.8

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ..-.||..|..       .++++.+|++.+ +++...+...|..|.+.|.|-.+.|.
T Consensus        36 w~l~IL~~L~~-------g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~   85 (131)
T 1yyv_A           36 WGVLILVALRD-------GTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYP   85 (131)
T ss_dssp             HHHHHHHHGGG-------CCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEEC
T ss_pred             cHHHHHHHHHc-------CCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecC
Confidence            44457777652       268999999999 79999999999999999999987764

>3pgz_A Single-stranded DNA-binding protein; ssgcid, single-strand binding protein, structural genomics center for infectious disease; 2.10A {Bartonella henselae}

Probab=83.55  E-value=2.2  Score=35.56  Aligned_cols=68  Identities=15%  Similarity=0.111  Sum_probs=40.8

Q ss_pred             CeEECCEEEeeEEEEEEEEE---eee---cCCeeEEEEE------cC-Cc-------eEEEEEecc-cccChhhhccCCC
Q 023576           62 NFMINGLEITNVTLVGLVYN---KEE---RASDVNFTLD------DG-TG-------RVVCKRWAS-EVFDTREMEAIQD  120 (280)
Q Consensus        62 ~~~i~g~~i~~V~iVG~V~~---~~~---~~t~~~~~Ld------Dg-TG-------~I~~~~w~~-~~~~~~~~~~~~~  120 (280)
                      .++.- ..++.|.|+|.|..   ++.   ....+.|+|-      |. +|       -|.|..|.. .++  .....++.
T Consensus        19 ~~~Ma-~~mNkV~LiGrLg~DPElR~t~~G~~Va~FsLAvnr~~kd~~~Ge~~e~Tdwi~Vvawgk~lAe--~~~~yL~K   95 (193)
T 3pgz_A           19 PGSMA-GSLNKVILIGNLGADPEIRRLNSGDQVANLRIATSESWRDRNTNERKERTEWHNIVIFNENLVK--VVEQYLKK   95 (193)
T ss_dssp             ----C-CCEEEEEEEEEESSCCEEEECTTSCEEEEEEEEEEEEECCC-----EEEEEEEEEEECCHHHHH--HHHHHCCT
T ss_pred             hhhHh-hhcCEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceeccCCCceeeeeEEEEEEEECHHHHH--HHHhhcCC
Confidence            44433 34789999999854   221   2245566553      11 23       488999974 321  12346999


Q ss_pred             CCEEEEEEEEee
Q 023576          121 GMYVRLIGNLKS  132 (280)
Q Consensus       121 G~yVrV~G~l~~  132 (280)
                      |+.|.|.|+|+.
T Consensus        96 Gs~V~VeGrL~t  107 (193)
T 3pgz_A           96 GSKIYIEGQLQT  107 (193)
T ss_dssp             TCEEEEEEEEEE
T ss_pred             CCEEEEEEEEEE
Confidence            999999999984

>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=83.55  E-value=1.3  Score=34.93  Aligned_cols=49  Identities=16%  Similarity=0.231  Sum_probs=37.9

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      -.+|-+|...    .+.-++.++|++++++++.-|++.+..|...|.|.++-.
T Consensus        17 l~~L~~La~~----~~~~~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~rG   65 (149)
T 1ylf_A           17 VHILSILKNN----PSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG   65 (149)
T ss_dssp             HHHHHHHHHS----CGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC--
T ss_pred             HHHHHHHHhC----CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEccC
Confidence            3455555432    123589999999999999999999999999999998643

>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=83.52  E-value=0.78  Score=41.84  Aligned_cols=44  Identities=20%  Similarity=0.288  Sum_probs=39.7

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +.||++|+ .+      .++..+|++.++++...|...+++|+++|.|.++
T Consensus        23 ~~il~~l~-~~------~~sr~~la~~~gls~~tv~~~v~~L~~~gli~~~   66 (380)
T 2hoe_A           23 SRILKRIM-KS------PVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEE   66 (380)
T ss_dssp             CCSHHHHH-HS------CBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHH-cC------CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            35899998 62      6899999999999999999999999999999885

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=83.36  E-value=1.4  Score=35.02  Aligned_cols=51  Identities=18%  Similarity=0.298  Sum_probs=43.9

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      .+.+..||.+|..       ..+++.+|++.++++...|...|..|.+.|.|-..-|.
T Consensus        57 ~p~R~~IL~~L~~-------~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~G  107 (151)
T 3f6v_A           57 EPTRRRLVQLLTS-------GEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRKDG  107 (151)
T ss_dssp             SHHHHHHHHHGGG-------CCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CHHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecC
Confidence            4577889999973       25899999999999999999999999999999876544

>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=83.19  E-value=0.92  Score=39.23  Aligned_cols=56  Identities=16%  Similarity=0.252  Sum_probs=48.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++.-|=.||.+|.+.    .+.|+++.+|++++.++...|...|+.|...|.|.-.-|+
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            4677888899999863    2358999999999999999999999999999999987665

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=83.15  E-value=1.4  Score=32.91  Aligned_cols=51  Identities=24%  Similarity=0.342  Sum_probs=41.8

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +..+..||.+|.+       .++++.+|++.++++...|...|..|.+.|.|...-|.
T Consensus        31 ~~~~~~il~~L~~-------~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~~~~~   81 (119)
T 2lkp_A           31 TPSRLMILTQLRN-------GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAG   81 (119)
T ss_dssp             CHHHHHHHHHHHH-------CCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEEEEET
T ss_pred             CHHHHHHHHHHHH-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecC
Confidence            3456678888764       25799999999999999999999999999999764433

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=82.70  E-value=1  Score=37.34  Aligned_cols=44  Identities=16%  Similarity=0.098  Sum_probs=37.9

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      =|+.|++.|++.      .-++++++++.|+.++..||.-|.+|...+.+
T Consensus        13 R~~~i~~~l~~~------~~~~~~~la~~~~vs~~TiRrDl~eL~~~~l~   56 (190)
T 4a0z_A           13 RREAIRQQIDSN------PFITDHELSDLFQVSIQTIRLDRTYLNIPELR   56 (190)
T ss_dssp             HHHHHHHHHHHC------TTCCHHHHHHHHTSCHHHHHHHHHHHTCCCHH
T ss_pred             HHHHHHHHHHHC------CCEeHHHHHHHHCCCHHHHHHHHHHhcCcchh
Confidence            567799999874      25899999999999999999999999887643

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=82.61  E-value=0.31  Score=37.58  Aligned_cols=52  Identities=21%  Similarity=0.312  Sum_probs=37.6

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +...|.+.|.... -....=+ +..+|++.|+++...|++|+..|.++|.|+..
T Consensus        16 i~~~l~~~I~~g~-~~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   68 (126)
T 3ic7_A           16 IADRICDDILLGQ-YEEEGRIPSVREYASIVEVNANTVMRSYEYLQSQEVIYNK   68 (126)
T ss_dssp             HHHHHHHHHHTTS-SCBTSEECCTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEE
T ss_pred             HHHHHHHHHHhCC-CCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            4455555554421 1223345 78999999999999999999999999999864

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=82.46  E-value=1.8  Score=30.85  Aligned_cols=42  Identities=17%  Similarity=0.277  Sum_probs=35.2

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      ..|++.+++|+.++.        .|.+..+|++.|++++..|+..+..+.
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            358889999999863        389999999999999999988776654

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=82.34  E-value=2.2  Score=29.20  Aligned_cols=41  Identities=15%  Similarity=0.247  Sum_probs=33.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      .|++.++.|+.++ .       .|.+..+|++.+++++..|+..+..+.
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            4677888899886 2       389999999999999999988776654

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=82.34  E-value=2.1  Score=27.77  Aligned_cols=36  Identities=19%  Similarity=0.356  Sum_probs=28.7

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      +++|+.++.        +|.+..+|++.+++++..|+..+..+.
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            566777753        388999999999999999988776554

>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=82.14  E-value=5  Score=31.72  Aligned_cols=55  Identities=20%  Similarity=0.322  Sum_probs=38.0

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCC---------------------c--eEEEEEecccccChhhhccCCCCCEEEEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGT---------------------G--RVVCKRWASEVFDTREMEAIQDGMYVRLI  127 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgT---------------------G--~I~~~~w~~~~~~~~~~~~~~~G~yVrV~  127 (280)
                      ..+.+++.|+.+-.....+.+.|-|.|                     |  +|.+.+|.+.+.  ...+.+++|+||++.
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            456778888887555577888888877                     3  467777766431  122459999999975

>1eqq_A Single stranded DNA binding protein; beta barrel, protein-DNA complex, replication/RNA complex; HET: 5MU; 3.20A {Escherichia coli} SCOP: b.40.4.3

Probab=81.99  E-value=0.76  Score=37.80  Aligned_cols=61  Identities=25%  Similarity=0.273  Sum_probs=39.4

Q ss_pred             EeeEEEEEEEEEe---ee---cCCeeEEEEE------c-CCc-------eEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576           70 ITNVTLVGLVYNK---EE---RASDVNFTLD------D-GTG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIGN  129 (280)
Q Consensus        70 i~~V~iVG~V~~~---~~---~~t~~~~~Ld------D-gTG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~  129 (280)
                      ++.|.|+|.|..-   +.   ....+.|+|-      | .||       -|.|+.|...++  .....|+.|+.|.|.|+
T Consensus         6 ~N~V~LiGrL~~dPelr~t~~G~~v~~f~LAv~~~~~d~~~Ge~~~~t~~i~vv~wg~~Ae--~~~~~l~KG~~V~VeGr   83 (178)
T 1eqq_A            6 VNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAE--VASEYLRKGSQVYIEGQ   83 (178)
T ss_dssp             EEEEEEEEEESSSCCCCEETTTEECCCCEEEEEECCCCSSSSSCCCEEEEEEEEECHHHHH--HHHHHCCTTCEEEECCE
T ss_pred             eeEEEEEEEECCCCEEEECCCCCEEEEEEEEEcCCeecCCCCceecccEEEEEEEccHHHH--HHHHhcCCCCEEEEEEE
Confidence            6788999998652   11   1234445442      1 123       488999976431  22345999999999999


Q ss_pred             Eee
Q 023576          130 LKS  132 (280)
Q Consensus       130 l~~  132 (280)
                      |+.
T Consensus        84 L~~   86 (178)
T 1eqq_A           84 LRT   86 (178)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            986

>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=81.98  E-value=4  Score=27.20  Aligned_cols=46  Identities=15%  Similarity=0.193  Sum_probs=34.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      .|++-++.|+.+.--..   ..+|.+..+|++.+++++..|+..+....
T Consensus         5 ~L~~~er~il~l~~~l~---~~~g~s~~eIA~~lgis~~tV~~~~~ra~   50 (68)
T 2p7v_B            5 GLTAREAKVLRMRFGID---MNTDYTLEEVGKQFDVTRERIRQIEAKAL   50 (68)
T ss_dssp             CCCHHHHHHHHHHTTTT---SSSCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHccC---CCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            47888899988765211   13599999999999999999887665443

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=81.92  E-value=0.11  Score=41.73  Aligned_cols=48  Identities=27%  Similarity=0.427  Sum_probs=41.9

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +..++..|++.|+..      .-++..+|+++++++...|+++|..|..+|.|.
T Consensus        11 ~d~l~~~Il~~l~~~------~~ls~~eLa~~lgvSr~~vr~al~~L~~~Gli~   58 (163)
T 2gqq_A           11 LDRIDRNILNELQKD------GRISNVELSKRVGLSPTPCLERVRRLERQGFIQ   58 (163)
T ss_dssp             CCSHHHHHHHHHHHC------SSCCTTGGGTSSSCCTTTSSSTHHHHHHHTSEE
T ss_pred             hhHHHHHHHHHHHhC------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence            567899999988752      346899999999999999999999999999995

>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=81.71  E-value=4.9  Score=34.79  Aligned_cols=80  Identities=16%  Similarity=0.256  Sum_probs=49.0

Q ss_pred             EeeEEEEEEEEEe---e---ecCCeeEEEEE------cCCc-------eEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576           70 ITNVTLVGLVYNK---E---ERASDVNFTLD------DGTG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIGNL  130 (280)
Q Consensus        70 i~~V~iVG~V~~~---~---~~~t~~~~~Ld------DgTG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l  130 (280)
                      ++.|.|+|.|..-   +   .....+.|+|.      |..|       -|.|..|...++  .....++.|+.|.|.|+|
T Consensus         5 ~N~v~L~G~l~~dpelr~t~~G~~v~~f~lA~~~~~~~~~G~~~~~t~~~~v~~~g~~Ae--~~~~~l~KG~~V~V~G~L   82 (264)
T 2fxq_A            5 LNQVFLIGTLTARPDMRYTPGGLAILDLNLAGQDAFTDESGQEREVPWYHRVRLLGRQAE--MWGDLLEKGQLIFVEGRL   82 (264)
T ss_dssp             EEEEEEEEEESSCCCCEECTTCCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHHH--HHTTTCCTTCEEEEEEEE
T ss_pred             eeEEEEEEEeccCCeEEECCCCCEEEEEEEEECCcEECCCCCEecccEEEEEEEEchHHH--HHHHhCCCCCEEEEEEEE
Confidence            5778888887542   1   12245555552      2223       478888865431  123468999999999999


Q ss_pred             ee--eC--Ce----eEEEEEEEeeCCCch
Q 023576          131 KS--FQ--GK----KQIVAFSVRPVTNFD  151 (280)
Q Consensus       131 ~~--f~--~~----~~i~~~~ir~v~d~N  151 (280)
                      +.  |.  |+    ..|.+..|..+...+
T Consensus        83 ~~~~~~~dG~~r~~~ev~a~~i~~l~~~~  111 (264)
T 2fxq_A           83 EYRQWEKDGEKKSEVQVRAEFIDPLEGRG  111 (264)
T ss_dssp             EEC---------CCEEEEEEEEEECCCC-
T ss_pred             EeeeEEeCCEEEEEEEEEEEEEEECcCCc
Confidence            65  54  22    348888898887654

>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=81.69  E-value=3.2  Score=30.87  Aligned_cols=51  Identities=16%  Similarity=0.269  Sum_probs=41.3

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +....||..|..     .+.-+++.+|++.+ +++...+...|..|.+.|.|-...+
T Consensus        27 ~wrl~IL~~L~~-----g~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~   78 (111)
T 3df8_A           27 KYTMLIISVLGN-----GSTRQNFNDIRSSIPGISSTILSRRIKDLIDSGLVERRSG   78 (111)
T ss_dssp             TTHHHHHHHHTS-----SSSCBCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEEES
T ss_pred             ccHHHHHHHHhc-----CCCCCCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEeec
Confidence            456678888863     12225599999999 8999999999999999999987654

>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=81.65  E-value=4.3  Score=27.44  Aligned_cols=47  Identities=15%  Similarity=0.292  Sum_probs=35.4

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHH----HHHHHH
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMD----SIASLE  261 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~----al~~L~  261 (280)
                      ..|++-++.|+...--..   .++|.+..+|++.+++++..|+.    |+..|-
T Consensus         9 ~~L~~~er~il~l~~~l~---~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A            9 SKLSEREAMVLKMRKGLI---DGREHTLEEVGAYFGVTRERIRQIENKALRKLK   59 (73)
T ss_dssp             TTSCHHHHHHHHHHHTTT---TSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHhcc---cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            357888899888755321   23599999999999999999887    555554

>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=81.59  E-value=1.3  Score=35.75  Aligned_cols=47  Identities=23%  Similarity=0.349  Sum_probs=38.9

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      -.+|-+|...    .+.-++.++|+++++++..-|+++|..|...|.|-++
T Consensus        15 lr~l~~La~~----~~~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~   61 (162)
T 3k69_A           15 VHSILYLDAH----RDSKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGT   61 (162)
T ss_dssp             HHHHHHHHTT----TTSCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEE
T ss_pred             HHHHHHHHhC----CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            4566666653    1345899999999999999999999999999999765

>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=81.56  E-value=5.2  Score=33.19  Aligned_cols=42  Identities=17%  Similarity=0.217  Sum_probs=29.9

Q ss_pred             eeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE
Q 023576           82 KEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG  128 (280)
Q Consensus        82 ~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G  128 (280)
                      ......++.|.|.|.||.++|...-.-.     .-..++||-+|++.
T Consensus       130 K~v~~~~~~YeI~DnTG~MeVvv~G~~~-----~i~CEeGDKLrL~c  171 (204)
T 3rlo_A          130 KNVRGEFTYYEIQDNTGKMEVVVHGRLT-----TINCEEGDKLKLTC  171 (204)
T ss_dssp             EEEETTEEEEEEEETTEEEEEEECGGGG-----GCCCCTTCEEEEEE
T ss_pred             EEeccceEEEEEecCCCcEEEEEeccCc-----ccccCCCCeeEEEE
Confidence            3445578999999999999999764321     23467888666553

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=81.52  E-value=3.5  Score=27.20  Aligned_cols=42  Identities=17%  Similarity=0.113  Sum_probs=32.9

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHH
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASL  260 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L  260 (280)
                      ..|++.++.|+.+.--       .|.+..+|++.+++++..|+..+...
T Consensus        14 ~~L~~~~r~il~l~~~-------~g~s~~eIA~~lgis~~tv~~~~~ra   55 (70)
T 2o8x_A           14 ADLTTDQREALLLTQL-------LGLSYADAAAVCGCPVGTIRSRVARA   55 (70)
T ss_dssp             TSSCHHHHHHHHHHHT-------SCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHH-------cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3577888888886432       38899999999999999887766543

>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=81.51  E-value=6.6  Score=37.37  Aligned_cols=68  Identities=16%  Similarity=0.214  Sum_probs=49.9

Q ss_pred             eeEEEEEEEEEeee----c--CCeeEEEEEcCC-c-------eE-----EEEEecccccChhhhccC-CCCCEEEE-EEE
Q 023576           71 TNVTLVGLVYNKEE----R--ASDVNFTLDDGT-G-------RV-----VCKRWASEVFDTREMEAI-QDGMYVRL-IGN  129 (280)
Q Consensus        71 ~~V~iVG~V~~~~~----~--~t~~~~~LdDgT-G-------~I-----~~~~w~~~~~~~~~~~~~-~~G~yVrV-~G~  129 (280)
                      ..|.|+|+|+.+..    +  .=.++|+|-|.+ .       -|     .|.+|.+..   +..+.+ .+||.|++ .-+
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            35889999988742    1  236789999954 2       16     999997754   235666 69999999 568


Q ss_pred             EeeeCCeeEEEE
Q 023576          130 LKSFQGKKQIVA  141 (280)
Q Consensus       130 l~~f~~~~~i~~  141 (280)
                      |+.|+++.++..
T Consensus       127 Iq~~ng~~~~v~  138 (495)
T 1jb7_A          127 LRLYNGQRQFNA  138 (495)
T ss_dssp             EEEETTEEEEEE
T ss_pred             EEEECCcEEEEe
Confidence            889999988644

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=80.85  E-value=1.8  Score=36.60  Aligned_cols=35  Identities=23%  Similarity=0.334  Sum_probs=31.1

Q ss_pred             CCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          234 ERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       234 e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .+=+ +..+|+++|+++..-||+||..|..+|.|-.
T Consensus        25 G~~LpsE~~La~~lgVSRtpVREAL~~L~~~GlV~~   60 (239)
T 2di3_A           25 GDHLPSERALSETLGVSRSSLREALRVLEALGTIST   60 (239)
T ss_dssp             TCBCCCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC
T ss_pred             CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEe
Confidence            3456 4779999999999999999999999999975

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=80.44  E-value=3.4  Score=29.37  Aligned_cols=40  Identities=13%  Similarity=0.211  Sum_probs=31.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS  259 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~  259 (280)
                      .|++.++.||.+.--       +|.+..+|++.|++++..|+..+..
T Consensus        37 ~L~~~~r~vl~l~~~-------~g~s~~eIA~~lgis~~tV~~~l~r   76 (92)
T 3hug_A           37 QLSAEHRAVIQRSYY-------RGWSTAQIATDLGIAEGTVKSRLHY   76 (92)
T ss_dssp             TSCHHHHHHHHHHHT-------SCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH-------cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            578888888876432       4899999999999999998776654

---

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	280
d2pi2a1	128	b.40.4.3 (A:44-171) Replication protein A 32 KDa s	3e-49
d1dpua_	69	a.4.5.16 (A:) C-terminal domain of RPA32 {Human (H	2e-14
d1j5ya1	65	a.4.5.1 (A:3-67) Putative transcriptional regulato	0.002

>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 =  157 bits (398), Expect = 3e-49
 Identities = 40/131 (30%), Positives = 73/131 (55%), Gaps = 4/131 (3%)

Query: 40  QGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGR 99
           Q +VP T+  +  A+   +    F I  +EI+ VT+VG++ + E+  +++ + +DD T  
Sbjct: 1   QHIVPCTISQLLSATLVDEV---FRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAA 57

Query: 100 VV-CKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYI 158
            +  ++W      + E   +    YV++ G+L+SFQ KK +VAF + P+ + +E T H +
Sbjct: 58  PMDVRQWVDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHIL 117

Query: 159 ECIYFHLQNSK 169
           E I  H+  SK
Sbjct: 118 EVINAHMVLSK 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 = 64.7 bits (158), Expect = 2e-14
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 4/66 (6%)

Query: 212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLK-IPQKKIMDSIASLENEGLIYSTI 270
           +GL      +L+ ++   +  R  G++  +L  QLK +    I  ++  L NEG IYST+
Sbjct: 2   NGLTVAQNQVLNLIK---ACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTV 58

Query: 271 DEFHYK 276
           D+ H+K
Sbjct: 59  DDDHFK 64

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 65

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]

 Score = 33.5 bits (77), Expect = 0.002
 Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 6/52 (11%)

Query: 219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGL-IYST 269
           + I+  L+       +  V   +L+E+L + ++ I+  IA L + G  I +T
Sbjct: 10  KSIVRILE-----RSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVAT 56

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	280
d2pi2a1	128	Replication protein A 32 KDa subunit (RPA32) fragm	100.0
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	99.89
d1nnxa_	106	Hypothetical protein YgiW {Escherichia coli [TaxId	97.93
d1o7ia_	115	Archaeal ssDNA-binding protein {Archaeon Sulfolobu	97.87
d1n9wa1	93	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	97.57
d1c0aa1	106	Aspartyl-tRNA synthetase (AspRS) {Escherichia coli	97.54
d1eova1	134	Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S	97.51
d1wjja_	145	Hypothetical protein At4g28440 (F20O9.120) {Thale	97.47
d1l0wa1	104	Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph	97.35
d1b8aa1	103	Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ	97.32
d1e1oa1	143	Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g	97.16
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.87
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	96.75
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	96.73
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	96.73
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	96.59
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.58
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	96.41
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.34
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	96.11
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	96.07
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	95.71
d1v1qa_	111	Primosomal replication protein N, PriB {Escherichi	95.61
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	95.45
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	95.43
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	95.36
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	95.33
d1gm5a2	180	RecG "wedge" domain {Thermotoga maritima [TaxId: 2	95.3
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	95.05
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	94.98
d1jmca1	116	Replication protein A 70 KDa subunit (RPA70) {Huma	94.8
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	94.73
d2oq0a1	88	Gamma-interferon-inducible protein Ifi-16 {Human (	94.56
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	94.48
d1l1oc_	178	Replication protein A 70 KDa subunit (RPA70) {Huma	94.39
d1xjva1	140	Protection of telomeres protein 1, Pot1 {Human (Ho	94.13
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	94.12
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	93.88
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	93.79
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	93.68
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	93.66
d1jmca2	122	Replication protein A 70 KDa subunit (RPA70) {Huma	93.63
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	93.33
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	93.28
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	93.15
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	93.0
d2pi2e1	115	Replication protein A 14 KDa (RPA14) subunit {Huma	92.94
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	92.93
d1qvca_	145	ssDNA-binding protein {Escherichia coli [TaxId: 56	92.89
d1qzga_	170	Protection of telomeres protein 1, Pot1 {Fission y	92.8
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	92.7
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	92.55
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	92.43
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	92.41
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	92.29
d1zyba1	73	Probable transcription regulator BT4300, C-termina	92.03
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	91.88
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	91.83
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	91.75
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	91.74
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	91.58
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	91.52
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	91.38
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	91.32
d1se8a_	231	ssDNA-binding protein {Deinococcus radiodurans [Ta	91.19
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	90.91
d2v9va2	73	C-terminal fragment of elongation factor SelB {Moo	90.58
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	90.44
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	90.43
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	90.07
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	89.76
d2dk8a1	68	DNA-directed RNA polymerase III subunit RPC6, RPO3	89.7
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	89.59
d1oyia_	62	dsRNA-binding protein E3 (E3L) {Vaccinia virus [Ta	89.56
d1ue1a_	118	ssDNA-binding protein {Mycobacterium tuberculosis	89.51
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	89.47
d1jb7a1	169	Telomere end binding protein alpha subunit {Oxytri	89.37
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	89.27
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	89.08
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	88.97
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	88.94
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	88.56
d1y0ua_	89	Putative arsenical resistance operon repressor AF0	88.38
d1se8a_	231	ssDNA-binding protein {Deinococcus radiodurans [Ta	88.26
d3ulla_	115	ssDNA-binding protein {Human (Homo sapiens), mitoc	87.88
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	87.41
d1ucra_	74	Dissimilatory sulfite reductase DsvD {Desulfovibri	87.4
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	87.26
d1sr3a_	114	Heme chaperone CcmE {Escherichia coli [TaxId: 562]	87.19
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	86.89
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	86.7
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	86.48
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	86.0
d1in4a1	75	Holliday junction helicase RuvB {Thermotoga mariti	85.88
d1j75a_	57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	85.65
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	85.28
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	84.65
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	84.56
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	84.34
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	84.28
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	83.7
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	82.63
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	82.44
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	82.21
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	81.97
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	81.5
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	81.3
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	80.47
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	80.42
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	80.33

>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=4e-39  Score=256.85  Aligned_cols=127  Identities=31%  Similarity=0.558  Sum_probs=114.1

Q ss_pred             CceeeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCc-eEEEEEecccccChhhhccC
Q 023576           40 QGLVPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAI  118 (280)
Q Consensus        40 ~~~~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~  118 (280)
                      |+|+|||||||++|.+.   ++.|+++|++|++|+|||+|++++..++++.|+|||+|| .|+|+.|.+++.+....+.+
T Consensus         1 q~i~PvtI~ql~~a~~~---~~~f~i~g~~v~~V~iVG~V~~i~~~~t~~~y~idDgTG~~i~v~~w~~~~~~~~~~~~i   77 (128)
T d2pi2a1           1 QHIVPCTISQLLSATLV---DEVFRIGNVEISQVTIVGIIRHAEKAPTNIVYKIDDMTAAPMDVRQWVDTDDTSSENTVV   77 (128)
T ss_dssp             CCCEECCHHHHHHCEEE---TTEEEETTEEESEEEEEEEEEEEEECSSEEEEEEECSSSSCEEEEEECC-------CCCC
T ss_pred             CceeeEEHHHHhcCcCC---CCCEEECCEEEEEEEEEEEEEEEEecCCEEEEEEECCCCCcEEEEEECCCCCCccccccc
Confidence            67999999999999764   358999999999999999999999999999999999999 69999998766554556789


Q ss_pred             CCCCEEEEEEEEeeeCCeeEEEEEEEeeCCCchHHHHHHHHHHHHHHHhcC
Q 023576          119 QDGMYVRLIGNLKSFQGKKQIVAFSVRPVTNFDEVTCHYIECIYFHLQNSK  169 (280)
Q Consensus       119 ~~G~yVrV~G~l~~f~~~~~i~~~~ir~v~d~Nei~~H~Le~i~~~l~~~~  169 (280)
                      ++|+||||+|+|+.|+++++|++++||||+|+||+++|+|||+++||+++|
T Consensus        78 ~~g~yVrV~G~lk~f~~~~~i~~~~i~~v~d~Nei~~H~Levi~~hL~~tk  128 (128)
T d2pi2a1          78 PPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSK  128 (128)
T ss_dssp             CTTCEEEEEEEEEEETTEEEEEEEEEEECSCTHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCEEEEEEEEEeeCCeEEEEEEEEEEeCCcCHHHHHHHHHHHHHHhhcC
Confidence            999999999999999999999999999999999999999999999999875

>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=99.89  E-value=5.5e-24  Score=149.30  Aligned_cols=66  Identities=30%  Similarity=0.547  Sum_probs=61.9

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCeeeecCCCccccccCC
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYSTIDEFHYKFARG  280 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~~  280 (280)
                      ++|++.|++||++|+..   .+++|+|+++|+++| +++.++|++|+++|++|||||+||||+|||+||.
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            47899999999999976   468899999999999 6999999999999999999999999999999984

>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=97.93  E-value=0.00011  Score=54.06  Aligned_cols=83  Identities=18%  Similarity=0.158  Sum_probs=62.4

Q ss_pred             eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCE
Q 023576           44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMY  123 (280)
Q Consensus        44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~y  123 (280)
                      ..|+++++++.    ++          ..|.|-|.|+..-...   .|.+.|+||.|.+-+=.+.    ..-..+.+++.
T Consensus        24 ~~tV~~a~~~~----Dd----------t~V~L~G~Iv~~l~~d---~Y~F~D~TG~I~VeId~~~----w~g~~v~p~~k   82 (106)
T d1nnxa_          24 VTTVESAKSLR----DD----------TWVTLRGNIVERISDD---LYVFKDASGTINVDIDHKR----WNGVTVTPKDT   82 (106)
T ss_dssp             CCCHHHHTTSC----SS----------EEEEEEEEEEEEEETT---EEEEEETTEEEEEECCGGG----STTCCCCTTSC
T ss_pred             EEhHHHHhhCc----CC----------CeEEEEEEEEEEeCCc---eEEEECCCCcEEEEEChhh----cCCcccCCCCE
Confidence            46899988763    12          5699999988876665   5678999999998852111    11246888999


Q ss_pred             EEEEEEEeeeCCeeEEEEEEEeeC
Q 023576          124 VRLIGNLKSFQGKKQIVAFSVRPV  147 (280)
Q Consensus       124 VrV~G~l~~f~~~~~i~~~~ir~v  147 (280)
                      |+|+|.+..-.....|-+.+|+.|
T Consensus        83 V~i~GevDk~~~~~eIdV~~I~~l  106 (106)
T d1nnxa_          83 VEIQGEVDKDWNSVEIDVKQIRKV  106 (106)
T ss_dssp             EEEEEEEEEETTEEEEEEEEEEEC
T ss_pred             EEEEEEEcCCCCceEEEEEEEEEC
Confidence            999999996667789999888765

>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=97.87  E-value=7.2e-05  Score=56.01  Aligned_cols=73  Identities=23%  Similarity=0.331  Sum_probs=57.1

Q ss_pred             eeEEEEEEEEEeee--------c-CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEE-EEEeeeCCeeEEE
Q 023576           71 TNVTLVGLVYNKEE--------R-ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI-GNLKSFQGKKQIV  140 (280)
Q Consensus        71 ~~V~iVG~V~~~~~--------~-~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~-G~l~~f~~~~~i~  140 (280)
                      ..|.|+|+|.++.+        . .....+.|-|.||+|.+.+|.+.      ...+++|+.|++. +.++.|++...|+
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            45788888888632        1 13467889999999999999753      3468999999995 8999999999999


Q ss_pred             EEE---EeeCCC
Q 023576          141 AFS---VRPVTN  149 (280)
Q Consensus       141 ~~~---ir~v~d  149 (280)
                      +.+   |.++.|
T Consensus        87 ~~~~s~i~~~~d   98 (115)
T d1o7ia_          87 AGSKTKIAEASE   98 (115)
T ss_dssp             ECTTCEEEECCC
T ss_pred             ECCCeEEEECCC
Confidence            854   666655

>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=97.57  E-value=0.00049  Score=49.32  Aligned_cols=71  Identities=17%  Similarity=0.126  Sum_probs=57.0

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC---CeeEEEEEEEeeC
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ---GKKQIVAFSVRPV  147 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~~~ir~v  147 (280)
                      ..|+|.|+|.+++......-+.|-|+||.+.|.+=..        ..+..++.|.|.|.+..-.   +...|.+..+..+
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            4789999999999888777779999999999875322        2356789999999998754   6678888888776


Q ss_pred             CC
Q 023576          148 TN  149 (280)
Q Consensus       148 ~d  149 (280)
                      ..
T Consensus        86 ~~   87 (93)
T d1n9wa1          86 SP   87 (93)
T ss_dssp             EC
T ss_pred             ec
Confidence            54

>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=97.54  E-value=0.00036  Score=51.31  Aligned_cols=78  Identities=17%  Similarity=0.245  Sum_probs=58.5

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC----------CeeEEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ----------GKKQIV  140 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~----------~~~~i~  140 (280)
                      ..|+|.|||..++......-+.|-|+||.+.|.+-.+..........+...+.|.|.|+|..-.          +...|.
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            6899999999998877777779999999999977544321112345788899999999997532          236788


Q ss_pred             EEEEeeCC
Q 023576          141 AFSVRPVT  148 (280)
Q Consensus       141 ~~~ir~v~  148 (280)
                      +..+..+.
T Consensus        96 v~~i~vl~  103 (106)
T d1c0aa1          96 ASSLTIIN  103 (106)
T ss_dssp             EEEEEEEE
T ss_pred             EeEEEEEe
Confidence            88776654

>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=97.51  E-value=0.00057  Score=52.31  Aligned_cols=80  Identities=13%  Similarity=0.039  Sum_probs=60.8

Q ss_pred             eeEEEEEEEEEeeecCC-eeEEEEEcCCceEEEEEecccccCh-----hhhccCCCCCEEEEEEEEeeeC--------Ce
Q 023576           71 TNVTLVGLVYNKEERAS-DVNFTLDDGTGRVVCKRWASEVFDT-----REMEAIQDGMYVRLIGNLKSFQ--------GK  136 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t-~~~~~LdDgTG~I~~~~w~~~~~~~-----~~~~~~~~G~yVrV~G~l~~f~--------~~  136 (280)
                      ..|+|.|+|..++.... ..-+.|-|+||.|.|.+-.+...+.     .....+..|+.|.|.|.|..-.        +.
T Consensus        37 ~~V~v~GwV~~~R~~G~kl~F~~LrD~sg~iQ~~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~  116 (134)
T d1eova1          37 KEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQN  116 (134)
T ss_dssp             CEEEEEEEEEEEEECSSSEEEEEEEETTEEEEEEEECCSSSSSCHHHHHHHTTCCTTCEEEEEEEEEECSSCCTTSSEEE
T ss_pred             CEEEEEEEEEEEEeCCCcEEEEEEEcCCCcEEEEEEeccccchhHHHHHHHhcCCCCCEEEEEEEEEeCCccCCCCCCCc
Confidence            57899999999988664 4567999999999999886543321     1246789999999999997643        33


Q ss_pred             eEEEEEEEeeCCCc
Q 023576          137 KQIVAFSVRPVTNF  150 (280)
Q Consensus       137 ~~i~~~~ir~v~d~  150 (280)
                      ..|.+..|..|...
T Consensus       117 ~Ei~v~~i~vls~a  130 (134)
T d1eova1         117 LEIHITKIYTISET  130 (134)
T ss_dssp             EEEEEEEEEEEECC
T ss_pred             EEEEEEEEEEEeCC
Confidence            57888888776543

>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=97.47  E-value=0.0004  Score=54.02  Aligned_cols=85  Identities=19%  Similarity=0.221  Sum_probs=63.2

Q ss_pred             eeeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeec-------------------CCeeEEEEEcCCceEEEE
Q 023576           43 VPVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEER-------------------ASDVNFTLDDGTGRVVCK  103 (280)
Q Consensus        43 ~PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~-------------------~t~~~~~LdDgTG~I~~~  103 (280)
                      ..++|++|...                -..|.|+++|.++...                   ..-....|-|.||+|.+.
T Consensus        15 ~~~kI~dL~pg----------------~~~vnl~vkVl~~~~~~~~~r~~~~~~~~~~~g~~~~v~~~~v~DeTG~i~~t   78 (145)
T d1wjja_          15 VFVKVEQLKPG----------------TTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETGCILFT   78 (145)
T ss_dssp             SSCCSTTCCTT----------------CCCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSCEEEEE
T ss_pred             ceeEHHHCCCC----------------CCCceEEEEEEEcccceeecccccccccccccCCCcEEEEEEEEccCCeEEEE
Confidence            35678887653                1567888889886421                   125567999999999999


Q ss_pred             EecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEEEEEE---EeeCCC
Q 023576          104 RWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQIVAFS---VRPVTN  149 (280)
Q Consensus       104 ~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i~~~~---ir~v~d  149 (280)
                      .|.+.      ...+++|+.|++.+ .++.|++..+|++.+   |.++.+
T Consensus        79 lW~~~------~~~l~~Gd~v~i~na~v~~~~G~~~L~vg~~g~I~~~~e  122 (145)
T d1wjja_          79 ARNDQ------VDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGA  122 (145)
T ss_dssp             ECTTH------HHHTCTTCEEEEEEEEEEEETTEEEEEECTTCCBCCCSC
T ss_pred             EEecc------ccccCcCCEEEEeeEEEEEECCEEEEEECCCEEEEECCC
Confidence            99763      34589999999875 566899999999874   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=97.35  E-value=0.0018  Score=47.27  Aligned_cols=76  Identities=17%  Similarity=0.192  Sum_probs=57.8

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEeeeC--------CeeEEEEE
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQ--------GKKQIVAF  142 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~--------~~~~i~~~  142 (280)
                      ..|+|.|||..++......-+.|-|+||.|.|.+-.+.+ .......+...+.|.|.|.|+.-.        +...|.+.
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            579999999999888877778999999999998743322 223456789999999999997421        23577777


Q ss_pred             EEeeC
Q 023576          143 SVRPV  147 (280)
Q Consensus       143 ~ir~v  147 (280)
                      .+..+
T Consensus        96 ~i~iL  100 (104)
T d1l0wa1          96 ALEVL  100 (104)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            77654

>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=97.32  E-value=0.00098  Score=48.61  Aligned_cols=78  Identities=13%  Similarity=0.070  Sum_probs=57.2

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccC--hhhhccCCCCCEEEEEEEEeeeC---CeeEEEEEEEe
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFD--TREMEAIQDGMYVRLIGNLKSFQ---GKKQIVAFSVR  145 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~--~~~~~~~~~G~yVrV~G~l~~f~---~~~~i~~~~ir  145 (280)
                      ..|+|.|+|.+++......-+.|-|+||.|.|.+-.+...+  -.....+..++.|.|.|.+..-.   ....|.+..|.
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            35899999999988877777799999999998865433211  12345789999999999997632   22447777766


Q ss_pred             eCC
Q 023576          146 PVT  148 (280)
Q Consensus       146 ~v~  148 (280)
                      -+.
T Consensus        97 ils   99 (103)
T d1b8aa1          97 VLN   99 (103)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            553

>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=97.16  E-value=0.0028  Score=48.84  Aligned_cols=101  Identities=17%  Similarity=0.150  Sum_probs=71.0

Q ss_pred             eeeHHHHhhcccCCCCCCCeEECCEEEeeEEEEEEEEEeeecCCeeEEEEEcCCceEEEEEecccccCh---hhhccCCC
Q 023576           44 PVTVKMISEASHSGDDKSNFMINGLEITNVTLVGLVYNKEERASDVNFTLDDGTGRVVCKRWASEVFDT---REMEAIQD  120 (280)
Q Consensus        44 PvtIkqi~~a~~~~~~~~~~~i~g~~i~~V~iVG~V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~---~~~~~~~~  120 (280)
                      -.++++|.......+ .....-.+   ..|+|.|+|..++....-+-+.|.|.||.|.+.+-.+.-.+.   .....+..
T Consensus        32 t~~~~ei~~~~~~~~-~~~~~~~~---~~V~vaGRI~~~R~~Gk~~F~~i~D~~g~iQi~~~~~~~~~~~~~~~~k~ld~  107 (143)
T d1e1oa1          32 DHTSDQLHEEFDAKD-NQELESLN---IEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDL  107 (143)
T ss_dssp             SCCHHHHHHHHTTCC-HHHHHHHC---CEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETTTSSTTHHHHTGGGCCT
T ss_pred             CccHHHHHHHHhccc-chhhhccC---ceEEEEEEEEEEcccCCeeEEEEEeCCceEEEEEccccchhhhHHHHHhcCCc
Confidence            367888887643221 00000001   248999999999887777788999999999988765433221   12367899


Q ss_pred             CCEEEEEEEEeee-CCeeEEEEEEEeeCC
Q 023576          121 GMYVRLIGNLKSF-QGKKQIVAFSVRPVT  148 (280)
Q Consensus       121 G~yVrV~G~l~~f-~~~~~i~~~~ir~v~  148 (280)
                      ||+|-|.|.+..= .|+..|.+..+..++
T Consensus       108 GDiIgv~G~~~~TktGElsi~~~~~~lLs  136 (143)
T d1e1oa1         108 GDIIGARGTLFKTQTGELSIHCTELRLLT  136 (143)
T ss_dssp             TCEEEEEEEEEECTTCCEEEEEEEEEEEE
T ss_pred             ccEEEeecccEECCCCcEEEEeeEEEEec
Confidence            9999999999755 488999998887654

>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=96.87  E-value=0.00065  Score=45.01  Aligned_cols=48  Identities=21%  Similarity=0.358  Sum_probs=43.4

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +.++.++||+.|+.++      -++..+|+++++++++.|...++.|.++|.|-
T Consensus         3 lD~~D~~IL~~L~~~~------r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~   50 (63)
T d2cg4a1           3 IDNLDRGILEALMGNA------RTAYAELAKQFGVSPETIHVRVEKMKQAGIIT   50 (63)
T ss_dssp             CCHHHHHHHHHHHHCT------TSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCHHHHHHHHHHHHcC------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            5678999999999753      56999999999999999999999999999984

>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=96.75  E-value=0.00081  Score=44.07  Aligned_cols=48  Identities=25%  Similarity=0.415  Sum_probs=42.8

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +.++.++|++.|++++      -+++.+|++++++++..|...+..|.++|.|-
T Consensus         1 lD~~D~~Il~~L~~n~------r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1           1 LDEIDKKIIKILQNDG------KAPLREISKITGLAESTIHERIRKLRESGVIK   48 (60)
T ss_dssp             CCHHHHHHHHHHHHCT------TCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHHHHHcC------CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            3568899999999853      45999999999999999999999999999984

>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=96.73  E-value=0.0014  Score=42.99  Aligned_cols=48  Identities=23%  Similarity=0.511  Sum_probs=42.8

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +.++.++||++|++++      =+++.+|+++++++++.|...++.|.++|.|-
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            3568899999999853      35999999999999999999999999999994

>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=96.73  E-value=0.0012  Score=43.67  Aligned_cols=48  Identities=25%  Similarity=0.452  Sum_probs=43.3

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +.++..+||+.|++++      -++..+|++.++++++.|...+..|.++|.|-
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            5678999999999753      45999999999999999999999999999993

>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=96.59  E-value=0.0018  Score=43.04  Aligned_cols=56  Identities=29%  Similarity=0.410  Sum_probs=45.9

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCe-eeecCCCccccccCC
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGL-IYSTIDEFHYKFARG  280 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~-IYsTiDd~hfk~t~~  280 (280)
                      +.+|+++|++.     +..++.++|++.|+++...|+.-|+.|.+.|. |+++- . -|...+|
T Consensus         9 ~~~Il~~L~~~-----~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~~I~~~~-g-GY~L~~G   65 (65)
T d1j5ya1           9 LKSIVRILERS-----KEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATP-R-GYVLAGG   65 (65)
T ss_dssp             HHHHHHHHHHC-----SSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEEET-T-EEECCTT
T ss_pred             HHHHHHHHHHc-----CCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEEeC-C-CEEeCCC
Confidence            45788888752     34699999999999999999999999999997 88763 3 6776655

>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=96.58  E-value=0.0013  Score=44.36  Aligned_cols=46  Identities=17%  Similarity=0.198  Sum_probs=41.3

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      ...||++|+..      ..++..+|++.++++...|...|+.|+++|.|.++
T Consensus         8 ~~~Il~~l~~~------g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           8 AGRVYKLIDQK------GPISRIDLSKESELAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHHH------CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            35799999874      37999999999999999999999999999999875

>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=96.41  E-value=0.003  Score=43.10  Aligned_cols=53  Identities=21%  Similarity=0.412  Sum_probs=45.1

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      +||++|...     +.++++.||++.++++.+.+...|..|++.|.+... ++..|..+
T Consensus         9 ~IL~~~a~~-----~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~-~~g~y~lG   61 (75)
T d1mkma1           9 EILDFIVKN-----PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK-KDKRYVPG   61 (75)
T ss_dssp             HHHHHHHHC-----SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC-TTSCEEEC
T ss_pred             HHHHHHHhC-----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC-CCCCEeec
Confidence            578888753     458999999999999999999999999999999997 45577653

>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=96.34  E-value=0.0035  Score=42.16  Aligned_cols=46  Identities=13%  Similarity=0.145  Sum_probs=41.6

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      ...||++|++.      ..++..+|++.++++...|...+++|+++|.|.++
T Consensus         7 ~~~Il~~i~~~------g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e~   52 (70)
T d1z6ra1           7 AGAVYRLIDQL------GPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQEL   52 (70)
T ss_dssp             HHHHHHHHHSS------CSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            35699999975      37899999999999999999999999999999876

>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=96.11  E-value=0.0016  Score=44.19  Aligned_cols=55  Identities=16%  Similarity=0.261  Sum_probs=44.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCC-CHHHHHHHHHHHHhCCeeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKI-PQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~-~~~~v~~al~~L~~eG~IYs  268 (280)
                      .|++-|++||++|++--. ....-.++.||++.|++ +...|...|..|.+.|+|-.
T Consensus         2 ~LT~rQ~~vL~~I~~~~~-~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r   57 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHIS-QTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEI   57 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHH-HHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHHHHH-HhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeec
Confidence            478899999999987410 11233589999999997 78999999999999999976

>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=96.07  E-value=0.0058  Score=40.39  Aligned_cols=55  Identities=11%  Similarity=0.181  Sum_probs=45.1

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccc
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHY  275 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hf  275 (280)
                      .+.++|..++++.+-    .--.+.||+..+++++.+++..|..|..+|.+.-- .+|+|
T Consensus         7 ~l~~~I~~~~~~~g~----~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI-~~d~y   61 (64)
T d1lvaa3           7 KLLKDLEDKYRVSRW----QPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKI-NDEFY   61 (64)
T ss_dssp             HHHHHHHHHHHHHTT----SCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEES-SSSBE
T ss_pred             HHHHHHHHHHHHcCC----CCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe-ccccc
Confidence            467788888877431    23489999999999999999999999999999995 44455

>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=95.71  E-value=0.015  Score=38.05  Aligned_cols=46  Identities=17%  Similarity=0.193  Sum_probs=40.2

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      +..+.+||++|++.      .-++.++|++.|+++...|+..|..|.+.|.+
T Consensus         4 ~~~~~~iL~~L~~~------~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~   49 (63)
T d1biaa1           4 NTVPLKLIALLANG------EFHSGEQLGETLGMSRAAINKHIQTLRDWGVD   49 (63)
T ss_dssp             CHHHHHHHHHHTTS------SCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCC
T ss_pred             cHHHHHHHHHHHHC------CcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCc
Confidence            34677899999753      36899999999999999999999999999984

>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=95.61  E-value=0.092  Score=38.07  Aligned_cols=83  Identities=16%  Similarity=0.190  Sum_probs=55.4

Q ss_pred             EEeeEEEEEEEEEeee------cCCeeEEEEEcC-----Cc-------eEEEEEecccccChhhhccCCCCCEEEEEEEE
Q 023576           69 EITNVTLVGLVYNKEE------RASDVNFTLDDG-----TG-------RVVCKRWASEVFDTREMEAIQDGMYVRLIGNL  130 (280)
Q Consensus        69 ~i~~V~iVG~V~~~~~------~~t~~~~~LdDg-----TG-------~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l  130 (280)
                      -.++|.|+|.|..-.+      +...+.|.|.=.     .|       .|+|+.|-..++  .....+..|+.|.|.|+|
T Consensus         5 m~N~v~L~G~l~~dpelr~T~~G~~v~~f~la~~~~~~e~~~~r~~~~~i~vv~~g~~Ae--~~~~~l~kG~~v~v~G~L   82 (111)
T d1v1qa_           5 MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQ--AITHSITVGSRITVQGFI   82 (111)
T ss_dssp             CCEEEEEEEEEEEEEEEEECTTCCEEEEEEEEEEEEEEETTEEEEEEEEEEEEEESTGGG--GGGTTCCTTCEEEEEEEE
T ss_pred             ceEEEEEEEEecCCcceEECCCCCEEEEEEEEeccEEecccceEEEEEEEEEEEeCHHHH--HHHHHhcCCCEEEEEEEE
Confidence            3577888888865421      224666666410     12       278888976542  223579999999999999


Q ss_pred             eee--C---CeeEEEEEEEeeCCCchHH
Q 023576          131 KSF--Q---GKKQIVAFSVRPVTNFDEV  153 (280)
Q Consensus       131 ~~f--~---~~~~i~~~~ir~v~d~Nei  153 (280)
                      +..  +   ++..|.|..|..++.-+++
T Consensus        83 ~~~~~~~~~~r~v~~a~~ie~l~s~~~~  110 (111)
T d1v1qa_          83 SCHKAKNGLSKMVLHAEQIELIDSVDKL  110 (111)
T ss_dssp             EEECTTTTSCEEEEEEEEEEETTSCSCC
T ss_pred             EEecccCCCCEEEEEEEEEEEecCCCcc
Confidence            974  3   3556778899888776553

>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=95.45  E-value=0.022  Score=38.47  Aligned_cols=51  Identities=14%  Similarity=0.242  Sum_probs=39.2

Q ss_pred             hHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          218 DQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+.|.+.|.... -....=+ +..+|+++|+++...|++|+..|.++|.|+..
T Consensus         9 ~e~i~~~I~~g~-~~~G~~LPs~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~   60 (74)
T d1hw1a1           9 EEYIIESIWNNR-FPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ   60 (74)
T ss_dssp             HHHHHHHHHTTS-SCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcCC-CCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE
Confidence            344555555432 1233456 79999999999999999999999999999974

>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=95.43  E-value=0.013  Score=39.11  Aligned_cols=36  Identities=8%  Similarity=0.232  Sum_probs=32.6

Q ss_pred             CCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          234 ERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       234 e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      ..=++..++++.++++...|++|+..|.++|.|+..
T Consensus        23 G~~l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~   58 (69)
T d2hs5a1          23 GARLSEPDICAALDVSRNTVREAFQILIEDRLVAHE   58 (69)
T ss_dssp             TCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCccCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE
Confidence            345789999999999999999999999999999874

>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=95.36  E-value=0.02  Score=38.12  Aligned_cols=52  Identities=19%  Similarity=0.194  Sum_probs=44.8

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .++++.|-+.+-..+   ..++++-.+||++|+++..+|+.+|-.|...|.|+..
T Consensus         6 ~~i~~lvk~~l~~L~---~~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~   57 (70)
T d1sfua_           6 AEIFSLVKKEVLSLN---TNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMV   57 (70)
T ss_dssp             HHHHHHHHHHHHTSC---TTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHhcC---CCCCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecC
Confidence            357777777777764   4569999999999999999999999999999999975

>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=95.33  E-value=0.0069  Score=39.70  Aligned_cols=44  Identities=18%  Similarity=0.268  Sum_probs=38.6

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      +||+.|++       ..++..||++.++++...|...+++|+++|.|.++-
T Consensus         3 ~Il~~i~~-------~pisr~eLa~~~gls~~TVs~~v~~L~~~GlV~e~~   46 (62)
T d2hoea1           3 RILKRIMK-------SPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEK   46 (62)
T ss_dssp             CSHHHHHH-------SCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHH-------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            47777764       148999999999999999999999999999999863

>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=95.30  E-value=0.013  Score=46.19  Aligned_cols=73  Identities=23%  Similarity=0.242  Sum_probs=49.8

Q ss_pred             eeEEEEEEEEEeee----cCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEee--eCCeeEEEEEEE
Q 023576           71 TNVTLVGLVYNKEE----RASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKS--FQGKKQIVAFSV  144 (280)
Q Consensus        71 ~~V~iVG~V~~~~~----~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~--f~~~~~i~~~~i  144 (280)
                      ..|++.|.|..+..    .-..+..++.|+||.|++++|...- - ...-...+|+.|.|.|+++.  |+++.++.-..+
T Consensus        61 ~~vti~g~V~~~~~~~~~~~~~~~~~v~D~~g~i~l~fFn~~~-~-~~~~k~~~G~~v~v~Gkvk~~~~~~~~q~~~p~~  138 (180)
T d1gm5a2          61 EKVTTQGKIVSVETKKFQNMNILTAVLSDGLVHVPLKWFNQDY-L-QTYLKQLTGKEVFVTGTVKSNAYTGQYEIHNAEV  138 (180)
T ss_dssp             CCCEEEECCCCCEEEECSSCEEEEEEECCSSCCEEEEECSCCT-T-HHHHHTTCSSCEEEEEEECSCCTTSSCCEEEEEE
T ss_pred             eeeeeeeEEEeeccccccccceeEEEEEeccceEEEEEeCcHH-H-HHHHhhhcCceEEEEEEEeeccccceeeccCcee
Confidence            35778888876542    2245688999999999998775421 1 11123357999999999965  788877765544


Q ss_pred             e
Q 023576          145 R  145 (280)
Q Consensus       145 r  145 (280)
                      .
T Consensus       139 ~  139 (180)
T d1gm5a2         139 T  139 (180)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=95.05  E-value=0.025  Score=38.42  Aligned_cols=36  Identities=22%  Similarity=0.417  Sum_probs=32.6

Q ss_pred             CCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          234 ERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       234 e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      .+=+ +..++++.|+.+...|++||..|.++|.|++-
T Consensus        19 G~~LPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~   55 (78)
T d3bwga1          19 GDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQV   55 (78)
T ss_dssp             TCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE
Confidence            3456 79999999999999999999999999999874

>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=94.98  E-value=0.015  Score=39.85  Aligned_cols=52  Identities=15%  Similarity=0.404  Sum_probs=46.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      ++++-.+.||.+|++.    ...|+-..+|..+.+++...|..+|..|.+.++|=+
T Consensus        10 ~l~~~E~lVY~~I~~a----g~~GIW~~dir~ktnL~~~~l~K~LK~Lesk~lIK~   61 (78)
T d2dk5a1          10 GSDNQEKLVYQIIEDA----GNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKA   61 (78)
T ss_dssp             CSCSSHHHHHHHHHHH----CTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHHc----cccceeHHHHHHHcCCCHHHHHHHHHHHHhcCCcee
Confidence            5677788999999986    357999999999999999999999999999998854

>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=94.80  E-value=0.021  Score=41.88  Aligned_cols=60  Identities=18%  Similarity=0.182  Sum_probs=42.0

Q ss_pred             eeEEEEEEEEEee------ec---CCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE-EEee
Q 023576           71 TNVTLVGLVYNKE------ER---ASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKS  132 (280)
Q Consensus        71 ~~V~iVG~V~~~~------~~---~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~  132 (280)
                      +.++|.|+|....      ..   ...+.+.|.|.||.|.|.+|.+...  .....|++|+.+.+.+ .|+.
T Consensus        13 ~~~~I~~RV~~k~~~r~f~~~~~~g~v~~~~l~De~G~I~~t~~~~~~~--~f~~~l~~G~vy~i~~~~V~~   82 (116)
T d1jmca1          13 SKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRATAFNEQVD--KFFPLIEVNKVYYFSKGTLKI   82 (116)
T ss_dssp             CCCEEEEEEEEECCCEEEECSSCEEEEEEEEEECSSCEEEEEEEHHHHH--HHGGGCCTTCEEEEECCEEEE
T ss_pred             CCEEEEEEEEEeccceEEECCCCCceEEEEEEEcCCCCEEEEEchhhhh--hhHhhcccCCEEEEcceEEEE
Confidence            4566777776542      11   2457889999999999999976542  2346799999888865 4544

>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=94.73  E-value=0.017  Score=41.90  Aligned_cols=53  Identities=23%  Similarity=0.399  Sum_probs=47.0

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      +|++-+-.||.+|.+.      .++++.+|++.++++...|..+|+.|.+.|.|-.+.+
T Consensus        17 Glt~~e~~v~~~L~~~------g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~~   69 (109)
T d1sfxa_          17 SFKPSDVRIYSLLLER------GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIV   69 (109)
T ss_dssp             CCCHHHHHHHHHHHHH------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCHHHHHHHHHHHhc------CCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEec
Confidence            6888999999999764      3789999999999999999999999999999976554

>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=94.56  E-value=0.26  Score=33.84  Aligned_cols=57  Identities=11%  Similarity=0.154  Sum_probs=37.3

Q ss_pred             EEEeeecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEE-EEeeeCCeeEEE
Q 023576           79 VYNKEERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIG-NLKSFQGKKQIV  140 (280)
Q Consensus        79 V~~~~~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G-~l~~f~~~~~i~  140 (280)
                      |-.......++.|.|.|.||.|+|...-.-.     .-..++||-+|++- .|+.-+++++|.
T Consensus        21 v~KK~~~~~~~~YeI~D~TG~MeVvv~G~~~-----ni~CeeGDKLrL~cFeL~~~~~~~qL~   78 (88)
T d2oq0a1          21 LHKKTVNQKTTIYEIQDDRGKMDVVGTGQCH-----NIPCEEGDKLQLFCFRLRKKNQMSKLI   78 (88)
T ss_dssp             EEEEEECSSEEEEEEEETTEEEEEEEEGGGS-----SCCCCTTCEEEEEEEEEEEETTEEEEE
T ss_pred             EEEEEEcCCeEEEEEecCCCcEEEEEeccEe-----ecccCCCCeEEEEEEEEEecCCeEEEE
Confidence            3445567789999999999999999764321     23467888666543 333444555544

>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=94.48  E-value=0.021  Score=41.22  Aligned_cols=55  Identities=24%  Similarity=0.369  Sum_probs=46.0

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|-..     +..+++.+|++.++++...|...|+.|.+.|.|...-+.
T Consensus        18 gLs~~~~~iL~~L~~~-----~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~~~~   72 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEI-----EKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKTE   72 (109)
T ss_dssp             TCCHHHHHHHHHHHHH-----CSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-
T ss_pred             CcCHHHHHHHHHHHHc-----CCCCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEeecC
Confidence            5788888999877432     235899999999999999999999999999999876544

>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=94.39  E-value=0.056  Score=42.70  Aligned_cols=75  Identities=9%  Similarity=0.114  Sum_probs=48.7

Q ss_pred             eeEEEEEcCCceEEEEEeccccc----------------Chhhhc---cCCCCCEEEEE--EEEeeeCCe--eEEEEEEE
Q 023576           88 DVNFTLDDGTGRVVCKRWASEVF----------------DTREME---AIQDGMYVRLI--GNLKSFQGK--KQIVAFSV  144 (280)
Q Consensus        88 ~~~~~LdDgTG~I~~~~w~~~~~----------------~~~~~~---~~~~G~yVrV~--G~l~~f~~~--~~i~~~~i  144 (280)
                      .+.++|+|.||.+.+..|.+.+.                +....+   .-..|.-+++.  ++...|+++  ...++.+|
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            56778999999999999975431                100010   11345544444  455578764  56889999


Q ss_pred             eeCCCchHHHHHHHHHHHH
Q 023576          145 RPVTNFDEVTCHYIECIYF  163 (280)
Q Consensus       145 r~v~d~Nei~~H~Le~i~~  163 (280)
                      .|| |+.+...|+|+-|..
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 478888999998764

>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=94.13  E-value=0.47  Score=35.66  Aligned_cols=69  Identities=19%  Similarity=0.283  Sum_probs=50.8

Q ss_pred             eeEEEEEEEEEeee----cC--CeeEEEEEcCCc-eEEEEEecccccChhhhccC-CCCCEEEEEE-EEeeeCCeeEEEE
Q 023576           71 TNVTLVGLVYNKEE----RA--SDVNFTLDDGTG-RVVCKRWASEVFDTREMEAI-QDGMYVRLIG-NLKSFQGKKQIVA  141 (280)
Q Consensus        71 ~~V~iVG~V~~~~~----~~--t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~-~~G~yVrV~G-~l~~f~~~~~i~~  141 (280)
                      ..|.++|+|.....    +.  =.++++|-|.|- -|.|.+|....   +..+.+ ..||.|++.. +++.|+++.+...
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 TIVNVYGVVKFFKPPYLSKGTDYCSVVTIVDQTNVKLTCLLFSGNY---EALPIIYKNGDIVRFHRLKIQVYKKETQGIT   92 (140)
T ss_dssp             EEEEEEEEEEEEEEEEECSSSSEEEEEEEECTTCCEEEEEEEESSG---GGSCCCCSTTCEEEEEEEEEEEETTEEEEEE
T ss_pred             CEEEEEEEEeecCCCEEcCCCeEEEEEEEEeCCCCCeEEEEECCCh---HHCCCCCCCCCEEEEEEEEEEEECCeEEEEe
Confidence            36788999988642    22  255689999875 49999997754   235555 5799999986 5778999988776


Q ss_pred             E
Q 023576          142 F  142 (280)
Q Consensus       142 ~  142 (280)
                      .
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=94.12  E-value=0.044  Score=40.62  Aligned_cols=57  Identities=19%  Similarity=0.360  Sum_probs=49.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++.-|-.||.+|...    .+.+++..+|++.++++...+..+|+.|.+.|.|....|++
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            4677888899998764    24579999999999999999999999999999999877654

>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=93.88  E-value=0.042  Score=40.76  Aligned_cols=56  Identities=14%  Similarity=0.223  Sum_probs=48.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...    .+.|+++.+|++.++++...+...|+.|.+.|.|...-|.
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            3566778899999763    3468999999999999999999999999999999876554

>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=93.79  E-value=0.019  Score=40.21  Aligned_cols=55  Identities=22%  Similarity=0.312  Sum_probs=43.6

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhC--CCHHHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLK--IPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~--~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      |++-|++||++|-+.= .....-++..+|++.++  ++...||..|..|..+|.|+..
T Consensus         2 Lt~Rq~~IL~~Ive~y-~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~~   58 (87)
T d1stza1           2 LNDRQRKVLYCIVREY-IENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQP   58 (87)
T ss_dssp             CCHHHHHHHHHHHHHH-HHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECC
T ss_pred             cCHHHHHHHHHHHHHH-HHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccCC
Confidence            5677888998775531 12345788999999975  6899999999999999999874

>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=93.68  E-value=0.034  Score=40.55  Aligned_cols=58  Identities=14%  Similarity=0.301  Sum_probs=49.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFH  274 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~h  274 (280)
                      +++.-|-.||.+|...    .+.+++..+|++.++++...|...|+.|.+.|+|..+.|.+.
T Consensus        30 ~Ls~~q~~vL~~l~~~----~~~~~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~~~~D   87 (115)
T d2frha1          30 SISFEEFAVLTYISEN----KEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHD   87 (115)
T ss_dssp             CCCHHHHHHHHHHHHT----CCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSS
T ss_pred             CCCHHHHHHHHHHHcC----CCCCCCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeeecccC
Confidence            3566777888888764    345799999999999999999999999999999999987754

>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=93.66  E-value=0.055  Score=40.71  Aligned_cols=55  Identities=20%  Similarity=0.346  Sum_probs=46.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      |++..+-+|+.+|-..     +.++++.+|++.++++...|...|+.|.+.|+|..+-+.
T Consensus        23 Gl~~~~~~i~~~L~~~-----~~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~~~   77 (151)
T d1ku9a_          23 GLNKSVGAVYAILYLS-----DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIK   77 (151)
T ss_dssp             TCCHHHHHHHHHHHHC-----SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             CCCHHHHHHHHHHHhC-----CCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEEcC
Confidence            5777888899888532     347999999999999999999999999999999876543

>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=93.63  E-value=0.15  Score=37.54  Aligned_cols=66  Identities=20%  Similarity=0.381  Sum_probs=44.8

Q ss_pred             eEEEEEEEEEeee------c-----CCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEE-EeeeCCeeE
Q 023576           72 NVTLVGLVYNKEE------R-----ASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGN-LKSFQGKKQ  138 (280)
Q Consensus        72 ~V~iVG~V~~~~~------~-----~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~-l~~f~~~~~  138 (280)
                      .|-|+|+|.++..      +     .....++|.|.|| .|++.+|.+.+.   .. ....+..|.+.|. ++.|+++ .
T Consensus        18 ~vDViGvv~~v~~~~~i~~k~~g~~~~kR~i~i~D~t~~~i~vtLWg~~a~---~~-~~~~~~Vi~~k~~~v~~~~g~-s   92 (122)
T d1jmca2          18 LVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTATLWGEDAD---KF-DGSRQPVLAIKGARVSDFGGR-S   92 (122)
T ss_dssp             EEEEEEEEEEECCCEEEEETTTTEEEEEEEEEEECTTCCEEEEEEEHHHHH---HC-CCTTCCEEEEEEEEEECTTSS-E
T ss_pred             eEEEEEEEEEccCcEEEEEcCCCCceeEEEEEEEcCCCCEEEEEEEchHhh---hh-CCCCCCEEEEeeeEEeeccCc-e
Confidence            4778888877632      1     1367999999999 599999976531   11 2345667766665 6779876 5


Q ss_pred             EEEE
Q 023576          139 IVAF  142 (280)
Q Consensus       139 i~~~  142 (280)
                      |...
T Consensus        93 L~~~   96 (122)
T d1jmca2          93 LSVL   96 (122)
T ss_dssp             EECC
T ss_pred             Eecc
Confidence            6553

>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=93.33  E-value=0.091  Score=39.29  Aligned_cols=54  Identities=22%  Similarity=0.359  Sum_probs=47.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...      .|+++.+|++.++++...|...|+.|.+.|+|...-|.
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            4677888899999753      37999999999999999999999999999999876654

>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=93.28  E-value=0.048  Score=35.37  Aligned_cols=44  Identities=11%  Similarity=0.296  Sum_probs=36.5

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +.|+++.++      ...+...+||+.|+++...|.++|..|.++|+|-.
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            446665543      23789999999999999999999999999999854

>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=93.15  E-value=0.065  Score=39.90  Aligned_cols=56  Identities=20%  Similarity=0.257  Sum_probs=45.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+-.||.+|.+.     +.+++..+|++.++++...|...|+.|...|+|..+-|.+
T Consensus        28 glt~~~~~~L~~l~~~-----~~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~~~~~   83 (140)
T d3deua1          28 ELTQTHWVTLHNIHQL-----PPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCAS   83 (140)
T ss_dssp             TCCHHHHHHHHHHHHS-----CSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC----
T ss_pred             CCCHHHHHHHHHHHHc-----CCCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEecccCC
Confidence            4667788899998752     3489999999999999999999999999999999887764

>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=93.00  E-value=0.086  Score=34.90  Aligned_cols=47  Identities=13%  Similarity=0.150  Sum_probs=40.5

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .-|..||++....      --|++..+...|+-+....+.+|+.|+.||.+.-
T Consensus         3 ~Dqt~vLe~a~~~------G~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~Wv   49 (68)
T d1u5ta2           3 SDQTKILEICSIL------GYSSISLLKANLGWEAVRSKSALDEMVANGLLWI   49 (68)
T ss_dssp             TTHHHHHHTTTTT------SCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEE
T ss_pred             chHHHHHHHHHHc------CceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEEE
Confidence            3467899987642      3789999999999999999999999999999874

>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=92.94  E-value=0.48  Score=34.34  Aligned_cols=64  Identities=20%  Similarity=0.216  Sum_probs=44.5

Q ss_pred             eeEEEEEEEEEeeecCCeeEEEEEcCCc-eEEEEEecccccChhhhccCCCCCEEEEEEEEeeeCCeeEEEEEEEeeC
Q 023576           71 TNVTLVGLVYNKEERASDVNFTLDDGTG-RVVCKRWASEVFDTREMEAIQDGMYVRLIGNLKSFQGKKQIVAFSVRPV  147 (280)
Q Consensus        71 ~~V~iVG~V~~~~~~~t~~~~~LdDgTG-~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~~f~~~~~i~~~~ir~v  147 (280)
                      ..|+|||+|.+++...  -.+++.+.-| .|.|.+-.+.        ....+.||.|+|++.   ++..|.+..+...
T Consensus        21 k~V~ivGkV~~v~~~g--~~~~~~s~D~~~V~v~l~~~~--------~~~~~~~vEViG~V~---~~~sI~~~~~~~f   85 (115)
T d2pi2e1          21 KPVCFVGRLEKIHPTG--KMFILSDGEGKNGTIELMEPL--------DEEISGIVEVVGRVT---AKATILCTSYVQF   85 (115)
T ss_dssp             CEEEEEEEEEEECTTS--SEEEEECTTSCEEEEECSSCC--------SSCCCSEEEEEEEEC---TTSCEEEEEEEEC
T ss_pred             CeEEEEEEEEEEcCCC--CEEEEEcCCCCEEEEEeCCCC--------CCccCCeEEEEEEEC---CCCcEEEEEEEEc
Confidence            4899999999886543  3456777655 6777755432        235678999999995   4556777766555

>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=92.93  E-value=0.097  Score=38.72  Aligned_cols=56  Identities=18%  Similarity=0.253  Sum_probs=47.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++.-+=.||.+|...     ..|+++.+|+..++++...|..+|+.|+..|.|..+.|.+
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            3555666788877542     2389999999999999999999999999999999988765

>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=92.89  E-value=0.14  Score=38.77  Aligned_cols=63  Identities=21%  Similarity=0.198  Sum_probs=44.6

Q ss_pred             EEEeeEEEEEEEEE---ee---ecCCeeEEEEE--------------cCCceEEEEEecccccChhhhccCCCCCEEEEE
Q 023576           68 LEITNVTLVGLVYN---KE---ERASDVNFTLD--------------DGTGRVVCKRWASEVFDTREMEAIQDGMYVRLI  127 (280)
Q Consensus        68 ~~i~~V~iVG~V~~---~~---~~~t~~~~~Ld--------------DgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~  127 (280)
                      +-++.|.|+|.|..   +.   .....+.|.|-              +.|--+.|..|...++  .....++.|+.|.|.
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   22357778773              2344589999965431  234679999999999


Q ss_pred             EEEee
Q 023576          128 GNLKS  132 (280)
Q Consensus       128 G~l~~  132 (280)
                      |+|+.
T Consensus        81 G~l~~   85 (145)
T d1qvca_          81 GQLRT   85 (145)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            99875

>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=92.80  E-value=0.87  Score=35.25  Aligned_cols=70  Identities=21%  Similarity=0.219  Sum_probs=51.2

Q ss_pred             eeEEEEEEEEEeee-----cCC---eeEEEEEcCC----c-eEEEEEecccccChhhhccC-CCCCEEEEEE-EEeeeCC
Q 023576           71 TNVTLVGLVYNKEE-----RAS---DVNFTLDDGT----G-RVVCKRWASEVFDTREMEAI-QDGMYVRLIG-NLKSFQG  135 (280)
Q Consensus        71 ~~V~iVG~V~~~~~-----~~t---~~~~~LdDgT----G-~I~~~~w~~~~~~~~~~~~~-~~G~yVrV~G-~l~~f~~  135 (280)
                      ..|.++|+|.....     +.+   .++|+|-|.|    . .|.|.+|....+   ..+.+ ..||.|++.. +++.|++
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            46888888887642     222   5679999977    3 399999987642   35555 5799999986 6779999


Q ss_pred             eeEEEEEE
Q 023576          136 KKQIVAFS  143 (280)
Q Consensus       136 ~~~i~~~~  143 (280)
                      +.+.....
T Consensus       114 ~~q~v~~~  121 (170)
T d1qzga_         114 RTQGLSKD  121 (170)
T ss_dssp             EEEEEEEE
T ss_pred             ceEEEecC
Confidence            99866544

>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=92.70  E-value=0.048  Score=38.44  Aligned_cols=52  Identities=17%  Similarity=0.218  Sum_probs=45.0

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ++.+..||.+|...      ..+++.+|++.++++...|...|..|.+.|.|-..-|.
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            45788899999753      36899999999999999999999999999999876543

>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=92.55  E-value=0.042  Score=38.02  Aligned_cols=39  Identities=26%  Similarity=0.394  Sum_probs=36.4

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      .=++++.|++.|++++++++..|..|+.+|.|...||..
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            358999999999999999999999999999999999874

>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=92.43  E-value=0.078  Score=34.55  Aligned_cols=33  Identities=15%  Similarity=0.324  Sum_probs=30.8

Q ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      .+...+||+.|+++...|.+++..|.++|+|=.
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

>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=92.41  E-value=0.038  Score=37.18  Aligned_cols=50  Identities=20%  Similarity=0.403  Sum_probs=42.9

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCH-HHHHHHHHHHHhCCeeeec
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQ-KKIMDSIASLENEGLIYST  269 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~-~~v~~al~~L~~eG~IYsT  269 (280)
                      +.+++++|+++|.+.+      ....-+|++.|+++- .+|+.+|-.|...|.+|..
T Consensus         3 ~~d~eekI~~~L~~~g------~~~Al~iak~lGl~kakeVN~~LY~L~k~g~v~k~   53 (73)
T d1xmka1           3 MAEIKEKICDYLFNVS------DSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQ   53 (73)
T ss_dssp             HHHHHHHHHHHHHHTC------CEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             hHHHHHHHHHHHHHcC------CchHHHHHHHhCCCcHHHHhHHHHHHHHCCCeecC
Confidence            3568899999998753      356788999999998 5899999999999999975

>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=92.29  E-value=0.19  Score=33.77  Aligned_cols=60  Identities=10%  Similarity=0.190  Sum_probs=47.6

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +.+.-..||..|.+.....+..--|..-|+++-++|++.+|..|..|.+-|.+-+++|||
T Consensus         2 lDP~lvavL~~L~eA~~e~~g~~WSLaklsKra~~PMS~LRR~LTqL~~aGl~~t~~~ed   61 (81)
T d2obpa1           2 IDPAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVSVEAD   61 (81)
T ss_dssp             CCHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTT
T ss_pred             CChHHHHHHHHHHHHhccCCCCCccHHHHHhhcCCcHHHHHHHHHHHhhcCceeeeeccC
Confidence            344555677777665432233345899999999999999999999999999999999997

>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=92.03  E-value=0.19  Score=33.42  Aligned_cols=52  Identities=21%  Similarity=0.366  Sum_probs=39.7

Q ss_pred             chhHHHHHHhcCCCCCCC-C--CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          216 DCDQMILDYLQQPSSSER-E--RGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~-e--~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      ++..+|..+|-....... +  --++.++||+.++.+.+.|..+|..|.++|.|=
T Consensus         4 dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~   58 (73)
T d1zyba1           4 DLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLIE   58 (73)
T ss_dssp             SHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSCE
T ss_pred             CHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            467778777654321111 1  236899999999999999999999999999984

>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=91.88  E-value=0.12  Score=38.73  Aligned_cols=55  Identities=22%  Similarity=0.356  Sum_probs=47.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..|-.||.+|.+.      .|++..+|++.++++...|...|+.|...|+|...-|.+
T Consensus        26 ~lt~~q~~iL~~i~~~------~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~~~~   80 (144)
T d1lj9a_          26 SLTRGQYLYLVRVCEN------PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDAS   80 (144)
T ss_dssp             TCTTTHHHHHHHHHHS------TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             CCCHHHHHHHHHHHhC------CCCCHHHHHHHHCccHhhHHHHHHHHHhhhcccccCCCC
Confidence            4667788899988753      389999999999999999999999999999999877754

>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=91.83  E-value=0.08  Score=39.26  Aligned_cols=55  Identities=20%  Similarity=0.273  Sum_probs=48.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+-.||.+|...      .++++.+|++.++++...|..+|+.|...|+|..+-|.+
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            5777888899999763      379999999999999999999999999999999876654

>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=91.75  E-value=0.15  Score=32.38  Aligned_cols=47  Identities=28%  Similarity=0.475  Sum_probs=40.2

Q ss_pred             hHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          218 DQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       218 ~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      +++|+.+|++..   ...-.+..+++.+|+++-.+|+.+|-.|..-|.+.
T Consensus         1 Eq~vl~~l~~lg---~~~~~tA~~LA~kl~vpKk~iNr~LYsL~~kgkl~   47 (59)
T d2gxba1           1 EQRILKFLEELG---EGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQ   47 (59)
T ss_dssp             HHHHHHHHHHHC---TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             ChHHHHHHHhcC---CccchhHHHHHHHhCCcHHHHHHHHHHHHHccchh
Confidence            357999998864   33578999999999999999999999999998775

>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=91.74  E-value=0.1  Score=37.77  Aligned_cols=56  Identities=11%  Similarity=0.155  Sum_probs=47.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..|=.||.+|...    .+.|+++.+|++.++++...+..+|+.|.+.|+|--+.|+
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            4566777899888653    2458999999999999999999999999999999866665

>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=91.58  E-value=0.096  Score=39.11  Aligned_cols=55  Identities=20%  Similarity=0.335  Sum_probs=48.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+-.||.+|...      .|+++.+|++.++++...|...++.|...|+|....|.+
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            4677888899999763      389999999999999999999999999999999777754

>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=91.52  E-value=0.066  Score=36.92  Aligned_cols=39  Identities=26%  Similarity=0.342  Sum_probs=35.3

Q ss_pred             CCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          233 RERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       233 ~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      ...++++.+|++.++++...|...|+.|...|+|-...|
T Consensus        18 ~~~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~~D   56 (85)
T d3ctaa1          18 NRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVT   56 (85)
T ss_dssp             SEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeecc
Confidence            446899999999999999999999999999999987544

>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=91.38  E-value=0.27  Score=31.73  Aligned_cols=41  Identities=10%  Similarity=0.152  Sum_probs=35.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      .|++-+.+||.++.+        |.+..+|++.|++++..|+..+..+.
T Consensus         4 ~Lt~rE~~vl~l~~~--------G~s~~eIA~~l~iS~~TV~~~~~~i~   44 (65)
T d1l3la1           4 WLDPKEATYLRWIAV--------GKTMEEIADVEGVKYNSVRVKLREAM   44 (65)
T ss_dssp             CCCHHHHHHHHHHTT--------TCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHh--------cCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            578889999999863        99999999999999999998877654

>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=91.32  E-value=0.19  Score=39.38  Aligned_cols=49  Identities=27%  Similarity=0.415  Sum_probs=42.8

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      ++...+||.+|+.       ...++.+|++.++++...|...|..|.+.|.|.+.-
T Consensus        18 ~p~R~~Il~~L~~-------~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~~~   66 (190)
T d1ulya_          18 EDTRRKILKLLRN-------KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKR   66 (190)
T ss_dssp             SHHHHHHHHHHTT-------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            4678889999964       247999999999999999999999999999997653

>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=91.19  E-value=0.54  Score=38.01  Aligned_cols=76  Identities=17%  Similarity=0.338  Sum_probs=49.4

Q ss_pred             EEeeEEEEEEEEEe---e---ecCCeeEEEEE------c-------CCceEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576           69 EITNVTLVGLVYNK---E---ERASDVNFTLD------D-------GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN  129 (280)
Q Consensus        69 ~i~~V~iVG~V~~~---~---~~~t~~~~~Ld------D-------gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~  129 (280)
                      .++.|.|+|.+..-   .   .....+.|.|-      |       .|--+.|..|-..+   +....++.|+.|.|.|+
T Consensus       126 ~~N~v~l~G~l~~dpe~r~t~~G~~~~~f~va~~~~~~~~~g~~~~~t~~~~v~~~g~~A---e~~~~l~KG~~V~V~G~  202 (231)
T d1se8a_         126 AMNEVLVLGNVTRDPEIRYTPAGDAVLSLSIAVNENYQDRQGQRQEKVHYIDATLWRDLA---ENMKELRKGDPVMIMGR  202 (231)
T ss_dssp             CEEEEEEEEEECSCCEEEECTTCCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEETHHH---HHHTTCCTTCEEEEEEE
T ss_pred             cceeEEEEEEeCCCcEEEECCCCCEEEEEEEEECCCeECCCCceeeeeEEEEeEecCcHH---HHhhhCCCCCEEEEEEE
Confidence            36899999999652   1   22346777772      2       23358999996544   22456899999999999


Q ss_pred             Eee--eCCe-------eEEEEEEEeeC
Q 023576          130 LKS--FQGK-------KQIVAFSVRPV  147 (280)
Q Consensus       130 l~~--f~~~-------~~i~~~~ir~v  147 (280)
                      |+.  |.++       ..|.+..|..+
T Consensus       203 l~~~~~~~kdG~~r~~~~i~a~~v~~L  229 (231)
T d1se8a_         203 LVNEGWTDKDGNKRNSTRVEATRVEAL  229 (231)
T ss_dssp             EEEEECC------CEEEEEEEEEEEEC
T ss_pred             eEeceEECCCCCEEEEEEEEEEEEEEc
Confidence            974  5432       23555665554

>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=90.91  E-value=0.13  Score=38.18  Aligned_cols=54  Identities=22%  Similarity=0.267  Sum_probs=46.6

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++.-+-.||..|...      .++++.+|++.++++...|...|+.|...|+|-.+-+.
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            4667778899999753      37899999999999999999999999999999877654

>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=90.58  E-value=0.13  Score=34.10  Aligned_cols=53  Identities=17%  Similarity=0.199  Sum_probs=41.2

Q ss_pred             hhHHHHHHhcCC-CCCCCCCccCHHHHHHHh--CCCHHHHHHHHHHHHhCCeeeec
Q 023576          217 CDQMILDYLQQP-SSSERERGVHVNELSEQL--KIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       217 ~~~~Vl~~i~~~-~~~~~e~Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +++.|++.|++= .......|++.+++.+++  ++++.-+...|+.|+.+|.|-..
T Consensus         6 l~~~i~~~L~~fH~~~P~~~G~~keeLr~~l~~~~~~~~f~~lL~~l~~~g~l~~~   61 (73)
T d2v9va2           6 WWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLA   61 (73)
T ss_dssp             HHHHHHHHHHHHHHHCTTSSCEEHHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHHHHHHCccccCCCHHHHHHHhcccCCHHHHHHHHHHHHHCCChhee
Confidence            556666666441 011356899999999999  59999999999999999999763

>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=90.44  E-value=0.28  Score=31.77  Aligned_cols=41  Identities=20%  Similarity=0.309  Sum_probs=35.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      -|++-+.+||.++.+        |.+..+|++.+++++..|+..+..+.
T Consensus         4 ~LT~rE~~vl~l~~~--------G~s~~eIA~~L~is~~TV~~~~~~i~   44 (67)
T d1fsea_           4 LLTKREREVFELLVQ--------DKTTKEIASELFISEKTVRNHISNAM   44 (67)
T ss_dssp             CCCHHHHHHHHHHTT--------TCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc--------cCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            378889999999863        99999999999999999998877654

>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=90.43  E-value=0.098  Score=37.14  Aligned_cols=52  Identities=17%  Similarity=0.293  Sum_probs=38.9

Q ss_pred             hhHHHHHHhcCCCCCCCCCcc-CHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          217 CDQMILDYLQQPSSSERERGV-HVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      +...|.+.|..-. -...+=+ +..+++++|+.+...|++|+..|.++|.|+.-
T Consensus        14 i~~~i~~~I~~g~-l~~G~~LPs~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~   66 (100)
T d1v4ra1          14 VATHFRTLIKSGE-LAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSR   66 (100)
T ss_dssp             HHHHHHHHTTTTS-CCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEE
T ss_pred             HHHHHHHHHHcCC-CCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEe
Confidence            4444445554432 2233456 89999999999999999999999999999864

>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=90.07  E-value=0.12  Score=37.93  Aligned_cols=56  Identities=16%  Similarity=0.252  Sum_probs=48.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++..+-.||.+|...    .+.++++.+|++.++++...|..+|+.|...|.|.-.-|.
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            4677888899998764    2457999999999999999999999999999999887665

>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=89.76  E-value=0.57  Score=30.32  Aligned_cols=31  Identities=16%  Similarity=0.296  Sum_probs=29.6

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          237 VHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       237 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      ++.++||..++.+.+.|...|..|.++|.|-
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            7899999999999999999999999999884

>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=89.70  E-value=0.2  Score=32.89  Aligned_cols=47  Identities=15%  Similarity=0.263  Sum_probs=41.9

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I  266 (280)
                      -++..+|+++++..     ..|++=++|.+.+ .++.++=-+||..|.+.|.|
T Consensus         6 ~~ie~~Ilel~k~~-----P~GitD~dl~~a~p~v~~~qRv~aiN~LLs~g~i   53 (68)
T d2dk8a1           6 VEIENRIIELCHQF-----PHGITDQVIQNEMPHIEAQQRAVAINRLLSMGQL   53 (68)
T ss_dssp             HHHHHHHHHHHHHC-----SSCEEHHHHHHHCTTSCHHHHHHHHHHHHHHTSE
T ss_pred             HhHHHHHHHHHHhC-----CCCCChHHHHHHCcCCCHHHHHHHHHHHHHcCCe
Confidence            35888999999974     4699999999999 69999999999999999976

>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=89.59  E-value=0.33  Score=31.48  Aligned_cols=42  Identities=17%  Similarity=0.298  Sum_probs=36.4

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHh
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLEN  262 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~  262 (280)
                      .|++-+.+|+.++.+        |.+..+|++++++++..|+.-+..+..
T Consensus         6 ~LT~rE~~vl~ll~~--------G~s~~eIA~~l~iS~~TV~~~~~~i~~   47 (67)
T d1a04a1           6 QLTPRERDILKLIAQ--------GLPNKMIARRLDITESTVKVHVKHMLK   47 (67)
T ss_dssp             GSCHHHHHHHHHHHT--------TCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHh--------CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            478889999999864        999999999999999999988876643

>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=89.56  E-value=0.2  Score=30.87  Aligned_cols=48  Identities=17%  Similarity=0.420  Sum_probs=40.8

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      .|-+.|+.-    .-+|....++.++|++...+|++||-.|-....+|+.-|
T Consensus         6 ivceaik~i----g~egata~qltrqlnmekrevnkalydlqrsamvy~s~d   53 (62)
T d1oyia_           6 IVCEAIKTI----GIEGATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDD   53 (62)
T ss_dssp             HHHHHHHHH----SSSTEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECSS
T ss_pred             HHHHHHHhc----cccchHHHHHHHHHhHHHHHHHHHHHHHHHhhheecCCC
Confidence            466667664    246999999999999999999999999999999999744

>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=89.51  E-value=0.4  Score=34.63  Aligned_cols=61  Identities=26%  Similarity=0.347  Sum_probs=41.7

Q ss_pred             eeEEEEEEEEE---ee---ecCCeeEEEEE--c-------------CCceEEEEEecccccChhhhccCCCCCEEEEEEE
Q 023576           71 TNVTLVGLVYN---KE---ERASDVNFTLD--D-------------GTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGN  129 (280)
Q Consensus        71 ~~V~iVG~V~~---~~---~~~t~~~~~Ld--D-------------gTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~  129 (280)
                      +.|.|+|.|..   +.   .....+.|+|-  +             .|--+.|..|...++  .....++.|+.|.|.|+
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            67899999954   22   12346678773  1             133499999976432  22356999999999999


Q ss_pred             Eeee
Q 023576          130 LKSF  133 (280)
Q Consensus       130 l~~f  133 (280)
                      |+..
T Consensus        81 L~~~   84 (118)
T d1ue1a_          81 LKQR   84 (118)
T ss_dssp             EEEE
T ss_pred             eeec
Confidence            9963

>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=89.47  E-value=0.23  Score=39.17  Aligned_cols=50  Identities=34%  Similarity=0.511  Sum_probs=43.0

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      ++...+||.+|+.       .-+++.+|++.|+++...|+.-|..|.+.|.|.+..+
T Consensus        14 ~~~R~~Il~~L~~-------~~~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~~~~~   63 (194)
T d2p4wa1          14 NETRRRILFLLTK-------RPYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVE   63 (194)
T ss_dssp             SHHHHHHHHHHHH-------SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CHHHHHHHHHHHh-------CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe
Confidence            3577889999974       2479999999999999999999999999999987544

>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=89.37  E-value=1.5  Score=33.82  Aligned_cols=69  Identities=16%  Similarity=0.222  Sum_probs=51.1

Q ss_pred             eeEEEEEEEEEeee----c--CCeeEEEEEcCC------------c-eEEEEEecccccChhhhccC-CCCCEEEEEE-E
Q 023576           71 TNVTLVGLVYNKEE----R--ASDVNFTLDDGT------------G-RVVCKRWASEVFDTREMEAI-QDGMYVRLIG-N  129 (280)
Q Consensus        71 ~~V~iVG~V~~~~~----~--~t~~~~~LdDgT------------G-~I~~~~w~~~~~~~~~~~~~-~~G~yVrV~G-~  129 (280)
                      ..|.|.|+|+....    +  .=.++|+|-|.|            + .|.|.+|.+..   +..+.+ ..||.|++.. +
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 QPQHFYAVVIDATFPYKTNQERYICSLKIVDPTLYLKQQKGAGDASDYATLVLYAKRF---EDLPIIHRAGDIIRVHRAT   91 (169)
T ss_dssp             SCEEEEEEEEEECCCEECSSSCEEEEEEEEBTTBSBCCTTSSCSCBCCEEEEEEESSG---GGSCCCCEETCEEEEEEEE
T ss_pred             CeEEEEEEEeecCCceecCCCcEEEEEEEEeCCCCccccccccccCCceEEEEECCCH---HHCCCCCCCCCEEEEEEEE
Confidence            34789999988642    2  236788999976            2 48999998764   235555 4799999985 6


Q ss_pred             EeeeCCeeEEEEE
Q 023576          130 LKSFQGKKQIVAF  142 (280)
Q Consensus       130 l~~f~~~~~i~~~  142 (280)
                      |+.|+++.+..+.
T Consensus        92 i~~~~g~~~~v~~  104 (169)
T d1jb7a1          92 LRLYNGQRQFNAN  104 (169)
T ss_dssp             EEEETTEEEEEEE
T ss_pred             EEEECCceeEEEc
Confidence            7889999998765

>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=89.27  E-value=0.26  Score=36.47  Aligned_cols=54  Identities=11%  Similarity=0.123  Sum_probs=46.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      +++.-|-.||.+|...      .+++..+|++.++++...+...|+.|.+.|+|-..-|.
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            4667788899999763      27999999999999999999999999999999876664

>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=89.08  E-value=0.28  Score=34.10  Aligned_cols=43  Identities=12%  Similarity=0.103  Sum_probs=37.9

Q ss_pred             CccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          235 RGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       235 ~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      +|+.+..|....+++-+.+.+.|+.|.+.|.|=.  ++..|..|+
T Consensus        17 ~g~~kT~i~~~aNLs~~~~~kyl~~L~~~GLI~~--~~~~Y~iT~   59 (90)
T d1r7ja_          17 SGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQ--EGKQYMLTK   59 (90)
T ss_dssp             TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE--ETTEEEECH
T ss_pred             CCCCccHHHHHcCCCHHHHHHHHHHHHHCCCeee--cCCEEEECc
Confidence            3778999999999999999999999999999953  667888875

>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=88.97  E-value=0.21  Score=36.95  Aligned_cols=56  Identities=20%  Similarity=0.346  Sum_probs=48.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFH  274 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~h  274 (280)
                      +++.-+-.||..|...      .++++.+|++.++++...|...|..|.+.|+|-..-|.++
T Consensus        29 ~lt~~q~~iL~~l~~~------~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~~D   84 (140)
T d2etha1          29 DMKTTELYAFLYVALF------GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVD   84 (140)
T ss_dssp             HSBHHHHHHHHHHHHH------CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTT
T ss_pred             CCCHHHHHHHHHHHHc------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeeecccc
Confidence            3566778899999763      3789999999999999999999999999999998777643

>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=88.94  E-value=0.19  Score=37.21  Aligned_cols=56  Identities=20%  Similarity=0.248  Sum_probs=48.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFH  274 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~h  274 (280)
                      +++.-|=.||.+|...      .|++..+|++.++++...|..+++.|+..|.|.-.-|.+.
T Consensus        30 gLt~~q~~vL~~l~~~------~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~~~~~D   85 (137)
T d1z91a1          30 NITYPQYLALLLLWEH------ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEED   85 (137)
T ss_dssp             CCCHHHHHHHHHHHHH------SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCSSC
T ss_pred             CcCHHHHHHHHHHHcC------CCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEeecCCC
Confidence            4677788899999763      3899999999999999999999999999999998877543

>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=88.56  E-value=0.17  Score=37.42  Aligned_cols=55  Identities=18%  Similarity=0.225  Sum_probs=47.9

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+-.||.+|...      .|++..+|++.++++...+...++.|...|+|=.+-|++
T Consensus        31 glt~~q~~vL~~i~~~------~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~~~~   85 (136)
T d2bv6a1          31 NLTYPQFLVLTILWDE------SPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEV   85 (136)
T ss_dssp             TCCHHHHHHHHHHHHS------SEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSS
T ss_pred             CCCHHHHHHHHHHHcC------CCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEeecCC
Confidence            4677888899999763      389999999999999999999999999999998776653

>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=88.38  E-value=0.52  Score=31.57  Aligned_cols=55  Identities=20%  Similarity=0.366  Sum_probs=45.5

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      .++.++||.+|..        |-+.++|-+.|+++..+.+=-|.-|. -|.+-+-.|+ .|+.|+
T Consensus        30 nPvRrkiLrmi~k--------grsedEIm~~l~LSkkqldYHLk~LE-~GfciErvge-~w~~T~   84 (89)
T d1y0ua_          30 NPVRRKILRMLDK--------GRSEEEIMQTLSLSKKQLDYHLKVLE-AGFCIERVGE-RWVVTD   84 (89)
T ss_dssp             CHHHHHHHHHHHT--------TCCHHHHHHHHTCCHHHHHHHHHHHH-HTTSEEEETT-EEEECT
T ss_pred             hHHHHHHHHHHHc--------cCCHHHHHHHhccCHHHHHHHHHHHH-ccceeEecCC-ceeecc
Confidence            4699999999963        67899999999999999998887664 5777777777 787775

>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=88.26  E-value=0.94  Score=36.49  Aligned_cols=79  Identities=13%  Similarity=0.140  Sum_probs=51.1

Q ss_pred             EeeEEEEEEEEE---ee---ecCCeeEEEEE------cC-------CceEEEEEecccccChhhh-ccCCCCCEEEEEEE
Q 023576           70 ITNVTLVGLVYN---KE---ERASDVNFTLD------DG-------TGRVVCKRWASEVFDTREM-EAIQDGMYVRLIGN  129 (280)
Q Consensus        70 i~~V~iVG~V~~---~~---~~~t~~~~~Ld------Dg-------TG~I~~~~w~~~~~~~~~~-~~~~~G~yVrV~G~  129 (280)
                      ++.|.|+|.|.+   +.   .....+.|.|-      |.       |--+.|..|-..++  ... ..++.|+.|.|.|+
T Consensus         3 mN~v~l~G~l~~dpe~r~t~~G~~~~~f~lA~~~~~~~~~g~~~~~t~~~~v~~~g~~Ae--~~~~~~l~KG~~V~V~G~   80 (231)
T d1se8a_           3 MNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGRERNLPWYHRVSILGKPAE--WQAERNLKGGDAVVVEGT   80 (231)
T ss_dssp             EEEEEEEEEESSCCEEEECTTSCEEEEEEEEEEEEC-------CEEEEEEEEEEESHHHH--HHHHTCCCTTCEEEEEEE
T ss_pred             ccEEEEEEEECcCCEEEECCCCCEEEEEEEEECCcEECCCCCEEeeeeeeeEEEeCchhh--hhhhhccCCCCEEEEEEE
Confidence            688999999964   22   12347778772      22       22488999966431  112 35899999999999


Q ss_pred             Eee--eC---Ce----eEEEEEEEeeCCCc
Q 023576          130 LKS--FQ---GK----KQIVAFSVRPVTNF  150 (280)
Q Consensus       130 l~~--f~---~~----~~i~~~~ir~v~d~  150 (280)
                      |+.  |.   |+    ..|.+..|..+..-
T Consensus        81 l~~~~~~~~dG~~r~~~~i~a~~v~~l~~~  110 (231)
T d1se8a_          81 LEYRQWEAPEGGKRSAVNVKALRMEQLGTQ  110 (231)
T ss_dssp             EEEEEEC-----CEEEEEEEEEEEEECSSC
T ss_pred             EEeeeeECCCCCEEEEEEEEEEEEEEccCC
Confidence            984  43   22    35777888777653

>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=87.88  E-value=1.3  Score=31.47  Aligned_cols=65  Identities=17%  Similarity=0.199  Sum_probs=39.0

Q ss_pred             EEEeeEEEEEEEEE---eee---cCCeeEEEEE------c------CCc-------eEEEEEecccccChhhhccCCCCC
Q 023576           68 LEITNVTLVGLVYN---KEE---RASDVNFTLD------D------GTG-------RVVCKRWASEVFDTREMEAIQDGM  122 (280)
Q Consensus        68 ~~i~~V~iVG~V~~---~~~---~~t~~~~~Ld------D------gTG-------~I~~~~w~~~~~~~~~~~~~~~G~  122 (280)
                      +.+++|.|+|.|.+   +..   ....+.|.|-      |      ..|       -+.|..|.....+ .....++.|+
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   221   2346677773      1      112       2455555432210 1123589999


Q ss_pred             EEEEEEEEeee
Q 023576          123 YVRLIGNLKSF  133 (280)
Q Consensus       123 yVrV~G~l~~f  133 (280)
                      .|.|.|+|+.-
T Consensus        82 ~V~V~Grl~~~   92 (115)
T d3ulla_          82 RIYLEGKIDYG   92 (115)
T ss_dssp             EEEEEEEEECC
T ss_pred             EEEEEEEEeee
Confidence            99999999863

>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=87.41  E-value=0.3  Score=37.52  Aligned_cols=55  Identities=16%  Similarity=0.108  Sum_probs=46.8

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      +++..+-.||.+|...      .|+++.+|++.++++...|..+|..|.+.|+|-.+-|++
T Consensus        38 ~Lt~~q~~vL~~l~~~------~~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~~~~   92 (162)
T d2fxaa1          38 DLNINEHHILWIAYQL------NGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLN   92 (162)
T ss_dssp             TCCHHHHHHHHHHHHH------TSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC--
T ss_pred             CCCHHHHHHHhhhccC------CCcCHHHHHHHHcCCchhhHHHHHHHHHCCCceeecccc
Confidence            4666777899999763      389999999999999999999999999999999877653

>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=87.40  E-value=0.26  Score=32.54  Aligned_cols=50  Identities=16%  Similarity=0.434  Sum_probs=39.6

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I  266 (280)
                      .++++.|+++|+....  .-.=.=+.|+.+.+ ..-+.+|++++..|++||.+
T Consensus         2 ee~k~~Ive~l~~k~~--~KsKfYfkDf~k~~Pd~k~R~vKK~~~~lV~e~~L   52 (74)
T d1ucra_           2 EEAKQKVVDFLNSKSG--SKSKFYFNDFTDLFPDMKQREVKKILTALVNDEVL   52 (74)
T ss_dssp             CHHHHHHHHHHSSHHH--HSSCEEHHHHHHHCTTSCHHHHHHHHHHHHHTTSE
T ss_pred             cHHHHHHHHHHHhccC--CcCceeHHHHHHHCCCccHHHHHHHHHHHhccceE
Confidence            4688999999976421  12245678898888 68899999999999999976

>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=87.26  E-value=0.67  Score=30.24  Aligned_cols=41  Identities=15%  Similarity=0.243  Sum_probs=35.7

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      .|++-+.+|+.+|..        |.+..+|+..|++++..|+.-+..+.
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            588899999999863        89999999999999999998877654

>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=87.19  E-value=1.6  Score=31.33  Aligned_cols=55  Identities=22%  Similarity=0.284  Sum_probs=42.0

Q ss_pred             eeEEEEEEEEE--ee--ecCCeeEEEEEcCCceEEEEEecccccChhhhccCCCCCEEEEEEEEe
Q 023576           71 TNVTLVGLVYN--KE--ERASDVNFTLDDGTGRVVCKRWASEVFDTREMEAIQDGMYVRLIGNLK  131 (280)
Q Consensus        71 ~~V~iVG~V~~--~~--~~~t~~~~~LdDgTG~I~~~~w~~~~~~~~~~~~~~~G~yVrV~G~l~  131 (280)
                      .+++|=|.|+.  +.  .....++|.|.|+...|.+.+---      -++.|++|.-|-|.|++.
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            46788888853  33  345689999999999999886422      246799999999999974

>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=86.89  E-value=0.48  Score=31.27  Aligned_cols=52  Identities=19%  Similarity=0.368  Sum_probs=44.9

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCc
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEF  273 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~  273 (280)
                      .+-.+.+++|+..      .=+.+++++..|++..+++.+.|++|..+|.|-=-+||.
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            3666778888864      368999999999999999999999999999999888883

>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=86.70  E-value=0.52  Score=32.02  Aligned_cols=55  Identities=13%  Similarity=0.141  Sum_probs=45.3

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCccccccC
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFAR  279 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t~  279 (280)
                      ++-.|++.|..       ..+++++|+++++.+++.+...++.|..-|.+=.+ .+..|+.|.
T Consensus        22 v~L~ifd~l~~-------gp~s~~eLA~~~g~~~~~l~rlLr~l~a~gl~~e~-~~~~y~lt~   76 (85)
T d1tw3a1          22 ATLRLVDHILA-------GARTVKALAARTDTRPEALLRLIRHLVAIGLLEED-APGEFVPTE   76 (85)
T ss_dssp             HHTTHHHHHHT-------TCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE-ETTEEEECT
T ss_pred             HHcCcHHHhcc-------CCCCHHHHHHHhCcChhHHHHHHHHHHHCCCeEec-CCCeEecCH
Confidence            55668888853       25899999999999999999999999999988665 345888663

>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=86.48  E-value=0.12  Score=40.12  Aligned_cols=58  Identities=28%  Similarity=0.307  Sum_probs=48.7

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      .+++..|=.||.+|...+   .+.|++..+|++.++++...|...|+.|...|+|..+-|.
T Consensus        58 ~gLt~~q~~vL~~L~~~~---~~~~lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~~~  115 (172)
T d2fbka1          58 SGLNAAGWDLLLTLYRSA---PPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDE  115 (172)
T ss_dssp             TTCCHHHHHHHHHHHHHC---CSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC--
T ss_pred             cCCCHHHHHHHHHHHhhC---CCCCcCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeeccc
Confidence            367888888999886542   3468999999999999999999999999999999988764

>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=86.00  E-value=0.63  Score=30.02  Aligned_cols=44  Identities=20%  Similarity=0.333  Sum_probs=38.0

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCee
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLI  266 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I  266 (280)
                      -++.++|++++.        +|++..+|+++|+++..-|.+.+..--+.|.|
T Consensus        17 ~DLR~Riv~~~~--------~G~s~r~aA~rf~VS~s~v~k~l~r~reTG~i   60 (63)
T d1k78a1          17 DVVRQRIVELAH--------QGVRPCDISRQLRVSHGCVSKILGRYYETGSI   60 (63)
T ss_dssp             HHHHHHHHHHHH--------TTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHH--------cCCCHHHHHHHhCCCHHHHHHHHHHHHHhcCC
Confidence            468899999875        38999999999999999999999888777755

>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=85.88  E-value=0.68  Score=30.89  Aligned_cols=54  Identities=24%  Similarity=0.350  Sum_probs=45.2

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHH-HHHhCCeeeec
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIA-SLENEGLIYST  269 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~-~L~~eG~IYsT  269 (280)
                      +|..+++++|+.|-+.-   ...-|.++-|+..++.+.+.|++.++ +|+..|.|=-|
T Consensus         2 GLd~~Dr~yL~~l~~~f---~ggPvGl~tlAa~l~e~~~TiEdviEPyLiq~G~i~RT   56 (75)
T d1in4a1           2 GLDEFDRKILKTIIEIY---RGGPVGLNALAASLGVEADTLSEVYEPYLLQAGFLART   56 (75)
T ss_dssp             CCCHHHHHHHHHHHHHS---TTCCBCHHHHHHHHTSCHHHHHHHTHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHHHh---CCCCCcHHHHHHHHcCChhHHHHHhhHHHHHhhHHhhC
Confidence            57889999999886542   23358899999999999999999998 89999999776

>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=85.65  E-value=0.64  Score=28.79  Aligned_cols=49  Identities=22%  Similarity=0.389  Sum_probs=41.6

Q ss_pred             chhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          216 DCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       216 ~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      ++.++||.+|+..+     .-+-...|++.+..|..++++.|-.|..|+.+-.+
T Consensus         1 ~LEQkILQVL~dag-----spvk~~ql~k~cqVpkk~lNqVL~rlkke~kVsl~   49 (57)
T d1j75a_           1 NLEQKILQVLSDDG-----GPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSSP   49 (57)
T ss_dssp             CHHHHHHHHHHHHC-----SCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHhcC-----CchHHHHHHHHHCCCHHHHHHHHHHHHhccccccC
Confidence            36789999999853     25677899999999999999999999999987654

>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=85.28  E-value=0.49  Score=35.02  Aligned_cols=47  Identities=17%  Similarity=0.257  Sum_probs=38.8

Q ss_pred             HHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeec
Q 023576          219 QMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYST  269 (280)
Q Consensus       219 ~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT  269 (280)
                      -.+|-+|...    .+.-++.++|++++++|..-+++.|..|...|.|-++
T Consensus        10 v~~L~~la~~----~~~~vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S~   56 (138)
T d1ylfa1          10 VHILSILKNN----PSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVN   56 (138)
T ss_dssp             HHHHHHHHHS----CGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHhC----CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence            3456666543    2346899999999999999999999999999999876

>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=84.65  E-value=0.62  Score=30.97  Aligned_cols=41  Identities=12%  Similarity=0.131  Sum_probs=31.9

Q ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCCcccccc
Q 023576          236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDEFHYKFA  278 (280)
Q Consensus       236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd~hfk~t  278 (280)
                      -++.++||..++.+.+.|..+|..|.++|.|-  ++..++...
T Consensus        30 ~lt~~elA~~~g~sretvsr~l~~l~~~glI~--~~~~~i~I~   70 (80)
T d3e5ua1          30 PLSQKSIGEITGVHHVTVSRVLASLKRENILD--KKKNKIIVY   70 (80)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE--C----CEES
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE--ecCCEEEEc
Confidence            46789999999999999999999999999984  355555443

>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=84.56  E-value=1.2  Score=30.94  Aligned_cols=51  Identities=16%  Similarity=0.253  Sum_probs=42.6

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ++.+.+|+.+|..       ..+++.+|++.++++.+.|..-|..|.+.|.|...-+.
T Consensus        22 ~p~Rl~Il~~L~~-------~~~~v~ela~~l~is~stvS~HL~~L~~aglV~~~r~G   72 (98)
T d1r1ta_          22 DPNRLRLLSLLAR-------SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQG   72 (98)
T ss_dssp             CHHHHHHHHHHTT-------CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CHHHHHHHHHHHc-------CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEC
Confidence            3567788888864       24799999999999999999999999999999765443

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=84.34  E-value=1.1  Score=29.43  Aligned_cols=35  Identities=17%  Similarity=0.251  Sum_probs=32.2

Q ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecC
Q 023576          236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTI  270 (280)
Q Consensus       236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi  270 (280)
                      -|....+++.++++|.-||.-+++|-+.|+|..+-
T Consensus        17 PiGRr~La~~L~l~Er~vRte~~~Lk~~gLI~~~~   51 (69)
T d2p8ta1          17 PLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKQ   51 (69)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             CccHHHHHHHcCCcHHHHHHHHHHHHHCCCeeeeC
Confidence            48899999999999999999999999999998863

>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=84.28  E-value=0.67  Score=31.63  Aligned_cols=41  Identities=22%  Similarity=0.276  Sum_probs=36.1

Q ss_pred             CCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHH
Q 023576          213 GLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLE  261 (280)
Q Consensus       213 ~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~  261 (280)
                      .|++-+.+|+.+|..        |.+..+|++.|++++..|+..+..+.
T Consensus        22 ~LT~rE~~vl~ll~~--------G~s~~eIA~~l~iS~~TV~~~~~~i~   62 (87)
T d1p4wa_          22 RLSPKESEVLRLFAE--------GFLVTEIAKKLNRSIKTISSQKKSAM   62 (87)
T ss_dssp             SCCHHHHHHHHHHHH--------TCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc--------CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            588999999999974        89999999999999999988877654

>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=83.70  E-value=0.89  Score=29.18  Aligned_cols=41  Identities=10%  Similarity=0.244  Sum_probs=33.1

Q ss_pred             CCCCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHH
Q 023576          212 DGLKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIAS  259 (280)
Q Consensus       212 ~~l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~  259 (280)
                      ..|++-++.|+.+.-.       .|++.++|++.+++++..|+..+..
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            3578888888887653       4899999999999999998876543

>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=82.63  E-value=0.72  Score=30.62  Aligned_cols=33  Identities=9%  Similarity=0.178  Sum_probs=30.2

Q ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeee
Q 023576          236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      -++.++||..++.+.+.|..+|..|.++|.|-.
T Consensus        29 ~lt~~eLA~~~G~sretvsr~L~~l~~~glI~~   61 (81)
T d2gaua1          29 YLSREELATLSNMTVSNAIRTLSTFVSERMLAL   61 (81)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            468899999999999999999999999998853

>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=82.44  E-value=0.57  Score=34.65  Aligned_cols=54  Identities=19%  Similarity=0.279  Sum_probs=44.3

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCCC
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTIDE  272 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  272 (280)
                      ++.-+-.||.+|...     +.++++.+|++.++++...|...|+.|...|+|...-|.
T Consensus        32 lt~~q~~vL~~L~~~-----~g~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~~~   85 (145)
T d2hr3a1          32 VQFSQLVVLGAIDRL-----GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP   85 (145)
T ss_dssp             HHHHHHHHHHHHHHT-----TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCHHHHHHHHHHHHc-----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeeeCc
Confidence            556777898888542     226999999999999999999999999999999877654

>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=82.21  E-value=1.2  Score=32.47  Aligned_cols=51  Identities=16%  Similarity=0.290  Sum_probs=41.9

Q ss_pred             CCchhHHHHHHhcCCCCCCCCCccCHHHHHHHh-----CCCHHHHHHHHHHHHhCCeeee
Q 023576          214 LKDCDQMILDYLQQPSSSERERGVHVNELSEQL-----KIPQKKIMDSIASLENEGLIYS  268 (280)
Q Consensus       214 l~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-----~~~~~~v~~al~~L~~eG~IYs  268 (280)
                      +++-+..||++|.+.    ...-+++++|.+.+     .++...|-..|+.|.+.|.|=.
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    23358999999988     3889999999999999999943

>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=81.97  E-value=1.6  Score=28.74  Aligned_cols=32  Identities=22%  Similarity=0.341  Sum_probs=29.4

Q ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHhCCeee
Q 023576          236 GVHVNELSEQLKIPQKKIMDSIASLENEGLIY  267 (280)
Q Consensus       236 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY  267 (280)
                      .++.++|+..++.+.+.|..+|..|.++|.|=
T Consensus        30 ~~t~~eiA~~lG~sretvsr~l~~l~~~g~I~   61 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTALNSLIKEGYIS   61 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHHHHHHHTTSSE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            45788999999999999999999999999883

>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=81.50  E-value=1.2  Score=32.26  Aligned_cols=46  Identities=11%  Similarity=0.168  Sum_probs=38.4

Q ss_pred             HHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          220 MILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       220 ~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      .+|-+|...      +.++.++|++.++.++.-|++.|..|...|.|-++--
T Consensus         8 ~~L~~la~~------~~~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s~rG   53 (127)
T d1xd7a_           8 HILSLISMD------EKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAG   53 (127)
T ss_dssp             HHHHHHHTC------SCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSS
T ss_pred             HHHHHHhcC------CCCCHHHHHHHhCcCHHHHHHHHHHHHHhCcccccCC
Confidence            466777542      3599999999999999999999999999999877643

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=80.47  E-value=1.4  Score=30.41  Aligned_cols=50  Identities=18%  Similarity=0.253  Sum_probs=41.5

Q ss_pred             CchhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCHHHHHHHHHHHHhCCeeeecCC
Q 023576          215 KDCDQMILDYLQQPSSSERERGVHVNELSEQLKIPQKKIMDSIASLENEGLIYSTID  271 (280)
Q Consensus       215 ~~~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiD  271 (280)
                      .+.+.+|+.+|...       -+++.+|++.++++.+.|-.-|..|.+.|.|-+.-+
T Consensus        17 d~~Rl~Il~~L~~~-------~~~v~el~~~l~~s~~~vS~HL~~L~~~glv~~~r~   66 (94)
T d1r1ua_          17 DYNRIRIMELLSVS-------EASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQ   66 (94)
T ss_dssp             SHHHHHHHHHHHHC-------CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CHHHHHHHHHHHcC-------CccHHHHHHHHCCCHHHHHHHHHHHHHCCceEEEEE
Confidence            34677899998752       378999999999999999999999999998855433

>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=80.42  E-value=0.99  Score=31.32  Aligned_cols=56  Identities=23%  Similarity=0.346  Sum_probs=44.4

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHh-CCCHHHHHHHHHHHHhCCeeeecCCCcc-----ccccC
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQL-KIPQKKIMDSIASLENEGLIYSTIDEFH-----YKFAR  279 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~IYsTiDd~h-----fk~t~  279 (280)
                      ..-.|+..|..       .-..+.+|.+.+ +++..-+.+.|.+|.++|.|.-+..++.     |..|+
T Consensus        12 W~l~Il~~L~~-------g~~rF~el~~~l~gis~~~Ls~rLk~Le~~glv~r~~~~~~p~~veY~LT~   73 (95)
T d2hzta1          12 WKCVILCHLTH-------GKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSE   73 (95)
T ss_dssp             THHHHHHHHTT-------CCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECT
T ss_pred             CHHHHHHHHHc-------CCCCHHHHHHHhhcCChhHHHHHHHHHHHhHHHhheeccccccchhhhhhh
Confidence            44456776643       125799999999 8999999999999999999998877765     76664

>d1fp2a1 a.4.5.29 (A:8-108) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

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: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=80.33  E-value=0.43  Score=33.76  Aligned_cols=57  Identities=18%  Similarity=0.322  Sum_probs=42.9

Q ss_pred             hhHHHHHHhcCCCCCCCCCccCHHHHHHHhCCCH---HHHHHHHHHHHhCCeeee-cCCCcccccc
Q 023576          217 CDQMILDYLQQPSSSERERGVHVNELSEQLKIPQ---KKIMDSIASLENEGLIYS-TIDEFHYKFA  278 (280)
Q Consensus       217 ~~~~Vl~~i~~~~~~~~e~Gv~v~~I~~~l~~~~---~~v~~al~~L~~eG~IYs-TiDd~hfk~t  278 (280)
                      ++-.|+++|.+.     ...++.++|+++++.++   +-+...|+.|...|.+-. +-++..|..|
T Consensus        30 veLgi~d~l~~~-----~~p~t~~eLa~~~~~~~~~~~~L~RlLR~L~~~gi~~~~~~~~~~Y~lt   90 (101)
T d1fp2a1          30 VEMNIPNIIQNH-----GKPISLSNLVSILQVPSSKIGNVRRLMRYLAHNGFFEIITKEEESYALT   90 (101)
T ss_dssp             HHTTHHHHHHHH-----TSCEEHHHHHHHHTCCGGGHHHHHHHHHHHHHTTSEEEEESSSEEEEEC
T ss_pred             HHcCcHHHHHHc-----CCCCCHHHHHHHcCCCCccchHHHHHHHHHHhCCceeeecCCCCeEecC
Confidence            555688888753     23699999999998654   348889999999999864 4455678765