Citrus Sinensis ID: 027236

---

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------
Protein Sequence
MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKKPKGGR
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHHccccccEEcccEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccccccccccccccHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHHHccccccHHHHHHHHHcccccHHHHHHHHHHHHHcccEEEEEEccEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccccccccccHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
mapksdntEAIVLNYVneqnrplnsQNVADALQKYNLKKAGIQKALDSLadngkisfkeYGKQKIYIARqdqfdipnseeLNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRggvtlvkpedrMAVEEMFLEKLSQWRKRKRMLRDIwdpimenspkNLKEFKEELGIEYDEDVGVSLQSFSDLLqrgkkpkggr
Flexible Loop (DISEMBL)
mapksdntEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRtlqsnltleqiREKEAQLVKEVKEMEnklaklrggvtlvkpedrMAVEEMFLEKLSQWRKRKRMLRDiwdpimenspkNLKEFKEELGIEYDEDVGVSLQsfsdllqrgkkpkggr
Low Complexity Region (SEG)
MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKKPKGGR
Disordered region (IsUnstruct)
**********IVLNYVN***********ADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQ**********************************************************************KLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIM*************LGIEYDEDVG********************
Disordered Region (DISOPRED)
******N***IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQD**********************************************LEQIREKEAQLVK*************************AVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSLQ****************
Disordered Region (DISEMBL)
MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDL***********
Disordered Region (DISPRO)
*****DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQR********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAPKSDNTEAIVLNYVNEQNRPLNSQNVADAxxxxxxxxxxxxxxxxxxxxxGKISFKEYGKQKIYIARQDQFDIPxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKKPKGGR
Positional Conservation
no confident homologs detected

---

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	226	2.2.26 [Sep-21-2011]
Q9FX64	226	Homologous-pairing protei	yes	no	0.991	0.991	0.751	4e-97
Q91ZY6	217	Homologous-pairing protei	yes	no	0.884	0.921	0.398	2e-33
O35047	217	Homologous-pairing protei	yes	no	0.884	0.921	0.388	3e-32
Q63ZL2	214	Homologous-pairing protei	N/A	no	0.871	0.920	0.372	2e-30
Q9P2W1	217	Homologous-pairing protei	yes	no	0.880	0.917	0.385	3e-30
Q54UM1	243	Homologous-pairing protei	yes	no	0.893	0.831	0.322	6e-20
Q9HGK2	216	Homologous-pairing protei	yes	no	0.862	0.902	0.297	8e-15

>sp|Q9FX64|HOP2_ARATH Homologous-pairing protein 2 homolog OS=Arabidopsis thaliana GN=HOP2 PE=1 SV=1

 Score =  353 bits (907), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 169/225 (75%), Positives = 204/225 (90%), Gaps = 1/225 (0%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSDNTEAIVLN+VNEQN+PLN+QN ADALQK+NLKK  +QKALDSLAD GKI+FKEY
Sbjct: 1   MAPKSDNTEAIVLNFVNEQNKPLNTQNAADALQKFNLKKTAVQKALDSLADAGKITFKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIYIARQDQF+IPNSEEL QMKE+NAKLQEQL+E++K IS +E EI++LQSNLTLE+
Sbjct: 61  GKQKIYIARQDQFEIPNSEELAQMKEDNAKLQEQLQEKKKTISDVESEIKSLQSNLTLEE 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           I+EK+A+L KEVKEME KL KLR G+TLV+PED+ AVE+M+ +K++QWRKRKRM RDIWD
Sbjct: 121 IQEKDAKLRKEVKEMEEKLVKLREGITLVRPEDKKAVEDMYADKINQWRKRKRMFRDIWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKK-PKG 224
            + ENSPK++KE KEELGIEYDEDVG+S Q+++DL+Q GKK P+G
Sbjct: 181 TVTENSPKDVKELKEELGIEYDEDVGLSFQAYADLIQHGKKRPRG 225

Involved in bivalent formation and segregation of homologous chromosomes in meiosis.
Arabidopsis thaliana (taxid: 3702)

>sp|Q91ZY6|HOP2_RAT Homologous-pairing protein 2 homolog OS=Rattus norvegicus GN=Psmc3ip PE=1 SV=1

 Score =  142 bits (357), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 80/201 (39%), Positives = 118/201 (58%), Gaps = 1/201 (0%)

Query: 10  AIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA 68
            IVL Y+ EQNRP ++Q+V   LQK + L KA + KALD LA  GKI  K YGKQKIY A
Sbjct: 14  GIVLRYLQEQNRPYSAQDVFGNLQKEHGLGKAAVVKALDQLAQQGKIKEKTYGKQKIYFA 73

Query: 69  RQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQL 128
            QDQFD  +  +L+ +      L  +++  +++   +E E++ L S LT  +++ +  +L
Sbjct: 74  DQDQFDTVSDADLHSLDASIMALTAKVQGLQQSCRHMEAELKELTSALTTPEMQTEIQEL 133

Query: 129 VKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPK 188
            KE      +L  ++     V PE++  V     +   +WRKRKRM  ++ D I+E  PK
Sbjct: 134 KKECARYTERLKNIKAATNHVTPEEKEKVYRERQKYCKEWRKRKRMTTELCDAILEGYPK 193

Query: 189 NLKEFKEELGIEYDEDVGVSL 209
           + K+F EE+GIE DED  V+L
Sbjct: 194 SKKQFFEEVGIETDEDHNVTL 214

Plays an important role in meiotic recombination. Stimulates DMC1-mediated strand exchange required for pairing homologous chromosomes during meiosis. The complex PSMC3IP/MND1 binds DNA, stimulates the recombinase activity of DMC1 as well as DMC1 D-loop formation from double-strand DNA. This complex stabilizes presynaptic RAD51 and DMC1 filaments formed on single strand DNA to capture double-strand DNA. This complex stimulates both synaptic and presynaptic critical steps in RAD51 and DMC1-promoted homologous pairing. May inhibit HIV-1 viral protein TAT activity and modulate the activity of proteasomes through association with PSMC3 (By similarity). Plays a role as a coactivator in nuclear receptor-mediated transcription.

Rattus norvegicus (taxid: 10116)

>sp|O35047|HOP2_MOUSE Homologous-pairing protein 2 homolog OS=Mus musculus GN=Psmc3ip PE=1 SV=1

 Score =  138 bits (348), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 78/201 (38%), Positives = 119/201 (59%), Gaps = 1/201 (0%)

Query: 10  AIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA 68
            I+L Y+ EQNRP ++Q+V   LQK + L KA + KALD LA  GKI  K YGKQKIY A
Sbjct: 14  GIILRYLQEQNRPYSAQDVFGNLQKEHGLGKAAVVKALDQLAQEGKIKEKTYGKQKIYFA 73

Query: 69  RQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQL 128
            Q+QFD  +  +L+ +      L  +++  +++   +E E++ L S LT  +++++  +L
Sbjct: 74  DQNQFDTVSDADLHGLDASIVALTAKVQSLQQSCRHMEAELKELTSALTTPEMQKEIQEL 133

Query: 129 VKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPK 188
            KE  +   +L  ++     V PE++  V     +   +WRKRKRM  ++ D I+E  PK
Sbjct: 134 KKECAQYTERLKNIKAATNHVTPEEKEKVYRDRQKYCKEWRKRKRMTTELCDAILEGYPK 193

Query: 189 NLKEFKEELGIEYDEDVGVSL 209
           + K+F EE+GIE DED  V L
Sbjct: 194 SKKQFFEEVGIETDEDHNVLL 214

Plays an important role in meiotic recombination. Stimulates DMC1-mediated strand exchange required for pairing homologous chromosomes during meiosis. The complex PSMC3IP/MND1 binds DNA, stimulates the recombinase activity of DMC1 as well as DMC1 D-loop formation from double-strand DNA. This complex stabilizes presynaptic RAD51 and DMC1 filaments formed on single strand DNA to capture double-strand DNA. This complex stimulates both synaptic and presynaptic critical steps in RAD51 and DMC1-promoted homologous pairing. May inhibit HIV-1 viral protein TAT activity and modulate the activity of proteasomes through association with PSMC3.

Mus musculus (taxid: 10090)

>sp|Q63ZL2|HOP2_XENLA Homologous-pairing protein 2 homolog OS=Xenopus laevis GN=psmc3ip PE=2 SV=1

 Score =  132 bits (331), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 76/204 (37%), Positives = 127/204 (62%), Gaps = 7/204 (3%)

Query: 10  AIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA 68
           +I+L Y+N+QNRP ++Q+V   LQ+ + L K  + K ++ LA  GKI  K YGKQKIY A
Sbjct: 11  SIILKYLNDQNRPYSTQDVFSNLQRDHGLGKTAVVKTMELLAQKGKIKEKVYGKQKIYFA 70

Query: 69  RQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQL 128
            Q+QF   +  EL  +  +  +L  +L+  +++  +LE E++ L S+LT E++ ++ + L
Sbjct: 71  DQEQFPSVSDSELKDLDAQVTELSSKLQSSQQSCRQLESELKDLTSSLTTEEMLKEVSCL 130

Query: 129 VKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEK---LSQWRKRKRMLRDIWDPIMEN 185
            +E    E+KL  ++     V P ++   E+++ E+     +W+KRKRM  DI+D I+E 
Sbjct: 131 KEECDRHEHKLTNIKSATNHVTPAEK---EKVYGERKHFCKEWKKRKRMATDIFDAILEG 187

Query: 186 SPKNLKEFKEELGIEYDEDVGVSL 209
            PK+ K+F EE+G+E DED  V++
Sbjct: 188 YPKSKKQFFEEVGVETDEDCNVTV 211

Plays an important role in meiotic recombination. Stimulates DMC1-mediated strand exchange required for pairing of homologous chromosomes during meiosis.

Xenopus laevis (taxid: 8355)

>sp|Q9P2W1|HOP2_HUMAN Homologous-pairing protein 2 homolog OS=Homo sapiens GN=PSMC3IP PE=1 SV=1

 Score =  132 bits (331), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 77/200 (38%), Positives = 119/200 (59%), Gaps = 1/200 (0%)

Query: 11  IVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR 69
           I+L Y+ EQNRP +SQ+V   LQ+ + L KA + K L+ LA  GKI  K YGKQKIY A 
Sbjct: 15  ILLRYLQEQNRPYSSQDVFGNLQREHGLGKAVVVKTLEQLAQQGKIKEKMYGKQKIYFAD 74

Query: 70  QDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLV 129
           QDQFD+ +  +L  +  +   L  +++  +++   +E E++ L S LT  +++++  +L 
Sbjct: 75  QDQFDMVSDADLQVLDGKIVALTAKVQSLQQSCRYMEAELKELSSALTTPEMQKEIQELK 134

Query: 130 KEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKN 189
           KE      +L  ++     V PE++  V     +   +WRKRKRM  ++ D I+E  PK+
Sbjct: 135 KECAGYRERLKNIKAATNHVTPEEKEQVYRERQKYCKEWRKRKRMATELSDAILEGYPKS 194

Query: 190 LKEFKEELGIEYDEDVGVSL 209
            K+F EE+GIE DED  V+L
Sbjct: 195 KKQFFEEVGIETDEDYNVTL 214

Plays an important role in meiotic recombination. Stimulates DMC1-mediated strand exchange required for pairing homologous chromosomes during meiosis. The complex PSMC3IP/MND1 binds DNA, stimulates the recombinase activity of DMC1 as well as DMC1 D-loop formation from double-strand DNA. This complex stabilizes presynaptic RAD51 and DMC1 filaments formed on single strand DNA to capture double-strand DNA. This complex stimulates both synaptic and presynaptic critical steps in RAD51 and DMC1-promoted homologous pairing. May inhibit HIV-1 viral protein TAT activity and modulate the activity of proteasomes through association with PSMC3. Acts as a tissue specific coactivator of hormone-dependent transcription mediated by nuclear receptors.

Homo sapiens (taxid: 9606)

>sp|Q54UM1|HOP2_DICDI Homologous-pairing protein 2 homolog OS=Dictyostelium discoideum GN=hop2 PE=3 SV=1

 Score = 97.4 bits (241), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 117/214 (54%), Gaps = 12/214 (5%)

Query: 4   KSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ 63
           K D  E  +LN +N+ NRP N Q +  A    ++ K  I K L SL + GK++FKEY K 
Sbjct: 7   KKDEVEENILNLINKANRPYNYQMIEAAFP--SMGKTQIVKTLKSLGEQGKLTFKEYNKA 64

Query: 64  KIYIARQDQ--------FDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSN 115
            IY   QD         ++IP  E ++ +  +   +  QLE ++  +  L  + + L + 
Sbjct: 65  IIYWRIQDTGPKLDEQGYEIP-QESIHDLNRKLDGINRQLEVEQDTLKSLISQSKQLNNQ 123

Query: 116 LTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRML 175
           L+ EQI+++  QL  E KE+E+KL   +    ++  +D+  +++   +  S+W KRK + 
Sbjct: 124 LSDEQIQKEVNQLSTENKELESKLLTFQTK-EIMSDKDKQRLDDTIKKARSEWVKRKALF 182

Query: 176 RDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSL 209
           RDI D ++E S K  K+ +E++G E DED+ + +
Sbjct: 183 RDILDQVLERSNKKKKDLQEDIGWETDEDLKIQM 216

Required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9HGK2|HOP2_SCHPO Homologous-pairing protein 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=meu13 PE=1 SV=1

 Score = 80.5 bits (197), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 59/198 (29%), Positives = 107/198 (54%), Gaps = 3/198 (1%)

Query: 4   KSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ 63
           K +  E +V  Y+ + NRP ++ +V+  L+    K+   QKAL+ L D G I  K YGKQ
Sbjct: 13  KGEEAEKLVYEYLRKTNRPYSATDVSANLKNVVSKQVA-QKALEQLRDTGLIHGKLYGKQ 71

Query: 64  KIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIRE 123
            +++  QD       EEL +M+++  +L++++   +    +   E++ L ++L+  +IRE
Sbjct: 72  SVFVCLQDDLAAATPEELAEMEKQIQELKDEVSVVKTLYKEKCIELQALNNSLSPAEIRE 131

Query: 124 KEAQLVKEVKEMENKLAKLRGG-VTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPI 182
           K   + KE++E  +KL  LR G V  +  E     ++ +      +  RK+M  D+W  +
Sbjct: 132 KIQSIDKEIEETSSKLESLRNGTVKQISKEAMQKTDKNYDFAKKGFSNRKKMFYDLWH-L 190

Query: 183 MENSPKNLKEFKEELGIE 200
           + +S +N K+  E+LG E
Sbjct: 191 ITDSLENPKQLWEKLGFE 208

Required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis. Acts indirectly in a process facilitating homologous recombination. Acts during mid-to late-horse-tail period.

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

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	226
224099357	226	predicted protein [Populus trichocarpa]	0.977	0.977	0.809	1e-99
15222250	226	homologous-pairing protein 2 [Arabidopsi	0.991	0.991	0.751	2e-95
297844240	226	hypothetical protein ARALYDRAFT_334636 [	0.991	0.991	0.746	2e-94
255576473	225	tbp-1 interacting protein, putative [Ric	0.995	1.0	0.795	6e-94
356526637	226	PREDICTED: homologous-pairing protein 2	0.991	0.991	0.755	6e-93
225423937	226	PREDICTED: homologous-pairing protein 2	0.977	0.977	0.751	7e-92
357488489	226	Homologous-pairing protein-like protein	0.991	0.991	0.755	9e-92
449434640	226	PREDICTED: homologous-pairing protein 2	0.991	0.991	0.773	5e-89
356495952	227	PREDICTED: homologous-pairing protein 2	0.991	0.986	0.725	2e-88
108710703	227	Tat binding protein 1 containing protein	0.955	0.951	0.708	4e-84

>gi|224099357|ref|XP_002311452.1| predicted protein [Populus trichocarpa] gi|222851272|gb|EEE88819.1| predicted protein [Populus trichocarpa]

 Score =  367 bits (943), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 179/221 (80%), Positives = 205/221 (92%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSD+ EAIVLN+VNEQN+PLNSQNVAD+LQK+NLKKAGIQKALD+LADNGKISFKEY
Sbjct: 1   MAPKSDSAEAIVLNFVNEQNKPLNSQNVADSLQKFNLKKAGIQKALDNLADNGKISFKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIY+ARQDQFDIP SEELNQMKEENA++Q+QL+EQ++AIS++EGEI+ LQSNLTLEQ
Sbjct: 61  GKQKIYLARQDQFDIPTSEELNQMKEENAQVQQQLDEQKRAISEVEGEIKNLQSNLTLEQ 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           IR KEA+L KEVKEME+KL KLR GVTLV+PE+R A+ EM+ EKLSQWRKRKRM +D+WD
Sbjct: 121 IRHKEAKLQKEVKEMEDKLVKLRKGVTLVRPEERKAIAEMYSEKLSQWRKRKRMFKDVWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKK 221
            I EN PK+LKEFKEELG+EYDEDVGVSLQSFS LLQ GKK
Sbjct: 181 AITENLPKDLKEFKEELGLEYDEDVGVSLQSFSGLLQHGKK 221

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15222250|ref|NP_172791.1| homologous-pairing protein 2 [Arabidopsis thaliana] gi|75172985|sp|Q9FX64.1|HOP2_ARATH RecName: Full=Homologous-pairing protein 2 homolog; AltName: Full=Protein AHP2; Short=AtAHP2; AltName: Full=Protein ARABIDOPSIS HOMOLOG PAIRING 2; AltName: Full=Protein HOP2; Short=AtHOP2 gi|9958066|gb|AAG09555.1|AC011810_14 Hypothetical Protein [Arabidopsis thaliana] gi|29293664|gb|AAO67519.1| AHP2 [Arabidopsis thaliana] gi|51971417|dbj|BAD44373.1| unknown protein [Arabidopsis thaliana] gi|92856625|gb|ABE77410.1| At1g13330 [Arabidopsis thaliana] gi|110735793|dbj|BAE99873.1| hypothetical protein [Arabidopsis thaliana] gi|121490118|emb|CAF28783.1| Hop2 protein [Arabidopsis thaliana] gi|332190880|gb|AEE29001.1| homologous-pairing protein 2 [Arabidopsis thaliana]

 Score =  353 bits (907), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 169/225 (75%), Positives = 204/225 (90%), Gaps = 1/225 (0%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSDNTEAIVLN+VNEQN+PLN+QN ADALQK+NLKK  +QKALDSLAD GKI+FKEY
Sbjct: 1   MAPKSDNTEAIVLNFVNEQNKPLNTQNAADALQKFNLKKTAVQKALDSLADAGKITFKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIYIARQDQF+IPNSEEL QMKE+NAKLQEQL+E++K IS +E EI++LQSNLTLE+
Sbjct: 61  GKQKIYIARQDQFEIPNSEELAQMKEDNAKLQEQLQEKKKTISDVESEIKSLQSNLTLEE 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           I+EK+A+L KEVKEME KL KLR G+TLV+PED+ AVE+M+ +K++QWRKRKRM RDIWD
Sbjct: 121 IQEKDAKLRKEVKEMEEKLVKLREGITLVRPEDKKAVEDMYADKINQWRKRKRMFRDIWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKK-PKG 224
            + ENSPK++KE KEELGIEYDEDVG+S Q+++DL+Q GKK P+G
Sbjct: 181 TVTENSPKDVKELKEELGIEYDEDVGLSFQAYADLIQHGKKRPRG 225

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297844240|ref|XP_002890001.1| hypothetical protein ARALYDRAFT_334636 [Arabidopsis lyrata subsp. lyrata] gi|297335843|gb|EFH66260.1| hypothetical protein ARALYDRAFT_334636 [Arabidopsis lyrata subsp. lyrata]

 Score =  350 bits (899), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 168/225 (74%), Positives = 203/225 (90%), Gaps = 1/225 (0%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSDNTEAIVLN+VNEQN+PLN+QN ADALQK+NLKK  +QKALDSLAD GKI+FKEY
Sbjct: 1   MAPKSDNTEAIVLNFVNEQNKPLNTQNAADALQKFNLKKTAVQKALDSLADAGKITFKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIYIARQDQF+IPNSEEL QMKEENAKLQEQL+E++K IS +E EI++LQSNLTLE+
Sbjct: 61  GKQKIYIARQDQFEIPNSEELAQMKEENAKLQEQLQEKKKTISDVESEIKSLQSNLTLEE 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           I+EK+A+L KEV+EME KL KLR G+TLV+PED+ AVE+M+ +K++QWRKRKRM RDIWD
Sbjct: 121 IQEKDAKLRKEVREMEEKLIKLREGITLVRPEDKKAVEDMYADKINQWRKRKRMFRDIWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKK-PKG 224
            + ENSPK++KE KEELGIEYDEDV +S Q+++DL+Q GKK P+G
Sbjct: 181 TVTENSPKDVKELKEELGIEYDEDVDLSFQAYADLIQHGKKRPRG 225

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255576473|ref|XP_002529128.1| tbp-1 interacting protein, putative [Ricinus communis] gi|223531407|gb|EEF33241.1| tbp-1 interacting protein, putative [Ricinus communis]

 Score =  349 bits (895), Expect = 6e-94,   Method: Compositional matrix adjust.
 Identities = 179/225 (79%), Positives = 204/225 (90%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSD+ EAIVLN+VNEQNRPLNSQ+VAD+LQKYNLKK  IQKALD+LAD GKISFKEY
Sbjct: 1   MAPKSDSAEAIVLNFVNEQNRPLNSQSVADSLQKYNLKKTAIQKALDTLADGGKISFKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIY+ARQDQFDIPNSEELN MK+EN+KLQ+QL++Q+KAI+ +EGEI+ LQSNLTLEQ
Sbjct: 61  GKQKIYLARQDQFDIPNSEELNCMKDENSKLQQQLQDQKKAINAVEGEIKALQSNLTLEQ 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           I EKEA+L  EVKE+E+KL KLRGGVTLV PE+R AVE+M+ E +SQWRKRKRM +D+WD
Sbjct: 121 IHEKEAKLRNEVKELEDKLVKLRGGVTLVSPEERHAVEKMYSELISQWRKRKRMFKDLWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKKPKGG 225
            I ENSPK+LKEFKEELGIEYDEDVGVSLQSFSDLLQRGKK   G
Sbjct: 181 SITENSPKDLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKKRARG 225

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526637|ref|XP_003531923.1| PREDICTED: homologous-pairing protein 2 homolog [Glycine max]

 Score =  345 bits (886), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 170/225 (75%), Positives = 201/225 (89%), Gaps = 1/225 (0%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSD+ EAIVLN+VNEQNRP+N+QNVADALQK+NLKKA IQKALD+LAD G+ISFKEY
Sbjct: 1   MAPKSDSAEAIVLNFVNEQNRPVNAQNVADALQKFNLKKAAIQKALDNLADGGRISFKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIY+ARQDQF IPN+EELNQMKE+NA+LQ+QLE+Q+KA S++E EI++LQSNLTLEQ
Sbjct: 61  GKQKIYLARQDQFQIPNTEELNQMKEQNAELQKQLEDQKKATSEVEAEIKSLQSNLTLEQ 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           I E+E  L  EV+EME KL KLRGGVTLVKPE+R AVE M  E + QWRKRKRM +D+WD
Sbjct: 121 IFEREVNLRLEVQEMEEKLTKLRGGVTLVKPEERKAVENMLSEMIGQWRKRKRMFKDLWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKK-PKG 224
            + ENSPK+ KEFKEELGIEYDEDVGVSLQS++DL+Q+GKK P+G
Sbjct: 181 TLTENSPKDPKEFKEELGIEYDEDVGVSLQSYNDLIQQGKKRPRG 225

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225423937|ref|XP_002279040.1| PREDICTED: homologous-pairing protein 2 homolog [Vitis vinifera] gi|297737839|emb|CBI27040.3| unnamed protein product [Vitis vinifera]

 Score =  342 bits (877), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 166/221 (75%), Positives = 198/221 (89%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSD+ E IVLN+VNEQNRPLNSQNVAD+LQK+NLKK+ +QKALD+LAD+G+IS KEY
Sbjct: 1   MAPKSDSVEGIVLNFVNEQNRPLNSQNVADSLQKFNLKKSSVQKALDALADSGRISSKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIY+ARQDQFDIPNSEEL++MKEENAKLQ+QLEEQ++AIS++EGEI+TLQSNLTLEQ
Sbjct: 61  GKQKIYLARQDQFDIPNSEELSRMKEENAKLQQQLEEQKRAISEVEGEIKTLQSNLTLEQ 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           IR KEA+L  EV+EME+KL  LRGGVTLVK EDR  VEEM+ ++++QWR+RKR+ +D+WD
Sbjct: 121 IRAKEAKLKMEVEEMEDKLNNLRGGVTLVKFEDRKVVEEMYSDRINQWRRRKRIFKDLWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKK 221
            I EN PK+LKEFKEEL IEYDEDVGVS QS  DL+Q  KK
Sbjct: 181 AITENLPKDLKEFKEELAIEYDEDVGVSFQSLCDLMQHRKK 221

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357488489|ref|XP_003614532.1| Homologous-pairing protein-like protein [Medicago truncatula] gi|355515867|gb|AES97490.1| Homologous-pairing protein-like protein [Medicago truncatula]

 Score =  342 bits (876), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 170/225 (75%), Positives = 199/225 (88%), Gaps = 1/225 (0%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSD+ EAIVLN+VNEQNRPLN+QNVADALQK+NLKKA IQKALDSL   GKISFKEY
Sbjct: 1   MAPKSDSAEAIVLNFVNEQNRPLNTQNVADALQKFNLKKAAIQKALDSLEKGGKISFKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIY+ARQDQF+IPN+EELNQMKE+NA LQ+QLEEQ+K I ++E EI++LQSNLT+EQ
Sbjct: 61  GKQKIYVARQDQFEIPNNEELNQMKEKNANLQKQLEEQKKVIGEVEAEIKSLQSNLTMEQ 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           I EKE  L  +V+E+E KL KLRGGVTLV+PE+R+AVE M  EK+SQWRKRKRM RD+WD
Sbjct: 121 ICEKEIDLRMQVQELEIKLNKLRGGVTLVRPEERVAVESMLSEKISQWRKRKRMFRDLWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKK-PKG 224
            + ENSPK+ KEFKEELG+EYDEDVGVSLQS SDL+ +GKK P+G
Sbjct: 181 TLTENSPKDPKEFKEELGLEYDEDVGVSLQSCSDLIPQGKKRPRG 225

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434640|ref|XP_004135104.1| PREDICTED: homologous-pairing protein 2 homolog [Cucumis sativus] gi|449493462|ref|XP_004159300.1| PREDICTED: homologous-pairing protein 2 homolog [Cucumis sativus]

 Score =  332 bits (852), Expect = 5e-89,   Method: Compositional matrix adjust.
 Identities = 174/225 (77%), Positives = 198/225 (88%), Gaps = 1/225 (0%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSD+ EAIVLN+VNEQNRP+NSQN AD+LQK+NLKK  +QKALDSLAD+G+ISFKEY
Sbjct: 1   MAPKSDSAEAIVLNFVNEQNRPINSQNAADSLQKFNLKKTAVQKALDSLADSGRISFKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIYIARQDQF IPNSEEL QMKE NAKLQ+QL E +KAIS++E EIRTLQSNLTLEQ
Sbjct: 61  GKQKIYIARQDQFQIPNSEELTQMKEANAKLQKQLGEHKKAISQVEEEIRTLQSNLTLEQ 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           +REKEA L  EVKE+E KL  LR GVTLV PEDR A+E+++ EKLSQWRKRKRM +DIWD
Sbjct: 121 MREKEAMLRMEVKELEEKLEVLRRGVTLVSPEDRKAIEQIYSEKLSQWRKRKRMFKDIWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLL-QRGKKPKG 224
            I ENS K+LKEFKEELGIEYDEDVGV+LQSFSD+L Q  K+P+G
Sbjct: 181 AITENSSKDLKEFKEELGIEYDEDVGVNLQSFSDMLPQNRKRPRG 225

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356495952|ref|XP_003516834.1| PREDICTED: homologous-pairing protein 2 homolog [Glycine max]

 Score =  330 bits (847), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 164/226 (72%), Positives = 198/226 (87%), Gaps = 2/226 (0%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           MAPKSD+ EAIVLN+VNEQNRP+N+QNVADALQK+NLKKA IQKALD LAD  +ISFKE+
Sbjct: 1   MAPKSDSAEAIVLNFVNEQNRPVNAQNVADALQKFNLKKAAIQKALDILADGKRISFKEF 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIY+ARQDQF IPN+EELN MK++NA LQ+QLE+Q+KA S++E EI++LQSNLTLEQ
Sbjct: 61  GKQKIYLARQDQFQIPNTEELNHMKKQNADLQKQLEDQKKATSEVEAEIKSLQSNLTLEQ 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           I E+E  L  EV+EME+KL KLRGGVTLVKPE+R AVE M  E + QWRKRKRM +D+WD
Sbjct: 121 IFEREVNLRLEVQEMEDKLTKLRGGVTLVKPEERKAVENMLSEMIGQWRKRKRMFKDLWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYD-EDVGVSLQSFSDLLQRG-KKPKG 224
            + ENSPK+ KEF+EELGIEYD EDVGVSLQS++DL+Q+G K+P+G
Sbjct: 181 TLTENSPKDPKEFQEELGIEYDEEDVGVSLQSYNDLIQQGQKRPRG 226

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|108710703|gb|ABF98498.1| Tat binding protein 1 containing protein, expressed [Oryza sativa Japonica Group] gi|215736883|dbj|BAG95812.1| unnamed protein product [Oryza sativa Japonica Group] gi|218193619|gb|EEC76046.1| hypothetical protein OsI_13231 [Oryza sativa Indica Group] gi|222625657|gb|EEE59789.1| hypothetical protein OsJ_12305 [Oryza sativa Japonica Group]

 Score =  316 bits (810), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 153/216 (70%), Positives = 189/216 (87%)

Query: 1   MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
           M PKSD+ E IVL++VNEQNRPLNSQNVADALQK++LKK  +QKALD+LAD+G+ISFKEY
Sbjct: 1   MPPKSDSVEGIVLSFVNEQNRPLNSQNVADALQKFSLKKTAVQKALDALADSGQISFKEY 60

Query: 61  GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
           GKQKIY+ARQDQF+IPN EEL +MK+ N KLQE+L +Q+KAIS++E E+R LQSNLTL +
Sbjct: 61  GKQKIYLARQDQFNIPNGEELEEMKKANIKLQEELADQKKAISEVESEVRGLQSNLTLAE 120

Query: 121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
           I+ KEA+L +EV+EME KL KLR GV LVKPED+  +EE F EK++QWRKRKRM +++WD
Sbjct: 121 IKSKEAKLQREVQEMEEKLNKLRNGVILVKPEDKKIIEESFSEKVNQWRKRKRMFKELWD 180

Query: 181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLL 216
            I ENSPK+ KEFKEELG+EYDEDVGV+LQS+SD+L
Sbjct: 181 NITENSPKDQKEFKEELGLEYDEDVGVNLQSYSDML 216

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	226
TAIR|locus:2205359	226	AHP2 "AT1G13330" [Arabidopsis	0.991	0.991	0.751	8.3e-90
RGD|621885	217	Psmc3ip "PSMC3 interacting pro	0.880	0.917	0.4	2.5e-33
MGI|MGI:1098610	217	Psmc3ip "proteasome (prosome,	0.880	0.917	0.39	8.5e-33
UNIPROTKB|F1S1D9	217	PSMC3IP "Uncharacterized prote	0.880	0.917	0.38	2.3e-32
UNIPROTKB|Q9P2W1	217	PSMC3IP "Homologous-pairing pr	0.880	0.917	0.385	3.7e-32
UNIPROTKB|E1BEL5	217	PSMC3IP "Uncharacterized prote	0.880	0.917	0.375	1.6e-31
UNIPROTKB|E2RCC0	217	PSMC3IP "Uncharacterized prote	0.880	0.917	0.38	2e-31
ZFIN|ZDB-GENE-040625-125	213	psmc3ip "PSMC3 interacting pro	0.924	0.981	0.352	4.2e-31
DICTYBASE|DDB_G0280989	243	hop2 "homologous-pairing prote	0.893	0.831	0.322	1.8e-25
POMBASE|SPAC222.15	216	meu13 "Tat binding protein 1(T	0.898	0.939	0.286	8e-21

TAIR|locus:2205359 AHP2 "AT1G13330" [Arabidopsis thaliana (taxid:3702)]

 Score = 896 (320.5 bits), Expect = 8.3e-90, P = 8.3e-90
 Identities = 169/225 (75%), Positives = 204/225 (90%)

Query:     1 MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY 60
             MAPKSDNTEAIVLN+VNEQN+PLN+QN ADALQK+NLKK  +QKALDSLAD GKI+FKEY
Sbjct:     1 MAPKSDNTEAIVLNFVNEQNKPLNTQNAADALQKFNLKKTAVQKALDSLADAGKITFKEY 60

Query:    61 GKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQ 120
             GKQKIYIARQDQF+IPNSEEL QMKE+NAKLQEQL+E++K IS +E EI++LQSNLTLE+
Sbjct:    61 GKQKIYIARQDQFEIPNSEELAQMKEDNAKLQEQLQEKKKTISDVESEIKSLQSNLTLEE 120

Query:   121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD 180
             I+EK+A+L KEVKEME KL KLR G+TLV+PED+ AVE+M+ +K++QWRKRKRM RDIWD
Sbjct:   121 IQEKDAKLRKEVKEMEEKLVKLREGITLVRPEDKKAVEDMYADKINQWRKRKRMFRDIWD 180

Query:   181 PIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLLQRGKK-PKG 224
              + ENSPK++KE KEELGIEYDEDVG+S Q+++DL+Q GKK P+G
Sbjct:   181 TVTENSPKDVKELKEELGIEYDEDVGLSFQAYADLIQHGKKRPRG 225

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0051026 "chiasma assembly" evidence=IMP

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

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

GO:0010332 "response to gamma radiation" evidence=RCA

RGD|621885 Psmc3ip "PSMC3 interacting protein" [Rattus norvegicus (taxid:10116)]

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 80/200 (40%), Positives = 118/200 (59%)

Query:    11 IVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR 69
             IVL Y+ EQNRP ++Q+V   LQK + L KA + KALD LA  GKI  K YGKQKIY A 
Sbjct:    15 IVLRYLQEQNRPYSAQDVFGNLQKEHGLGKAAVVKALDQLAQQGKIKEKTYGKQKIYFAD 74

Query:    70 QDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLV 129
             QDQFD  +  +L+ +      L  +++  +++   +E E++ L S LT  +++ +  +L 
Sbjct:    75 QDQFDTVSDADLHSLDASIMALTAKVQGLQQSCRHMEAELKELTSALTTPEMQTEIQELK 134

Query:   130 KEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKN 189
             KE      +L  ++     V PE++  V     +   +WRKRKRM  ++ D I+E  PK+
Sbjct:   135 KECARYTERLKNIKAATNHVTPEEKEKVYRERQKYCKEWRKRKRMTTELCDAILEGYPKS 194

Query:   190 LKEFKEELGIEYDEDVGVSL 209
              K+F EE+GIE DED  V+L
Sbjct:   195 KKQFFEEVGIETDEDHNVTL 214

GO:0000502 "proteasome complex" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0006310 "DNA recombination" evidence=IEA

GO:0007126 "meiosis" evidence=IEA

GO:0030331 "estrogen receptor binding" evidence=IDA

GO:0030374 "ligand-dependent nuclear receptor transcription coactivator activity" evidence=IEA;ISO;IDA

GO:0035259 "glucocorticoid receptor binding" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IMP

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0046966 "thyroid hormone receptor binding" evidence=IDA

GO:0046983 "protein dimerization activity" evidence=TAS

GO:0050681 "androgen receptor binding" evidence=IDA

GO:0050692 "DBD domain binding" evidence=IDA

MGI|MGI:1098610 Psmc3ip "proteasome (prosome, macropain) 26S subunit, ATPase 3, interacting protein" [Mus musculus (taxid:10090)]

 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 78/200 (39%), Positives = 119/200 (59%)

Query:    11 IVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR 69
             I+L Y+ EQNRP ++Q+V   LQK + L KA + KALD LA  GKI  K YGKQKIY A 
Sbjct:    15 IILRYLQEQNRPYSAQDVFGNLQKEHGLGKAAVVKALDQLAQEGKIKEKTYGKQKIYFAD 74

Query:    70 QDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLV 129
             Q+QFD  +  +L+ +      L  +++  +++   +E E++ L S LT  +++++  +L 
Sbjct:    75 QNQFDTVSDADLHGLDASIVALTAKVQSLQQSCRHMEAELKELTSALTTPEMQKEIQELK 134

Query:   130 KEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKN 189
             KE  +   +L  ++     V PE++  V     +   +WRKRKRM  ++ D I+E  PK+
Sbjct:   135 KECAQYTERLKNIKAATNHVTPEEKEKVYRDRQKYCKEWRKRKRMTTELCDAILEGYPKS 194

Query:   190 LKEFKEELGIEYDEDVGVSL 209
              K+F EE+GIE DED  V L
Sbjct:   195 KKQFFEEVGIETDEDHNVLL 214

GO:0000502 "proteasome complex" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0006310 "DNA recombination" evidence=IEA

GO:0007126 "meiosis" evidence=IEA

GO:0030331 "estrogen receptor binding" evidence=ISO

GO:0030374 "ligand-dependent nuclear receptor transcription coactivator activity" evidence=ISO

GO:0035259 "glucocorticoid receptor binding" evidence=ISO

GO:0042803 "protein homodimerization activity" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0046966 "thyroid hormone receptor binding" evidence=ISO

GO:0050681 "androgen receptor binding" evidence=ISO

GO:0050692 "DBD domain binding" evidence=ISO

UNIPROTKB|F1S1D9 PSMC3IP "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 354 (129.7 bits), Expect = 2.3e-32, P = 2.3e-32
 Identities = 76/200 (38%), Positives = 120/200 (60%)

Query:    11 IVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR 69
             I+L Y+ EQNRP ++Q+V   LQ+ + L KA + KAL+ LA  GKI  K YGKQKIY A 
Sbjct:    15 ILLKYLQEQNRPYSAQDVFGNLQREHGLGKAAVVKALEQLAQQGKIKEKVYGKQKIYFAD 74

Query:    70 QDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLV 129
             QDQFD+ +  +L  +  +   L  +++  +++   +E E++ L S LT  +++++  +L 
Sbjct:    75 QDQFDMVSDADLQGLDAKIVALTAKVQSLQQSCRHMEAELKELTSALTTPEMQKEIQELK 134

Query:   130 KEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKN 189
             KE      +L  ++     V PE++  V         +WRKRKRM  +++D I+E  P++
Sbjct:   135 KECTGYTERLKNIKAATNHVTPEEKEQVHRERQRYCKEWRKRKRMATELFDAILEGYPRS 194

Query:   190 LKEFKEELGIEYDEDVGVSL 209
              K+F EE+GIE DED  V+L
Sbjct:   195 KKQFFEEVGIETDEDHKVTL 214

GO:0030374 "ligand-dependent nuclear receptor transcription coactivator activity" evidence=IEA

UNIPROTKB|Q9P2W1 PSMC3IP "Homologous-pairing protein 2 homolog" [Homo sapiens (taxid:9606)]

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 77/200 (38%), Positives = 119/200 (59%)

Query:    11 IVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR 69
             I+L Y+ EQNRP +SQ+V   LQ+ + L KA + K L+ LA  GKI  K YGKQKIY A 
Sbjct:    15 ILLRYLQEQNRPYSSQDVFGNLQREHGLGKAVVVKTLEQLAQQGKIKEKMYGKQKIYFAD 74

Query:    70 QDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLV 129
             QDQFD+ +  +L  +  +   L  +++  +++   +E E++ L S LT  +++++  +L 
Sbjct:    75 QDQFDMVSDADLQVLDGKIVALTAKVQSLQQSCRYMEAELKELSSALTTPEMQKEIQELK 134

Query:   130 KEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKN 189
             KE      +L  ++     V PE++  V     +   +WRKRKRM  ++ D I+E  PK+
Sbjct:   135 KECAGYRERLKNIKAATNHVTPEEKEQVYRERQKYCKEWRKRKRMATELSDAILEGYPKS 194

Query:   190 LKEFKEELGIEYDEDVGVSL 209
              K+F EE+GIE DED  V+L
Sbjct:   195 KKQFFEEVGIETDEDYNVTL 214

GO:0003677 "DNA binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0007126 "meiosis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0030374 "ligand-dependent nuclear receptor transcription coactivator activity" evidence=IMP

UNIPROTKB|E1BEL5 PSMC3IP "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 75/200 (37%), Positives = 119/200 (59%)

Query:    11 IVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR 69
             I+L Y+ EQNRP ++Q+V   LQ+ + L K  + KAL+ LA  GKI  K YGKQKIY A 
Sbjct:    15 ILLKYLQEQNRPYSAQDVFGNLQREHGLGKTAVVKALEQLAQQGKIKEKMYGKQKIYFAD 74

Query:    70 QDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLV 129
             QDQFD+ +  +L  +  +   L  +++  +++   +E E++ L S LT  +++++  +L 
Sbjct:    75 QDQFDVVSDADLQGLDAKILALTAKVQSLQQSCRHMEAELKELTSALTTPEMQKEIEELK 134

Query:   130 KEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKN 189
             KE      +L  ++     V PE++  V +   +   +WR+RKRM  ++ D I+E  PK+
Sbjct:   135 KECAGYRERLKNIKAATNHVTPEEKEQVYKERQKYHKEWRQRKRMATELSDAILEGYPKS 194

Query:   190 LKEFKEELGIEYDEDVGVSL 209
              K+F EE+GIE DED  V L
Sbjct:   195 KKQFFEEVGIETDEDHNVKL 214

GO:0030374 "ligand-dependent nuclear receptor transcription coactivator activity" evidence=IEA

UNIPROTKB|E2RCC0 PSMC3IP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 345 (126.5 bits), Expect = 2.0e-31, P = 2.0e-31
 Identities = 76/200 (38%), Positives = 117/200 (58%)

Query:    11 IVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR 69
             I+L Y+ EQNRP ++Q+V   LQ+ + L KA + KAL+ LA  GKI  K YGKQKIY A 
Sbjct:    15 ILLRYLQEQNRPYSAQDVFGNLQREHGLGKAAVVKALEQLAQQGKIKEKMYGKQKIYFAD 74

Query:    70 QDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLV 129
             QDQF   +  +L  +  +   L  +++  +++   +E E++ L S LT  +++++  +L 
Sbjct:    75 QDQFATVSDADLQGLDAKIVALTAKVQSLQQSCRHMEAELKELTSALTTPEMQKEIQELK 134

Query:   130 KEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKN 189
             KE      +L  ++     V PE++  V     +   +WRKRKRM  ++ D I+E  PK+
Sbjct:   135 KECAAYRERLKNIKAASNHVTPEEKEQVYRERQKYCKEWRKRKRMATELSDAILEGYPKS 194

Query:   190 LKEFKEELGIEYDEDVGVSL 209
              K+F EE+GIE DED  V L
Sbjct:   195 KKQFFEEVGIETDEDYNVKL 214

GO:0030374 "ligand-dependent nuclear receptor transcription coactivator activity" evidence=IEA

ZFIN|ZDB-GENE-040625-125 psmc3ip "PSMC3 interacting protein" [Danio rerio (taxid:7955)]

 Score = 342 (125.4 bits), Expect = 4.2e-31, P = 4.2e-31
 Identities = 74/210 (35%), Positives = 121/210 (57%)

Query:     1 MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKY-NLKKAGIQKALDSLADNGKISFKE 59
             M+ K     A +L Y+NE+NRP ++Q+V   LQK   L K  + KA++ LA  GKI  K 
Sbjct:     1 MSKKDSAAVARILAYLNEKNRPFSAQDVFTNLQKQCGLGKTAVVKAMEQLAQEGKIKEKV 60

Query:    60 YGKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLE 119
             YGKQKIY A Q QF+  +  +L +M +   ++  +++   ++  +L+ E++ L S+LT  
Sbjct:    61 YGKQKIYFADQSQFEDVSDADLRKMDDRIGEINTEVQSISQSCRQLDTELKELNSSLTTA 120

Query:   120 QIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIW 179
             +++ +  +L  E+     +L  ++     V PE+R  V +     + +WRKRKR++ D+ 
Sbjct:   121 EMKAQIQELQAEISGYRERLENIKSATNHVTPEEREKVYKERETYVKEWRKRKRLVSDMM 180

Query:   180 DPIMENSPKNLKEFKEELGIEYDEDVGVSL 209
               I+E  PK+ K F EE GIE DED  V++
Sbjct:   181 GAILEGYPKSKKHFLEEAGIETDEDHKVTM 210

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

DICTYBASE|DDB_G0280989 hop2 "homologous-pairing protein 2" [Dictyostelium discoideum (taxid:44689)]

 Score = 289 (106.8 bits), Expect = 1.8e-25, P = 1.8e-25
 Identities = 69/214 (32%), Positives = 117/214 (54%)

Query:     4 KSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ 63
             K D  E  +LN +N+ NRP N Q +  A    ++ K  I K L SL + GK++FKEY K 
Sbjct:     7 KKDEVEENILNLINKANRPYNYQMIEAAFP--SMGKTQIVKTLKSLGEQGKLTFKEYNKA 64

Query:    64 KIYIARQDQ--------FDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSN 115
              IY   QD         ++IP  E ++ +  +   +  QLE ++  +  L  + + L + 
Sbjct:    65 IIYWRIQDTGPKLDEQGYEIPQ-ESIHDLNRKLDGINRQLEVEQDTLKSLISQSKQLNNQ 123

Query:   116 LTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRML 175
             L+ EQI+++  QL  E KE+E+KL   +    ++  +D+  +++   +  S+W KRK + 
Sbjct:   124 LSDEQIQKEVNQLSTENKELESKLLTFQTK-EIMSDKDKQRLDDTIKKARSEWVKRKALF 182

Query:   176 RDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSL 209
             RDI D ++E S K  K+ +E++G E DED+ + +
Sbjct:   183 RDILDQVLERSNKKKKDLQEDIGWETDEDLKIQM 216

GO:0007126 "meiosis" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

POMBASE|SPAC222.15 meu13 "Tat binding protein 1(TBP-1)-interacting protein (TBPIP) homolog (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 59/206 (28%), Positives = 111/206 (53%)

Query:     4 KSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ 63
             K +  E +V  Y+ + NRP ++ +V+  L+    K+   QKAL+ L D G I  K YGKQ
Sbjct:    13 KGEEAEKLVYEYLRKTNRPYSATDVSANLKNVVSKQVA-QKALEQLRDTGLIHGKLYGKQ 71

Query:    64 KIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIRE 123
              +++  QD       EEL +M+++  +L++++   +    +   E++ L ++L+  +IRE
Sbjct:    72 SVFVCLQDDLAAATPEELAEMEKQIQELKDEVSVVKTLYKEKCIELQALNNSLSPAEIRE 131

Query:   124 KEAQLVKEVKEMENKLAKLRGG-VTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPI 182
             K   + KE++E  +KL  LR G V  +  E     ++ +      +  RK+M  D+W  +
Sbjct:   132 KIQSIDKEIEETSSKLESLRNGTVKQISKEAMQKTDKNYDFAKKGFSNRKKMFYDLWH-L 190

Query:   183 MENSPKNLKEFKEELGIEYDEDVGVS 208
             + +S +N K+  E+LG E +  + ++
Sbjct:   191 ITDSLENPKQLWEKLGFETEGPIDLN 216

GO:0000790 "nuclear chromatin" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005819 "spindle" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0007129 "synapsis" evidence=IMP

GO:0007131 "reciprocal meiotic recombination" evidence=IMP

GO:0044732 "mitotic spindle pole body" 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)
Q9FX64	HOP2_ARATH	No assigned EC number	0.7511	0.9911	0.9911	yes	no
Q91ZY6	HOP2_RAT	No assigned EC number	0.3980	0.8849	0.9216	yes	no
Q9P2W1	HOP2_HUMAN	No assigned EC number	0.385	0.8805	0.9170	yes	no
O35047	HOP2_MOUSE	No assigned EC number	0.3880	0.8849	0.9216	yes	no
Q54UM1	HOP2_DICDI	No assigned EC number	0.3224	0.8938	0.8312	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

Your Input:
	eugene3.00081109	hypothetical protein (227 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.145.162.1	hypothetical protein (206 aa)				•	•	•	•		0.848

---

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	226
pfam07106	169	pfam07106, TBPIP, Tat binding protein 1(TBP-1)-int	7e-43
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	0.002

>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein (TBPIP)

 Score =  142 bits (359), Expect = 7e-43
 Identities = 76/170 (44%), Positives = 115/170 (67%), Gaps = 1/170 (0%)

Query: 7   NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIY 66
             EA++L Y+NEQNRP + Q+V D LQ   L K  +QKALD L D GKI  KEYGKQKIY
Sbjct: 1   EAEALILKYLNEQNRPYSVQDVVDNLQN-GLGKTAVQKALDELVDEGKIICKEYGKQKIY 59

Query: 67  IARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEA 126
           +  QDQF++P+ EELN++  E  +L+E+++  ++  S LE E+++L S+LT E+++E+  
Sbjct: 60  LCNQDQFELPSDEELNKLDMEIEELREEVQLLKQDCSTLEIELKSLTSDLTTEELQEEIQ 119

Query: 127 QLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLR 176
           +L KEV+E+E KL  L  G   V PE+   V++ + +   +W+KRK++  
Sbjct: 120 ELKKEVREIEEKLESLEEGWKPVTPEEMEKVKKEYKDLHKEWKKRKKLCN 169

This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. 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. Length = 169

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 38.1 bits (89), Expect = 0.002
 Identities = 21/104 (20%), Positives = 51/104 (49%), Gaps = 11/104 (10%)

Query: 76  PNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEM 135
              E + +++EEN++L+ +LEE ++ I KLE E+   +  +        + +  +E++  
Sbjct: 426 KLEETVERLEEENSELKRELEELKREIEKLESELERFRREV------RDKVRKDREIRAR 479

Query: 136 ENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIW 179
           + ++ +L       + E++    E    KL++ RK +++     
Sbjct: 480 DRRIERLE-----KELEEKKKRVEELERKLAELRKMRKLELSGK 518

Length = 652

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	226
KOG4603	201	consensus TBP-1 interacting protein [Signal transd	100.0
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	100.0
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	99.97
KOG3433	203	consensus Protein involved in meiotic recombinatio	99.95
COG5124	209	Protein predicted to be involved in meiotic recomb	99.95
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	98.12
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	97.8
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	97.72
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	97.72
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.69
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	97.56
PRK06474	178	hypothetical protein; Provisional	97.43
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	97.4
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	97.15
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	97.1
PHA00738	108	putative HTH transcription regulator	97.05
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	96.91
PRK09462	148	fur ferric uptake regulator; Provisional	96.87
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.85
PF07061	83	Swi5: Swi5; InterPro: IPR010760 This entry represe	96.79
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	96.74
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	96.72
COG3355	126	Predicted transcriptional regulator [Transcription	96.71
PF08679	67	DsrD: Dissimilatory sulfite reductase D (DsrD); In	96.64
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	96.56
PRK11639	169	zinc uptake transcriptional repressor; Provisional	96.48
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.4
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.39
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.35
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	96.35
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.32
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	96.29
COG4565	224	CitB Response regulator of citrate/malate metaboli	96.12
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	95.99
COG1378	247	Predicted transcriptional regulators [Transcriptio	95.9
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	95.79
COG2345	218	Predicted transcriptional regulator [Transcription	95.61
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	95.59
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	95.57
COG3682	123	Predicted transcriptional regulator [Transcription	95.53
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.47
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	95.24
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	95.23
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	95.2
PHA02943	165	hypothetical protein; Provisional	95.19
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	95.14
PRK06266	178	transcription initiation factor E subunit alpha; V	95.08
COG1510	177	Predicted transcriptional regulators [Transcriptio	95.05
PRK11546	143	zraP zinc resistance protein; Provisional	95.04
PRK14127	109	cell division protein GpsB; Provisional	94.99
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	94.88
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	94.87
PRK03573	144	transcriptional regulator SlyA; Provisional	94.84
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	94.52
PRK11569	274	transcriptional repressor IclR; Provisional	94.52
PF13730	55	HTH_36: Helix-turn-helix domain	94.44
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	94.43
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	94.41
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	94.34
PF05812	118	Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro:	94.0
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	93.97
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	93.92
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	93.89
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	93.87
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	93.61
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	93.4
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	93.31
PF05584	72	Sulfolobus_pRN: Sulfolobus plasmid regulatory prot	93.2
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	93.18
PF05557	722	MAD: Mitotic checkpoint protein; InterPro: IPR0086	93.17
PF02295	66	z-alpha: Adenosine deaminase z-alpha domain; Inter	93.09
PRK11637	428	AmiB activator; Provisional	92.9
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	92.81
COG3937	108	Uncharacterized conserved protein [Function unknow	92.71
PRK10884	206	SH3 domain-containing protein; Provisional	92.67
PRK11637	428	AmiB activator; Provisional	92.59
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	92.49
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	92.47
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	92.46
COG1777	217	Predicted transcriptional regulators [Transcriptio	92.28
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	92.18
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	92.17
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	92.11
PRK03902	142	manganese transport transcriptional regulator; Pro	92.04
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	91.9
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	91.86
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	91.75
PRK05431	425	seryl-tRNA synthetase; Provisional	91.52
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	91.44
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	91.4
PRK10870	176	transcriptional repressor MprA; Provisional	91.37
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	91.12
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	90.92
PF07848	70	PaaX: PaaX-like protein; InterPro: IPR012906 This	90.9
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	90.86
PLN02678	448	seryl-tRNA synthetase	90.81
COG2433	652	Uncharacterized conserved protein [Function unknow	90.79
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	90.67
PF14282	106	FlxA: FlxA-like protein	90.56
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	90.39
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	90.33
TIGR00414	418	serS seryl-tRNA synthetase. This model represents	90.23
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	90.21
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	90.14
PRK00215	205	LexA repressor; Validated	90.13
COG5185	622	HEC1 Protein involved in chromosome segregation, i	89.63
PF09744	158	Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; Inte	89.54
COG2512	258	Predicted membrane-associated trancriptional regul	89.32
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	89.31
PF10552	116	ORF6C: ORF6C domain; InterPro: IPR018878 This entr	89.29
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	89.1
KOG4603	201	consensus TBP-1 interacting protein [Signal transd	89.04
PF08657	259	DASH_Spc34: DASH complex subunit Spc34 ; InterPro:	89.0
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	88.98
PF14389	88	Lzipper-MIP1: Leucine-zipper of ternary complex fa	88.94
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	88.71
PLN02320	502	seryl-tRNA synthetase	88.59
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	88.58
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	88.48
PRK10046	225	dpiA two-component response regulator DpiA; Provis	88.02
PRK09954	362	putative kinase; Provisional	87.93
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	87.93
PF10458	66	Val_tRNA-synt_C: Valyl tRNA synthetase tRNA bindin	87.89
COG1414	246	IclR Transcriptional regulator [Transcription]	87.81
COG1497	260	Predicted transcriptional regulator [Transcription	87.64
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	87.58
COG4189	308	Predicted transcriptional regulator [Transcription	87.41
PRK09391	230	fixK transcriptional regulator FixK; Provisional	87.23
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	86.8
COG0640	110	ArsR Predicted transcriptional regulators [Transcr	86.51
PRK12423	202	LexA repressor; Provisional	86.39
PRK11050	152	manganese transport regulator MntR; Provisional	86.11
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	86.1
KOG0971	1243	consensus Microtubule-associated protein dynactin	86.09
PF15188	85	CCDC-167: Coiled-coil domain-containing protein 16	86.04
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	86.04
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	86.03
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	85.97
PF14257	262	DUF4349: Domain of unknown function (DUF4349)	85.92
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	85.88
KOG4809	654	consensus Rab6 GTPase-interacting protein involved	85.85
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	85.78
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	85.78
PRK15422	79	septal ring assembly protein ZapB; Provisional	85.53
PRK11014	141	transcriptional repressor NsrR; Provisional	85.49
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	85.46
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	85.41
PRK14137	195	recX recombination regulator RecX; Provisional	85.29
PRK11642	813	exoribonuclease R; Provisional	85.11
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	84.98
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	84.75
KOG3647	338	consensus Predicted coiled-coil protein [General f	84.34
PF00038	312	Filament: Intermediate filament protein; InterPro:	84.08
KOG0979	1072	consensus Structural maintenance of chromosome pro	83.78
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	83.77
COG3398	240	Uncharacterized protein conserved in archaea [Func	83.74
PHA03162	135	hypothetical protein; Provisional	83.73
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	83.68
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	83.64
PF01486	100	K-box: K-box region; InterPro: IPR002487 MADS gene	83.53
PF06008	264	Laminin_I: Laminin Domain I; InterPro: IPR009254 L	83.35
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	83.33
COG4026	290	Uncharacterized protein containing TOPRIM domain,	83.05
COG1846	126	MarR Transcriptional regulators [Transcription]	83.02
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	82.83
PHA03155	115	hypothetical protein; Provisional	82.83
PRK04984	239	fatty acid metabolism regulator; Provisional	82.81
PF03938	158	OmpH: Outer membrane protein (OmpH-like); InterPro	82.77
PF03551	75	PadR: Transcriptional regulator PadR-like family;	82.67
PHA02562	562	46 endonuclease subunit; Provisional	82.62
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	82.35
COG4026	290	Uncharacterized protein containing TOPRIM domain,	82.23
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	82.23
PF15456	124	Uds1: Up-regulated During Septation	82.22
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	82.19
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	82.15
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	82.09
PF07544	83	Med9: RNA polymerase II transcription mediator com	82.02
PRK03918	880	chromosome segregation protein; Provisional	81.8
KOG4302	660	consensus Microtubule-associated protein essential	81.79
COG4942	420	Membrane-bound metallopeptidase [Cell division and	81.45
PRK00117	157	recX recombination regulator RecX; Reviewed	81.36
PRK14165	217	winged helix-turn-helix domain-containing protein/	81.33
PRK05638	442	threonine synthase; Validated	81.29
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	81.25
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	81.22
PF04065	233	Not3: Not1 N-terminal domain, CCR4-Not complex com	81.22
COG1654	79	BirA Biotin operon repressor [Transcription]	80.92
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	80.84
PRK13777	185	transcriptional regulator Hpr; Provisional	80.66
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	80.44
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	80.38
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	80.2

>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]

Probab=100.00  E-value=5.8e-51  Score=321.20  Aligned_cols=201  Identities=44%  Similarity=0.665  Sum_probs=197.2

Q ss_pred             CCCCcchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHH
Q 027236            1 MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEE   80 (226)
Q Consensus         1 M~~kg~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee   80 (226)
                      |+|..++++..||.||++||||||-+||++||++..++|++|+++||+|.+.|+|..|.||||+||+++|+.|..+|+++
T Consensus         1 mae~~~~~e~ivl~~~~eqNrP~ssq~v~~~lq~e~lgktavqk~Ld~La~~Gki~~K~YGKqKIY~a~QDqF~~~~~ee   80 (201)
T KOG4603|consen    1 MAEAAEDAEGIVLRYLQEQNRPYSSQDVFGNLQREHLGKTAVQKTLDQLAQQGKIKEKMYGKQKIYFADQDQFDMVSDEE   80 (201)
T ss_pred             CCccccccHHHHHHHHHHhcCCCchHHHHHHHHHHhccchHHHHHHHHHHHcCchhHHhccceeeEeecHHhhcCCChHH
Confidence            88888999999999999999999999999999984479999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHH
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEM  160 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~  160 (226)
                      +..|+.+|..|++++.++++.++..+++|+.|.+.+|.+|+...|++|.+++...+++|.++++|...|+|++++.+.+.
T Consensus        81 l~~ld~~i~~l~ek~q~l~~t~s~veaEik~L~s~Lt~eemQe~i~~L~kev~~~~erl~~~k~g~~~vtpedk~~v~~~  160 (201)
T KOG4603|consen   81 LQVLDGKIVALTEKVQSLQQTCSYVEAEIKELSSALTTEEMQEEIQELKKEVAGYRERLKNIKAGTNHVTPEDKEQVYRE  160 (201)
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCccc
Q 027236          161 FLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEY  201 (226)
Q Consensus       161 ~~~~~~~w~kRkri~~~i~~~i~e~~~~~~k~l~e~lGie~  201 (226)
                      |.+++++|++|+|||++||+.+++++|+++++|++++|||+
T Consensus       161 y~~~~~~wrk~krmf~ei~d~~~e~~pk~ksel~eelGIE~  201 (201)
T KOG4603|consen  161 YQKYCKEWRKRKRMFREIIDKLLEGLPKKKSELYEELGIEA  201 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHhCcCC
Confidence            99999999999999999999999999999999999999985

>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=100.00  E-value=6.5e-49  Score=319.34  Aligned_cols=169  Identities=43%  Similarity=0.716  Sum_probs=166.5

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHHHHHHH
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKE   86 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~~~l~~   86 (226)
                      ||++.|++||..||||||++||++|||+ +|+|++|+++|++||++|.|++|.||||+||||+|+.|+++|++++..|+.
T Consensus         1 eAe~~Il~y~~~qNRPys~~di~~nL~~-~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~~~~~~s~eel~~ld~   79 (169)
T PF07106_consen    1 EAEDAILEYMKEQNRPYSAQDIFDNLHN-KVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFANQDELEVPSPEELAELDA   79 (169)
T ss_pred             ChHHHHHHHHHHcCCCCcHHHHHHHHHh-hccHHHHHHHHHHHHhCCCeeeeeecceEEEeeCccccCCCCchhHHHHHH
Confidence            6899999999999999999999999998 899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHH
Q 027236           87 ENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLS  166 (226)
Q Consensus        87 ~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~~  166 (226)
                      +|.+|++++.+++.+++.++++|+.|.+.||+++|...|.+|++++..++++|..|++++.++|+++++++.+.|.+|++
T Consensus        80 ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~k  159 (169)
T PF07106_consen   80 EIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSGSKPVSPEEKEKLEKEYKKWRK  159 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999998889999999999999999999


Q ss_pred             HHHHHHHHHH
Q 027236          167 QWRKRKRMLR  176 (226)
Q Consensus       167 ~w~kRkri~~  176 (226)
                      +|++|||||+
T Consensus       160 ~w~kRKri~k  169 (169)
T PF07106_consen  160 EWKKRKRICK  169 (169)
T ss_pred             HHHHHHHHhC
Confidence            9999999995

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 [].

>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast)

Probab=99.97  E-value=1.5e-28  Score=202.49  Aligned_cols=180  Identities=23%  Similarity=0.352  Sum_probs=164.0

Q ss_pred             HHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHHHHHHHHHHH
Q 027236           12 VLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENAK   90 (226)
Q Consensus        12 Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~~~l~~~i~~   90 (226)
                      ||++||++..||+++||++.+++ .||+-++|+++|++||++|+|.+.++|.+++|||    ||   +++...+...+..
T Consensus         1 il~~f~e~~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~EKiGssn~YWs----Fp---s~~~~~~~~~~~~   73 (188)
T PF03962_consen    1 ILEIFHESKDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVEKIGSSNYYWS----FP---SQAKQKRQNKLEK   73 (188)
T ss_pred             ChHHHhhcCCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhhhccCeeEEEe----cC---hHHHHHHHHHHHH
Confidence            68999999999999999999999 7999999999999999999999999999999999    99   6999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccC----CHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHH---HHHH
Q 027236           91 LQEQLEEQRKAISKLEGEIRTLQSNL----TLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEE---MFLE  163 (226)
Q Consensus        91 l~~~l~~l~~~~k~l~~el~~l~~~~----t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~---~~~~  163 (226)
                      |++++..++..+..++.+|..+....    ....+.+.+.+|+.++..++.+|..+..++    |+.++.+..   .+..
T Consensus        74 l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~~~~~~D----p~~i~~~~~~~~~~~~  149 (188)
T PF03962_consen   74 LQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKELEKYSEND----PEKIEKLKEEIKIAKE  149 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----HHHHHHHHHHHHHHHH
Confidence            99999999999999999999998642    237788899999999999999999888764    666665554   5889


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCccccccc
Q 027236          164 KLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDV  205 (226)
Q Consensus       164 ~~~~w~kRkri~~~i~~~i~e~~~~~~k~l~e~lGie~Ded~  205 (226)
                      ++++||++.   ..|.+||...++++.++|..+|||+.|+||
T Consensus       150 ~anrwTDNI---~~l~~~~~~k~~~~~~~i~k~f~Ip~d~dy  188 (188)
T PF03962_consen  150 AANRWTDNI---FSLKSYLKKKFGMDEEDIRKEFGIPEDFDY  188 (188)
T ss_pred             HHHHHHhhH---HHHHHHHHHhcCCCHHHHHHHcCCccccCC
Confidence            999999997   456699999999999999999999999987

The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].

>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=99.95  E-value=8.8e-27  Score=186.02  Aligned_cols=194  Identities=21%  Similarity=0.272  Sum_probs=172.4

Q ss_pred             CCCC--cchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCH
Q 027236            1 MAPK--SDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNS   78 (226)
Q Consensus         1 M~~k--g~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~   78 (226)
                      ||||  .++++..++++|+++...|-+++|++..++.||.-+.|+.+|++|||+|+|.++++|.+++||+    ||   +
T Consensus         1 m~~kls~~ekr~~l~eIf~eskDff~LkelEKlG~kKgIv~~tvKdvLQsLvDD~lV~~eKIgtSnyyws----fp---s   73 (203)
T KOG3433|consen    1 MTVKLSSDEKRMILLEIFQESKDFFQLKELEKLGSKKGIVWQTVKDVLQSLVDDGLVIKEKIGTSNYYWS----FP---S   73 (203)
T ss_pred             CCcccchHHHHHHHHHHHHhhHhHHHHHHHHHhCCccceehhHHHHHHHHHhccchHHHHHhcccccccc----cc---h
Confidence            7886  4999999999999999999999999988888999999999999999999999999999999999    99   5


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC-----HHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHH
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLT-----LEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPED  153 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t-----~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee  153 (226)
                      +.+-.....+.+|.++|+...+....+...+.+.+....     +++|...+..|+..++.++.+|..++.+++ ..-+.
T Consensus        74 ~a~~~~ks~~qeLe~~L~~~~qk~~tl~e~~en~K~~~e~tEer~~el~kklnslkk~~e~lr~el~k~~e~dp-qv~~k  152 (203)
T KOG3433|consen   74 EAICDRKSVLQELESQLATGSQKKATLGESIENRKAGREETEERTDELTKKLNSLKKILESLRWELAKIQETDP-QVFEK  152 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHhHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCH-HHHHH
Confidence            888888899999999999999999999988877765422     257788888999999999999999997753 22445


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCccccccc
Q 027236          154 RMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDV  205 (226)
Q Consensus       154 ~~~~~~~~~~~~~~w~kRkri~~~i~~~i~e~~~~~~k~l~e~lGie~Ded~  205 (226)
                      +..+.+.+..++|+|+++.   .-++++|+..+|+.+.++.+.|||+.|+||
T Consensus       153 ~~~~~K~~~eaanrwtDnI---~il~dy~~rkf~~e~nqi~~~fgIPed~d~  201 (203)
T KOG3433|consen  153 KVHLEKTMAEAANRWTDNI---FILIDYLYRKFGLEPNQIRKEFGIPEDFDY  201 (203)
T ss_pred             HHHHHHHHHHHHhhhhhhH---HHHHHHHHHhcCCCHHHHhHhcCCCccccc
Confidence            5567788999999999997   556799999999999999999999999998

>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]

Probab=99.95  E-value=3.4e-26  Score=181.86  Aligned_cols=197  Identities=19%  Similarity=0.238  Sum_probs=162.7

Q ss_pred             CCCCc---chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCC
Q 027236            1 MAPKS---DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPN   77 (226)
Q Consensus         1 M~~kg---~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~   77 (226)
                      |||+|   ++++.+++.+||.+..+|-+++|+...++.+|+-++|+++|++|||+|.|.+.++|.+++||+    |+   
T Consensus         1 M~~~~ls~~eKrr~L~aI~~~SKdFFqLkEvEkLGSKK~IVl~tVKd~lQqlVDDgvV~~EK~GtsN~YWs----F~---   73 (209)
T COG5124           1 MPPKGLSLAEKRRRLEAIFHDSKDFFQLKEVEKLGSKKQIVLMTVKDLLQQLVDDGVVSVEKCGTSNIYWS----FK---   73 (209)
T ss_pred             CCCccccHHHHHHHHHHHHhccHHHHHHHHHHHhccccccHHHHHHHHHHHHhhcCceeeeeeccceeEEe----cc---
Confidence            99998   899999999999999999999999999888999999999999999999999999999999999    99   


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCH-------HHHHHHHHHH-HHHHHHHHHHHHHhhCCCCCC
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTL-------EQIREKEAQL-VKEVKEMENKLAKLRGGVTLV  149 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~-------~el~~~i~~L-~~e~~~l~~kL~~l~~~~~~v  149 (226)
                      ++.+..+......|++++..+++.++.+..+|..-.+....       .+....+..+ +.+..+++.+|..|+... |+
T Consensus        74 s~~~qk~~~~~~~l~~~~~~~kqdi~t~~e~i~~ek~~r~k~~Te~~~n~~~~~Ll~~~k~eqd~~k~~l~~l~~~~-pi  152 (209)
T COG5124          74 SQTLQKLYDSSELLKKKIQEVKQDIATYKEEIDKEKATRRKKFTEGQKNYNREALLEKRKKEQDEIKKKLNSLQKIE-PI  152 (209)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhcccccchhhHHHHHHHHHHHHHHHHHHHHhccccccC-ch
Confidence            58899999999999999999999999999998887754322       3444444333 444455555776666432 23


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCcccccccccch
Q 027236          150 KPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSL  209 (226)
Q Consensus       150 s~ee~~~~~~~~~~~~~~w~kRkri~~~i~~~i~e~~~~~~k~l~e~lGie~Ded~~v~~  209 (226)
                      .-+....-.+.+...++.|+++.   .-+++++|..+|++++++.+++||+.|.|+ +..
T Consensus       153 ~~d~~~~~~kk~~~~~n~~tDnI---~ilidy~c~kf~~~~~qir~~fgIPedld~-~q~  208 (209)
T COG5124         153 RWDAAKIQEKKKKVHLNKTTDNI---EILIDYLCKKFFLKPEQIRKEFGIPEDLDE-FQE  208 (209)
T ss_pred             hHHHHhhhHHHHHHHHHhhhhhH---HHHHHHHHHHcCCCHHHHHHhcCCCcchhh-hcc
Confidence            33333333345888899999997   557799999999999999999999999998 543

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

Probab=98.12  E-value=6.1e-06  Score=56.02  Aligned_cols=57  Identities=32%  Similarity=0.502  Sum_probs=47.1

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCcee-EEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQK-IYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~k-iY~~   68 (226)
                      .+.|++||+.++.|.+..||.+.+   |++..+|-..|..|+.+|.|..-..|+.+ .||-
T Consensus         2 ke~Il~~i~~~~~p~~T~eiA~~~---gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~   59 (62)
T PF04703_consen    2 KEKILEYIKEQNGPLKTREIADAL---GLSIYQARYYLEKLEKEGKVERSPVRRGKSTYWR   59 (62)
T ss_dssp             HHCHHHHHHHHTS-EEHHHHHHHH---TS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EEE
T ss_pred             cHHHHHHHHHcCCCCCHHHHHHHh---CCCHHHHHHHHHHHHHCCCEEEecCCCCcceeee
Confidence            367999999999999999999998   89999999999999999999887775443 4775

>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea

Probab=97.80  E-value=0.0012  Score=50.04  Aligned_cols=61  Identities=16%  Similarity=0.326  Sum_probs=54.9

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +++..|++++-+... -++.+|.+.++. ++.+.++|..+|..|+++|.|..+..|++.+|.+
T Consensus         3 ~~E~~IM~~lW~~~~-~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p   64 (115)
T PF03965_consen    3 DLELEIMEILWESGE-ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIGRAYVYSP   64 (115)
T ss_dssp             HHHHHHHHHHHHHSS-EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETTCEEEEE
T ss_pred             HHHHHHHHHHHhCCC-CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecCCceEEEe
Confidence            578899999998887 999999999987 4799999999999999999999999999999988

Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....

>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=97.72  E-value=9.9e-05  Score=50.62  Aligned_cols=58  Identities=29%  Similarity=0.513  Sum_probs=52.4

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+-+..|+.+|. .+.|.++.+|...+   +++++.|-++|..|++.|+|.... |+..+|.+
T Consensus         7 s~~E~~vy~~Ll-~~~~~t~~eIa~~l---~i~~~~v~~~L~~L~~~GlV~~~~-~~~~~Y~a   64 (68)
T PF01978_consen    7 SENEAKVYLALL-KNGPATAEEIAEEL---GISRSTVYRALKSLEEKGLVEREE-GRPKVYRA   64 (68)
T ss_dssp             HHHHHHHHHHHH-HHCHEEHHHHHHHH---TSSHHHHHHHHHHHHHTTSEEEEE-ECCEEEEE
T ss_pred             CHHHHHHHHHHH-HcCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEc-CceEEEEE
Confidence            356788999998 88999999999988   899999999999999999998888 77888887

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.

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

Probab=97.72  E-value=0.00015  Score=54.75  Aligned_cols=62  Identities=19%  Similarity=0.308  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCce-eEEEee
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGKQ-KIYIAR   69 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK~-kiY~~~   69 (226)
                      .+..|+++|..+++|+|+.+|.+.+...  .++.++|=.+|+.|++.|+|..-.++.. ..|..+
T Consensus         2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~   66 (116)
T cd07153           2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELN   66 (116)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence            4678999999999999999999999763  6899999999999999999999888655 555443

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.

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

Probab=97.69  E-value=0.0002  Score=49.44  Aligned_cols=58  Identities=21%  Similarity=0.283  Sum_probs=49.0

Q ss_pred             chHHHHHHHHHHhcCCC-CcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEE
Q 027236            6 DNTEAIVLNYVNEQNRP-LNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIY   66 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrP-ys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY   66 (226)
                      +.-++.||.+|.....| +++.+|...|   |+++..|.++|..|.+.|+|....-....++
T Consensus         5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l---gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~   63 (68)
T smart00550        5 DSLEEKILEFLENSGDETSTALQLAKNL---GLPKKEVNRVLYSLEKKGKVCKQGGTPPLWK   63 (68)
T ss_pred             hHHHHHHHHHHHHCCCCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEecCCCCCceE
Confidence            56788999999999875 9999999998   8999999999999999999987554334333

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

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=97.56  E-value=0.00037  Score=53.05  Aligned_cols=63  Identities=24%  Similarity=0.375  Sum_probs=52.9

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecC-ceeEEEee
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYG-KQKIYIAR   69 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~G-K~kiY~~~   69 (226)
                      ..+..||++|.++++|+|+.+|.+.|...  .|+.++|=.+|+.|++.|+|..-..+ ....|-..
T Consensus         8 ~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~   73 (120)
T PF01475_consen    8 PQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELS   73 (120)
T ss_dssp             HHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEES
T ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeec
Confidence            46889999999999999999999999763  69999999999999999999998887 44555443

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 ....

>PRK06474 hypothetical protein; Provisional

Probab=97.43  E-value=0.011  Score=48.49  Aligned_cols=73  Identities=14%  Similarity=0.264  Sum_probs=60.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec-----CceeEEEeecCCCCCCCHHH
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY-----GKQKIYIARQDQFDIPNSEE   80 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~-----GK~kiY~~~Q~~~~~~~~ee   80 (226)
                      ..-+..|+++|...+.|+|+.+|...+.  +|+.++|=..|..|++.|+|..-..     |..++|.++...+.. ++++
T Consensus        10 ~p~R~~Il~~L~~~~~~~ta~el~~~l~--~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~~-~~~~   86 (178)
T PRK06474         10 HPVRMKICQVLMRNKEGLTPLELVKILK--DVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAKI-EGSE   86 (178)
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHhc--CCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceeee-CHHH
Confidence            5568899999999888899999999885  6999999999999999999998665     345899998887653 3444


Q ss_pred             H
Q 027236           81 L   81 (226)
Q Consensus        81 ~   81 (226)
                      +
T Consensus        87 ~   87 (178)
T PRK06474         87 W   87 (178)
T ss_pred             H
Confidence            3

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=97.40  E-value=0.009  Score=46.42  Aligned_cols=61  Identities=23%  Similarity=0.318  Sum_probs=53.2

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +++-.|+.++-.. .|-++.+|.+.|.. .++..++|...|..|+++|.|..+..|...+|.+
T Consensus         4 ~~E~~VM~vlW~~-~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr~~~Y~p   65 (130)
T TIGR02698         4 DAEWEVMRVVWTL-GETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGRKFIYTA   65 (130)
T ss_pred             HHHHHHHHHHHcC-CCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCCCcEEEEe
Confidence            4677899999864 48899999998865 4789999999999999999999999999888876

This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=97.15  E-value=0.0021  Score=42.22  Aligned_cols=52  Identities=21%  Similarity=0.368  Sum_probs=45.1

Q ss_pred             HHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           12 VLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        12 Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      |+.++.  ++|.+..+|...+   +++++.|.++|+.|.+.|.|....-|...+|..
T Consensus         2 il~~l~--~~~~~~~~i~~~l---~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~   53 (66)
T smart00418        2 ILKLLA--EGELCVCELAEIL---GLSQSTVSHHLKKLREAGLVESRREGKRVYYSL   53 (66)
T ss_pred             HHHHhh--cCCccHHHHHHHH---CCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEE
Confidence            677776  8899999998888   799999999999999999999877677677766

>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=97.10  E-value=0.00085  Score=43.58  Aligned_cols=46  Identities=26%  Similarity=0.444  Sum_probs=41.3

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      --.||++|..+..|.++.+|...+   |+++++|...|.+|++.|.|..
T Consensus         5 al~iL~~l~~~~~~~t~~eia~~~---gl~~stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen    5 ALRILEALAESGGPLTLSEIARAL---GLPKSTVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             HHHHHHCHHCTBSCEEHHHHHHHH---TS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCcCeec
Confidence            357999999999999999999988   8999999999999999999864

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.

>PHA00738 putative HTH transcription regulator

Probab=97.05  E-value=0.009  Score=44.81  Aligned_cols=65  Identities=18%  Similarity=0.274  Sum_probs=57.1

Q ss_pred             CcchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCC
Q 027236            4 KSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQ   72 (226)
Q Consensus         4 kg~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~   72 (226)
                      .|+..|-.|+.+|.. +.|.++.+|...+   +++.++|-+-|.-|.+-|+|....-|+..+|..+.+.
T Consensus         9 ~~dptRr~IL~lL~~-~e~~~V~eLae~l---~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~~   73 (108)
T PHA00738          9 RAKILRRKILELIAE-NYILSASLISHTL---LLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIRENS   73 (108)
T ss_pred             cCCHHHHHHHHHHHH-cCCccHHHHHHhh---CCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCCc
Confidence            367889999999964 5579988998877   7999999999999999999999999999999996554

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

Probab=96.91  E-value=0.0054  Score=48.56  Aligned_cols=66  Identities=17%  Similarity=0.273  Sum_probs=57.1

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc--ccccHHHHHHHHHHHHHcCCcceeecCc-eeEEEeecC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK--YNLKKAGIQKALDSLADNGKISFKEYGK-QKIYIARQD   71 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~--~~v~K~~v~k~L~~Lv~~g~i~~K~~GK-~kiY~~~Q~   71 (226)
                      -.-|..|++||.++..|+|+.+|.+.|..  -+|+.++|=.+|+.|++.|+|..=.++. ...|..++.
T Consensus        20 T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~   88 (145)
T COG0735          20 TPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSE   88 (145)
T ss_pred             CHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCC
Confidence            45688999999999999999999999986  3699999999999999999999999955 466655555

>PRK09462 fur ferric uptake regulator; Provisional

Probab=96.87  E-value=0.0048  Score=48.80  Aligned_cols=64  Identities=13%  Similarity=0.286  Sum_probs=53.2

Q ss_pred             chHHHHHHHHHHhc-CCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecC-ceeEEEee
Q 027236            6 DNTEAIVLNYVNEQ-NRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYG-KQKIYIAR   69 (226)
Q Consensus         6 ~ea~~~Il~y~~~~-nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~G-K~kiY~~~   69 (226)
                      -..+..||++|..+ .+|+|+.+|.+.|.+.  +|+.++|=.+|+.|++.|+|..=.+| ....|-++
T Consensus        16 T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~~~   83 (148)
T PRK09462         16 TLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFELT   83 (148)
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEEeC
Confidence            46789999999986 5899999999999763  58999999999999999999877764 34556443

>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=96.85  E-value=0.0059  Score=38.70  Aligned_cols=46  Identities=26%  Similarity=0.554  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      +-+..|+.|+.+ |.+.|..+|...+   |++.++|...|..|.++|.|.
T Consensus         3 ~~~~~Il~~l~~-~~~~t~~ela~~~---~is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    3 ETQRKILNYLRE-NPRITQKELAEKL---GISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHHHHH-CTTS-HHHHHHHH---TS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHh---CCCHHHHHHHHHHHHHCcCcC
Confidence            456789999998 5559999999988   899999999999999999873

...

>PF07061 Swi5: Swi5; InterPro: IPR010760 This entry represents Swi5 and is involved in meiotic DNA repair synthesis and meiotic joint molecule formation []

Probab=96.79  E-value=0.025  Score=40.58  Aligned_cols=78  Identities=15%  Similarity=0.350  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCcc
Q 027236          121 IREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIE  200 (226)
Q Consensus       121 l~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~~~w~kRkri~~~i~~~i~e~~~~~~k~l~e~lGie  200 (226)
                      +...+..|++++..+...+..+.+.-    +.......+.|.+....|.+=|-++-.+++.|++.-+....++++++|++
T Consensus         5 l~~~~~~L~~~~~~l~~~i~~~~~~l----~~~~~~~v~~hI~lLheYNeiKD~gQ~Lig~iA~~rgvt~~~v~~e~gl~   80 (83)
T PF07061_consen    5 LEAEIQELKEQIEQLEKEISELEAEL----IEDPEKIVKRHIKLLHEYNEIKDIGQGLIGLIADQRGVTVKDVYEEFGLD   80 (83)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhc----ccCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCcHHHHHHHcCCC
Confidence            44455555555555555555554321    12334566777777889999999999999999999999999999999998


Q ss_pred             cc
Q 027236          201 YD  202 (226)
Q Consensus       201 ~D  202 (226)
                      .+
T Consensus        81 ~~   82 (83)
T PF07061_consen   81 MN   82 (83)
T ss_pred             CC
Confidence            64

It is known to interact with Swi2, Rhp51 and Swi6 [].

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=96.74  E-value=0.042  Score=42.02  Aligned_cols=61  Identities=23%  Similarity=0.260  Sum_probs=54.8

Q ss_pred             cchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            5 SDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         5 g~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      ++..+-.|+.++... .|.++.+|.+.+   +++.++|.+-|.-|.+-|+|....-|...+|..+
T Consensus        14 adptRl~IL~~L~~~-~~~~v~ela~~l---~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~   74 (117)
T PRK10141         14 SDETRLGIVLLLRES-GELCVCDLCTAL---DQSQPKISRHLALLRESGLLLDRKQGKWVHYRLS   74 (117)
T ss_pred             CCHHHHHHHHHHHHc-CCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEEC
Confidence            478888999999753 489999999888   7999999999999999999999999999999884

>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=96.72  E-value=0.0082  Score=40.15  Aligned_cols=53  Identities=23%  Similarity=0.444  Sum_probs=46.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCc
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGK   62 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK   62 (226)
                      +..+-.|+.++ ..+.|.++.+|...+   +++.+++-.-|..|.+-|+|....-|+
T Consensus         9 ~p~R~~Il~~L-~~~~~~t~~ela~~l---~~~~~t~s~hL~~L~~aGli~~~~~gr   61 (61)
T PF12840_consen    9 DPTRLRILRLL-ASNGPMTVSELAEEL---GISQSTVSYHLKKLEEAGLIEVEREGR   61 (61)
T ss_dssp             SHHHHHHHHHH-HHCSTBEHHHHHHHH---TS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             CHHHHHHHHHH-hcCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCeEEeccCC
Confidence            45677899999 679999999999988   799999999999999999999988774

...

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=96.71  E-value=0.035  Score=42.91  Aligned_cols=52  Identities=21%  Similarity=0.377  Sum_probs=44.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .++.-.|+.-|.+.|.|.++-+|...|   +.++++|+++|+.|++-|+|.-...
T Consensus        26 s~~Dv~v~~~LL~~~~~~tvdelae~l---nr~rStv~rsl~~L~~~GlV~Rek~   77 (126)
T COG3355          26 SELDVEVYKALLEENGPLTVDELAEIL---NRSRSTVYRSLQNLLEAGLVEREKV   77 (126)
T ss_pred             cHHHHHHHHHHHhhcCCcCHHHHHHHH---CccHHHHHHHHHHHHHcCCeeeeee
Confidence            455566777777799999999999988   6799999999999999999987765

>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=96.64  E-value=0.0087  Score=40.83  Aligned_cols=60  Identities=15%  Similarity=0.377  Sum_probs=49.5

Q ss_pred             hHHHHHHHHHH---hcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVN---EQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~---~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      |+.+.|++||.   .....|=.+|+.+..+  ....-.|+|++..||.+|.+..=--|++..|-.
T Consensus         1 e~K~~Ile~L~~k~~~KskfYfkD~~k~~p--d~k~R~vKKi~~~LV~Eg~l~yWSSGSTTmYgl   63 (67)
T PF08679_consen    1 EAKQKILEFLEAKKKKKSKFYFKDFYKAFP--DAKPREVKKIVNELVNEGKLEYWSSGSTTMYGL   63 (67)
T ss_dssp             HHHHHHHHHHSSCCCHSS-EEHHHHHHH-T--TS-HHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHhccCCCCceeHHHHHHHCC--CcCHHHHHHHHHHHHhhCeEEEEcCCCcEEecC
Confidence            57889999987   3355788999999886  578999999999999999999988999999965

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

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=96.56  E-value=0.011  Score=37.37  Aligned_cols=49  Identities=16%  Similarity=0.369  Sum_probs=41.6

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ...|+.|+.. +.|+++.++...+   +++.++|.+.|+.|.+.|.|....-|
T Consensus         2 ~~~il~~l~~-~~~~s~~~l~~~l---~~s~~tv~~~l~~L~~~g~i~~~~~~   50 (53)
T smart00420        2 QQQILELLAQ-QGKVSVEELAELL---GVSEMTIRRDLNKLEEQGLLTRVHGG   50 (53)
T ss_pred             HHHHHHHHHH-cCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEeecC
Confidence            3578999885 5789999999988   79999999999999999998765544

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=96.48  E-value=0.011  Score=48.06  Aligned_cols=57  Identities=21%  Similarity=0.239  Sum_probs=51.2

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCc
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGK   62 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK   62 (226)
                      -..+..||++|..+.+|+|+.+|.+.|...  .|+.++|=.+|+.|++.|+|..=..|.
T Consensus        25 T~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~~~   83 (169)
T PRK11639         25 TPQRLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTN   83 (169)
T ss_pred             CHHHHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEecCC
Confidence            456889999999999999999999999773  589999999999999999998877754

>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=96.40  E-value=0.017  Score=38.86  Aligned_cols=57  Identities=18%  Similarity=0.361  Sum_probs=43.0

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      +-.||.++..+++|-+..+|.+.+   +++++++-++|+.|++.|+|....-   |...+|-.
T Consensus         5 q~~vL~~l~~~~~~~t~~~l~~~~---~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~L   64 (68)
T PF13463_consen    5 QWQVLRALAHSDGPMTQSDLAERL---GISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRL   64 (68)
T ss_dssp             HHHHHHHHT--TS-BEHHHHHHHT---T--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE
T ss_pred             HHHHHHHHHccCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEe
Confidence            457899999999999999999988   7999999999999999999965533   55555544

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

Probab=96.39  E-value=0.029  Score=37.65  Aligned_cols=59  Identities=24%  Similarity=0.425  Sum_probs=50.0

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      ...+..|+.++...  |.+..+|...+   +++.+.+.++|+.|++.|.|.....|...+|.+.
T Consensus         6 ~~~~~~il~~l~~~--~~~~~ei~~~~---~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~   64 (78)
T cd00090           6 DPTRLRILRLLLEG--PLTVSELAERL---GLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLT   64 (78)
T ss_pred             ChHHHHHHHHHHHC--CcCHHHHHHHH---CcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeC
Confidence            46678899998864  48999988877   7899999999999999999999888877777774

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.

>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=96.35  E-value=0.013  Score=37.09  Aligned_cols=46  Identities=26%  Similarity=0.484  Sum_probs=40.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      ++.+-.|+.++.+  .|+++.+|.+.+   ++++++|..-|..|.+.|+|.
T Consensus         1 d~~R~~Il~~L~~--~~~~~~el~~~l---~~s~~~vs~hL~~L~~~glV~   46 (47)
T PF01022_consen    1 DPTRLRILKLLSE--GPLTVSELAEEL---GLSQSTVSHHLKKLREAGLVE   46 (47)
T ss_dssp             SHHHHHHHHHHTT--SSEEHHHHHHHH---TS-HHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHHHHh--CCCchhhHHHhc---cccchHHHHHHHHHHHCcCee
Confidence            3567789999987  999999999988   899999999999999999985

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 ....

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=96.35  E-value=0.014  Score=41.73  Aligned_cols=48  Identities=23%  Similarity=0.319  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      .--.|+++|.....|.++.+|...+   ++++++|.+.|..|++.|.|...
T Consensus         6 r~~~Il~~l~~~~~~~t~~~ia~~l---~i~~~tv~r~l~~L~~~g~l~~~   53 (91)
T smart00346        6 RGLAVLRALAEEPGGLTLAELAERL---GLSKSTAHRLLNTLQELGYVEQD   53 (91)
T ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHh---CCCHHHHHHHHHHHHHCCCeeec
Confidence            3456899998877899999999988   89999999999999999999875

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.32  E-value=0.25  Score=41.04  Aligned_cols=59  Identities=24%  Similarity=0.440  Sum_probs=47.5

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee----cCc-eeEEEeec
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE----YGK-QKIYIARQ   70 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~----~GK-~kiY~~~Q   70 (226)
                      .+..||.++... .|.|..+|.+.+   +|+.++|.+.|+.|+++|+|....    -|. ..+|....
T Consensus         2 tr~~IL~~L~~~-~~~t~~eLA~~l---gis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~   65 (203)
T TIGR02702         2 TKEDILSYLLKQ-GQATAAALAEAL---AISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSR   65 (203)
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECc
Confidence            367899999875 568999999988   899999999999999999998662    344 45565543

All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.

>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=96.29  E-value=0.019  Score=38.52  Aligned_cols=50  Identities=16%  Similarity=0.437  Sum_probs=41.7

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCc
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGK   62 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK   62 (226)
                      -..|+..-. .+.|-+..+|...|   +|++++|.++|..|.++|+|....||-
T Consensus        10 L~~Iy~l~~-~~~~v~~~~iA~~L---~vs~~tvt~ml~~L~~~GlV~~~~y~g   59 (60)
T PF01325_consen   10 LKAIYELSE-EGGPVRTKDIAERL---GVSPPTVTEMLKRLAEKGLVEYEPYKG   59 (60)
T ss_dssp             HHHHHHHHH-CTSSBBHHHHHHHH---TS-HHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             HHHHHHHHc-CCCCccHHHHHHHH---CCChHHHHHHHHHHHHCCCEEecCCCC
Confidence            344555544 78999999999999   799999999999999999999998873

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 ....

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=96.12  E-value=0.023  Score=47.71  Aligned_cols=64  Identities=27%  Similarity=0.469  Sum_probs=55.5

Q ss_pred             CCc--chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee-ecCc----eeEEEee
Q 027236            3 PKS--DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK-EYGK----QKIYIAR   69 (226)
Q Consensus         3 ~kg--~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K-~~GK----~kiY~~~   69 (226)
                      |||  .---..|.+.+..+.-|||+.++...+   |++++++.+.|+-|++.|.+... .||+    ...||..
T Consensus       152 PkGi~~~Tl~~i~~~~~~~~~~~Taeela~~~---giSRvTaRRYLeyl~~~~~l~a~i~yG~vGRP~r~Y~~~  222 (224)
T COG4565         152 PKGLDELTLQKVREALKEPDQELTAEELAQAL---GISRVTARRYLEYLVSNGILEAEIHYGKVGRPERRYRLK  222 (224)
T ss_pred             CCCcCHHHHHHHHHHHhCcCCccCHHHHHHHh---CccHHHHHHHHHHHHhcCeeeEEeeccccCCcceeeecc
Confidence            577  566788999999999999999998877   89999999999999999999988 6785    4777764

>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=95.99  E-value=0.035  Score=36.02  Aligned_cols=44  Identities=18%  Similarity=0.422  Sum_probs=38.3

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCc
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKI   55 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i   55 (226)
                      ...|+.+|..++.|+|+.++.+.|   +|+..+|.+.|+.|-+.|..
T Consensus         2 ~~~il~~L~~~~~~it~~eLa~~l---~vS~rTi~~~i~~L~~~~~~   45 (55)
T PF08279_consen    2 QKQILKLLLESKEPITAKELAEEL---GVSRRTIRRDIKELREWGIP   45 (55)
T ss_dssp             HHHHHHHHHHTTTSBEHHHHHHHC---TS-HHHHHHHHHHHHHTT-E
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHh---CCCHHHHHHHHHHHHHCCCe
Confidence            357999999999999999999988   79999999999999999933

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 ....

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=95.90  E-value=0.17  Score=43.57  Aligned_cols=93  Identities=25%  Similarity=0.310  Sum_probs=67.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHHHHHHH
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKE   86 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~~~l~~   86 (226)
                      +=+..|+-.|.. ..|-++.+|....   ||+.+-|=++|.+|.++|.|..- -|+-++|.|    .|   ++++  ++.
T Consensus        16 ~yEa~vY~aLl~-~g~~tA~eis~~s---gvP~~kvY~vl~sLe~kG~v~~~-~g~P~~y~a----v~---p~~~--i~~   81 (247)
T COG1378          16 EYEAKVYLALLC-LGEATAKEISEAS---GVPRPKVYDVLRSLEKKGLVEVI-EGRPKKYRA----VP---PEEL--IER   81 (247)
T ss_pred             HHHHHHHHHHHH-hCCccHHHHHHHc---CCCchhHHHHHHHHHHCCCEEee-CCCCceEEe----CC---HHHH--HHH
Confidence            345566666663 4588999998876   89999999999999999999988 899999999    65   5663  345


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           87 ENAKLQEQLEEQRKAISKLEGEIRTLQ  113 (226)
Q Consensus        87 ~i~~l~~~l~~l~~~~k~l~~el~~l~  113 (226)
                      ...+++..+..+......+..++....
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (247)
T COG1378          82 IKEELQELLRELESELEELERELARRE  108 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhcccccc
Confidence            555565556666655555555444433

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []

Probab=95.79  E-value=0.21  Score=44.67  Aligned_cols=86  Identities=21%  Similarity=0.357  Sum_probs=67.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHH
Q 027236           73 FDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPE  152 (226)
Q Consensus        73 ~~~~~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~e  152 (226)
                      ...++++++..+..++..+..++...+..+.+++.++..+...  .+++.+++.++..+|.+++..+..-+    ..|..
T Consensus       203 ~~~~D~~eL~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~--i~~~~~~k~~l~~eI~e~~~~~~~~r----~~t~~  276 (325)
T PF08317_consen  203 IESCDQEELEALRQELAEQKEEIEAKKKELAELQEELEELEEK--IEELEEQKQELLAEIAEAEKIREECR----GWTRS  276 (325)
T ss_pred             hhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhc----CCCHH
Confidence            4567788899999999999999999999999998888888765  46777778888888887777665543    34788


Q ss_pred             HHHHHHHHHHHH
Q 027236          153 DRMAVEEMFLEK  164 (226)
Q Consensus       153 e~~~~~~~~~~~  164 (226)
                      |+..++..+...
T Consensus       277 Ev~~Lk~~~~~L  288 (325)
T PF08317_consen  277 EVKRLKAKVDAL  288 (325)
T ss_pred             HHHHHHHHHHHH
Confidence            888888877543

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=95.61  E-value=0.76  Score=38.90  Aligned_cols=58  Identities=19%  Similarity=0.439  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC-----ceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG-----KQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G-----K~kiY~~   68 (226)
                      .-++.|+.++.+ --|-|+.++.+.|   ||++++|..-|+.|+.+|+|......     .+++|-.
T Consensus        11 ~tr~~il~lL~~-~g~~sa~elA~~L---gis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~L   73 (218)
T COG2345          11 STRERILELLKK-SGPVSADELAEEL---GISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRL   73 (218)
T ss_pred             cHHHHHHHHHhc-cCCccHHHHHHHh---CCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeee
Confidence            356778888774 4699999999999   89999999999999999999998543     2466644

>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=95.59  E-value=0.065  Score=35.35  Aligned_cols=49  Identities=16%  Similarity=0.298  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHhcCCC-CcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236            8 TEAIVLNYVNEQNRP-LNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus         8 a~~~Il~y~~~~nrP-ys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      .+-.||.|+.....+ .++.+|...+   ++++++|..++..|++.|+|....
T Consensus         6 ~q~~vL~~l~~~~~~~~t~~~la~~l---~~~~~~vs~~v~~L~~~Glv~r~~   55 (62)
T PF12802_consen    6 SQFRVLMALARHPGEELTQSELAERL---GISKSTVSRIVKRLEKKGLVERER   55 (62)
T ss_dssp             HHHHHHHHHHHSTTSGEEHHHHHHHH---TS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEeC
Confidence            455788888877776 8999999988   799999999999999999998764

...

>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []

Probab=95.57  E-value=0.44  Score=36.60  Aligned_cols=87  Identities=22%  Similarity=0.309  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCH-HHHHHHHHHHHHHHHHHHHHHHHhhC--CCCCCCHHHHHHH
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTL-EQIREKEAQLVKEVKEMENKLAKLRG--GVTLVKPEDRMAV  157 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~-~el~~~i~~L~~e~~~l~~kL~~l~~--~~~~vs~ee~~~~  157 (226)
                      +..++.++..++.++..+...-..+..+|-.+...... ......+..|+.++.+++.++..+-.  |-   -.++++.+
T Consensus        25 lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~~~~~~~~~~L~~el~~l~~ry~t~LellGE---K~E~veEL  101 (120)
T PF12325_consen   25 LRRLEGELASLQEELARLEAERDELREEIVKLMEENEELRALKKEVEELEQELEELQQRYQTLLELLGE---KSEEVEEL  101 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc---hHHHHHHH
Confidence            33445555555555555555555566666555543222 45556788888888888888876643  32   25777777


Q ss_pred             HHHHHHHHHHHHH
Q 027236          158 EEMFLEKLSQWRK  170 (226)
Q Consensus       158 ~~~~~~~~~~w~k  170 (226)
                      ..++.+...+|+.
T Consensus       102 ~~Dv~DlK~myr~  114 (120)
T PF12325_consen  102 RADVQDLKEMYRE  114 (120)
T ss_pred             HHHHHHHHHHHHH
Confidence            7777666655544

The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].

>COG3682 Predicted transcriptional regulator [Transcription]

Probab=95.53  E-value=0.12  Score=39.85  Aligned_cols=62  Identities=16%  Similarity=0.269  Sum_probs=57.1

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ..|+..|++++=... |-++.||...+++ ...+.++|+-.|..|+.+|.|.++.=|+.-+|-+
T Consensus         5 s~aE~eVM~ilW~~~-~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdgr~~~y~p   67 (123)
T COG3682           5 SAAEWEVMEILWSRG-PATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDGRAFRYSP   67 (123)
T ss_pred             cHHHHHHHHHHHHcC-CccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhcCCeeeeec
Confidence            468889999999877 9999999999987 5799999999999999999999999999999977

>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=95.47  E-value=0.066  Score=35.72  Aligned_cols=40  Identities=33%  Similarity=0.532  Sum_probs=34.6

Q ss_pred             cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236           19 QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus        19 ~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .+.|.+..+|.+.+   |++.++|.++|..|.++|+|.....|
T Consensus        22 ~~~~~s~~ela~~~---g~s~~tv~r~l~~L~~~g~i~~~~~~   61 (67)
T cd00092          22 VQLPLTRQEIADYL---GLTRETVSRTLKELEEEGLISRRGRG   61 (67)
T ss_pred             ccCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEecCCC
Confidence            34689999999888   79999999999999999999876544

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=95.24  E-value=0.12  Score=37.74  Aligned_cols=50  Identities=18%  Similarity=0.173  Sum_probs=42.3

Q ss_pred             cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCC
Q 027236           19 QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQF   73 (226)
Q Consensus        19 ~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~   73 (226)
                      ...|.|.++|...+   |+++++|.++|..|..+|+|...  |....|.+|++.+
T Consensus        44 ~~~~is~~eLa~~~---g~sr~tVsr~L~~Le~~GlI~r~--~~~~~~~~n~~~~   93 (95)
T TIGR01610        44 KQDRVTATVIAELT---GLSRTHVSDAIKSLARRRIIFRQ--GMMGIVGVNTPLS   93 (95)
T ss_pred             cCCccCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeeee--cCCceeecCCCcc
Confidence            57899999998877   79999999999999999999743  5578888887653

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6

Probab=95.23  E-value=0.3  Score=36.32  Aligned_cols=66  Identities=30%  Similarity=0.494  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSN-LTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~-~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      -+++..++.+..++..++..++.+.+.+..++..+... ...+++.++...+..++.+++..+..+.
T Consensus        28 vd~i~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~~e   94 (108)
T PF02403_consen   28 VDEIIELDQERRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKELE   94 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57788899999999999999999999999999999987 5778899998888888888888887654

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....

>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea

Probab=95.20  E-value=0.063  Score=36.73  Aligned_cols=51  Identities=18%  Similarity=0.383  Sum_probs=44.0

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecC
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .||++|.+++.|.+...|.+.|...  .++..+|..-|..|-.+|++...-|+
T Consensus         2 ~IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~g~~   54 (66)
T PF08461_consen    2 FILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKVGRQ   54 (66)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccccCCc
Confidence            5899999999999999999999764  57789999999999999966654454

>PHA02943 hypothetical protein; Provisional

Probab=95.19  E-value=0.47  Score=37.88  Aligned_cols=63  Identities=19%  Similarity=0.239  Sum_probs=52.3

Q ss_pred             CCCCc----chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            1 MAPKS----DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         1 M~~kg----~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ||.+-    -+-...||+|+  ..-+-|..+|...|   |++-.+|+-+|--|.-+|.|..-.+|+..+|++
T Consensus         1 MPr~~sd~v~~R~~eILE~L--k~G~~TtseIAkaL---GlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l   67 (165)
T PHA02943          1 MPRGMSDTVHTRMIKTLRLL--ADGCKTTSRIANKL---GVSHSMARNALYQLAKEGMVLKVEIGRAAIWCL   67 (165)
T ss_pred             CCcchhHHHHHHHHHHHHHH--hcCCccHHHHHHHH---CCCHHHHHHHHHHHHHcCceEEEeecceEEEEE
Confidence            66542    35567799999  33345577888888   899999999999999999999999999999998

>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=95.14  E-value=0.075  Score=36.28  Aligned_cols=49  Identities=27%  Similarity=0.467  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhccccc-HHHHHHHHHHHHHcCCccee
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLK-KAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~-K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      +.-+-|.+|+.+...|=|+.+|.+.+   |+. .++|+..|+.|.+.|.|...
T Consensus        10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~---g~~S~~tv~~~L~~Le~kG~I~r~   59 (65)
T PF01726_consen   10 EVLEFIREYIEENGYPPTVREIAEAL---GLKSTSTVQRHLKALERKGYIRRD   59 (65)
T ss_dssp             HHHHHHHHHHHHHSS---HHHHHHHH---TSSSHHHHHHHHHHHHHTTSEEEG
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHh---CCCChHHHHHHHHHHHHCcCccCC
Confidence            34455666677788999999999988   665 99999999999999999753

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.

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=95.08  E-value=0.41  Score=39.24  Aligned_cols=59  Identities=17%  Similarity=0.175  Sum_probs=48.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee-----cCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE-----YGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~-----~GK~kiY~~   68 (226)
                      ++....|++.|.... +.+..++...|   ||+...|-++|..|.++|+|....     .|--.+||.
T Consensus        21 ~~~~~~Vl~~L~~~g-~~tdeeLA~~L---gi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~   84 (178)
T PRK06266         21 DEEGFEVLKALIKKG-EVTDEEIAEQT---GIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWK   84 (178)
T ss_pred             CccHhHHHHHHHHcC-CcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEE
Confidence            455677888888544 89999998888   899999999999999999998432     466678888

>COG1510 Predicted transcriptional regulators [Transcription]

Probab=95.05  E-value=0.11  Score=42.19  Aligned_cols=59  Identities=20%  Similarity=0.343  Sum_probs=48.4

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec-C-ceeEEEeecC
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY-G-KQKIYIARQD   71 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~-G-K~kiY~~~Q~   71 (226)
                      ..|+-.|+-+++|.++.+|..++   |++|+.|--+|..|.+-|+|.-... | .-.+|.+.++
T Consensus        29 G~iYgilyls~~Pmtl~Ei~E~l---g~Sks~vS~~lkkL~~~~lV~~~~~~G~Rk~~F~a~~d   89 (177)
T COG1510          29 GQIYGILYLSRKPLTLDEIAEAL---GMSKSNVSMGLKKLQDWNLVKKVFEKGDRKDYFEAEKD   89 (177)
T ss_pred             HHHhhhheecCCCccHHHHHHHH---CCCcchHHHHHHHHHhcchHHhhhccCcchhhhcccch
Confidence            46888888899999999999988   8999999999999999999876544 4 4456666443

>PRK11546 zraP zinc resistance protein; Provisional

Probab=95.04  E-value=0.32  Score=38.46  Aligned_cols=72  Identities=17%  Similarity=0.186  Sum_probs=57.9

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           70 QDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        70 Q~~~~~~~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +.....+|+|.-+.++.-..+...+...|++++-..+.||+.|...+..+  .+.|.+|.+||..|+.+|...+
T Consensus        38 ~~~~~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD--~~kI~aL~kEI~~Lr~kL~e~r  109 (143)
T PRK11546         38 QQNAAPLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPD--SSKINAVAKEMENLRQSLDELR  109 (143)
T ss_pred             ccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHHHHHHHHHHH
Confidence            33456678999999999999999999999999999999999998774443  3457777788888888775543

>PRK14127 cell division protein GpsB; Provisional

Probab=94.99  E-value=0.64  Score=35.07  Aligned_cols=83  Identities=17%  Similarity=0.283  Sum_probs=60.0

Q ss_pred             CCcHHHHHH-HHhc--ccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 027236           22 PLNSQNVAD-ALQK--YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQ   98 (226)
Q Consensus        22 Pys~~di~~-~l~~--~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~~~l~~~i~~l~~~l~~l   98 (226)
                      +++..||.. -++.  .|+....|-..||..++                            ++..+..++.+|++++..+
T Consensus         5 ~LTp~DI~~KeF~~~~RGYd~~EVD~FLd~V~~----------------------------dye~l~~e~~~Lk~e~~~l   56 (109)
T PRK14127          5 KLTPKDILEKEFKTSMRGYDQDEVDKFLDDVIK----------------------------DYEAFQKEIEELQQENARL   56 (109)
T ss_pred             CCCHHHHhhCccCCCCCCCCHHHHHHHHHHHHH----------------------------HHHHHHHHHHHHHHHHHHH
Confidence            466666633 2222  38888888888887764                            5566677888888888888


Q ss_pred             HHHHHHHHHHHHHHhc-----------cCCHHHHHHHHHHHHHHH
Q 027236           99 RKAISKLEGEIRTLQS-----------NLTLEQIREKEAQLVKEV  132 (226)
Q Consensus        99 ~~~~k~l~~el~~l~~-----------~~t~~el~~~i~~L~~e~  132 (226)
                      +.++.+++.++....+           ..|+-+++..|..|++++
T Consensus        57 ~~~l~e~~~~~~~~~~~~~~~~~~~~~~~tn~DiLKRls~LEk~V  101 (109)
T PRK14127         57 KAQVDELTKQVSVGASSSSVATTQPSSSATNYDILKRLSNLEKHV  101 (109)
T ss_pred             HHHHHHHHHhhccccccccccccCCCCCcchHHHHHHHHHHHHHH
Confidence            8888888887776542           257788889998888876

>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=94.88  E-value=0.15  Score=33.69  Aligned_cols=49  Identities=18%  Similarity=0.420  Sum_probs=41.0

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCc
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGK   62 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK   62 (226)
                      ...|++|+.+ +.+.++.++...+   +|+..++-.-|+.|.+.|+|. +.+|-
T Consensus         2 ~~~Il~~l~~-~~~~s~~ela~~~---~VS~~TiRRDl~~L~~~g~i~-r~~GG   50 (57)
T PF08220_consen    2 QQQILELLKE-KGKVSVKELAEEF---GVSEMTIRRDLNKLEKQGLIK-RTHGG   50 (57)
T ss_pred             HHHHHHHHHH-cCCEEHHHHHHHH---CcCHHHHHHHHHHHHHCCCEE-EEcCE
Confidence            4679999865 6789999999888   899999999999999999854 45553

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

>smart00787 Spc7 Spc7 kinetochore protein

Probab=94.87  E-value=0.46  Score=42.37  Aligned_cols=87  Identities=25%  Similarity=0.338  Sum_probs=63.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHH
Q 027236           73 FDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPE  152 (226)
Q Consensus        73 ~~~~~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~e  152 (226)
                      +..++++++..+..++..+..++.....++.+++.++..+....  ++..+++.++..+|.+++..++..+    ..|..
T Consensus       198 ~~~~d~~eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I--~~~~~~k~e~~~~I~~ae~~~~~~r----~~t~~  271 (312)
T smart00787      198 LEDCDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKI--EDLTNKKSELNTEIAEAEKKLEQCR----GFTFK  271 (312)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhcC----CCCHH
Confidence            45667888888888888888888888888888888887777543  4556667777777777777665544    34688


Q ss_pred             HHHHHHHHHHHHH
Q 027236          153 DRMAVEEMFLEKL  165 (226)
Q Consensus       153 e~~~~~~~~~~~~  165 (226)
                      |+..+...+..+.
T Consensus       272 Ei~~Lk~~~~~Le  284 (312)
T smart00787      272 EIEKLKEQLKLLQ  284 (312)
T ss_pred             HHHHHHHHHHHHH
Confidence            8888888765433

This domain is found in cell division proteins which are required for kinetochore-spindle association.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=94.84  E-value=1.1  Score=34.72  Aligned_cols=52  Identities=19%  Similarity=0.346  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ..+-.||.++...+.|-+..+|.+.+   ++++++|.++++.|+..|+|.-..-.
T Consensus        31 ~~q~~vL~~l~~~~~~~t~~eLa~~l---~~~~~tvt~~v~~Le~~GlV~r~~~~   82 (144)
T PRK03573         31 QTHWVTLHNIHQLPPEQSQIQLAKAI---GIEQPSLVRTLDQLEEKGLISRQTCA   82 (144)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHh---CCChhhHHHHHHHHHHCCCEeeecCC
Confidence            34557888888766678899999988   79999999999999999999988653

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=94.52  E-value=0.085  Score=34.11  Aligned_cols=37  Identities=19%  Similarity=0.390  Sum_probs=30.9

Q ss_pred             CCCC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           20 NRPL-NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        20 nrPy-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      +..+ |..++...+   +++.++|.++|..|.++|.|....
T Consensus        17 ~~~l~s~~~la~~~---~vs~~tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       17 GDKLPSERELAAQL---GVSRTTVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             CCcCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEec
Confidence            3345 888888877   799999999999999999987543

>PRK11569 transcriptional repressor IclR; Provisional

Probab=94.52  E-value=0.078  Score=46.09  Aligned_cols=49  Identities=14%  Similarity=0.268  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      +.--.||++|.+.++|.++.+|...+   |++|++|-..|.+|++.|.|...
T Consensus        28 ~ral~IL~~l~~~~~~~~lseia~~l---glpksTv~RlL~tL~~~G~l~~~   76 (274)
T PRK11569         28 TRGLKLLEWIAESNGSVALTELAQQA---GLPNSTTHRLLTTMQQQGFVRQV   76 (274)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEc
Confidence            34457899999999999999999988   89999999999999999999754

>PF13730 HTH_36: Helix-turn-helix domain

Probab=94.44  E-value=0.1  Score=33.72  Aligned_cols=32  Identities=22%  Similarity=0.452  Sum_probs=27.2

Q ss_pred             CCC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCc
Q 027236           21 RPL-NSQNVADALQKYNLKKAGIQKALDSLADNGKI   55 (226)
Q Consensus        21 rPy-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i   55 (226)
                      ..| |...|.+.+   |+++.+|+++++.|++.|.|
T Consensus        23 ~~~pS~~~la~~~---g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   23 GCFPSQETLAKDL---GVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             CCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCcCC
Confidence            344 777787777   89999999999999999986

>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=94.43  E-value=0.17  Score=35.90  Aligned_cols=56  Identities=23%  Similarity=0.402  Sum_probs=43.1

Q ss_pred             HHHHHHHhcCC--CCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeec
Q 027236           11 IVLNYVNEQNR--PLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQ   70 (226)
Q Consensus        11 ~Il~y~~~~nr--Pys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q   70 (226)
                      .++-|+-.++.  |.|..+|...+   +++...+.++|+.|+..|+|.+.. |..-=|+...
T Consensus        12 ~~l~~la~~~~~~~~s~~eiA~~~---~i~~~~l~kil~~L~~~Gli~s~~-G~~GGy~L~~   69 (83)
T PF02082_consen   12 RILLYLARHPDGKPVSSKEIAERL---GISPSYLRKILQKLKKAGLIESSR-GRGGGYRLAR   69 (83)
T ss_dssp             HHHHHHHCTTTSC-BEHHHHHHHH---TS-HHHHHHHHHHHHHTTSEEEET-STTSEEEESS
T ss_pred             HHHHHHHhCCCCCCCCHHHHHHHH---CcCHHHHHHHHHHHhhCCeeEecC-CCCCceeecC
Confidence            45666665555  89999999987   799999999999999999998776 7765566533

(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.

>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation

Probab=94.41  E-value=0.71  Score=32.19  Aligned_cols=59  Identities=20%  Similarity=0.250  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHH
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENK  138 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~k  138 (226)
                      -+.+..+..+|..+-+.+..|+.++..|..+-..+.  -.+.+|..+..+|+.+-....++
T Consensus         3 ~E~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~--~e~~~L~~en~~L~~e~~~~~~r   61 (72)
T PF06005_consen    3 LELLEQLEEKIQQAVETIALLQMENEELKEKNNELK--EENEELKEENEQLKQERNAWQER   61 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH--HHHHHHHHHHHHHHHHHHHHHHH
Confidence            455677777788777777777777777776655555  22333333444444333333333

It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.

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

Probab=94.34  E-value=0.088  Score=44.93  Aligned_cols=48  Identities=21%  Similarity=0.280  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      .--.||++|-...+|.++.||...+   |++|++|-..|.+|++.|.|...
T Consensus        10 ral~IL~~l~~~~~~~~l~eia~~l---glpksT~~RlL~tL~~~G~l~~~   57 (248)
T TIGR02431        10 RGLAVIEAFGAERPRLTLTDVAEAT---GLTRAAARRFLLTLVELGYVTSD   57 (248)
T ss_pred             HHHHHHHHHhcCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEeC
Confidence            3457899999999999999999988   89999999999999999999753

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.

>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins

Probab=94.00  E-value=0.84  Score=34.81  Aligned_cols=47  Identities=21%  Similarity=0.328  Sum_probs=33.5

Q ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHhhC-----CCCCCCHHHHHHHHHHH
Q 027236          115 NLTLEQIREKEAQLVKEVKEMENKLAKLRG-----GVTLVKPEDRMAVEEMF  161 (226)
Q Consensus       115 ~~t~~el~~~i~~L~~e~~~l~~kL~~l~~-----~~~~vs~ee~~~~~~~~  161 (226)
                      .+|.+||.+++..|+-||+.|..+|..--+     +...+||.+.+.+...|
T Consensus         2 ~~t~EeLaaeL~kLqmENk~LKkkl~~~~~p~~~p~~~~LTp~qKe~~I~s~   53 (118)
T PF05812_consen    2 DMTMEELAAELQKLQMENKALKKKLRQSVGPGPSPDDEVLTPAQKEAMITSA   53 (118)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHHTT---S-TT--B--HHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCccccChHHHHHHHHHH
Confidence            357799999999999999999999976542     33568888877666554

; PDB: 2OA5_B 2H3R_D.

>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A

Probab=93.97  E-value=0.71  Score=32.65  Aligned_cols=73  Identities=18%  Similarity=0.312  Sum_probs=51.7

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec--Cc--eeEEEeecCCCCCCCHHHHHHH
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY--GK--QKIYIARQDQFDIPNSEELNQM   84 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~--GK--~kiY~~~Q~~~~~~~~ee~~~l   84 (226)
                      +-.|+.|+.. ++.-+..+|.+.+   ++++..+-+.|..|.+.|.|..++-  |+  ..+|..        |+.-...+
T Consensus         2 Rl~Il~~L~~-~~~~~f~~L~~~l---~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~l--------T~~Gr~~~   69 (80)
T PF13601_consen    2 RLAILALLYA-NEEATFSELKEEL---GLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSL--------TDKGREAF   69 (80)
T ss_dssp             HHHHHHHHHH-HSEEEHHHHHHHT---T--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE---------HHHHHHH
T ss_pred             HHHHHHHHhh-cCCCCHHHHHHHh---CcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEE--------CHHHHHHH
Confidence            3468888886 7778888998888   8999999999999999999999865  22  344444        34556555


Q ss_pred             HHHHHHHHH
Q 027236           85 KEENAKLQE   93 (226)
Q Consensus        85 ~~~i~~l~~   93 (226)
                      ...+..|++
T Consensus        70 ~~~~~~L~~   78 (80)
T PF13601_consen   70 ERYVAALRE   78 (80)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555543

>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length

Probab=93.92  E-value=0.7  Score=37.01  Aligned_cols=58  Identities=14%  Similarity=0.302  Sum_probs=44.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHHHHHHHH
Q 027236           80 ELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSN-LTLEQIREKEAQLVKEVKEMEN  137 (226)
Q Consensus        80 e~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~-~t~~el~~~i~~L~~e~~~l~~  137 (226)
                      ++.....+...+.+++..++.++.....+|..|... ..+++|..+|..|+.++....+
T Consensus        14 ~i~~~K~~~~~~~~e~~~~k~ql~~~d~~i~~Lk~~~~d~eeLk~~i~~lq~~~~~~~~   72 (155)
T PF06810_consen   14 DIEAPKAKVDKVKEERDNLKTQLKEADKQIKDLKKSAKDNEELKKQIEELQAKNKTAKE   72 (155)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHH
Confidence            344455677777888888888888888888888874 7789999999999998884333

The function of this family is unknown.; GO: 0005198 structural molecule activity

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=93.89  E-value=0.16  Score=43.82  Aligned_cols=52  Identities=15%  Similarity=0.263  Sum_probs=45.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      +.--.||++|.....|.++.+|...+   |++|++|-..|+.|++.|.|....-+
T Consensus        11 ~ral~iL~~l~~~~~~ls~~eia~~l---gl~kstv~RlL~tL~~~g~v~~~~~~   62 (263)
T PRK09834         11 SRGLMVLRALNRLDGGATVGLLAELT---GLHRTTVRRLLETLQEEGYVRRSASD   62 (263)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEecCC
Confidence            44557899999888899999999988   89999999999999999999876543

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=93.87  E-value=0.58  Score=31.75  Aligned_cols=62  Identities=18%  Similarity=0.394  Sum_probs=44.3

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHH
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEEL   81 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~   81 (226)
                      .|+..+.  ++|++..++...+   +|+.++|.+.+..|.+.|...... |+  -|+. +...+.++++.+
T Consensus         4 ~il~~L~--~~~~~~~eLa~~l---~vS~~tv~~~l~~L~~~g~~i~~~-~~--g~~l-~~~~~ll~~~~i   65 (69)
T TIGR00122         4 RLLALLA--DNPFSGEKLGEAL---GMSRTAVNKHIQTLREWGVDVLTV-GK--GYRL-PPPIPLLNAKQI   65 (69)
T ss_pred             HHHHHHH--cCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCeEEec-CC--ceEe-cCccccCCHHHH
Confidence            4677766  5578888888888   899999999999999999977666 43  4443 222344444433

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.

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=93.61  E-value=1.8  Score=37.10  Aligned_cols=88  Identities=19%  Similarity=0.352  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCH-----HHHHHHHHHHHHHHHHHHHHHHHhhCC-CCCCCHHHH
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTL-----EQIREKEAQLVKEVKEMENKLAKLRGG-VTLVKPEDR  154 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~-----~el~~~i~~L~~e~~~l~~kL~~l~~~-~~~vs~ee~  154 (226)
                      +..+|.++..+..........++.+.+++..++....+     +++..++.+++.++.++++++...+.. +..-+..+.
T Consensus        12 iq~lD~e~~rl~~~~~~~~~~l~k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~~~~e~   91 (239)
T COG1579          12 IQKLDLEKDRLEPRIKEIRKALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDEREL   91 (239)
T ss_pred             HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHH
Confidence            34455555555555555555555555555555543322     555666666666666666666555431 122234444


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 027236          155 MAVEEMFLEKLSQWRKRK  172 (226)
Q Consensus       155 ~~~~~~~~~~~~~w~kRk  172 (226)
                      ..+..+.    ..|.+|.
T Consensus        92 ~aL~~E~----~~ak~r~  105 (239)
T COG1579          92 RALNIEI----QIAKERI  105 (239)
T ss_pred             HHHHHHH----HHHHHHH
Confidence            4444443    3444544

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=93.40  E-value=0.2  Score=43.54  Aligned_cols=57  Identities=11%  Similarity=0.146  Sum_probs=47.8

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +.--.||++|-..++|.++.+|...+   |++|++|-..|.+|++.|.|....  ...-|..
T Consensus        25 ~r~l~IL~~~~~~~~~~tl~eIa~~l---glpkStv~RlL~tL~~~G~l~~~~--~~~~Y~l   81 (271)
T PRK10163         25 ERGIAILQYLEKSGGSSSVSDISLNL---DLPLSTTFRLLKVLQAADFVYQDS--QLGWWHI   81 (271)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEcC--CCCeEEe
Confidence            45567999999999999999999988   899999999999999999996653  2344655

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=93.31  E-value=2  Score=30.31  Aligned_cols=50  Identities=26%  Similarity=0.384  Sum_probs=42.2

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|.+..+|...+   +++.++|.+.|..|++.|.|.....
T Consensus        10 ~~~~~il~~l~~-~~~~~~~~la~~~---~~s~~~i~~~l~~L~~~g~v~~~~~   59 (101)
T smart00347       10 PTQFLVLRILYE-EGPLSVSELAKRL---GVSPSTVTRVLDRLEKKGLIRRLPS   59 (101)
T ss_pred             HHHHHHHHHHHH-cCCcCHHHHHHHH---CCCchhHHHHHHHHHHCCCeEecCC
Confidence            456678888886 4589999998877   7899999999999999999987754

>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus

Probab=93.20  E-value=0.71  Score=32.15  Aligned_cols=56  Identities=20%  Similarity=0.301  Sum_probs=44.4

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee--ecC--ceeEEEee
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK--EYG--KQKIYIAR   69 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K--~~G--K~kiY~~~   69 (226)
                      .+.|+-++-..  -.++.++...   .||++..+.-.|-.|+++|+|.-+  .||  |-.+||..
T Consensus         7 ~~~IL~~ls~~--c~TLeeL~ek---Tgi~k~~LlV~LsrL~k~GiI~Rkw~~~~gkk~R~YclK   66 (72)
T PF05584_consen    7 TQKILIILSKR--CCTLEELEEK---TGISKNTLLVYLSRLAKRGIIERKWRKFGGKKYREYCLK   66 (72)
T ss_pred             HHHHHHHHHhc--cCCHHHHHHH---HCCCHHHHHHHHHHHHHCCCeeeeeEEecCeEEEEEEec
Confidence            45677776644  7776666554   489999999999999999999999  776  66888873

>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=93.18  E-value=0.22  Score=36.61  Aligned_cols=47  Identities=26%  Similarity=0.514  Sum_probs=38.6

Q ss_pred             chHHHHHHHHHHh---cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCc
Q 027236            6 DNTEAIVLNYVNE---QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKI   55 (226)
Q Consensus         6 ~ea~~~Il~y~~~---~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i   55 (226)
                      .....+||+|++.   ...-.++.+|..-|   +++...|.++|+.|+++|.|
T Consensus        46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l---~~~~~~v~~al~~L~~eG~I   95 (102)
T PF08784_consen   46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQL---GMSENEVRKALDFLSNEGHI   95 (102)
T ss_dssp             -HHHHHHHHHHHC----TTTEEHHHHHHHS---TS-HHHHHHHHHHHHHTTSE
T ss_pred             CHHHHHHHHHHHhcCCCCCcccHHHHHHHh---CcCHHHHHHHHHHHHhCCeE
Confidence            4568999999999   44557888888877   79999999999999999987

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.

>PF05557 MAD: Mitotic checkpoint protein; InterPro: IPR008672 This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins

Probab=93.17  E-value=2.7  Score=41.65  Aligned_cols=68  Identities=29%  Similarity=0.425  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--c--------------cCCH---HHHHHHHHHHHHHHHHHHHH
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQ--S--------------NLTL---EQIREKEAQLVKEVKEMENK  138 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~--~--------------~~t~---~el~~~i~~L~~e~~~l~~k  138 (226)
                      .+.+..+..++.+|+.++..|..++..|+.+|..+.  +              .|+.   .-....+..|+.|+..|..+
T Consensus       502 ~e~~~~L~~~~~~Le~e~~~L~~~~~~Le~~l~~~~L~g~~~~~~trVL~lr~NP~~~~~~~k~~~l~~L~~En~~L~~~  581 (722)
T PF05557_consen  502 SEELNELQKEIEELERENERLRQELEELESELEKLTLQGEFNPSKTRVLHLRDNPTSKAEQIKKSTLEALQAENEDLLAR  581 (722)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCT--BTTTEEEEEESS-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccCCCCceeeeeCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            466788899999999999999999999999998732  1              1222   12346789999999999999


Q ss_pred             HHHhhCC
Q 027236          139 LAKLRGG  145 (226)
Q Consensus       139 L~~l~~~  145 (226)
                      |..+..+
T Consensus       582 l~~le~~  588 (722)
T PF05557_consen  582 LRSLEEG  588 (722)
T ss_dssp             HHHHTTT
T ss_pred             HHhcccC
Confidence            9888754

The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in Saccharomyces cerevisiae and higher eukaryotes. In Saccharomyces cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated [].; PDB: 1GO4_F 4DZO_A.

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

Probab=93.09  E-value=0.3  Score=33.42  Aligned_cols=50  Identities=22%  Similarity=0.392  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      +-++.|++||.... |-++..+..+++ .+++|..|-.+|=+|..+|+|.+.
T Consensus         4 ~~ee~Il~~L~~~g-~~~a~~ia~~~~-L~~~kk~VN~~LY~L~k~g~v~k~   53 (66)
T PF02295_consen    4 DLEEKILDFLKELG-GSTATAIAKALG-LSVPKKEVNRVLYRLEKQGKVCKE   53 (66)
T ss_dssp             HHHHHHHHHHHHHT-SSEEEHHHHHHH-HTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             hHHHHHHHHHHhcC-CccHHHHHHHhC-cchhHHHHHHHHHHHHHCCCEeeC
Confidence            56789999999999 888888888774 356799999999999999999753

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 ....

>PRK11637 AmiB activator; Provisional

Probab=92.90  E-value=5.9  Score=36.64  Aligned_cols=63  Identities=11%  Similarity=0.306  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      .+++..+..++.+++.++..++.+++.+..++..+...+  ..+...|..++.++..++.++..+
T Consensus        46 ~~~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi--~~~~~~i~~~~~~i~~~~~ei~~l  108 (428)
T PRK11637         46 RDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAI--SQASRKLRETQNTLNQLNKQIDEL  108 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666666666666666666666666555432  223444444444444444444443

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=92.81  E-value=0.27  Score=37.67  Aligned_cols=56  Identities=21%  Similarity=0.374  Sum_probs=43.8

Q ss_pred             HHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            9 EAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      --.|+.||-.. +.|.|+.+|.+.+   +++.+.|.++|..|+..|+|... -|..--|..
T Consensus        11 al~~l~~la~~~~~~~s~~eia~~l---~is~~~v~~~l~~L~~~Gli~~~-~g~~ggy~l   67 (130)
T TIGR02944        11 ATLVLTTLAQNDSQPYSAAEIAEQT---GLNAPTVSKILKQLSLAGIVTSK-RGVEGGYTL   67 (130)
T ss_pred             HHHHHHHHHhCCCCCccHHHHHHHH---CcCHHHHHHHHHHHHHCCcEEec-CCCCCChhh
Confidence            34567777654 5689999998888   89999999999999999999764 344445655

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.

>COG3937 Uncharacterized conserved protein [Function unknown]

Probab=92.71  E-value=2.7  Score=31.45  Aligned_cols=81  Identities=22%  Similarity=0.365  Sum_probs=49.5

Q ss_pred             cccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 027236           36 NLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEE-LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQS  114 (226)
Q Consensus        36 ~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee-~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~  114 (226)
                      ..+...+++..|.||.+|.+.                     .++ ..-.+.-+.+.+.+-.++...   ....+..+.+
T Consensus        20 a~~~ek~~klvDelVkkGeln---------------------~eEak~~vddl~~q~k~~~~e~e~K---~~r~i~~ml~   75 (108)
T COG3937          20 AETAEKVQKLVDELVKKGELN---------------------AEEAKRFVDDLLRQAKEAQGELEEK---IPRKIEEMLS   75 (108)
T ss_pred             HHHHHHHHHHHHHHHHcCCCC---------------------HHHHHHHHHHHHHHHHHHhhhHHHh---hhHHHHHHHh
Confidence            356778999999999999874                     233 333344444444433333322   2233333333


Q ss_pred             c------CCHHHHHHHHHHHHHHHHHHHHHHH
Q 027236          115 N------LTLEQIREKEAQLVKEVKEMENKLA  140 (226)
Q Consensus       115 ~------~t~~el~~~i~~L~~e~~~l~~kL~  140 (226)
                      .      -+..++...|..|++++..|++++.
T Consensus        76 ~~~~~r~~~~~~l~~rvd~Lerqv~~Lenk~k  107 (108)
T COG3937          76 DLEVARQSEMDELTERVDALERQVADLENKLK  107 (108)
T ss_pred             hccccccchHHHHHHHHHHHHHHHHHHHHHhc
Confidence            2      2237888889999999999988763

>PRK10884 SH3 domain-containing protein; Provisional

Probab=92.67  E-value=4.4  Score=33.98  Aligned_cols=58  Identities=14%  Similarity=0.207  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +..++.+++++++++.++..+.....+++..-.     .+....+.+|+.+++.|.++|..++
T Consensus        95 lp~le~el~~l~~~l~~~~~~~~~~~~~l~~~~-----~~~~~~~~~L~~~n~~L~~~l~~~~  152 (206)
T PRK10884         95 VPDLENQVKTLTDKLNNIDNTWNQRTAEMQQKV-----AQSDSVINGLKEENQKLKNQLIVAQ  152 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566677777777777666666554444443322     2345556667777777777776655

>PRK11637 AmiB activator; Provisional

Probab=92.59  E-value=3.4  Score=38.25  Aligned_cols=59  Identities=17%  Similarity=0.348  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           83 QMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        83 ~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      ....++.+++.++..++.++..++.++..+...  ...+..+|..+..++..++.+|..+.
T Consensus        44 ~~~~~l~~l~~qi~~~~~~i~~~~~~~~~~~~~--l~~l~~qi~~~~~~i~~~~~~i~~~~  102 (428)
T PRK11637         44 DNRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQ--LKKQEEAISQASRKLRETQNTLNQLN  102 (428)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666666666666666666655544  23455566666666666666665544

>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=92.49  E-value=2.1  Score=35.35  Aligned_cols=22  Identities=32%  Similarity=0.424  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 027236          151 PEDRMAVEEMFLEKLSQWRKRK  172 (226)
Q Consensus       151 ~ee~~~~~~~~~~~~~~w~kRk  172 (226)
                      .+...+++.+......+|-+++
T Consensus       164 e~k~~~l~~En~~Lv~Rwm~~k  185 (194)
T PF08614_consen  164 EEKLRKLEEENRELVERWMQRK  185 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3456678888899999999986

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=92.47  E-value=0.38  Score=38.46  Aligned_cols=57  Identities=12%  Similarity=0.339  Sum_probs=47.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEE
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIY   66 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY   66 (226)
                      ++=-..|+.+.. .+-|-..+||...|   +|+.++|.+.|..|...|+|....||....+
T Consensus         9 edYL~~Iy~l~~-~~~~~~~~diA~~L---~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT   65 (154)
T COG1321           9 EDYLETIYELLE-EKGFARTKDIAERL---KVSPPSVTEMLKRLERLGLVEYEPYGGVTLT   65 (154)
T ss_pred             HHHHHHHHHHHh-ccCcccHHHHHHHh---CCCcHHHHHHHHHHHHCCCeEEecCCCeEEC
Confidence            455566777777 66677788998888   7999999999999999999999999987665

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=92.46  E-value=0.42  Score=29.45  Aligned_cols=34  Identities=32%  Similarity=0.565  Sum_probs=30.1

Q ss_pred             CCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236           22 PLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus        22 Pys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      |.+..+|.+.+   +++.++|.++|..|.+.|.|...
T Consensus         8 ~~s~~~la~~l---~~s~~tv~~~l~~L~~~g~l~~~   41 (48)
T smart00419        8 PLTRQEIAELL---GLTRETVSRTLKRLEKEGLISRE   41 (48)
T ss_pred             ccCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEe
Confidence            67888888877   79999999999999999999754

>COG1777 Predicted transcriptional regulators [Transcription]

Probab=92.28  E-value=3.4  Score=34.73  Aligned_cols=48  Identities=19%  Similarity=0.344  Sum_probs=40.2

Q ss_pred             cchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            5 SDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         5 g~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      |.+-+-.|+..+.  ++||=+.++..-+   ||+-++|.+.|+-|...|+|.+
T Consensus        13 GNetRR~Il~lLt--~~p~yvsEiS~~l---gvsqkAVl~HL~~LE~AGlveS   60 (217)
T COG1777          13 GNETRRRILQLLT--RRPCYVSEISREL---GVSQKAVLKHLRILERAGLVES   60 (217)
T ss_pred             cCcHHHHHHHHHh--cCchHHHHHHhhc---CcCHHHHHHHHHHHHHcCCchh
Confidence            4566778888876  8897766666555   8999999999999999999999

>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=92.18  E-value=0.55  Score=30.55  Aligned_cols=47  Identities=15%  Similarity=0.346  Sum_probs=38.4

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      +-.||.++. ++.|-+..+|...+   +++++++..+++.|++.|+|....
T Consensus         5 q~~iL~~l~-~~~~~~~~~la~~~---~~~~~~~t~~i~~L~~~g~I~r~~   51 (59)
T PF01047_consen    5 QFRILRILY-ENGGITQSELAEKL---GISRSTVTRIIKRLEKKGLIERER   51 (59)
T ss_dssp             HHHHHHHHH-HHSSEEHHHHHHHH---TS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHH-HcCCCCHHHHHHHH---CCChhHHHHHHHHHHHCCCEEecc
Confidence            346777776 46679999998888   799999999999999999998653

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 ....

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=92.17  E-value=1.6  Score=32.72  Aligned_cols=57  Identities=11%  Similarity=0.166  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC---ceeEEEe
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG---KQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G---K~kiY~~   68 (226)
                      .+-.||.++.. +.|-+..+|.+.+   ++++++|...|+.|..+|+|......   ..++|..
T Consensus        29 ~q~~iL~~l~~-~~~~t~~ela~~~---~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~L   88 (118)
T TIGR02337        29 QQWRILRILAE-QGSMEFTQLANQA---CILRPSLTGILARLERDGLVTRLKASNDQRRVYISL   88 (118)
T ss_pred             HHHHHHHHHHH-cCCcCHHHHHHHh---CCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEE
Confidence            34468888765 6688999999888   79999999999999999999988764   4445544

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.

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=92.11  E-value=0.41  Score=36.59  Aligned_cols=54  Identities=17%  Similarity=0.238  Sum_probs=41.4

Q ss_pred             HHHHHHHhc--CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNEQ--NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~~--nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .++-|+...  ..|.|..+|...+   +++.+.|.++|+.|+..|+|.... |..--|..
T Consensus        12 ~~l~~la~~~~~~~~s~~eia~~~---~i~~~~v~~il~~L~~~gli~~~~-g~~ggy~l   67 (132)
T TIGR00738        12 RALLDLALNPDEGPVSVKEIAERQ---GISRSYLEKILRTLRRAGLVESVR-GPGGGYRL   67 (132)
T ss_pred             HHHHHHHhCCCCCcCcHHHHHHHH---CcCHHHHHHHHHHHHHCCcEEecc-CCCCCccC
Confidence            455555543  2399999998888   799999999999999999998753 54435655

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.

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=92.04  E-value=0.59  Score=36.46  Aligned_cols=52  Identities=12%  Similarity=0.305  Sum_probs=40.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ++--..|+.++. ++.|-++.+|...|   +|++++|..+|+.|.+.|+|....++
T Consensus         7 edyL~~I~~l~~-~~~~~~~~ela~~l---~vs~~svs~~l~~L~~~Gli~~~~~~   58 (142)
T PRK03902          7 EDYIEQIYLLIE-EKGYARVSDIAEAL---SVHPSSVTKMVQKLDKDEYLIYEKYR   58 (142)
T ss_pred             HHHHHHHHHHHh-cCCCcCHHHHHHHh---CCChhHHHHHHHHHHHCCCEEEecCc
Confidence            455566666665 45566888898888   79999999999999999999866543

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

Probab=91.90  E-value=0.99  Score=29.52  Aligned_cols=49  Identities=12%  Similarity=0.242  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHHhc----CCC-CcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            7 NTEAIVLNYVNEQ----NRP-LNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         7 ea~~~Il~y~~~~----nrP-ys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      +..+.|..++...    +.+ .+..+|.+.+   +++.++|.++|..|.+.|.|...
T Consensus         5 ~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~---~is~~~v~~~l~~L~~~G~i~~~   58 (66)
T cd07377           5 QIADQLREAILSGELKPGDRLPSERELAEEL---GVSRTTVREALRELEAEGLVERR   58 (66)
T ss_pred             HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEec
Confidence            3445555554432    222 3488887777   79999999999999999997644

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

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

Probab=91.86  E-value=0.35  Score=33.06  Aligned_cols=46  Identities=13%  Similarity=0.298  Sum_probs=36.2

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .|.+|+. .+..+|+.+|...+   +++..+|...|+.|+..|.|..-..
T Consensus         4 ~i~~~l~-~~~~~S~~eLa~~~---~~s~~~ve~mL~~l~~kG~I~~~~~   49 (69)
T PF09012_consen    4 EIRDYLR-ERGRVSLAELAREF---GISPEAVEAMLEQLIRKGYIRKVDM   49 (69)
T ss_dssp             HHHHHHH-HS-SEEHHHHHHHT---T--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred             HHHHHHH-HcCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCcEEEecC
Confidence            5778887 46678998998877   7999999999999999999986544

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

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=91.75  E-value=2.2  Score=29.44  Aligned_cols=59  Identities=22%  Similarity=0.271  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCH-----HHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           84 MKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTL-----EQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        84 l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~-----~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      |+..+..|+..+..+...+......++.|...-+.     .++-..+..|+.++..+...|+.+
T Consensus         3 Lea~~~~Lr~rLd~~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~   66 (69)
T PF14197_consen    3 LEAEIATLRNRLDSLTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEEL   66 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45566666666666666666666666666653222     334445555666666666655544

>PRK05431 seryl-tRNA synthetase; Provisional

Probab=91.52  E-value=1.6  Score=40.59  Aligned_cols=66  Identities=29%  Similarity=0.385  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL-TLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~-t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      -+++..++.+..+++.++..|+.+.+.+..++..+.... ..+++.++..++.+++.++++++..+.
T Consensus        27 vd~i~~ld~~~r~l~~~~~~lr~~rn~~sk~i~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~   93 (425)
T PRK05431         27 VDELLELDEERRELQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKALEAELDELE   93 (425)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467778899999999999999999999999998865554 445677777777777777766665544

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=91.44  E-value=0.5  Score=40.51  Aligned_cols=56  Identities=14%  Similarity=0.262  Sum_probs=45.1

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +.--.||++|-.. +|.++.+|...+   |++|++|-..|.+|++.|.|...  +...-|..
T Consensus        14 ~r~l~IL~~l~~~-~~l~l~eia~~l---gl~kstv~Rll~tL~~~G~l~~~--~~~~~Y~l   69 (257)
T PRK15090         14 LKVFGILQALGEE-REIGITELSQRV---MMSKSTVYRFLQTMKTLGYVAQE--GESEKYSL   69 (257)
T ss_pred             HHHHHHHHHhhcC-CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEc--CCCCcEEe
Confidence            4455789999764 699999999988   89999999999999999999875  22333555

>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=91.40  E-value=3.4  Score=32.56  Aligned_cols=90  Identities=23%  Similarity=0.337  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC-------C-HHHHHHHHHHHHHHHHHHHHHHHHhhCC--CCCCCH
Q 027236           82 NQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL-------T-LEQIREKEAQLVKEVKEMENKLAKLRGG--VTLVKP  151 (226)
Q Consensus        82 ~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~-------t-~~el~~~i~~L~~e~~~l~~kL~~l~~~--~~~vs~  151 (226)
                      ...+.+|..|+..+..+..++..+...|..+...+       + ++.|...|..|+.++...+.+|......  ..-+.+
T Consensus        31 ~~~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~~lee~~~~~~~~E~l~rriq~LEeele~ae~~L~e~~ekl~e~d~~a  110 (143)
T PF12718_consen   31 EQKEQEITSLQKKNQQLEEELDKLEEQLKEAKEKLEESEKRKSNAEQLNRRIQLLEEELEEAEKKLKETTEKLREADVKA  110 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33444555555555555555555555555444432       2 2445556666666666666655443221  111234


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 027236          152 EDRMAVEEMFLEKLSQWRKR  171 (226)
Q Consensus       152 ee~~~~~~~~~~~~~~w~kR  171 (226)
                      +.+.+-...+..-...|=.|
T Consensus       111 e~~eRkv~~le~~~~~~E~k  130 (143)
T PF12718_consen  111 EHFERKVKALEQERDQWEEK  130 (143)
T ss_pred             HHHHHHHHHHHhhHHHHHHH
Confidence            44444444555555566665

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].

>PRK10870 transcriptional repressor MprA; Provisional

Probab=91.37  E-value=6.7  Score=31.77  Aligned_cols=53  Identities=21%  Similarity=0.271  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCc
Q 027236            7 NTEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGK   62 (226)
Q Consensus         7 ea~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK   62 (226)
                      ..+-.||.++... +.|-+..+|...+   ++++++|..+++.|+..|+|....-+.
T Consensus        55 ~~q~~iL~~L~~~~~~~it~~eLa~~l---~l~~~tvsr~v~rLe~kGlV~R~~~~~  108 (176)
T PRK10870         55 ETLFMALITLESQENHSIQPSELSCAL---GSSRTNATRIADELEKRGWIERRESDN  108 (176)
T ss_pred             HHHHHHHHHHhcCCCCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence            3455677777754 5678889999988   799999999999999999999887754

>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length

Probab=91.12  E-value=1.4  Score=32.00  Aligned_cols=63  Identities=24%  Similarity=0.306  Sum_probs=51.9

Q ss_pred             hHHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHH----------HHHHHcCCc-ceeecCceeEEEeecCC
Q 027236            7 NTEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKAL----------DSLADNGKI-SFKEYGKQKIYIARQDQ   72 (226)
Q Consensus         7 ea~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L----------~~Lv~~g~i-~~K~~GK~kiY~~~Q~~   72 (226)
                      ..+..||.||.+. -+|+.+.+|....   ++.-+.|.-||          ++|+.-|+| .+...+-.++|-..+..
T Consensus         9 ~~R~~vl~~L~~~yp~~~~~~eIar~v---~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~lT~~G   83 (90)
T PF07381_consen    9 KVRKKVLEYLCSIYPEPAYPSEIARSV---GSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRLTEKG   83 (90)
T ss_pred             HHHHHHHHHHHHcCCCcCCHHHHHHHH---CCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEeChhh
Confidence            4678999999999 8899999998877   67888888888          579999999 66676888888774443

The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=90.92  E-value=2.1  Score=31.77  Aligned_cols=57  Identities=21%  Similarity=0.420  Sum_probs=44.9

Q ss_pred             HHHHHHHHH--hc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCce--eEEEe
Q 027236            9 EAIVLNYVN--EQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ--KIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~--~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~--kiY~~   68 (226)
                      +-.||.++.  .. ..|-+.++|...+   ++.+++|.++++.|++.|.|.-..-..-  .+|+.
T Consensus        27 q~~vL~~l~~~~~~~~~~t~~eL~~~l---~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~   88 (109)
T TIGR01889        27 ELLILYYLGKLENNEGKLTLKEIIKEI---LIKQSALVKIIKKLSKKGYLSKERSEDDERKVIIS   88 (109)
T ss_pred             HHHHHHHHHhhhccCCcCcHHHHHHHH---CCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEE
Confidence            345677766  33 3679999999988   7999999999999999999998777643  45544

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.

>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT)

Probab=90.90  E-value=0.59  Score=32.37  Aligned_cols=55  Identities=15%  Similarity=0.320  Sum_probs=45.8

Q ss_pred             HHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           14 NYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        14 ~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +|+.....|.++.++...+...||+-++|--+|--|+.+|.|....-|...+|-.
T Consensus        12 dy~~~~g~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~L   66 (70)
T PF07848_consen   12 DYLRPRGGWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLESERRGRRSYYRL   66 (70)
T ss_dssp             HHCCTTTS-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE
T ss_pred             HHhccCCCceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceeeeecCccceEee
Confidence            3445566777899999999888999999999999999999999999999998865

PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=90.86  E-value=3.9  Score=32.76  Aligned_cols=55  Identities=24%  Similarity=0.293  Sum_probs=42.2

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce---e--ecCceeEEEe
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF---K--EYGKQKIYIA   68 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~---K--~~GK~kiY~~   68 (226)
                      -.|++.+.. ..+.+--+|...|   |++...|-++|..|.++|+|..   +  .-|-..+||.
T Consensus        17 v~Vl~aL~~-~~~~tdEeLa~~L---gi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~   76 (158)
T TIGR00373        17 GLVLFSLGI-KGEFTDEEISLEL---GIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWR   76 (158)
T ss_pred             HHHHHHHhc-cCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEE
Confidence            445665553 3378988888877   8999999999999999999932   2  2366788887

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.

>PLN02678 seryl-tRNA synthetase

Probab=90.81  E-value=2.1  Score=40.18  Aligned_cols=65  Identities=23%  Similarity=0.334  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL-TLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~-t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +++..++.+..+++.++..++.+.+.+..++..+.... ..+++.++..+|.+++..++.++..+.
T Consensus        33 d~il~ld~~~r~l~~~~e~lr~erN~~sk~I~~~k~~~~~~~~l~~~~~~Lk~ei~~le~~~~~~~   98 (448)
T PLN02678         33 DEVIALDKEWRQRQFELDSLRKEFNKLNKEVAKLKIAKEDATELIAETKELKKEITEKEAEVQEAK   98 (448)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66778889999999999999999999999998755443 346676666677666666666665543

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=90.79  E-value=3.8  Score=39.57  Aligned_cols=16  Identities=13%  Similarity=0.268  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHHHHHHH
Q 027236          124 KEAQLVKEVKEMENKL  139 (226)
Q Consensus       124 ~i~~L~~e~~~l~~kL  139 (226)
                      ++.+++.+|..|+.+|
T Consensus       475 ei~~~~~~I~~L~~~L  490 (652)
T COG2433         475 EIRARDRRIERLEKEL  490 (652)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3444444555554444

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

Probab=90.67  E-value=0.56  Score=27.44  Aligned_cols=31  Identities=32%  Similarity=0.607  Sum_probs=25.9

Q ss_pred             CCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCc
Q 027236           22 PLNSQNVADALQKYNLKKAGIQKALDSLADNGKI   55 (226)
Q Consensus        22 Pys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i   55 (226)
                      |.+-+||.+.+   |.+..+|-++|..|..+|+|
T Consensus         2 ~mtr~diA~~l---G~t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    2 PMTRQDIADYL---GLTRETVSRILKKLERQGLI   32 (32)
T ss_dssp             E--HHHHHHHH---TS-HHHHHHHHHHHHHTTSE
T ss_pred             CcCHHHHHHHh---CCcHHHHHHHHHHHHHcCCC
Confidence            67889999988   89999999999999999986

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 ....

>PF14282 FlxA: FlxA-like protein

Probab=90.56  E-value=2.2  Score=31.90  Aligned_cols=52  Identities=19%  Similarity=0.413  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--cCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRTLQS--NLTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~l~~--~~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +..|..|+.++..|..+       |..|..  .++.++....+..|+.+|..|+..|..+.
T Consensus        18 ~~~I~~L~~Qi~~Lq~q-------l~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq   71 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQ-------LQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQ   71 (106)
T ss_pred             HHHHHHHHHHHHHHHHH-------HHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555555544444444       444444  36777788888888888888888887765

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=90.39  E-value=4  Score=27.85  Aligned_cols=62  Identities=24%  Similarity=0.289  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      +..+..+++.|-..+..|+.+...|..++..+.+.  +..|..+.+.-...+..+-++|..+..
T Consensus         2 L~~Le~kle~Li~~~~~L~~EN~~Lr~q~~~~~~E--R~~L~ekne~Ar~rvEamI~RLk~leq   63 (65)
T TIGR02449         2 LQALAAQVEHLLEYLERLKSENRLLRAQEKTWREE--RAQLLEKNEQARQKVEAMITRLKALEQ   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHhhhhhcc
Confidence            45677888888888888888888888888877753  567778888888888888888877653

Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.

>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=90.33  E-value=0.59  Score=31.98  Aligned_cols=33  Identities=30%  Similarity=0.581  Sum_probs=30.3

Q ss_pred             CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236           21 RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus        21 rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      -|+|-++|.+.+   |++..+|.++|..|.++|.|.
T Consensus        27 ~~lt~~~iA~~~---g~sr~tv~r~l~~l~~~g~I~   59 (76)
T PF13545_consen   27 LPLTQEEIADML---GVSRETVSRILKRLKDEGIIE   59 (76)
T ss_dssp             EESSHHHHHHHH---TSCHHHHHHHHHHHHHTTSEE
T ss_pred             ecCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE
Confidence            478999998888   899999999999999999888

...

>TIGR00414 serS seryl-tRNA synthetase

Probab=90.23  E-value=2.5  Score=39.14  Aligned_cols=65  Identities=25%  Similarity=0.397  Sum_probs=49.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC--HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLT--LEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t--~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +++..++.+..++..++..++.+...+..++..+.....  .+++.++..++.+++.+++.++..+.
T Consensus        30 d~i~~ld~~~r~~~~~~~~l~~erN~~sk~i~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~   96 (418)
T TIGR00414        30 EKLIALDDERKKLLSEIEELQAKRNELSKQIGKAKGQKKDKIEEIKKELKELKEELTELSAALKALE   96 (418)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            667788899999999999999999999999988655433  45777777777777777766665543

This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=90.21  E-value=1.4  Score=36.52  Aligned_cols=58  Identities=24%  Similarity=0.287  Sum_probs=48.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ...+-.||.|+... .|-+..+|.+.+   ++++++|.+.|+.|.+.|+|.... +..+.|..
T Consensus       142 s~~~~~IL~~l~~~-g~~s~~eia~~l---~is~stv~r~L~~Le~~GlI~r~~-~r~~~~~l  199 (203)
T TIGR01884       142 SREELKVLEVLKAE-GEKSVKNIAKKL---GKSLSTISRHLRELEKKGLVEQKG-RKGKRYSL  199 (203)
T ss_pred             CHHHHHHHHHHHHc-CCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEc-CCccEEEe
Confidence            56677999999854 567999999888   799999999999999999999886 46666665

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.

>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures

Probab=90.14  E-value=3.5  Score=28.75  Aligned_cols=61  Identities=28%  Similarity=0.432  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +..-|..|..|+++-..|....-.+...+..|+..  +.++...+..+...+......+..++
T Consensus         7 l~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~--~~e~e~~~~~l~~~~~~~e~~~~~l~   67 (74)
T PF12329_consen    7 LAEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAK--IKELEKQIKELKKKLEELEKELESLE   67 (74)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55667888888888888877777777777777754  23444555555555555555554443

The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.

>PRK00215 LexA repressor; Validated

Probab=90.13  E-value=1.2  Score=36.85  Aligned_cols=57  Identities=21%  Similarity=0.362  Sum_probs=44.9

Q ss_pred             HHHHHHHHHH----hcCCCCcHHHHHHHHhcccc-cHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            8 TEAIVLNYVN----EQNRPLNSQNVADALQKYNL-KKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~----~~nrPys~~di~~~l~~~~v-~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+..||.|+.    ..+.|-++.+|.+.+   |+ ++++|...|..|.+.|.|....-+ ...+..
T Consensus         5 ~q~~il~~i~~~~~~~~~~~s~~ela~~~---~~~~~~tv~~~l~~L~~~g~i~~~~~~-~r~~~l   66 (205)
T PRK00215          5 RQQEILDFIRDHIEETGYPPSRREIADAL---GLRSPSAVHEHLKALERKGFIRRDPGR-SRAIEV   66 (205)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHh---CCCChHHHHHHHHHHHHCCCEEeCCCC-cceEEe
Confidence            4556677665    457899999999888   89 999999999999999999776644 444444

>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]

Probab=89.63  E-value=13  Score=35.00  Aligned_cols=81  Identities=10%  Similarity=0.133  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhC--CCCCCCHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHH
Q 027236          119 EQIREKEAQLVKEVKEMENKLAKLRG--GVTLVKPEDRMAVEEM--------------FLEKLSQWRKRKRMLRDIWDPI  182 (226)
Q Consensus       119 ~el~~~i~~L~~e~~~l~~kL~~l~~--~~~~vs~ee~~~~~~~--------------~~~~~~~w~kRkri~~~i~~~i  182 (226)
                      ..|..+|..-+.+++.|+++...|+.  ....+|+++++....+              ..+..+.-.+|++-+..+++.+
T Consensus       333 ~kl~~eie~kEeei~~L~~~~d~L~~q~~kq~Is~e~fe~mn~Ere~L~reL~~i~~~~~~L~k~V~~~~leaq~~~~sl  412 (622)
T COG5185         333 EKLKSEIELKEEEIKALQSNIDELHKQLRKQGISTEQFELMNQEREKLTRELDKINIQSDKLTKSVKSRKLEAQGIFKSL  412 (622)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhHHHHHHHHHHHH
Confidence            33444444444444444444444432  1245888877754332              3445566667776666555554


Q ss_pred             HhcCCCCHHHHHHHhCcc
Q 027236          183 MENSPKNLKEFKEELGIE  200 (226)
Q Consensus       183 ~e~~~~~~k~l~e~lGie  200 (226)
                      ...+- .-+-+...+|+-
T Consensus       413 ek~~~-~~~sl~~~i~~~  429 (622)
T COG5185         413 EKTLR-QYDSLIQNITRS  429 (622)
T ss_pred             HHHHH-HHHHHHHHhccc
Confidence            44321 123455555554

>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans

Probab=89.54  E-value=9.6  Score=30.63  Aligned_cols=102  Identities=20%  Similarity=0.292  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--CCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHH
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSN--LTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMA  156 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~--~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~  156 (226)
                      .++..+......|..+...-+...+..+.++-.+.-.  -...+|...+.+|+.++..|+.++..+..-.....+. -..
T Consensus        50 ~e~~~L~~d~e~L~~q~~~ek~~r~~~e~~l~~~Ed~~~~e~k~L~~~v~~Le~e~r~L~~~~~~~~~q~~rlee~-e~~  128 (158)
T PF09744_consen   50 VELELLREDNEQLETQYEREKELRKQAEEELLELEDQWRQERKDLQSQVEQLEEENRQLELKLKNLSDQSSRLEER-EAE  128 (158)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccccchh-HHH
Confidence            4566667777777777766666666666666544322  3446788899999999999998887766432222222 223


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 027236          157 VEEMFLEKLSQWRKRKRMLRDIWDP  181 (226)
Q Consensus       157 ~~~~~~~~~~~w~kRkri~~~i~~~  181 (226)
                      +...+...+.+.+.=.+..++.++.
T Consensus       129 l~~e~~~l~er~~e~l~~~~e~ver  153 (158)
T PF09744_consen  129 LKKEYNRLHERERELLRKLKEHVER  153 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555666666655554445555554

Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=89.32  E-value=1.3  Score=38.54  Aligned_cols=60  Identities=22%  Similarity=0.373  Sum_probs=48.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+.+..|++|+.++.-=-.-.|+-..+   |++|+.|-++|..|...|+|.-.+.|+.+++-.
T Consensus       194 ~~~e~~il~~i~~~GGri~Q~eL~r~l---glsktTvsR~L~~LEk~GlIe~~K~G~~n~V~l  253 (258)
T COG2512         194 NEDEKEILDLIRERGGRITQAELRRAL---GLSKTTVSRILRRLEKRGLIEKEKKGRTNIVEL  253 (258)
T ss_pred             CHHHHHHHHHHHHhCCEEeHHHHHHhh---CCChHHHHHHHHHHHhCCceEEEEeCCeeEEEE
Confidence            456677788877765544445666655   899999999999999999999999999999866

>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=89.31  E-value=1.7  Score=39.07  Aligned_cols=79  Identities=19%  Similarity=0.291  Sum_probs=55.0

Q ss_pred             CCCCc--chHHHHHHHHHHhc--CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee-cCC---
Q 027236            1 MAPKS--DNTEAIVLNYVNEQ--NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR-QDQ---   72 (226)
Q Consensus         1 M~~kg--~ea~~~Il~y~~~~--nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~-Q~~---   72 (226)
                      |+.-+  .+.++.|++.+...  .+.|+..+|...++  +.....+..+|+.|.++|+|..-.-|...+|-+. ++.   
T Consensus         1 m~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~--~~~~~~~~~~in~Ll~~~~~~~~~~~~~l~~~~~~~~~a~k   78 (327)
T PF05158_consen    1 MASIDKLSELEKKLLELCRENPSPKGFSQEDLQQLIP--GLDLQELVKAINELLSSGLLKLLKKGGGLSYKAVSEEEAKK   78 (327)
T ss_dssp             ------HHHHHHHHHHHHHH---SS-EEHHHHHHH-T--TS-HHHHHHHHHHHHHHTSEEEEE-SSSEEEEE--SSS---
T ss_pred             CcccchHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcC--CCCHHHHHHHHHHHHhCCCEEEEEcCCEEEEEEeCHHHHhh
Confidence            55433  68899999999998  99999999999865  6899999999999999999999997777777554 222   


Q ss_pred             CCCCCHHHH
Q 027236           73 FDIPNSEEL   81 (226)
Q Consensus        73 ~~~~~~ee~   81 (226)
                      +..++++|.
T Consensus        79 ~~~l~~~e~   87 (327)
T PF05158_consen   79 LKGLSDEER   87 (327)
T ss_dssp             --SSSCCHH
T ss_pred             hcCCCHHHH
Confidence            455556664

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.

>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 []

Probab=89.29  E-value=7.8  Score=29.24  Aligned_cols=68  Identities=12%  Similarity=0.317  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHH---------HH---HHHHHHHHHHHHHhcCCCC
Q 027236          122 REKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQW---------RK---RKRMLRDIWDPIMENSPKN  189 (226)
Q Consensus       122 ~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~~~w---------~k---Rkri~~~i~~~i~e~~~~~  189 (226)
                      ...+.++.+++.+++.++..|..+ .++++.+-..+.+....-...|         .+   |++.|.+||..+..-++.+
T Consensus         7 ~~~~~~~~~ki~~ve~~V~~l~~~-~~i~~~q~~~i~~~v~~rv~~~lgg~~s~ay~~~~~~~k~f~~i~~~lk~~F~V~   85 (116)
T PF10552_consen    7 MQATEEHNEKIEEVENRVDDLEEN-MPIDPGQQKEIQKAVKSRVYELLGGKGSPAYKDKSFRRKLFSDIYRDLKRHFGVP   85 (116)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHHHHHHHhccccchhhhhHHhHHHHHHHHHHHHHHhCCc
Confidence            345666777778888888777754 3567777776666544333333         44   8889999999998888775


Q ss_pred             H
Q 027236          190 L  190 (226)
Q Consensus       190 ~  190 (226)
                      .
T Consensus        86 s   86 (116)
T PF10552_consen   86 S   86 (116)
T ss_pred             h
Confidence            3

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=89.10  E-value=6.2  Score=28.06  Aligned_cols=33  Identities=21%  Similarity=0.532  Sum_probs=28.3

Q ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236           26 QNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus        26 ~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .++.+.+   +|++++|.++|+.|++.|+|.....+
T Consensus         3 ~ela~~l---~is~stvs~~l~~L~~~glI~r~~~~   35 (96)
T smart00529        3 SEIAERL---NVSPPTVTQMLKKLEKDGLVEYEPYR   35 (96)
T ss_pred             HHHHHHh---CCChHHHHHHHHHHHHCCCEEEcCCC
Confidence            4566666   79999999999999999999998754

iron dependent repressor

>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]

Probab=89.04  E-value=2.8  Score=34.09  Aligned_cols=23  Identities=9%  Similarity=-0.090  Sum_probs=13.5

Q ss_pred             cccHHHHHHHHHHHHHcCCccee
Q 027236           36 NLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus        36 ~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      -++++.|-..|+.-+-.+-++.|
T Consensus        22 P~ssq~v~~~lq~e~lgktavqk   44 (201)
T KOG4603|consen   22 PYSSQDVFGNLQREHLGKTAVQK   44 (201)
T ss_pred             CCchHHHHHHHHHHhccchHHHH
Confidence            46677777777766644444444

>PF08657 DASH_Spc34: DASH complex subunit Spc34 ; InterPro: IPR013966 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []

Probab=89.00  E-value=3.5  Score=35.81  Aligned_cols=64  Identities=14%  Similarity=0.288  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHH---------------HHHHHHHHHHHHHHHHHHHHHHh
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLE---------------QIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~---------------el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      +.+..+..+...+..+++.++.++..-+.+|..+....+..               ...+.|..-+.+|.+|+.++..|
T Consensus       180 eki~~Lr~~y~~l~~~i~~lE~~VaeQ~~qL~~~n~~~~~~~~~~~~~~~~~~~~~~~de~I~rEeeEIreLE~k~~~L  258 (259)
T PF08657_consen  180 EKIAALRQRYNQLSNSIAYLEAEVAEQEAQLERMNRSSSDSSSDDEESEESSEDSVDTDEDIRREEEEIRELERKKREL  258 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccccccccccccccchhHHHHHHHHHHHHHHHHHHHHhc
Confidence            34677777777788888888888888888888876643332               45566777777788887777655

In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].

>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=88.98  E-value=1.2  Score=29.70  Aligned_cols=36  Identities=19%  Similarity=0.348  Sum_probs=28.4

Q ss_pred             CC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236           22 PL-NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus        22 Py-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .+ |..++...+   +|+.+.|.++|..|+++|+|....-
T Consensus        23 ~lps~~~la~~~---~vsr~tvr~al~~L~~~g~i~~~~~   59 (64)
T PF00392_consen   23 RLPSERELAERY---GVSRTTVREALRRLEAEGLIERRPG   59 (64)
T ss_dssp             BE--HHHHHHHH---TS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred             EeCCHHHHHHHh---ccCCcHHHHHHHHHHHCCcEEEECC
Confidence            45 777777666   8999999999999999999987644

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 ....

>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1

Probab=88.94  E-value=4.7  Score=29.08  Aligned_cols=65  Identities=29%  Similarity=0.371  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC---------CHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL---------TLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~---------t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +-...+..++..|+.++..-..-...|+.-+..-.+..         ...+|..+|+.++.+|..|+.++..|.
T Consensus         8 ~~r~~LeqeV~~Lq~~L~~E~~~r~aLe~al~~~~~~~~~~~~~lp~~~keLL~EIA~lE~eV~~LE~~v~~L~   81 (88)
T PF14389_consen    8 ERRSALEQEVAELQKQLQEEQDLRRALEKALGRSSGSLPSSPSSLPKKAKELLEEIALLEAEVAKLEQKVLSLY   81 (88)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcccCCccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44567788888888888877777777776665543322         338999999999999999999998875

>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.71  E-value=10  Score=32.32  Aligned_cols=100  Identities=21%  Similarity=0.372  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHH
Q 027236           90 KLQEQLEEQRKAISKLEGEIRTLQSN-LTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQW  168 (226)
Q Consensus        90 ~l~~~l~~l~~~~k~l~~el~~l~~~-~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~~~w  168 (226)
                      +++.....+..-...+..++..+... .-..|+..+++.|.+|-....+.|....        +|+..++..+.   ..|
T Consensus         5 ~ir~K~~~lek~k~~i~~e~~~~e~ee~~L~e~~kE~~~L~~Er~~h~eeLrqI~--------~DIn~lE~iIk---qa~   73 (230)
T PF10146_consen    5 EIRNKTLELEKLKNEILQEVESLENEEKCLEEYRKEMEELLQERMAHVEELRQIN--------QDINTLENIIK---QAE   73 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHH---HHH
Confidence            34444444444444444444444433 2235666677777777777766665544        34555555554   333


Q ss_pred             HHHHHHHHHHHHHHHhc-CCCC--HHHHHHH-hCccc
Q 027236          169 RKRKRMLRDIWDPIMEN-SPKN--LKEFKEE-LGIEY  201 (226)
Q Consensus       169 ~kRkri~~~i~~~i~e~-~~~~--~k~l~e~-lGie~  201 (226)
                      ..|.++...+ ..+.+. .+..  ..++..+ +|++.
T Consensus        74 ~er~~~~~~i-~r~~eey~~Lk~~in~~R~e~lgl~~  109 (230)
T PF10146_consen   74 SERNKRQEKI-QRLYEEYKPLKDEINELRKEYLGLEP  109 (230)
T ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence            4444432333 222233 2221  2455556 77763

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.

>PLN02320 seryl-tRNA synthetase

Probab=88.59  E-value=3.9  Score=38.89  Aligned_cols=65  Identities=18%  Similarity=0.227  Sum_probs=50.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      -+++..++.+..++..++..++.+.+.+..++.........++|.++..+|.+++.++++.+..+
T Consensus        92 vd~l~~ld~~~r~~~~~~~~lr~ern~~sk~i~~~~~~~~~~~l~~~~k~lk~~i~~le~~~~~~  156 (502)
T PLN02320         92 LELVLELYENMLALQKEVERLRAERNAVANKMKGKLEPSERQALVEEGKNLKEGLVTLEEDLVKL  156 (502)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47788889999999999999999999999999873333455777777777777777777766554

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=88.58  E-value=1.5  Score=34.01  Aligned_cols=49  Identities=14%  Similarity=0.161  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .+-.||..+.. +.|-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        41 ~q~~vL~~l~~-~~~~t~~eLa~~l---~i~~~tvsr~l~~Le~~GlI~R~~~   89 (144)
T PRK11512         41 AQFKVLCSIRC-AACITPVELKKVL---SVDLGALTRMLDRLVCKGWVERLPN   89 (144)
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEeccC
Confidence            45567777764 5678889999888   7999999999999999999998765

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=88.48  E-value=1.9  Score=34.86  Aligned_cols=60  Identities=20%  Similarity=0.346  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHhcCC-----CCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCC
Q 027236            8 TEAIVLNYVNEQNR-----PLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQF   73 (226)
Q Consensus         8 a~~~Il~y~~~~nr-----Pys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~   73 (226)
                      +...|+.|+.+.-.     ..|..+|.+.+   ++++++|.+++..|.+.|.|...   ++.+|++|.+.+
T Consensus        56 k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l---~iS~~Tv~r~ik~L~e~~iI~k~---~~G~Y~iNP~~~  120 (165)
T PF05732_consen   56 KAFRVLMYILENMDKDNAVVATQKEIAEKL---GISKPTVSRAIKELEEKNIIKKI---RNGAYMINPNFF  120 (165)
T ss_pred             hHHHHHHHHHHhcCCCCeEEeeHHHHHHHh---CCCHHHHHHHHHHHHhCCcEEEc---cCCeEEECcHHh
Confidence            34566666665322     34555666665   89999999999999999988764   456999987753

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=88.02  E-value=1.4  Score=36.58  Aligned_cols=49  Identities=22%  Similarity=0.242  Sum_probs=43.8

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee-ecCc
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK-EYGK   62 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K-~~GK   62 (226)
                      .|+.++..-...++.++|...|   +|+..+|.+.+..|+..|++... .||+
T Consensus       166 ~Vl~~~~~g~~g~s~~eIa~~l---~iS~~Tv~~~~~~~~~~~~~~~~~~~~~  215 (225)
T PRK10046        166 AVRKLFKEPGVQHTAETVAQAL---TISRTTARRYLEYCASRHLIIAEIVHGK  215 (225)
T ss_pred             HHHHHHHcCCCCcCHHHHHHHh---CccHHHHHHHHHHHHhCCeEEEEeecCC
Confidence            7888888777789999999988   89999999999999999999998 6664

>PRK09954 putative kinase; Provisional

Probab=87.93  E-value=1.4  Score=39.45  Aligned_cols=50  Identities=24%  Similarity=0.418  Sum_probs=42.8

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      +-...||.+|++ |-+.|.++|.+.|   +|++++|.+.|..|.++|.|....|
T Consensus         3 ~~~~~il~~l~~-~~~~s~~~la~~l---~~s~~~v~~~i~~L~~~g~i~~~~~   52 (362)
T PRK09954          3 NREKEILAILRR-NPLIQQNEIADIL---QISRSRVAAHIMDLMRKGRIKGKGY   52 (362)
T ss_pred             hHHHHHHHHHHH-CCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCcCCcEE
Confidence            456679999995 4589999999999   7999999999999999999975544

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=87.93  E-value=2.1  Score=33.13  Aligned_cols=54  Identities=9%  Similarity=0.169  Sum_probs=40.8

Q ss_pred             HHHHHHHh--cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNE--QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~--~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .++-||-.  ...|+++.+|...+   +|+...+.++|..|+..|+|.+.. |+.==|+.
T Consensus        12 ~~l~~La~~~~~~~~s~~~ia~~~---~ip~~~l~kil~~L~~~glv~s~~-G~~Ggy~l   67 (135)
T TIGR02010        12 TAMLDLALNAETGPVTLADISERQ---GISLSYLEQLFAKLRKAGLVKSVR-GPGGGYQL   67 (135)
T ss_pred             HHHHHHHhCCCCCcCcHHHHHHHH---CcCHHHHHHHHHHHHHCCceEEEe-CCCCCEec
Confidence            34555543  34599999998877   799999999999999999998843 44334555

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6

Probab=87.89  E-value=3.9  Score=27.69  Aligned_cols=58  Identities=29%  Similarity=0.462  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH---HhccCCH--HHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRT---LQSNLTL--EQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~---l~~~~t~--~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      +.++..|+.++..++.++..+...|.+   +.+.|..  +.-...+..+..++..+...|..|
T Consensus         3 ~~E~~rL~Kel~kl~~~i~~~~~kL~n~~F~~kAP~eVve~er~kl~~~~~~~~~l~~~l~~L   65 (66)
T PF10458_consen    3 EAEIERLEKELEKLEKEIERLEKKLSNENFVEKAPEEVVEKEREKLEELEEELEKLEEALEQL   65 (66)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCSTTHHHHS-CCHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcCccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            456666777777777776666666654   2233433  555667777888888888877665

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=87.81  E-value=1.4  Score=37.86  Aligned_cols=48  Identities=21%  Similarity=0.348  Sum_probs=42.3

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      --.||++|.....+-++.+|...+   |++|++|-..|..|++.|.|....
T Consensus         6 al~iL~~l~~~~~~l~l~ela~~~---glpksT~~RlL~tL~~~G~v~~d~   53 (246)
T COG1414           6 ALAILDLLAEGPGGLSLAELAERL---GLPKSTVHRLLQTLVELGYVEQDP   53 (246)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHh---CcCHHHHHHHHHHHHHCCCEEEcC
Confidence            347999999977777799998877   899999999999999999998775

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=87.64  E-value=13  Score=31.95  Aligned_cols=81  Identities=19%  Similarity=0.235  Sum_probs=52.5

Q ss_pred             CCCcchHHHHHHH-HHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHH
Q 027236            2 APKSDNTEAIVLN-YVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEE   80 (226)
Q Consensus         2 ~~kg~ea~~~Il~-y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee   80 (226)
                      .|| +.-+-.||- +...|.+ -+-+||.++|   |||-++|...+..|+.+|+|..+.=   --|-+        |.+-
T Consensus         6 ~kk-~~t~fqIL~ei~~~qp~-v~q~eIA~~l---giT~QaVsehiK~Lv~eG~i~~~gR---~~Y~i--------TkkG   69 (260)
T COG1497           6 SKK-NLTRFQILSEIAVRQPR-VKQKEIAKKL---GITLQAVSEHIKELVKEGLIEKEGR---GEYEI--------TKKG   69 (260)
T ss_pred             ccc-cchHHHHHHHHHHhCCC-CCHHHHHHHc---CCCHHHHHHHHHHHHhccceeecCC---eeEEE--------ehhH
Confidence            344 333444444 4443333 3567999988   8999999999999999999998322   23444        2455


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 027236           81 LNQMKEENAKLQEQLEEQ   98 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l   98 (226)
                      ...+.+++.+++.=..+.
T Consensus        70 ~e~l~~~~~dlr~f~~ev   87 (260)
T COG1497          70 AEWLLEQLSDLRRFSEEV   87 (260)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            666666666665544444

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=87.58  E-value=8  Score=32.99  Aligned_cols=54  Identities=24%  Similarity=0.447  Sum_probs=46.4

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCcee
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQK   64 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~k   64 (226)
                      .+-+..|++|+.+ +.+.+..++...|   +|+..+|.+-|..|.+.|+|.. .+|...
T Consensus         3 ~~R~~~Il~~l~~-~~~~~~~eLa~~l---~VS~~TiRRdL~~L~~~~~l~r-~~Gga~   56 (240)
T PRK10411          3 AARQQAIVDLLLN-HTSLTTEALAEQL---NVSKETIRRDLNELQTQGKILR-NHGRAK   56 (240)
T ss_pred             hHHHHHHHHHHHH-cCCCcHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEE-ecCeEE
Confidence            3567889999995 6699999999998   7999999999999999999875 677654

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=87.41  E-value=2.2  Score=36.66  Aligned_cols=63  Identities=27%  Similarity=0.480  Sum_probs=54.4

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec----CceeEEEeecCC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY----GKQKIYIARQDQ   72 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~----GK~kiY~~~Q~~   72 (226)
                      ...+-.||+.|+.. -|.|+++|...+   |.+.+.+.--+..|++-|+|..+..    |.|+|.++.-+.
T Consensus        22 S~vRv~Il~lL~~k-~plNvneiAe~l---gLpqst~s~~ik~Le~aGlirT~t~karkG~QKiC~s~~~e   88 (308)
T COG4189          22 SKVRVAILQLLHRK-GPLNVNEIAEAL---GLPQSTMSANIKVLEKAGLIRTETVKARKGSQKICISTTDE   88 (308)
T ss_pred             HHHHHHHHHHHHHh-CCCCHHHHHHHh---CCchhhhhhhHHHHHhcCceeeeeeccccCceeEeEeecce
Confidence            45677899999854 599999998888   7899999999999999999999876    999999886664

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=87.23  E-value=1.9  Score=36.15  Aligned_cols=52  Identities=25%  Similarity=0.383  Sum_probs=40.8

Q ss_pred             hHHHHHHHHHHhc----------CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            7 NTEAIVLNYVNEQ----------NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         7 ea~~~Il~y~~~~----------nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .++++|..||...          .-|++-++|.+.+   |++..+|.++|..|.++|+|.....|
T Consensus       154 ~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~l---GisretlsR~L~~L~~~GlI~~~~~~  215 (230)
T PRK09391        154 TAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYL---GLTIETVSRALSQLQDRGLIGLSGAR  215 (230)
T ss_pred             CHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHH---CCCHHHHHHHHHHHHHCCcEEecCCc
Confidence            4677777777652          2367888998888   89999999999999999999544333

>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=86.80  E-value=1.9  Score=34.71  Aligned_cols=60  Identities=25%  Similarity=0.473  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      ..++..+..++..++.++..+..++..|.+.+.+-.-.-...+|...+..++.++..+.+
T Consensus        71 ~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~  130 (169)
T PF07106_consen   71 PEELAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEE  130 (169)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHH
Confidence            345666666666666666666666666665544333333345566666666666655553

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 [].

>COG0640 ArsR Predicted transcriptional regulators [Transcription]

Probab=86.51  E-value=5.1  Score=27.77  Aligned_cols=58  Identities=24%  Similarity=0.445  Sum_probs=48.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEE
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYI   67 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~   67 (226)
                      +..+..|+..+... .+.++.++..++   +++..+|...|..|.+.|+|....-|...+|-
T Consensus        24 ~~~r~~il~~l~~~-~~~~~~~l~~~~---~~~~~~v~~hL~~L~~~glv~~~~~~~~~~~~   81 (110)
T COG0640          24 DPTRLEILSLLAEG-GELTVGELAEAL---GLSQSTVSHHLKVLREAGLVELRREGRLRLYR   81 (110)
T ss_pred             CHHHHHHHHHHHhc-CCccHHHHHHHH---CCChhHHHHHHHHHHHCCCeEEEecccEEEEe
Confidence            55678888888876 567777888877   78999999999999999999998888886665

>PRK12423 LexA repressor; Provisional

Probab=86.39  E-value=3.4  Score=34.25  Aligned_cols=59  Identities=19%  Similarity=0.343  Sum_probs=46.4

Q ss_pred             HHHHHHHHHH----hcCCCCcHHHHHHHHhccc-ccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            8 TEAIVLNYVN----EQNRPLNSQNVADALQKYN-LKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         8 a~~~Il~y~~----~~nrPys~~di~~~l~~~~-v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      .+..||+++.    +..-|=|..+|.+.+   | ++.++|.+.|+.|+..|+|....-|...++...
T Consensus         7 ~q~~il~~l~~~i~~~g~~Ps~~eia~~~---g~~s~~~v~~~l~~L~~~G~l~~~~~~~~~~~v~~   70 (202)
T PRK12423          7 KRAAILAFIRERIAQAGQPPSLAEIAQAF---GFASRSVARKHVQALAEAGLIEVVPNQARGIRLPG   70 (202)
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHh---CCCChHHHHHHHHHHHHCCCEEecCCCcceeeecc
Confidence            4455555554    455567999999888   6 489999999999999999999888877777653

>PRK11050 manganese transport regulator MntR; Provisional

Probab=86.11  E-value=3.8  Score=32.42  Aligned_cols=51  Identities=18%  Similarity=0.391  Sum_probs=40.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ++.-..|+.++.. +-|.+..+|...+   +|++++|.++|+.|.+.|+|....+
T Consensus        36 e~~l~~I~~~l~~-~~~~t~~eLA~~l---~is~stVsr~l~~Le~~GlI~r~~~   86 (152)
T PRK11050         36 EDYVELIADLIAE-VGEARQVDIAARL---GVSQPTVAKMLKRLARDGLVEMRPY   86 (152)
T ss_pred             HHHHHHHHHHHHh-cCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEecC
Confidence            3444566666654 5688999999888   7999999999999999999877654

>TIGR00498 lexA SOS regulatory protein LexA

Probab=86.10  E-value=1.5  Score=35.98  Aligned_cols=54  Identities=22%  Similarity=0.383  Sum_probs=43.3

Q ss_pred             chHHHHHHHHHHhc----CCCCcHHHHHHHHhccccc-HHHHHHHHHHHHHcCCcceeecCce
Q 027236            6 DNTEAIVLNYVNEQ----NRPLNSQNVADALQKYNLK-KAGIQKALDSLADNGKISFKEYGKQ   63 (226)
Q Consensus         6 ~ea~~~Il~y~~~~----nrPys~~di~~~l~~~~v~-K~~v~k~L~~Lv~~g~i~~K~~GK~   63 (226)
                      ...+..||+|+.+.    ..|-++.+|...+   +++ +++|...|+.|.+.|.|.... |..
T Consensus         5 t~~q~~iL~~l~~~~~~~~~~~~~~ela~~~---~~~s~~tv~~~l~~L~~~g~i~~~~-~~~   63 (199)
T TIGR00498         5 TARQQEVLDLIRAHIESTGYPPSIREIARAV---GLRSPSAAEEHLKALERKGYIERDP-GKP   63 (199)
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCcHHHHHHHh---CCCChHHHHHHHHHHHHCCCEecCC-CCC
Confidence            45677888888754    4577788998888   787 999999999999999998764 443

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.

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=86.09  E-value=11  Score=38.15  Aligned_cols=96  Identities=18%  Similarity=0.293  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHhccCCH------HHHHHHHHHHHHHHHHHHHHHHHhhCCC
Q 027236           78 SEELNQMKEEN-----AKLQEQLEEQRKAISKLEGEIRTLQSNLTL------EQIREKEAQLVKEVKEMENKLAKLRGGV  146 (226)
Q Consensus        78 ~ee~~~l~~~i-----~~l~~~l~~l~~~~k~l~~el~~l~~~~t~------~el~~~i~~L~~e~~~l~~kL~~l~~~~  146 (226)
                      .-|+..+|.++     +.|+.++..++..+.+|+..|..|++...+      .-=.-+..+|++++..|++-|-.|++-.
T Consensus       312 ~iEmaTldKEmAEERaesLQ~eve~lkEr~deletdlEILKaEmeekG~~~~~~ss~qfkqlEqqN~rLKdalVrLRDls  391 (1243)
T KOG0971|consen  312 AIEMATLDKEMAEERAESLQQEVEALKERVDELETDLEILKAEMEEKGSDGQAASSYQFKQLEQQNARLKDALVRLRDLS  391 (1243)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            34555555444     457778888888888888888887764332      1112357889999999999999998621


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 027236          147 TLVKPEDRMAVEEMFLEKLSQWRKRKRM  174 (226)
Q Consensus       147 ~~vs~ee~~~~~~~~~~~~~~w~kRkri  174 (226)
                      . -...+..++.+...+-..+...=+|+
T Consensus       392 A-~ek~d~qK~~kelE~k~sE~~eL~r~  418 (1243)
T KOG0971|consen  392 A-SEKQDHQKLQKELEKKNSELEELRRQ  418 (1243)
T ss_pred             h-HHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            1 12334556666655555444443334

>PF15188 CCDC-167: Coiled-coil domain-containing protein 167

Probab=86.04  E-value=4  Score=29.36  Aligned_cols=59  Identities=20%  Similarity=0.325  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC-HHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236           86 EENAKLQEQLEEQRKAISKLEGEIRTLQSNLT-LEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus        86 ~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t-~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      .+|+.+.+.+......+..++..|..-.-+|. ...+..+...+.......+.+|..|+.
T Consensus         5 ~eId~lEekl~~cr~~le~ve~rL~~~eLs~e~R~~lE~E~~~l~~~l~~~E~eL~~Lrk   64 (85)
T PF15188_consen    5 KEIDGLEEKLAQCRRRLEAVESRLRRRELSPEARRSLEKELNELKEKLENNEKELKLLRK   64 (85)
T ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHcccCCChHHHHHHHHHHHHHHHHhhccHHHHHHHHH
Confidence            56777888888888888888777776665543 367777778888888888888877764

>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=86.04  E-value=7.2  Score=30.73  Aligned_cols=21  Identities=19%  Similarity=0.327  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 027236           91 LQEQLEEQRKAISKLEGEIRT  111 (226)
Q Consensus        91 l~~~l~~l~~~~k~l~~el~~  111 (226)
                      +.+++..++.....+..+|..
T Consensus        19 ~e~~~K~le~~~~~~E~EI~s   39 (143)
T PF12718_consen   19 LEAKVKQLEQENEQKEQEITS   39 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes

Probab=86.03  E-value=11  Score=37.26  Aligned_cols=66  Identities=23%  Similarity=0.440  Sum_probs=53.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236           77 NSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus        77 ~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      +++....|..++..|+.++...++...+|+..|..+.+.  .-.+..++.+++.++..|+.++..|..
T Consensus       416 ~~~a~~rLE~dvkkLraeLq~~Rq~E~ELRsqis~l~~~--Er~lk~eL~qlr~ene~Lq~Kl~~L~~  481 (697)
T PF09726_consen  416 EPDAISRLEADVKKLRAELQSSRQSEQELRSQISSLTNN--ERSLKSELSQLRQENEQLQNKLQNLVQ  481 (697)
T ss_pred             ChHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhhcccc--chHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356677888899999999998888888888887777652  347788899999999999999988853

; GO: 0016021 integral to membrane

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=85.97  E-value=2.9  Score=30.55  Aligned_cols=46  Identities=13%  Similarity=0.322  Sum_probs=38.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      +..-.|+.+|... .+-+..+|...+   |++.++|.+.++.|.++|.|.
T Consensus         3 ~~D~~il~~L~~~-~~~~~~~la~~l---~~s~~tv~~~l~~L~~~g~i~   48 (108)
T smart00344        3 EIDRKILEELQKD-ARISLAELAKKV---GLSPSTVHNRVKRLEEEGVIK   48 (108)
T ss_pred             HHHHHHHHHHHHh-CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCee
Confidence            3456788888864 467777888877   899999999999999999988

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

>PF14257 DUF4349: Domain of unknown function (DUF4349)

Probab=85.92  E-value=6  Score=34.03  Aligned_cols=118  Identities=17%  Similarity=0.266  Sum_probs=71.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHH-----------HHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVAD-----------ALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFD   74 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~-----------~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~   74 (226)
                      +.+...|.+...+.+ .|-...-..           ++. ..|+...+..+|+.|..-|.|......             
T Consensus        62 ~~a~~~i~~~~~~~g-G~i~~~~~~~~~~~~~~~~~~lt-iRVP~~~~~~~l~~l~~~g~v~~~~~~-------------  126 (262)
T PF14257_consen   62 EKAVKKIENLVESYG-GYIESSSSSSSGGSDDERSASLT-IRVPADKFDSFLDELSELGKVTSRNIS-------------  126 (262)
T ss_pred             HHHHHHHHHHHHHcC-CEEEEEeeecccCCCCcceEEEE-EEECHHHHHHHHHHHhccCceeeeecc-------------
Confidence            466667777776654 332211111           111 279999999999999976655544322             


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236           75 IPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus        75 ~~~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                         .+++.   .++..+..+++.++.....|.+-|++....-..-++..++.+.+.+|..++.++..|..
T Consensus       127 ---~~DvT---~~y~D~~arl~~l~~~~~rl~~ll~ka~~~~d~l~ie~~L~~v~~eIe~~~~~~~~l~~  190 (262)
T PF14257_consen  127 ---SEDVT---EQYVDLEARLKNLEAEEERLLELLEKAKTVEDLLEIERELSRVRSEIEQLEGQLKYLDD  190 (262)
T ss_pred             ---ccchH---HHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence               12221   44455666666666666666555553332222246667888888999999998888865

>PF13851 GAS: Growth-arrest specific micro-tubule binding

Probab=85.88  E-value=19  Score=29.97  Aligned_cols=16  Identities=25%  Similarity=0.362  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHHHHH
Q 027236          125 EAQLVKEVKEMENKLA  140 (226)
Q Consensus       125 i~~L~~e~~~l~~kL~  140 (226)
                      +..++.++.+|+..|.
T Consensus        64 L~~a~~e~~eL~k~L~   79 (201)
T PF13851_consen   64 LKKAEEEVEELRKQLK   79 (201)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3333333333333333

>KOG4809 consensus Rab6 GTPase-interacting protein involved in endosome-to-TGN transport [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.85  E-value=26  Score=33.70  Aligned_cols=60  Identities=18%  Similarity=0.135  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027236          120 QIREKEAQLVKEVKEMENKLAKLRG--GVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWD  180 (226)
Q Consensus       120 el~~~i~~L~~e~~~l~~kL~~l~~--~~~~vs~ee~~~~~~~~~~~~~~w~kRkri~~~i~~  180 (226)
                      .+.-.+++-..+|..++..|.+...  .+..++|+ +....+.+...++.|++=-.++...++
T Consensus       384 ~leIalEqkkEec~kme~qLkkAh~~~ddar~~pe-~~d~i~~le~e~~~y~de~~kaqaevd  445 (654)
T KOG4809|consen  384 SLEIALEQKKEECSKMEAQLKKAHNIEDDARMNPE-FADQIKQLEKEASYYRDECGKAQAEVD  445 (654)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhcChh-hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444566777888888888877754  33445553 233333344444555444333333333

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=85.78  E-value=2.5  Score=34.75  Aligned_cols=61  Identities=13%  Similarity=0.249  Sum_probs=51.1

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQ   70 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q   70 (226)
                      +-+.+|++||.....+-.|.+|...|   |+.|..|-+.|=.|-..|.|.+-.--.-.+|.-.+
T Consensus         4 ~~~~~i~~~l~~~~~~~~a~~i~k~l---~i~k~~vNr~LY~L~~~~~v~~~~~~pP~W~~~~~   64 (183)
T PHA02701          4 DCASLILTLLSSSGDKLPAKRIAKEL---GISKHEANRCLYRLLESDAVSCEDGCPPLWSVECE   64 (183)
T ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHh---CccHHHHHHHHHHHhhcCcEecCCCCCCccccccC
Confidence            45789999999888679999999988   89999999999999999999887555556665543

>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]

Probab=85.78  E-value=6.2  Score=41.00  Aligned_cols=73  Identities=19%  Similarity=0.352  Sum_probs=63.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCH-----HHHHHHHHHHHHHHHHHHHHHHHhhCCC
Q 027236           74 DIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTL-----EQIREKEAQLVKEVKEMENKLAKLRGGV  146 (226)
Q Consensus        74 ~~~~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~-----~el~~~i~~L~~e~~~l~~kL~~l~~~~  146 (226)
                      ++++.+++++|...+.+|+.++..+...+.+++..|.....+.+.     +-|+.....|..-..+|+++++.+++++
T Consensus      1220 ~svs~~~i~~l~~~~~~lr~~l~~~~e~L~~~E~~Lsdi~~~~~~a~~~LesLq~~~~~l~~~~keL~e~~~~ik~sd 1297 (1758)
T KOG0994|consen 1220 PSVSAEDIAQLASATESLRRQLQALTEDLPQEEETLSDITNSLPLAGKDLESLQREFNGLLTTYKELREQLEKIKESD 1297 (1758)
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence            566789999999999999999999999999999999988876553     6677778888888999999999998754

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=85.53  E-value=11  Score=26.74  Aligned_cols=21  Identities=0%  Similarity=0.109  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 027236           81 LNQMKEENAKLQEQLEEQRKA  101 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~  101 (226)
                      +..+..+|...-+.+.-|+-+
T Consensus         6 leqLE~KIqqAvdtI~LLqmE   26 (79)
T PRK15422          6 FEKLEAKVQQAIDTITLLQME   26 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444443333333

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=85.49  E-value=2.5  Score=32.92  Aligned_cols=47  Identities=13%  Similarity=0.222  Sum_probs=38.5

Q ss_pred             cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           19 QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        19 ~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+.|.|..+|...+   +|+.+.|.++|..|...|+|....-...-++.+
T Consensus        22 ~g~~~s~~~ia~~~---~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~   68 (141)
T PRK11014         22 EGRMTSISEVTEVY---GVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLG   68 (141)
T ss_pred             CCCccCHHHHHHHH---CcCHHHHHHHHHHHHhCCEEEEecCCCCCeeec
Confidence            44688988888877   899999999999999999999987654445554

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=85.46  E-value=3.5  Score=32.71  Aligned_cols=54  Identities=15%  Similarity=0.201  Sum_probs=41.1

Q ss_pred             HHHHH-HhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           12 VLNYV-NEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        12 Il~y~-~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ++-|| ....+|.++.+|.+..   +|+...+.|+|..|+..|+|.+..--..=++.+
T Consensus        13 ~L~~LA~~~~~~~s~~eIA~~~---~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La   67 (153)
T PRK11920         13 MLMYCAANDGKLSRIPEIARAY---GVSELFLFKILQPLVEAGLVETVRGRNGGVRLG   67 (153)
T ss_pred             HHHHHHhCCCCcCcHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEeecCCCCCeeec
Confidence            44455 3456688999998866   899999999999999999999988433344444

>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=85.41  E-value=14  Score=31.60  Aligned_cols=60  Identities=20%  Similarity=0.296  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236           83 QMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus        83 ~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      ..+.+++.+.++-..+..++..+..++..|...  +..+...+..+++++..++.++..+..
T Consensus        39 ~sQ~~id~~~~e~~~L~~e~~~l~~e~e~L~~~--~~~l~~~v~~q~~el~~L~~qi~~~~~   98 (251)
T PF11932_consen   39 QSQKRIDQWDDEKQELLAEYRQLEREIENLEVY--NEQLERQVASQEQELASLEQQIEQIEE   98 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566666667777777777777777777653  667777777777777777777777654

However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.

>PRK14137 recX recombination regulator RecX; Provisional

Probab=85.29  E-value=2.5  Score=35.10  Aligned_cols=56  Identities=14%  Similarity=0.255  Sum_probs=48.3

Q ss_pred             chHHHHHHHHHHh--cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            6 DNTEAIVLNYVNE--QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         6 ~ea~~~Il~y~~~--~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      +++...++.|-..  +.|+||-.+|..-|...++.-..|..+|+.|.+.|.|.=..|.
T Consensus        36 ~e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfA   93 (195)
T PRK14137         36 DEAREALLAYAFRALAARAMTAAELRAKLERRSEDEALVTEVLERVQELGYQDDAQVA   93 (195)
T ss_pred             HHHHHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHH
Confidence            7888888887765  5999999999999988899999999999999999987655553

>PRK11642 exoribonuclease R; Provisional

Probab=85.11  E-value=2.2  Score=43.01  Aligned_cols=49  Identities=14%  Similarity=0.389  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhccc-ccHHHHHHHHHHHHHcCCcce
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYN-LKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~-v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      ++.||+||..+++|++..+|...|.-.+ -.+..+..+|+.|+.+|.|..
T Consensus        21 ~~~Il~~l~~~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~   70 (813)
T PRK11642         21 REFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVF   70 (813)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEE
Confidence            5779999999899999999999883211 236779999999999999974

>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins

Probab=84.98  E-value=5.8  Score=29.57  Aligned_cols=56  Identities=25%  Similarity=0.413  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           88 NAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        88 i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +..+.+.+......+..++.++..+=..-....|...+.+++-++..+..+|..+.
T Consensus        37 ~~~l~~~~~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~   92 (106)
T PF10805_consen   37 IEKLEERLDEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVS   92 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            33344444444555555555544442222235566677777777777777776653

The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.75  E-value=4.7  Score=35.09  Aligned_cols=28  Identities=18%  Similarity=0.375  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRTL  112 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~l  112 (226)
                      +.++.+++.+...+..++..|..++..+
T Consensus        37 ds~l~~~~~~~~~~q~ei~~L~~qi~~~   64 (265)
T COG3883          37 DSKLSELQKEKKNIQNEIESLDNQIEEI   64 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444443333

>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]

Probab=84.34  E-value=28  Score=30.53  Aligned_cols=95  Identities=16%  Similarity=0.148  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------Hh
Q 027236          119 EQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPI--------------ME  184 (226)
Q Consensus       119 ~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~~~w~kRkri~~~i~~~i--------------~e  184 (226)
                      ..|..+|+.-+.++..++.+|+.|++-. |.--.+.++.++++.+.-..|.-|.+...-+-..+              ..
T Consensus       136 a~L~~Kierrk~ElEr~rkRle~LqsiR-P~~MdEyE~~EeeLqkly~~Y~l~f~nl~yL~~qldd~~rse~~rqeeaen  214 (338)
T KOG3647|consen  136 AALGSKIERRKAELERTRKRLEALQSIR-PAHMDEYEDCEEELQKLYQRYFLRFHNLDYLKSQLDDRTRSEPIRQEEAEN  214 (338)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcc-hHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhhhhHHHHHHHHh
Confidence            6778889999999999999999998632 22234555555555444444444433222111111              12


Q ss_pred             cCCCCHHHHHH------HhCcccccccccchhhchh
Q 027236          185 NSPKNLKEFKE------ELGIEYDEDVGVSLQSFSD  214 (226)
Q Consensus       185 ~~~~~~k~l~e------~lGie~Ded~~v~~~~~~~  214 (226)
                      .||+-++.|.+      ..|.-.|+|..+.+|+.++
T Consensus       215 sm~~i~ekl~ee~~~~d~~g~~DD~d~D~~~~D~rd  250 (338)
T KOG3647|consen  215 SMPFIPEKLIEEDDDDDDEGDLDDEDLDSEIPDIRD  250 (338)
T ss_pred             cchhhHHHhhhhhhhccccccccccccCCCCCchhh
Confidence            24443443432      3566677777777777654

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope

Probab=84.08  E-value=7.3  Score=34.17  Aligned_cols=10  Identities=20%  Similarity=0.607  Sum_probs=4.3

Q ss_pred             hhhchhhhhC
Q 027236          209 LQSFSDLLQR  218 (226)
Q Consensus       209 ~~~~~~~~~~  218 (226)
                      +.+|++|+.+
T Consensus       299 IatYR~LLEg  308 (312)
T PF00038_consen  299 IATYRKLLEG  308 (312)
T ss_dssp             HHHHHHHHTC
T ss_pred             HHHHHHHHhC
Confidence            3444444433

They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....

>KOG0979 consensus Structural maintenance of chromosome protein SMC5/Spr18, SMC superfamily [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=83.78  E-value=19  Score=36.83  Aligned_cols=107  Identities=20%  Similarity=0.238  Sum_probs=75.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHH
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVE  158 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~  158 (226)
                      +-...+..++.++-..+.++.+.+..-.+.  .+.-.-.++....+....++++.+++.++..+.        ++++.+.
T Consensus       821 ek~~~~~~e~~e~p~t~~eld~~I~~e~t~--~~~~~n~ne~~vq~y~~r~~el~~l~~~~~~~~--------~~le~i~  890 (1072)
T KOG0979|consen  821 EKSLVLMKELAEEPTTMDELDQAITDELTR--ALKFENVNEDAVQQYEVREDELRELETKLEKLS--------EDLERIK  890 (1072)
T ss_pred             hhHHHHHHHHHhCCCcHHHHHHHHHHHHHH--HHHHhcCChHHHHHHHHHHHHHHHHHhhhhhhh--------hhHHHHH
Confidence            334445556666666666776665443331  222234445578888999999999999987754        4577788


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCcccc
Q 027236          159 EMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYD  202 (226)
Q Consensus       159 ~~~~~~~~~w~kRkri~~~i~~~i~e~~~~~~k~l~e~lGie~D  202 (226)
                      +......+.|..+.   .+++..|.+.+    ..|+..+|.-+.
T Consensus       891 ~kl~~~ke~w~~~l---e~~V~~In~~F----s~~F~~mg~aGe  927 (1072)
T KOG0979|consen  891 DKLSDVKEVWLPKL---EEMVEQINERF----SQLFSSMGCAGE  927 (1072)
T ss_pred             HHHhhHHHHHHHHH---HHHHHHHHHHH----HHHHhhcccCce
Confidence            88888889999986   88999998887    368888887654

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=83.77  E-value=3  Score=35.86  Aligned_cols=54  Identities=17%  Similarity=0.367  Sum_probs=46.4

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCcee
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQK   64 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~k   64 (226)
                      .+-+..|++|+. ++...++.++...|   +|+..+|-+-|..|.++|+|. +.+|-..
T Consensus         4 ~~R~~~Il~~l~-~~~~~~~~ela~~l---~vS~~TiRRdL~~Le~~g~l~-r~~GGa~   57 (252)
T PRK10906          4 TQRHDAIIELVK-QQGYVSTEELVEHF---SVSPQTIRRDLNDLAEQNKIL-RHHGGAA   57 (252)
T ss_pred             HHHHHHHHHHHH-HcCCEeHHHHHHHh---CCCHHHHHHHHHHHHHCCCEE-EecCCEE
Confidence            466789999995 46679999999988   799999999999999999985 7888873

>COG3398 Uncharacterized protein conserved in archaea [Function unknown]

Probab=83.74  E-value=5.3  Score=33.93  Aligned_cols=65  Identities=15%  Similarity=0.258  Sum_probs=56.1

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFD   74 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~   74 (226)
                      ...+..|++|++. |--|++.++..|+   ++.+.++.=.|..|-..++|....+|-...|+++-..+-
T Consensus       100 ns~R~~Iy~~i~~-nPG~~lsEl~~nl---~i~R~TlRyhlriLe~~~li~a~~~~g~~~yfpa~~t~~  164 (240)
T COG3398         100 NSKRDGIYNYIKP-NPGFSLSELRANL---YINRSTLRYHLRILESNPLIEAGRVGGALRYFPADMTYG  164 (240)
T ss_pred             hhhHHHHHHHhcc-CCCccHHHHHHhc---CCChHHHHHHHHHHHhCcchhhhccCCceEEccCCCCcc
Confidence            4678999999984 4557889999988   789999999999999999999999999999988655544

>PHA03162 hypothetical protein; Provisional

Probab=83.73  E-value=19  Score=28.04  Aligned_cols=49  Identities=18%  Similarity=0.221  Sum_probs=37.6

Q ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC-----CCCCCHHHHHHHHHHHH
Q 027236          114 SNLTLEQIREKEAQLVKEVKEMENKLAKLRGG-----VTLVKPEDRMAVEEMFL  162 (226)
Q Consensus       114 ~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~~-----~~~vs~ee~~~~~~~~~  162 (226)
                      ..+|.+||.+++..|+-||+.|..+|..--++     +...||.+.+.+...|.
T Consensus        11 ~~~tmEeLaaeL~kLqmENK~LKkkl~~~~~~~~~p~d~~LTp~qKea~I~s~v   64 (135)
T PHA03162         11 AQPTMEDLAAEIAKLQLENKALKKKIKEGTDDDPLPGDPILTPAAKEAMIGAAT   64 (135)
T ss_pred             cCCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccCCHHHHHHHHHHHH
Confidence            46899999999999999999999998543222     34588888877665543

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=83.68  E-value=20  Score=29.70  Aligned_cols=38  Identities=13%  Similarity=0.183  Sum_probs=31.7

Q ss_pred             CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236           20 NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus        20 nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      +...+..++...+   ||+++.|-.+|..|..+|+|.....
T Consensus        28 G~~L~e~eLae~l---gVSRtpVREAL~~L~~eGlv~~~~~   65 (224)
T PRK11534         28 DEKLRMSLLTSRY---ALGVGPLREALSQLVAERLVTVVNQ   65 (224)
T ss_pred             CCcCCHHHHHHHH---CCChHHHHHHHHHHHHCCCEEEeCC
Confidence            5567766766666   8999999999999999999988654

>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT)

Probab=83.64  E-value=9.3  Score=29.47  Aligned_cols=30  Identities=27%  Similarity=0.479  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIR  110 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~  110 (226)
                      +..+..++..++.++..++.........|.
T Consensus        61 L~~lr~e~~~~~~~~~~l~~~~~~a~~~l~   90 (132)
T PF07926_consen   61 LQQLREELQELQQEINELKAEAESAKAELE   90 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444444444444333

These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore

>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development

Probab=83.53  E-value=9.2  Score=27.93  Aligned_cols=54  Identities=24%  Similarity=0.377  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 027236          119 EQIREKEAQLVKEVKEMENKLAKLRGG-VTLVKPEDRMAVEEMFLEKLSQWRKRK  172 (226)
Q Consensus       119 ~el~~~i~~L~~e~~~l~~kL~~l~~~-~~~vs~ee~~~~~~~~~~~~~~w~kRk  172 (226)
                      ..+..++..|+.++..|+..+..+.+. -...|..++..++..+..+.+.-+.||
T Consensus        15 e~~~~e~~~L~~~~~~L~~~~R~~~GedL~~Ls~~eL~~LE~~Le~aL~~VR~rK   69 (100)
T PF01486_consen   15 EELQQEIAKLRKENESLQKELRHLMGEDLESLSLKELQQLEQQLESALKRVRSRK   69 (100)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHhhhhhHHHHHHHH
Confidence            556667777777777777777777652 245677888888888877777777776

The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells

Probab=83.35  E-value=27  Score=30.07  Aligned_cols=52  Identities=15%  Similarity=0.174  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 027236          119 EQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRK  170 (226)
Q Consensus       119 ~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~~~w~k  170 (226)
                      .+|...|..+...|.++-+++..|..+....+..++...-.+...+..+-++
T Consensus        90 ~~L~~~i~~l~~~i~~l~~~~~~l~~~~~~~~~~~l~~~l~ea~~mL~emr~  141 (264)
T PF06008_consen   90 QDLEQFIQNLQDNIQELIEQVESLNENGDQLPSEDLQRALAEAQRMLEEMRK  141 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            5666677777777777777777776533344555555544444444444333

Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex

>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []

Probab=83.33  E-value=4.9  Score=27.60  Aligned_cols=38  Identities=32%  Similarity=0.462  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL  116 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~  116 (226)
                      .....+..++..++.+++.++.+...|+.++..+++.|
T Consensus        17 ~~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~   54 (80)
T PF04977_consen   17 SRYYQLNQEIAELQKEIEELKKENEELKEEIERLKNDP   54 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCH
Confidence            45667778888888888888888888888888885544

These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle

>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]

Probab=83.05  E-value=22  Score=30.38  Aligned_cols=27  Identities=22%  Similarity=0.352  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236          118 LEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus       118 ~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      +++|...+..|+.+..+.+++|+.++.
T Consensus       151 keeL~~eleele~e~ee~~erlk~le~  177 (290)
T COG4026         151 KEELLKELEELEAEYEEVQERLKRLEV  177 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566666666666666666666553

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=83.02  E-value=3.9  Score=29.78  Aligned_cols=48  Identities=23%  Similarity=0.256  Sum_probs=36.3

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      +-.|+.++......-. .+|.+.+   ++++++|..+|+.|++.|+|....-
T Consensus        24 q~~~L~~l~~~~~~~~-~~la~~l---~i~~~~vt~~l~~Le~~glv~r~~~   71 (126)
T COG1846          24 QYQVLLALYEAGGITV-KELAERL---GLDRSTVTRLLKRLEDKGLIERLRD   71 (126)
T ss_pred             HHHHHHHHHHhCCCcH-HHHHHHH---CCCHHHHHHHHHHHHHCCCeeecCC
Confidence            4456666665443332 6777766   8999999999999999999988766

>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=82.83  E-value=3.5  Score=30.33  Aligned_cols=57  Identities=25%  Similarity=0.412  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee-----ecCceeEEEe
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK-----EYGKQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K-----~~GK~kiY~~   68 (226)
                      ....|++.|... ..-+-.+|...+   +++...|-++|..|.++|+|...     .-|-..+||.
T Consensus        14 ~~~~Il~~L~~~-~~l~de~la~~~---~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~   75 (105)
T PF02002_consen   14 EAVRILDALLRK-GELTDEDLAKKL---GLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWY   75 (105)
T ss_dssp             TTHHHHHHHHHH---B-HHHHHHTT----S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE
T ss_pred             hHHHHHHHHHHc-CCcCHHHHHHHh---CCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEE
Confidence            345667777643 345655665544   89999999999999999999766     3477788898

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.

>PHA03155 hypothetical protein; Provisional

Probab=82.83  E-value=18  Score=27.35  Aligned_cols=48  Identities=19%  Similarity=0.255  Sum_probs=37.2

Q ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHHHHHhh-CCCCCCCHHHHHHHHHHH
Q 027236          114 SNLTLEQIREKEAQLVKEVKEMENKLAKLR-GGVTLVKPEDRMAVEEMF  161 (226)
Q Consensus       114 ~~~t~~el~~~i~~L~~e~~~l~~kL~~l~-~~~~~vs~ee~~~~~~~~  161 (226)
                      ..+|.+||.+++..|+-|++.|..+|..-- .++..+||.+.+.+...+
T Consensus         6 ~~~tvEeLaaeL~kL~~ENK~LKkkl~~~~~p~d~~LT~~qKea~I~s~   54 (115)
T PHA03155          6 ACADVEELEKELQKLKIENKALKKKLLQHGNPEDELLTPAQKDAIINSL   54 (115)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCccccCHHHHHHHHHHH
Confidence            357889999999999999999999985422 245678888877665553

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=82.81  E-value=6.4  Score=33.02  Aligned_cols=53  Identities=11%  Similarity=0.290  Sum_probs=37.9

Q ss_pred             chHHHHHHHHHHhc----CCCC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            6 DNTEAIVLNYVNEQ----NRPL-NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         6 ~ea~~~Il~y~~~~----nrPy-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      +.+.+.|.+.+...    +.+. |-.++...+   ||+++.|-+||..|..+|+|......
T Consensus        10 ~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~---gVSRt~VReAL~~L~~eGlv~~~~g~   67 (239)
T PRK04984         10 GFAEEYIIESIWNNRFPPGSILPAERELSELI---GVTRTTLREVLQRLARDGWLTIQHGK   67 (239)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEeCCC
Confidence            34444444444432    3456 666777666   89999999999999999999987553

>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others

Probab=82.77  E-value=6.2  Score=30.95  Aligned_cols=60  Identities=18%  Similarity=0.398  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 027236           82 NQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAK  141 (226)
Q Consensus        82 ~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~  141 (226)
                      ..++......+.++.....++..+..++......+|.++....-.++.....+++.....
T Consensus        39 ~~l~~~~~~~~~~l~~~~~el~~~~~~l~~~~~~ls~~~~~~~~~~l~~~~~~l~~~~~~   98 (158)
T PF03938_consen   39 AKLQEKFKALQKELQAKQKELQKLQQKLQSQKATLSEEERQKRQQELQQKEQELQQFQQQ   98 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS----SSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555666666677777776666666666666777777766666666555555554433

OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.

>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles

Probab=82.67  E-value=6.5  Score=26.91  Aligned_cols=55  Identities=20%  Similarity=0.367  Sum_probs=42.0

Q ss_pred             HHHHHHhcCCCCcHHHHHHHHhcc-----cccHHHHHHHHHHHHHcCCcceeecC-----ceeEEEe
Q 027236           12 VLNYVNEQNRPLNSQNVADALQKY-----NLKKAGIQKALDSLADNGKISFKEYG-----KQKIYIA   68 (226)
Q Consensus        12 Il~y~~~~nrPys~~di~~~l~~~-----~v~K~~v~k~L~~Lv~~g~i~~K~~G-----K~kiY~~   68 (226)
                      ||..+..  +|.+--+|...+...     .|+..+|=.+|+.|.++|+|.+..-.     ..++|.+
T Consensus         1 iL~~L~~--~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~i   65 (75)
T PF03551_consen    1 ILGLLSE--GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRI   65 (75)
T ss_dssp             HHHHHHH--S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEE
T ss_pred             Chhhhcc--CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEE
Confidence            4556654  777777777666552     58899999999999999999998775     4678877

In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....

>PHA02562 46 endonuclease subunit; Provisional

Probab=82.62  E-value=25  Score=33.30  Aligned_cols=63  Identities=14%  Similarity=0.330  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--CCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSN--LTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~--~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +..+..++..+..++..+..++..++..+..+.+.  ...+++..++..+..+...++.++..++
T Consensus       176 ~~e~~~~i~~l~~~i~~l~~~i~~~~~~i~~~~~~~~~~i~~l~~e~~~l~~~~~~l~~~l~~l~  240 (562)
T PHA02562        176 IRELNQQIQTLDMKIDHIQQQIKTYNKNIEEQRKKNGENIARKQNKYDELVEEAKTIKAEIEELT  240 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555555555444444443  2234555555555555444444444443

>PF07200 Mod_r: Modifier of rudimentary (Mod(r)) protein; InterPro: IPR009851 This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins

Probab=82.35  E-value=22  Score=27.78  Aligned_cols=90  Identities=20%  Similarity=0.220  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHH
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVE  158 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~  158 (226)
                      .++..+..++..+..++..+..+...+..++..+....+..-+...+.   ..+.+.++.=+.+..... -..-++....
T Consensus        55 ~~l~~~r~~l~~~~~~~~~L~~~~~~k~~~~~~l~~~~s~~~l~~~L~---~~~~e~eeeSe~lae~fl-~g~~d~~~Fl  130 (150)
T PF07200_consen   55 PELEELRSQLQELYEELKELESEYQEKEQQQDELSSNYSPDALLARLQ---AAASEAEEESEELAEEFL-DGEIDVDDFL  130 (150)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH---HHHHHHHHHHHHHC-S-S-SSHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHH---HHHHHHHHHHHHHHHHHh-CCCCCHHHHH
Confidence            567777888888888888888888888888888866555555555444   444444444434432111 1245677788


Q ss_pred             HHHHHHHHHHHHHH
Q 027236          159 EMFLEKLSQWRKRK  172 (226)
Q Consensus       159 ~~~~~~~~~w~kRk  172 (226)
                      +.|...++.|-.|+
T Consensus       131 ~~f~~~R~~yH~R~  144 (150)
T PF07200_consen  131 KQFKEKRKLYHLRR  144 (150)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            88888888888876

The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [], and both of these regions are represented in this family.; PDB: 2CAZ_F 2P22_C 2F66_F.

>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]

Probab=82.23  E-value=11  Score=32.05  Aligned_cols=56  Identities=34%  Similarity=0.486  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      .....++++.+.++..+..+|..++..+.+.  -+++...+..|+.+++.|++.+..+
T Consensus       134 ke~~ee~kekl~E~~~EkeeL~~eleele~e--~ee~~erlk~le~E~s~LeE~~~~l  189 (290)
T COG4026         134 KEDYEELKEKLEELQKEKEELLKELEELEAE--YEEVQERLKRLEVENSRLEEMLKKL  189 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3444444444444444444444444444432  2455566666666666666665443

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=82.23  E-value=7.1  Score=36.77  Aligned_cols=57  Identities=11%  Similarity=0.202  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236           86 EENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus        86 ~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      ..+.+-+....+|++++..++.++..+....  .++..+|++|+.++..|+.+++.+..
T Consensus        69 SALteqQ~kasELEKqLaaLrqElq~~saq~--~dle~KIkeLEaE~~~Lk~Ql~a~~~  125 (475)
T PRK13729         69 HATTEMQVTAAQMQKQYEEIRRELDVLNKQR--GDDQRRIEKLGQDNAALAEQVKALGA  125 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh--hhHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            4444555556666666666655555444332  46688889999999999999865543

>PF15456 Uds1: Up-regulated During Septation

Probab=82.22  E-value=21  Score=27.51  Aligned_cols=70  Identities=30%  Similarity=0.408  Sum_probs=46.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHhccCC---------HHHHHHHHHHHHHHHHHHH
Q 027236           73 FDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEI-------RTLQSNLT---------LEQIREKEAQLVKEVKEME  136 (226)
Q Consensus        73 ~~~~~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el-------~~l~~~~t---------~~el~~~i~~L~~e~~~l~  136 (226)
                      |..++.+|++.+..++..|...+..++..+. ++..+       ..+...++         ..+-...+.+....|.++.
T Consensus        16 feiLs~eEVe~LKkEl~~L~~R~~~lr~kl~-le~k~RdAa~sl~~l~~~~~~~~~~~~~~~~~~eeel~~~~rk~ee~~   94 (124)
T PF15456_consen   16 FEILSFEEVEELKKELRSLDSRLEYLRRKLA-LESKIRDAAHSLSRLYSSSSRRARFSRESSLKAEEELAESDRKCEELA   94 (124)
T ss_pred             CcccCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhcCCCccccCCCcchHHHHHHHHHHHHhhHHHHH
Confidence            6777889999998888888888887776666 44444       33333333         3445555666666666666


Q ss_pred             HHHHHhh
Q 027236          137 NKLAKLR  143 (226)
Q Consensus       137 ~kL~~l~  143 (226)
                      .+|..+.
T Consensus        95 ~eL~~le  101 (124)
T PF15456_consen   95 QELWKLE  101 (124)
T ss_pred             HHHHHHH
Confidence            6665554

>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=82.19  E-value=27  Score=28.72  Aligned_cols=32  Identities=25%  Similarity=0.396  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 027236           83 QMKEENAKLQEQLEEQRKAISKLEGEIRTLQS  114 (226)
Q Consensus        83 ~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~  114 (226)
                      .+..++.++.....++...+..+..++..+..
T Consensus        78 ~l~~ELael~r~~~el~~~L~~~~~~l~~l~~  109 (194)
T PF08614_consen   78 KLQEELAELYRSKGELAQQLVELNDELQELEK  109 (194)
T ss_dssp             --------------------------------
T ss_pred             cccccccccccccccccccccccccccchhhh
Confidence            33444444444444444444444444444443

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=82.15  E-value=4.6  Score=34.78  Aligned_cols=58  Identities=21%  Similarity=0.352  Sum_probs=48.5

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEE
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYI   67 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~   67 (226)
                      +|-+.||+-|...+--.+..++.+.+   ||+.+.|..++..|...|.|....-|..-.|+
T Consensus       183 eAv~~IL~~L~~~egrlse~eLAerl---GVSRs~ireAlrkLE~aGvIe~r~LG~kGt~V  240 (251)
T TIGR02787       183 EAVEHIFEELDGNEGLLVASKIADRV---GITRSVIVNALRKLESAGVIESRSLGMKGTYI  240 (251)
T ss_pred             HHHHHHHHHhccccccccHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEeccCCCCccEe
Confidence            67788888888766667877888877   89999999999999999999999988544444

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.

>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure

Probab=82.09  E-value=15  Score=26.10  Aligned_cols=47  Identities=15%  Similarity=0.331  Sum_probs=38.1

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .|+..+..  .|-...++...++  +|+...+.+.|..|.+.|+|....+.
T Consensus         9 ~IL~~l~~--g~~rf~el~~~l~--~is~~~L~~~L~~L~~~GLv~r~~~~   55 (90)
T PF01638_consen    9 LILRALFQ--GPMRFSELQRRLP--GISPKVLSQRLKELEEAGLVERRVYP   55 (90)
T ss_dssp             HHHHHHTT--SSEEHHHHHHHST--TS-HHHHHHHHHHHHHTTSEEEEEES
T ss_pred             HHHHHHHh--CCCcHHHHHHhcc--hhHHHHHHHHHHHHHHcchhhccccc
Confidence            45666665  6888788988885  79999999999999999999888773

The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.

>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=82.02  E-value=15  Score=26.04  Aligned_cols=54  Identities=19%  Similarity=0.308  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236           91 LQEQLEEQRKAISKLEGEIRTLQSN-LTLEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus        91 l~~~l~~l~~~~k~l~~el~~l~~~-~t~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      +......++..+...++-+..+-.. .|.++-..+|.+|++++....+-|..|++
T Consensus        26 ~~~~~~~lk~Klq~ar~~i~~lpgi~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~   80 (83)
T PF07544_consen   26 LDTATGSLKHKLQKARAAIRELPGIDRSVEEQEEEIEELEEQIRKKREVLQKFKE   80 (83)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444455555555555555543 77789999999999999999998888874

Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex

>PRK03918 chromosome segregation protein; Provisional

Probab=81.80  E-value=29  Score=34.94  Aligned_cols=30  Identities=33%  Similarity=0.480  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           84 MKEENAKLQEQLEEQRKAISKLEGEIRTLQ  113 (226)
Q Consensus        84 l~~~i~~l~~~l~~l~~~~k~l~~el~~l~  113 (226)
                      +..++..++.++..++.++..+..++..+.
T Consensus       624 ~~~~l~~~~~~i~~l~~~i~~l~~~~~~l~  653 (880)
T PRK03918        624 LEEELDKAFEELAETEKRLEELRKELEELE  653 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444555555555555555554

>KOG4302 consensus Microtubule-associated protein essential for anaphase spindle elongation [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=81.79  E-value=56  Score=32.23  Aligned_cols=76  Identities=21%  Similarity=0.288  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhC--CC------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236          119 EQIREKEAQLVKEVKEMENKLAKLRG--GV------------TLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIME  184 (226)
Q Consensus       119 ~el~~~i~~L~~e~~~l~~kL~~l~~--~~------------~~vs~ee~~~~~~~~~~~~~~w~kRkri~~~i~~~i~e  184 (226)
                      ++|.++..+-..++.++..+++.|..  |.            ..+|-+.++.+...+..++++...|.+-+.+++..|  
T Consensus       113 e~lr~qk~eR~~ef~el~~qie~l~~~l~g~~~~~~~~~~D~~dlsl~kLeelr~~L~~L~~ek~~Rlekv~~~~~~I--  190 (660)
T KOG4302|consen  113 EGLRKQKDERRAEFKELYHQIEKLCEELGGPEDLPSFLIADESDLSLEKLEELREHLNELQKEKSDRLEKVLELKEEI--  190 (660)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccCCcccccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
Confidence            55555666666666666666666642  11            245667888888999999999999986555554443  


Q ss_pred             cCCCCHHHHHHHhCcccc
Q 027236          185 NSPKNLKEFKEELGIEYD  202 (226)
Q Consensus       185 ~~~~~~k~l~e~lGie~D  202 (226)
                            ..+++.||++..
T Consensus       191 ------~~l~~~Lg~~~~  202 (660)
T KOG4302|consen  191 ------KSLCSVLGLDFS  202 (660)
T ss_pred             ------HHHHHHhCCCcc
Confidence                  346666666654

>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

Probab=81.45  E-value=46  Score=30.99  Aligned_cols=20  Identities=20%  Similarity=0.287  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhc
Q 027236          166 SQWRKRKRMLRDIWDPIMEN  185 (226)
Q Consensus       166 ~~w~kRkri~~~i~~~i~e~  185 (226)
                      ..-+.|++.+-.+++++.-.
T Consensus       108 ~q~r~qr~~La~~L~A~~r~  127 (420)
T COG4942         108 VQEREQRRRLAEQLAALQRS  127 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHhc
Confidence            33366777777788876554

>PRK00117 recX recombination regulator RecX; Reviewed

Probab=81.36  E-value=3.8  Score=32.33  Aligned_cols=54  Identities=17%  Similarity=0.281  Sum_probs=45.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ..|....+.|+-  .|+||..+|..-|...|++...|..+|+.|.+.|.|.-..|.
T Consensus        11 ~~a~~~al~~L~--~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a   64 (157)
T PRK00117         11 ASARARALRLLA--RREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFA   64 (157)
T ss_pred             HHHHHHHHHHHc--cchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHH
Confidence            567777888886  779999999999988899999999999999999887544443

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=81.33  E-value=22  Score=30.07  Aligned_cols=48  Identities=17%  Similarity=0.215  Sum_probs=38.1

Q ss_pred             hcCCC--CcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           18 EQNRP--LNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        18 ~~nrP--ys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ..++|  -|..++.+.+   +++++++.+.|+.|.+.|+|.....+....++.
T Consensus        15 ~l~~~~~IS~~eLA~~L---~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~L   64 (217)
T PRK14165         15 AVNNTVKISSSEFANHT---GTSSKTAARILKQLEDEGYITRTIVPRGQLITI   64 (217)
T ss_pred             ccCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEE
Confidence            34444  5788888888   799999999999999999999887765544444

>PRK05638 threonine synthase; Validated

Probab=81.29  E-value=4.8  Score=37.45  Aligned_cols=60  Identities=22%  Similarity=0.300  Sum_probs=49.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee-ecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK-EYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K-~~GK~kiY~~   68 (226)
                      +..+-.||.+|.+.  |.+..+|...+.. .++.++|-..|..|.+.|+|... .-|+.++|..
T Consensus       370 ~~~r~~IL~~L~~~--~~~~~el~~~l~~-~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~L  430 (442)
T PRK05638        370 GGTKLEILKILSER--EMYGYEIWKALGK-PLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKL  430 (442)
T ss_pred             cchHHHHHHHHhhC--CccHHHHHHHHcc-cCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEE
Confidence            46688999999844  8889999998853 48999999999999999999874 4488666666

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=81.25  E-value=3.1  Score=34.61  Aligned_cols=49  Identities=16%  Similarity=0.335  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHHhc--------------CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            7 NTEAIVLNYVNEQ--------------NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         7 ea~~~Il~y~~~~--------------nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      .++++|..||..-              .-|++-++|.+.|   |++..+|.++|..|..+|+|...
T Consensus       155 ~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~l---G~sr~tvsR~l~~l~~~g~I~~~  217 (235)
T PRK11161        155 NAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYL---GLTVETISRLLGRFQKSGMLAVK  217 (235)
T ss_pred             CHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHh---CCcHHHHHHHHHHHHHCCCEEec
Confidence            5677777777652              1378889999988   89999999999999999999844

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=81.22  E-value=4.5  Score=35.15  Aligned_cols=53  Identities=13%  Similarity=0.310  Sum_probs=45.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ   63 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~   63 (226)
                      .+-...|++++....+ .++.++...|   +|+..+|.+=|..|.+.|++. +.+|-.
T Consensus        16 ~eR~~~Il~~L~~~~~-vtv~eLa~~l---~VS~~TIRRDL~~Le~~G~l~-r~~GGa   68 (269)
T PRK09802         16 SERREQIIQRLRQQGS-VQVNDLSALY---GVSTVTIRNDLAFLEKQGIAV-RAYGGA   68 (269)
T ss_pred             HHHHHHHHHHHHHcCC-EeHHHHHHHH---CCCHHHHHHHHHHHHhCCCeE-EEeCCE
Confidence            5668899999997665 8999999988   899999999999999999998 666664

>PF04065 Not3: Not1 N-terminal domain, CCR4-Not complex component ; InterPro: IPR007207 The Ccr4-Not complex (Not1, Not2, Not3, Not4 and Not5) is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID []

Probab=81.22  E-value=34  Score=29.30  Aligned_cols=82  Identities=17%  Similarity=0.223  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCH----HHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHH
Q 027236           83 QMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTL----EQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVE  158 (226)
Q Consensus        83 ~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~----~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~  158 (226)
                      -+..-|.+|..++..+..++-.|......-+...+.    +++...+...+-=+..|+.-|..|.++.  ++|+.+..++
T Consensus       126 wl~~~Id~L~~QiE~~E~E~E~L~~~~kKkk~~~~~~~r~~~l~~~ierhk~Hi~kLE~lLR~L~N~~--l~~e~V~~ik  203 (233)
T PF04065_consen  126 WLKDSIDELNRQIEQLEAEIESLSSQKKKKKKDSTKQERIEELESRIERHKFHIEKLELLLRLLDNDE--LDPEQVEDIK  203 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhccCccCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC--CCHHHHHHHH
Confidence            345555666666666665555555433222111222    5666667777777778888777777654  7899988888


Q ss_pred             HHHHHHHH
Q 027236          159 EMFLEKLS  166 (226)
Q Consensus       159 ~~~~~~~~  166 (226)
                      ..+..+..
T Consensus       204 edieyYve  211 (233)
T PF04065_consen  204 EDIEYYVE  211 (233)
T ss_pred             HHHHHHHH
Confidence            77754443

This domain is the N-terminal region of the Not proteins.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=80.92  E-value=7  Score=27.71  Aligned_cols=54  Identities=15%  Similarity=0.212  Sum_probs=40.6

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ....-+....++|.|=..|.+.|   |++.++|-|.+++|-+.|.=+.-.-  ++-|-.
T Consensus         7 ~~~~ll~~~~~~~~SGe~La~~L---giSRtaVwK~Iq~Lr~~G~~I~s~~--~kGY~L   60 (79)
T COG1654           7 MLLLLLLLLTGNFVSGEKLAEEL---GISRTAVWKHIQQLREEGVDIESVR--GKGYLL   60 (79)
T ss_pred             HHHHHHHHcCCCcccHHHHHHHH---CccHHHHHHHHHHHHHhCCceEecC--CCceec
Confidence            33444556678899999999988   8999999999999999997554433  334544

>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]

Probab=80.84  E-value=16  Score=37.69  Aligned_cols=51  Identities=31%  Similarity=0.507  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhccC------CHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236           94 QLEEQRKAISKLEGEIRTLQSNL------TLEQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus        94 ~l~~l~~~~k~l~~el~~l~~~~------t~~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      .+..++..+..++..+..+....      ..+|+..+++.|++++..+++.+..|+.
T Consensus       366 ~i~~~k~~~d~l~k~I~~~~~~~~~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~  422 (1074)
T KOG0250|consen  366 SIRKLKKEVDRLEKQIADLEKQTNNELGSELEERENKLEQLKKEVEKLEEQINSLRE  422 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444432      2267778888888888888888877764

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=80.66  E-value=30  Score=28.41  Aligned_cols=57  Identities=16%  Similarity=0.180  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC--ceeEEEe
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG--KQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G--K~kiY~~   68 (226)
                      .+-.||.++.. +.+-+.++|.+.+   ++.+++|..+|+.|..+|+|....-.  +=.+|..
T Consensus        46 ~q~~iL~~L~~-~~~itq~eLa~~l---~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~  104 (185)
T PRK13777         46 NEHHILWIAYH-LKGASISEIAKFG---VMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIE  104 (185)
T ss_pred             HHHHHHHHHHh-CCCcCHHHHHHHH---CCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEE
Confidence            34568877765 5588999998866   68999999999999999999976543  3344444

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

Probab=80.44  E-value=15  Score=25.41  Aligned_cols=49  Identities=20%  Similarity=0.286  Sum_probs=31.7

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .||.++.  +.|-+.++|...+   +++-..+.+.|..|.+.|+|.  .  ....|..
T Consensus        10 ~IL~~l~--~~~~~~t~i~~~~---~L~~~~~~~yL~~L~~~gLI~--~--~~~~Y~l   58 (77)
T PF14947_consen   10 DILKILS--KGGAKKTEIMYKA---NLNYSTLKKYLKELEEKGLIK--K--KDGKYRL   58 (77)
T ss_dssp             HHHHHH---TT-B-HHHHHTTS---T--HHHHHHHHHHHHHTTSEE--E--ETTEEEE
T ss_pred             HHHHHHH--cCCCCHHHHHHHh---CcCHHHHHHHHHHHHHCcCee--C--CCCEEEE
Confidence            3555554  5666666675433   789999999999999999992  1  4566666

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=80.38  E-value=3.2  Score=33.45  Aligned_cols=49  Identities=14%  Similarity=0.270  Sum_probs=39.3

Q ss_pred             hcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeec
Q 027236           18 EQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQ   70 (226)
Q Consensus        18 ~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q   70 (226)
                      ....|.++.+|...+   +++...+.++|..|+..|+|.+ .-|..==|....
T Consensus        21 ~~~~~vs~~eIA~~~---~ip~~~l~kIl~~L~~aGLv~s-~rG~~GGy~Lar   69 (164)
T PRK10857         21 SEAGPVPLADISERQ---GISLSYLEQLFSRLRKNGLVSS-VRGPGGGYLLGK   69 (164)
T ss_pred             CCCCcCcHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEe-CCCCCCCeeccC
Confidence            344699999998877   7999999999999999999998 435444576633

>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]

Probab=80.20  E-value=56  Score=31.49  Aligned_cols=26  Identities=19%  Similarity=0.492  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236          119 EQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus       119 ~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      .++.+++..++..+..+++.+..|+.
T Consensus       151 ~~leAe~~~~krr~~~le~e~~~Lk~  176 (546)
T KOG0977|consen  151 SELEAEINTLKRRIKALEDELKRLKA  176 (546)
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            56677777788888888888887765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	226
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.7 bits (102), Expect = 3e-05
 Identities = 30/223 (13%), Positives = 65/223 (29%), Gaps = 68/223 (30%)

Query: 6   DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLAD---NGKISFKEYGK 62
              E +V  +V E  R  N + +   ++    + + + +      D   N    F +Y  
Sbjct: 73  SKQEEMVQKFVEEVLRI-NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY-- 129

Query: 63  QKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAI------------SKLEGEIR 110
               ++R   +                KL++ L E R A             + +  +  
Sbjct: 130 ---NVSRLQPYL---------------KLRQALLELRPAKNVLIDGVLGSGKTWVALD-- 169

Query: 111 TLQSN------------LTLEQIREKEAQLVKEVKEMENKLAKLRGGVT-----LVKPED 153
              S             L L+     E  L    + ++  L ++    T         + 
Sbjct: 170 VCLSYKVQCKMDFKIFWLNLKNCNSPETVL----EMLQKLLYQIDPNWTSRSDHSSNIKL 225

Query: 154 RMAVEEMFLEKLSQWRKRKRML---RDIWDPIMENSPKNLKEF 193
           R+   +  L +L + +  +  L    ++ +       K    F
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQN------AKAWNAF 262

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 27/153 (17%), Positives = 59/153 (38%), Gaps = 12/153 (7%)

Query: 53   GKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTL 112
              ++ +E  K KI     +++     +    ++ +  +LQ +++EQ K    L  ++  L
Sbjct: 899  RMMAKRELKKLKIEARSVERYK----KLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNL 954

Query: 113  QSNLT--LEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRK 170
            +   +   E++R    +L    +E +N   ++         ++ +A     L +    +K
Sbjct: 955  EITYSTETEKLRSDVERLRMSEEEAKNATNRVL------SLQEEIAKLRKELHQTQTEKK 1008

Query: 171  RKRMLRDIWDPIMENSPKNLKEFKEELGIEYDE 203
                  D +    E     LKE    L  E +E
Sbjct: 1009 TIEEWADKYKHETEQLVSELKEQNTLLKTEKEE 1041

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 21/131 (16%), Positives = 55/131 (41%), Gaps = 21/131 (16%)

Query: 79   EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQS----------NLT--LEQIREKEA 126
            E   Q++ E  K+Q+Q+ +  + + + E   + LQ            +   +  + ++  
Sbjct: 941  ERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNN 1000

Query: 127  QLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENS 186
            +L KE K +E +++ L            +A EE   + L++ + +   +    +  ++  
Sbjct: 1001 KLTKERKLLEERVSDL---------TTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKE 1051

Query: 187  PKNLKEFKEEL 197
             K+ +E ++  
Sbjct: 1052 EKSRQELEKIK 1062

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	226
1p6r_A	82	Penicillinase repressor; transcription regulation,	97.81
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.77
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	97.71
3viq_B	85	Mating-type switching protein SWI5; recombination	97.67
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	97.65
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	97.54
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	97.47
3jth_A	98	Transcription activator HLYU; transcription factor	97.45
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	97.38
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	97.38
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	97.36
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	97.3
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	97.28
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	97.27
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	97.26
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	97.22
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	97.16
3r0a_A	123	Putative transcriptional regulator; structural gen	97.16
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	97.16
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.13
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	97.11
1ucr_A	78	Protein DSVD; dissimilatory sulfite reductase D, D	97.1
2kko_A	108	Possible transcriptional regulatory protein (possi	97.08
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	97.07
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	97.05
2w57_A	150	Ferric uptake regulation protein; gene regulation,	97.03
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	96.92
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.9
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	96.9
4ets_A	162	Ferric uptake regulation protein; metal binding pr	96.87
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	96.85
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	96.79
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.79
1okr_A	123	MECI, methicillin resistance regulatory protein ME	96.75
1y0u_A	96	Arsenical resistance operon repressor, putative; s	96.74
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.71
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	96.71
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	96.68
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	96.68
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.61
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	96.55
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	96.55
1ku9_A	152	Hypothetical protein MJ223; putative transcription	96.49
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	96.44
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	96.43
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	96.4
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	96.38
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	96.37
2gxg_A	146	146AA long hypothetical transcriptional regulator;	96.3
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	96.26
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	96.26
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	96.25
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	96.21
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	96.19
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.19
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.19
2eth_A	154	Transcriptional regulator, putative, MAR family; M	96.06
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	96.04
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	95.83
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	95.69
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	95.66
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	95.6
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	95.58
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	95.55
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	95.54
2pg4_A	95	Uncharacterized protein; structural genomics, join	95.54
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	95.34
2nnn_A	140	Probable transcriptional regulator; structural gen	95.33
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	95.32
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	95.32
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	95.3
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	95.28
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	95.26
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	95.21
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	95.07
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	95.04
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	94.92
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	94.87
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	94.79
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	94.73
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	94.72
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.63
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	94.59
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	94.58
3s2w_A	159	Transcriptional regulator, MARR family; structural	94.55
1yyv_A	131	Putative transcriptional regulator; reductive meth	94.53
3df8_A	111	Possible HXLR family transcriptional factor; APC89	94.53
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	94.52
3bja_A	139	Transcriptional regulator, MARR family, putative;	94.52
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	94.51
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	94.44
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	94.42
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	94.37
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	94.35
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	94.32
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	94.2
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	94.1
1z91_A	147	Organic hydroperoxide resistance transcriptional;	94.03
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	94.02
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	93.97
3nqo_A	189	MARR-family transcriptional regulator; structural	93.9
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	93.88
1mkm_A	249	ICLR transcriptional regulator; structural genomic	93.84
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	93.53
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	93.52
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	93.19
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	93.17
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	93.15
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	92.99
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	92.89
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	92.82
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	92.82
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	92.8
2pex_A	153	Transcriptional regulator OHRR; transcription regu	92.78
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	92.76
3f3x_A	144	Transcriptional regulator, MARR family, putative;	92.69
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	92.67
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	92.62
2g7u_A	257	Transcriptional regulator; ICLR family, structural	92.6
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	92.6
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	92.59
2dk8_A	81	DNA-directed RNA polymerase III 39 kDa polypeptide	92.47
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	92.36
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	92.34
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	92.3
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	92.12
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	92.11
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	92.04
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	92.0
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	91.98
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	91.96
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	91.94
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	91.84
2qc0_A	373	Uncharacterized protein; NP_719793.1, uncharacteri	91.77
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	91.62
2hgc_A	102	YJCQ protein; SR346, structure, autostructure, NES	91.6
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	91.45
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	91.34
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	91.31
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	91.29
2oa5_A	110	Hypothetical protein BQLF2; MHR28B, NESG, structur	90.95
1bia_A	321	BIRA bifunctional protein; transcription regulatio	90.84
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	90.84
3lay_A	175	Zinc resistance-associated protein; salmonella typ	90.82
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	90.8
2h09_A	155	Transcriptional regulator MNTR; transcription regu	90.75
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	90.63
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	90.62
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	90.46
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	90.44
3qne_A	485	Seryl-tRNA synthetase, cytoplasmic; amino acid bio	90.4
1u5t_B	169	Defective in vacuolar protein sorting; VPS36P; ESC	90.39
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	90.37
1ylf_A	149	RRF2 family protein; structural genomics, transcri	90.25
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	90.24
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	90.12
2dq0_A	455	Seryl-tRNA synthetase; coiled-coil, homodimer, str	90.1
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	89.79
3eyi_A	72	Z-DNA-binding protein 1; alternative splicing, DNA	89.66
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	89.3
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	89.3
2w25_A	150	Probable transcriptional regulatory protein; trans	89.09
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	88.85
3eqx_A	373	FIC domain containing transcriptional regulator; F	88.74
3k69_A	162	Putative transcription regulator; putative transcr	88.67
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	88.65
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	88.5
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	88.47
3dfg_A	162	Xcrecx, regulatory protein RECX; RECX RECA, homolo	88.46
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	88.24
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	88.19
2vn2_A	128	DNAD, chromosome replication initiation protein; D	88.05
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	88.04
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	87.95
1xma_A	145	Predicted transcriptional regulator; southea colla	87.93
2fxa_A	207	Protease production regulatory protein HPR; protea	87.73
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	87.71
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	87.47
4g6q_A	182	Putative uncharacterized protein; structural genom	87.47
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	87.25
1wle_A	501	Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bo	87.15
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	86.73
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	86.45
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	86.1
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	86.06
4fx0_A	148	Probable transcriptional repressor protein; helix-	85.9
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	85.87
1bja_A	95	Transcription regulatory protein MOTA; activation	85.86
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	85.6
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	85.53
1g6u_A	48	Domain swapped dimer; designed three helix bundle,	85.49
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	85.34
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	85.34
1w7p_D	566	VPS36P, YLR417W; ESCRT-II complex, endosomal prote	85.26
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	85.21
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	84.78
1z05_A	429	Transcriptional regulator, ROK family; structural	84.69
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	84.06
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	83.94
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	83.72
3kn1_A	249	Golgi phosphoprotein 3; beta hairpin, phosphoinosi	83.48
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	83.24
3by6_A	126	Predicted transcriptional regulator; structural ge	83.21
1xd7_A	145	YWNA; structural genomics, protein structure initi	83.19
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	83.11
1ses_A	421	Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A	82.92
2dq3_A	425	Seryl-tRNA synthetase; coiled-coil, homodimer, str	82.88
4esf_A	117	PADR-like transcriptional regulator; PADR family,	82.8
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	82.62
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	82.35
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	82.27
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	81.87
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	81.79
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	81.7
3eet_A	272	Putative GNTR-family transcriptional regulator; st	81.55
2co5_A	99	Viral protein F93; viral protein-winged helix comp	81.44
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	81.21
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	80.96
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	80.88
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	80.61
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	80.54
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	80.49
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	80.41
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	80.18
3lss_A	484	Seryl-tRNA synthetase; aminoacyl-tRNA synthetase,	80.01

>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=97.81  E-value=0.00012  Score=50.65  Aligned_cols=64  Identities=20%  Similarity=0.313  Sum_probs=56.8

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEeec
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQ   70 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q   70 (226)
                      ...+..||.++.. +.|.++.+|.+.++. .+++.++|...|+.|++.|+|.....|...+|.+..
T Consensus         8 t~~e~~vL~~L~~-~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~gr~~~y~~~~   72 (82)
T 1p6r_A            8 SDAELEVMKVIWK-HSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKEGRVFVYTPNI   72 (82)
T ss_dssp             CHHHHHHHHHHHT-SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESC
T ss_pred             CHHHHHHHHHHHc-CCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEecCCEEEEEeec
Confidence            5788899999987 789999999998864 258999999999999999999999999999998743

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=97.77  E-value=9.1e-05  Score=49.89  Aligned_cols=53  Identities=17%  Similarity=0.267  Sum_probs=46.8

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ++.+..||++|....+|.|+.+|...+   ++++++|.+.|..|.+.|.|....-|
T Consensus         9 ~~~~~~IL~~L~~~~~~~s~~eLA~~l---glsr~tv~~~l~~L~~~G~I~~~~~G   61 (67)
T 2heo_A            9 DNLEQKILQVLSDDGGPVAIFQLVKKC---QVPKKTLNQVLYRLKKEDRVSSPSPK   61 (67)
T ss_dssp             CHHHHHHHHHHHHHCSCEEHHHHHHHH---CSCHHHHHHHHHHHHHTTSEEEEETT
T ss_pred             cHHHHHHHHHHHHcCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCcEecCCCc
Confidence            567889999999877899999999988   89999999999999999998765444

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=97.71  E-value=7.5e-05  Score=51.47  Aligned_cols=57  Identities=14%  Similarity=0.197  Sum_probs=52.2

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      ++.+++||+.|.+...|.++.+|...+   ||.|-.|-++|..|-.+|+|.+-    ...||+.
T Consensus        18 ~d~eekVLe~LkeaG~PlkageIae~~---GvdKKeVdKaik~LKkEgkI~SP----kRCyw~~   74 (80)
T 2lnb_A           18 GHLEQRILQVLTEAGSPVKLAQLVKEC---QAPKRELNQVLYRMKKELKVSLT----SPATWCL   74 (80)
T ss_dssp             HHHHHHHHHHHHHHTSCEEHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEE----ETTEEEE
T ss_pred             chHHHHHHHHHHHcCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHcCCccCC----CCceeeC
Confidence            788999999999999999999999988   89999999999999999998876    5677774

>3viq_B Mating-type switching protein SWI5; recombination activator; 2.20A {Schizosaccharomyces pombe} PDB: 3vir_A*

Probab=97.67  E-value=0.001  Score=46.79  Aligned_cols=83  Identities=10%  Similarity=0.167  Sum_probs=66.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Q 027236          117 TLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEE  196 (226)
Q Consensus       117 t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~~~w~kRkri~~~i~~~i~e~~~~~~k~l~e~  196 (226)
                      +.+.|...|..|+.++..++..+..+.+.-...+|+   .+.+.|......|..=|-++-.+++.|++.-+...++++++
T Consensus         2 ~~~~L~~~i~~L~~q~~~L~~ei~~~~a~L~~~~~~---~~~~~hI~~Lh~YNeiKD~gq~L~g~iA~~rgv~~~~v~~e   78 (85)
T 3viq_B            2 EKSQLESRVHLLEQQKEQLESSLQDALAKLKNRDAK---QTVQKHIDLLHTYNEIRDIALGMIGKVAEHEKCTSVELFDR   78 (85)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSSCHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGGHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHH---HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCcHHHHHHH
Confidence            346778888888888888888888887532223344   35666777778999999999999999999999999999999


Q ss_pred             hCcccc
Q 027236          197 LGIEYD  202 (226)
Q Consensus       197 lGie~D  202 (226)
                      ||++.+
T Consensus        79 ~g~~~~   84 (85)
T 3viq_B           79 FGVNGS   84 (85)
T ss_dssp             HTCCTT
T ss_pred             hCCCCC
Confidence            999875

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=97.65  E-value=0.00015  Score=50.28  Aligned_cols=62  Identities=11%  Similarity=0.295  Sum_probs=53.0

Q ss_pred             chHHHHHHHHHHhcC-CCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCc-eeEEE
Q 027236            6 DNTEAIVLNYVNEQN-RPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGK-QKIYI   67 (226)
Q Consensus         6 ~ea~~~Il~y~~~~n-rPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK-~kiY~   67 (226)
                      ...+..||++|...+ +|+++.+|...+...  +|++++|-..|+.|++.|+|..-..+. ...|-
T Consensus        16 t~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~~~~~~y~   81 (83)
T 2fu4_A           16 TLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE   81 (83)
T ss_dssp             CHHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeCCCceEee
Confidence            567889999999887 899999999999653  799999999999999999999888744 44553

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=97.54  E-value=0.0016  Score=47.25  Aligned_cols=58  Identities=22%  Similarity=0.306  Sum_probs=51.4

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.|+.++  .+.|.++.+|...+   ++++++|...|..|.+.|+|.....|...+|..
T Consensus        20 ~~~r~~IL~~L--~~~~~~~~ela~~l---~is~~tv~~~l~~L~~~gli~~~~~gr~~~y~l   77 (114)
T 2oqg_A           20 DETRWEILTEL--GRADQSASSLATRL---PVSRQAIAKHLNALQACGLVESVKVGREIRYRA   77 (114)
T ss_dssp             CHHHHHHHHHH--HHSCBCHHHHHHHS---SSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             ChHHHHHHHHH--HcCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeeEEecCCEEEEEe
Confidence            45677899999  46789999998887   799999999999999999999988899888877

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=97.47  E-value=0.00042  Score=47.94  Aligned_cols=59  Identities=15%  Similarity=0.253  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee--ecCceeEEEeecC
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK--EYGKQKIYIARQD   71 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K--~~GK~kiY~~~Q~   71 (226)
                      +..|+.++.. +.|.+..+|.+.+   ||++++|.+.|+.|.+.|+|...  ..|+..+|..+..
T Consensus         2 r~~Il~~L~~-~~~~s~~eLa~~l---gvs~~tv~r~L~~L~~~GlI~~~~~~~gr~~~y~l~~~   62 (81)
T 2htj_A            2 KNEILEFLNR-HNGGKTAEIAEAL---AVTDYQARYYLLLLEKAGMVQRSPLRRGMATYWFLKGE   62 (81)
T ss_dssp             HHHHHHHHHH-SCCCCHHHHHHHH---TSCHHHHHHHHHHHHHHTSEEEECCSSSSSCEEEESSC
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEeccCCCCcEEEEEChh
Confidence            4679999975 4689999999988   89999999999999999999854  4466666666544

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=97.45  E-value=0.00078  Score=47.95  Aligned_cols=58  Identities=14%  Similarity=0.292  Sum_probs=52.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.|+.++..  .|.++.+|...+   |+++++|...|..|.+.|+|.....|+..+|..
T Consensus        22 ~~~r~~Il~~L~~--~~~~~~ela~~l---~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l   79 (98)
T 3jth_A           22 NERRLQILCMLHN--QELSVGELCAKL---QLSQSALSQHLAWLRRDGLVTTRKEAQTVYYTL   79 (98)
T ss_dssp             SHHHHHHHHHTTT--SCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEECCTTCCEEEE
T ss_pred             CHHHHHHHHHHhc--CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEE
Confidence            5667789999975  799999999988   799999999999999999999999999988887

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=97.38  E-value=0.00042  Score=52.53  Aligned_cols=62  Identities=16%  Similarity=0.269  Sum_probs=53.4

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCce-eEEE
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGKQ-KIYI   67 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK~-kiY~   67 (226)
                      -..+..||++|..+++|+|+.+|...+...  +|+.++|=..|+.|++.|+|..-.+|.. ..|-
T Consensus        10 T~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~~~~~~~y~   74 (131)
T 2o03_A           10 TRQRAAISTLLETLDDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHTDTGESVYR   74 (131)
T ss_dssp             HHHHHHHHHHHHHCCSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEECTTSCEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEeCCCceEEE
Confidence            356789999999999999999999999653  7999999999999999999999888644 4443

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=97.38  E-value=0.00016  Score=52.55  Aligned_cols=62  Identities=16%  Similarity=0.245  Sum_probs=54.6

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      -..+-.||.++.+ +.|-++.+|.+.+.. .++++++|..+|+.|+++|+|.....|...+|++
T Consensus        34 T~~e~~VL~~L~~-~~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~~gR~~~Y~p   96 (99)
T 2k4b_A           34 SNAELIVMRVIWS-LGEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKEGRKFVYRP   96 (99)
T ss_dssp             CCSCSHHHHHHHH-HSCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEEETTEEEEEC
T ss_pred             CHHHHHHHHHHHh-CCCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEeCCCEEEEEE
Confidence            3556789999997 669999999998864 2588999999999999999999999999999987

>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=97.36  E-value=0.00066  Score=47.30  Aligned_cols=53  Identities=17%  Similarity=0.248  Sum_probs=47.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHH-HHHHHHHHHHHcCCcceeecCce
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKA-GIQKALDSLADNGKISFKEYGKQ   63 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~-~v~k~L~~Lv~~g~i~~K~~GK~   63 (226)
                      +-++.||.|++... |-++.+|.+.|   ||+++ +|...|..|..+|+|.....|.-
T Consensus        11 ~~~~~IL~~Lk~~g-~~ta~eiA~~L---git~~~aVr~hL~~Le~eGlV~~~~~gRP   64 (79)
T 1xmk_A           11 EIKEKICDYLFNVS-DSSALNLAKNI---GLTKARDINAVLIDMERQGDVYRQGTTPP   64 (79)
T ss_dssp             HHHHHHHHHHHHTC-CEEHHHHHHHH---CGGGHHHHHHHHHHHHHTTSEEEECSSSC
T ss_pred             hHHHHHHHHHHHcC-CcCHHHHHHHc---CCCcHHHHHHHHHHHHHCCCEEecCCCCC
Confidence            56889999988654 99999999999   89999 99999999999999997777876

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=97.30  E-value=0.0025  Score=44.90  Aligned_cols=59  Identities=12%  Similarity=0.224  Sum_probs=52.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.|+.++. .+.|.+..+|...+   ++++++|...|..|.+.|+|.....|...+|..
T Consensus        23 ~~~~~~il~~l~-~~~~~s~~ela~~l---~is~~tvs~~l~~L~~~glv~~~~~~r~~~y~l   81 (99)
T 3cuo_A           23 HPKRLLILCMLS-GSPGTSAGELTRIT---GLSASATSQHLARMRDEGLIDSQRDAQRILYSI   81 (99)
T ss_dssp             SHHHHHHHHHHT-TCCSEEHHHHHHHH---CCCHHHHHHHHHHHHHTTSEEEEECSSCEEEEE
T ss_pred             ChHHHHHHHHHH-hCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEE
Confidence            456778998885 46699999999988   799999999999999999999999999888877

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=97.28  E-value=0.00073  Score=52.13  Aligned_cols=64  Identities=16%  Similarity=0.244  Sum_probs=54.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCc-eeEEEee
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGK-QKIYIAR   69 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK-~kiY~~~   69 (226)
                      -..+..||++|..+.+|+|+.+|.+.+...  +|+.++|=..|+.|++.|+|..-.+|. ...|-.+
T Consensus        21 T~qR~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~~   87 (145)
T 2fe3_A           21 TPQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFV   87 (145)
T ss_dssp             CHHHHHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCTTSCCEEEEC
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeCCCceEEECC
Confidence            467889999999999999999999999653  699999999999999999999888864 4556443

>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=97.27  E-value=0.0007  Score=48.65  Aligned_cols=61  Identities=13%  Similarity=0.235  Sum_probs=53.9

Q ss_pred             cchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeec
Q 027236            5 SDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQ   70 (226)
Q Consensus         5 g~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q   70 (226)
                      ++..+-.|+.++..  .|.++.+|...+   |+++++|...|..|.+.|+|.....|+..+|..+.
T Consensus        21 ~~~~r~~Il~~L~~--~~~~~~ela~~l---~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~   81 (102)
T 3pqk_A           21 SHPVRLMLVCTLVE--GEFSVGELEQQI---GIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTE   81 (102)
T ss_dssp             CSHHHHHHHHHHHT--CCBCHHHHHHHH---TCCTTHHHHHHHHHHHTTSEEEECSSSCCEEEECS
T ss_pred             CCHHHHHHHHHHHh--CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECc
Confidence            36677889999963  789999999988   79999999999999999999999999988888844

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=97.26  E-value=0.0021  Score=47.52  Aligned_cols=59  Identities=20%  Similarity=0.321  Sum_probs=53.5

Q ss_pred             cchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            5 SDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         5 g~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ++..+-.|+.++.  +.|.++.+|...+   |+++++|...|..|.+.|+|.....|...+|..
T Consensus        16 ~~~~R~~Il~~L~--~~~~~~~eLa~~l---~is~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l   74 (118)
T 3f6o_A           16 ADPTRRAVLGRLS--RGPATVSELAKPF---DMALPSFMKHIHFLEDSGWIRTHKQGRVRTCAI   74 (118)
T ss_dssp             TSHHHHHHHHHHH--TCCEEHHHHHTTC---CSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             CCHHHHHHHHHHH--hCCCCHHHHHHHh---CcCHHHHHHHHHHHHHCCCeEEEecCCEEEEEE
Confidence            3677889999998  5899999988877   899999999999999999999999999999988

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=97.22  E-value=0.0074  Score=45.71  Aligned_cols=63  Identities=17%  Similarity=0.241  Sum_probs=53.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      -..+-.||.++...+.|.++.+|...+.. .++++++|..+|+.|+++|+|.....|...+|++
T Consensus         8 t~~e~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~~r~~~~~~   71 (138)
T 2g9w_A            8 GDLERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDDRAHRYAP   71 (138)
T ss_dssp             CHHHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC---CCEEEE
T ss_pred             CHHHHHHHHHHHhcCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEecCCeEEEEe
Confidence            56788999999987789999999999953 2589999999999999999999999899888876

>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=97.16  E-value=0.0014  Score=47.47  Aligned_cols=58  Identities=17%  Similarity=0.282  Sum_probs=52.0

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.|+.++.  +.|.++.+|...+   |+++++|...|..|.+.|+|.....|+..+|..
T Consensus        25 ~~~r~~IL~~L~--~~~~~~~ela~~l---~is~stvs~~L~~L~~~Glv~~~~~gr~~~y~l   82 (106)
T 1r1u_A           25 DYNRIRIMELLS--VSEASVGHISHQL---NLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSL   82 (106)
T ss_dssp             SHHHHHHHHHHH--HCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHH--hCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEE
Confidence            566788999997  5789999999888   799999999999999999999999998877777

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=97.16  E-value=0.0039  Score=46.56  Aligned_cols=60  Identities=13%  Similarity=0.266  Sum_probs=50.2

Q ss_pred             chHHHHHHHHHHhcCCC-CcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec-----CceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRP-LNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY-----GKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrP-ys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~-----GK~kiY~~   68 (226)
                      ...+..||.+|.....| .++.+|.+.+   ++++++|.+.|+.|++.|+|.....     |...+|.+
T Consensus        25 t~~e~~il~~L~~~~~~~~t~~eLa~~l---~~s~sTV~r~L~~L~~~GlV~r~~~~~d~~~~~~~y~~   90 (123)
T 3r0a_A           25 TKADLNVMKSFLNEPDRWIDTDALSKSL---KLDVSTVQRSVKKLHEKEILQRSQQNLDGGGYVYIYKI   90 (123)
T ss_dssp             CHHHHHHHHHHHHSTTCCEEHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEE
T ss_pred             CHHHHHHHHHHHHCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEeeCCccCCCcceEEEec
Confidence            45678899999999999 9999999988   7999999999999999999987642     33445555

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=97.16  E-value=0.0013  Score=51.06  Aligned_cols=63  Identities=16%  Similarity=0.241  Sum_probs=53.8

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCc-eeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGK-QKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK-~kiY~~   68 (226)
                      -..+..||++|....+|+|+.+|.+.+...  +|+.++|=..|+.|++.|+|..-.+|. ...|-.
T Consensus        26 T~qR~~IL~~l~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   91 (150)
T 2xig_A           26 SKQREEVVSVLYRSGTHLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVLETSKSGRRYEI   91 (150)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEETTTEEEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            456789999999999999999999999652  699999999999999999999888743 455644

>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=97.13  E-value=0.0017  Score=45.39  Aligned_cols=59  Identities=22%  Similarity=0.426  Sum_probs=48.0

Q ss_pred             chHHHHHHHHHHhcC--CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQN--RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~n--rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ++....||++|.+..  .+.++.+|...|   ||+++.|.+.|..|.++|+|..-- |+--.|++
T Consensus         9 ~~~~~~IL~~L~~~~pg~~~t~~eLA~~L---gvsr~tV~~~L~~Le~~G~I~~~g-~~~~~W~i   69 (81)
T 1qbj_A            9 QDQEQRILKFLEELGEGKATTAHDLSGKL---GTPKKEINRVLYSLAKKGKLQKEA-GTPPLWKI   69 (81)
T ss_dssp             HHHHHHHHHHHHHHCTTCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEES-SSSCEEEE
T ss_pred             hHHHHHHHHHHHHcCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEecC-CCCCeeEE
Confidence            567889999999654  489999999988   799999999999999999997653 44434444

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=97.11  E-value=0.0011  Score=50.87  Aligned_cols=64  Identities=20%  Similarity=0.266  Sum_probs=54.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecC-ceeEEEee
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYG-KQKIYIAR   69 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~G-K~kiY~~~   69 (226)
                      -..+..||++|..+++|+|+.+|.+.|...  +|+.++|=..|+.|++.|+|..-.+| ....|-..
T Consensus        13 T~qR~~Il~~L~~~~~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~g~~~Y~~~   79 (139)
T 3mwm_A           13 TRQRAAVSAALQEVEEFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVLRTAEGESVYRRC   79 (139)
T ss_dssp             HHHHHHHHHHHTTCSSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEEECTTSCEEEECC
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCceEEEEC
Confidence            356889999999999999999999999652  69999999999999999999988884 34566543

>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=97.10  E-value=0.0013  Score=45.26  Aligned_cols=61  Identities=15%  Similarity=0.385  Sum_probs=54.9

Q ss_pred             chHHHHHHHHHHhc---CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQ---NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~---nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +++.+.|++||...   ...|=.+|+.+.++  +...-.|++++..||.+|.+..=-.|++..|-.
T Consensus         2 ee~K~~Ile~l~~k~~~KskfYf~D~~k~~P--~~k~r~vKK~~~~LV~Eg~leywSSGSTTmygl   65 (78)
T 1ucr_A            2 EEAKQKVVDFLNSKSGSKSKFYFNDFTDLFP--DMKQREVKKILTALVNDEVLEYWSSGSTTMYGL   65 (78)
T ss_dssp             CHHHHHHHHHHSSHHHHSSCEEHHHHHHHCT--TSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             hHHHHHHHHHHHhcccccccchHHHHHHHcc--ccCHHHHHHHHHHHHhcCceEEEecCCeEEEec
Confidence            57899999999985   44788999999887  578999999999999999999999999999976

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=97.08  E-value=0.0037  Score=45.52  Aligned_cols=58  Identities=14%  Similarity=0.256  Sum_probs=51.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.|+.++.  +.|.++.+|...+   |+++++|...|..|.+.|+|.....|+..+|..
T Consensus        24 ~~~r~~IL~~L~--~~~~s~~eLa~~l---gis~stvs~~L~~L~~~GlV~~~~~gr~~~y~l   81 (108)
T 2kko_A           24 NGRRLQILDLLA--QGERAVEAIATAT---GMNLTTASANLQALKSGGLVEARREGTRQYYRI   81 (108)
T ss_dssp             TSTTHHHHHHHT--TCCEEHHHHHHHH---TCCHHHHHHHHHHHHHHTSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHH--cCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEE
Confidence            455678899886  4899999999988   799999999999999999999999999888877

>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=97.07  E-value=0.036  Score=40.64  Aligned_cols=62  Identities=15%  Similarity=0.185  Sum_probs=54.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      -.++-.|+.++.. +.|-+..+|.+.++. .++++++|..+|+.|+++|+|....-|...+|++
T Consensus         9 t~~q~~vL~~L~~-~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~~r~~~~~~   71 (126)
T 1sd4_A            9 SMAEWDVMNIIWD-KKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSENIYFYSS   71 (126)
T ss_dssp             CHHHHHHHHHHHH-SSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHHh-cCCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeCCCeEEEEE
Confidence            5678899999998 569999999999964 3589999999999999999999998899888887

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=97.05  E-value=0.0011  Score=50.48  Aligned_cols=63  Identities=13%  Similarity=0.279  Sum_probs=52.9

Q ss_pred             chHHHHHHHHHHhcC-CCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecC-ceeEEEe
Q 027236            6 DNTEAIVLNYVNEQN-RPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYG-KQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~n-rPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~G-K~kiY~~   68 (226)
                      -..+..||++|..+. +|+|+.+|.+.+...  +|+.++|=..|+.|++.|+|..-.++ ....|-.
T Consensus        17 T~qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   83 (136)
T 1mzb_A           17 TLPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDGGHAVFEL   83 (136)
T ss_dssp             CHHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSSSSCEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            456889999999988 999999999999653  69999999999999999999988874 3455643

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=97.03  E-value=0.0011  Score=51.50  Aligned_cols=63  Identities=10%  Similarity=0.269  Sum_probs=53.7

Q ss_pred             chHHHHHHHHHHhcC-CCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCc-eeEEEe
Q 027236            6 DNTEAIVLNYVNEQN-RPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGK-QKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~n-rPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK-~kiY~~   68 (226)
                      -..+..||++|..+. +|+|+.+|.+.|...  +|+.++|=..|+.|++.|+|..-.++. ...|-.
T Consensus        16 T~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   82 (150)
T 2w57_A           16 TLPRLKILEVLQQPECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFEL   82 (150)
T ss_dssp             CHHHHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEEECGGGCEEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            456889999999888 999999999999653  699999999999999999999888843 455643

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=96.92  E-value=0.0038  Score=48.48  Aligned_cols=58  Identities=16%  Similarity=0.297  Sum_probs=52.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.||.+|.  +.|.++.+|...+   ++++++|...|..|.+.|+|.....|...+|..
T Consensus        57 ~p~R~~IL~~L~--~~~~t~~eLa~~l---gls~stvs~hL~~L~~aGlV~~~~~Gr~~~y~l  114 (151)
T 3f6v_A           57 EPTRRRLVQLLT--SGEQTVNNLAAHF---PASRSAISQHLRVLTEAGLVTPRKDGRFRYYRL  114 (151)
T ss_dssp             SHHHHHHHHHGG--GCCEEHHHHHTTS---SSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHH--hCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEE
Confidence            566889999997  6899999998877   899999999999999999999999999988887

>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=96.90  E-value=0.0022  Score=47.81  Aligned_cols=59  Identities=22%  Similarity=0.361  Sum_probs=48.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.|+.++.. +.|.++.+|...+   |+++++|...|..|.+.|+|.....|+..+|..
T Consensus        41 ~~~rl~IL~~L~~-~~~~s~~eLa~~l---~is~stvs~~L~~L~~~Glv~~~~~gr~~~y~l   99 (122)
T 1u2w_A           41 DENRAKITYALCQ-DEELCVCDIANIL---GVTIANASHHLRTLYKQGVVNFRKEGKLALYSL   99 (122)
T ss_dssp             SHHHHHHHHHHHH-SSCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEC----CCEEEE
T ss_pred             CHHHHHHHHHHHH-CCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEEEECCEEEEEE
Confidence            4456678988874 6799999999988   799999999999999999999999999888887

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=96.87  E-value=0.0015  Score=51.47  Aligned_cols=64  Identities=13%  Similarity=0.247  Sum_probs=51.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcc----cccHHHHHHHHHHHHHcCCcceeecCce-eEEEee
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKY----NLKKAGIQKALDSLADNGKISFKEYGKQ-KIYIAR   69 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~----~v~K~~v~k~L~~Lv~~g~i~~K~~GK~-kiY~~~   69 (226)
                      -..+..||++|.++.+|+|+.+|.+.+...    .|+.++|=.+|+.|++.|+|..=.+|.. ..|-.+
T Consensus        32 T~qR~~IL~~L~~~~~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~~i~~~~~~~~Y~~~  100 (162)
T 4ets_A           32 TKQREVLLKTLYHSDTHYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVTSISFGSAGKKYELA  100 (162)
T ss_dssp             CHHHHHHHHHHHSCCSCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEEECC-----CCEEEC
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEEEEEeCCCceEEEeC
Confidence            346889999999999999999999988643    5999999999999999999998877654 346443

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=96.85  E-value=0.004  Score=42.92  Aligned_cols=58  Identities=22%  Similarity=0.428  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHhcC--CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQN--RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~n--rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +-+..||.+|....  .+.++.+|...|   ||++++|.+.|..|..+|+|...- |+--.|++
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~L---gvs~~tV~~~L~~L~~~G~I~~~g-~~~~~W~i   73 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKL---GTPKKEINRVLYSLAKKGKLQKEA-GTPPLWKI   73 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHH---CCCHHHHHHHHHHHHHHTSEEEEC-SSSCEEEE
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEecC-CCCCceEe
Confidence            44678999999776  489999999988   799999999999999999997764 44334444

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=96.79  E-value=0.003  Score=40.88  Aligned_cols=46  Identities=22%  Similarity=0.411  Sum_probs=41.0

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      +..||+|++.++-.+.+.++.+.+   ||.|..|-++|..|.++|+|.-
T Consensus        12 e~~lL~yIr~sGGildI~~~a~ky---gV~kdeV~~~LrrLe~KGLI~l   57 (59)
T 2xvc_A           12 ERELLDYIVNNGGFLDIEHFSKVY---GVEKQEVVKLLEALKNKGLIAV   57 (59)
T ss_dssp             HHHHHHHHHHTTSEEEHHHHHHHH---CCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHcCCEEeHHHHHHHh---CCCHHHHHHHHHHHHHCCCeec
Confidence            678999999999999977776655   9999999999999999999964

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=96.79  E-value=0.0034  Score=43.41  Aligned_cols=52  Identities=23%  Similarity=0.380  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHhc-----CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            7 NTEAIVLNYVNEQ-----NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         7 ea~~~Il~y~~~~-----nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .....||+|+.+.     +.|.|+.+|.+.+   ||+.++|.+-|..|.++|+|....-|
T Consensus         4 ~r~~~IL~~I~~~i~~~~g~~psv~EIa~~l---gvS~~TVrr~L~~Le~kG~I~R~~gg   60 (77)
T 2jt1_A            4 SIVTKIISIVQERQNMDDGAPVKTRDIADAA---GLSIYQVRLYLEQLHDVGVLEKVNAG   60 (77)
T ss_dssp             THHHHHHHHHHHHHHHHTTSCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEESCS
T ss_pred             HHHHHHHHHHHHHHhhccCCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCcEEecCCC
Confidence            4567899999998     7899999999999   79999999999999999999877544

>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=96.75  E-value=0.011  Score=43.28  Aligned_cols=62  Identities=19%  Similarity=0.213  Sum_probs=53.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ...+-.||.++.. +.|.+..+|...+.. .++++++|..+|+.|++.|+|.....|...+|++
T Consensus         9 t~~~~~vL~~l~~-~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~~rr~~~~~   71 (123)
T 1okr_A            9 SSAEWEVMNIIWM-KKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYS   71 (123)
T ss_dssp             CHHHHHHHHHHHH-HSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHHh-CCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEecCCeEEEEE
Confidence            4567789999987 789999999998853 2489999999999999999999887799888887

>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=96.74  E-value=0.0048  Score=43.73  Aligned_cols=56  Identities=13%  Similarity=0.186  Sum_probs=47.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQD   71 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~   71 (226)
                      +..+..|+.++   +.|.++.+|...+   ++++++|.+.|+.|.+.|+|.... |   .|..+..
T Consensus        30 ~~~r~~Il~~L---~~~~~~~eLa~~l---~is~~tv~~~L~~L~~~Glv~~~~-g---~y~l~~~   85 (96)
T 1y0u_A           30 NPVRRKILRML---DKGRSEEEIMQTL---SLSKKQLDYHLKVLEAGFCIERVG-E---RWVVTDA   85 (96)
T ss_dssp             CHHHHHHHHHH---HTTCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEET-T---EEEECTT
T ss_pred             CHHHHHHHHHH---cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEC-C---EEEECCC
Confidence            45567899999   5789999999888   799999999999999999999877 7   6666443

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=96.71  E-value=0.0023  Score=44.87  Aligned_cols=57  Identities=12%  Similarity=0.188  Sum_probs=48.5

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .-...||.||.. +- .++.+|...|   ||++++|...|..|..+|.|....-..-++|+.
T Consensus        17 ~~~~~IL~lL~~-~g-~sa~eLAk~L---giSk~aVr~~L~~Le~eG~I~~~~~~PP~W~~~   73 (82)
T 1oyi_A           17 EIVCEAIKTIGI-EG-ATAAQLTRQL---NMEKREVNKALYDLQRSAMVYSSDDIPPRWFMT   73 (82)
T ss_dssp             HHHHHHHHHHSS-ST-EEHHHHHHHS---SSCHHHHHHHHHHHHHHTSSEECSSSSCEEESC
T ss_pred             HHHHHHHHHHHH-cC-CCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEeCCCCCCcceec
Confidence            556789999994 33 9999998888   899999999999999999999876666677766

>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=96.71  E-value=0.004  Score=47.97  Aligned_cols=62  Identities=16%  Similarity=0.299  Sum_probs=52.6

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCce-eEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGKQ-KIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK~-kiY~~   68 (226)
                      -..+..||++|.... |.|+.+|.+.+...  .|+.++|=.+|+.|++.|+|..=.+|.. ..|-.
T Consensus        18 T~qR~~Il~~l~~~~-h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~~~~~~~Y~~   82 (145)
T 3eyy_A           18 TPQRQLVLEAVDTLE-HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHLGHGAPTYHL   82 (145)
T ss_dssp             CHHHHHHHHHHHHHS-SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEEE
T ss_pred             CHHHHHHHHHHHhcC-CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            457889999999988 99999999999763  6999999999999999999998877544 45543

>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=96.68  E-value=0.0064  Score=45.34  Aligned_cols=58  Identities=19%  Similarity=0.353  Sum_probs=51.1

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.||.++.  +.|.++.+|...+   |+++++|...|..|.+.|+|.....|+..+|..
T Consensus        45 ~~~rl~IL~~L~--~~~~s~~ela~~l---gis~stvs~~L~~Le~~Glv~~~~~gr~~~y~l  102 (122)
T 1r1t_A           45 DPNRLRLLSLLA--RSELCVGDLAQAI---GVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQL  102 (122)
T ss_dssp             CHHHHHHHHHHT--TCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHH--cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEE
Confidence            445667888886  3799999999988   799999999999999999999999999888877

>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=96.68  E-value=0.024  Score=39.66  Aligned_cols=59  Identities=10%  Similarity=0.167  Sum_probs=49.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee---cCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE---YGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~---~GK~kiY~~   68 (226)
                      +..+-.||.++.. +.|.+..+|...+   ++++++|...|+.|.+.|+|....   -|...+|..
T Consensus        15 ~~~~~~iL~~L~~-~~~~~~~ela~~l---~is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~l   76 (100)
T 1ub9_A           15 NPVRLGIMIFLLP-RRKAPFSQIQKVL---DLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEI   76 (100)
T ss_dssp             SHHHHHHHHHHHH-HSEEEHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             ChHHHHHHHHHHh-cCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEE
Confidence            4556778998875 4589999998888   799999999999999999999766   677677766

>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=96.61  E-value=0.016  Score=40.92  Aligned_cols=58  Identities=16%  Similarity=0.179  Sum_probs=46.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec-CceeEEE
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY-GKQKIYI   67 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~-GK~kiY~   67 (226)
                      ...+-.|+.++.. +.|.+..+|...+   ++++++|...|+.|++.|+|..... ++-..|+
T Consensus        19 ~~~~~~il~~l~~-~~~~s~~ela~~l---~is~~tv~~~l~~L~~~glv~~~~~~~~r~~~~   77 (109)
T 1sfx_A           19 KPSDVRIYSLLLE-RGGMRVSEIAREL---DLSARFVRDRLKVLLKRGFVRREIVEKGWVGYI   77 (109)
T ss_dssp             CHHHHHHHHHHHH-HCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEE
T ss_pred             CHHHHHHHHHHHH-cCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEEeecCCceEEE
Confidence            4567789999975 5689999999988   7999999999999999999988654 3333333

>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=96.55  E-value=0.018  Score=40.70  Aligned_cols=51  Identities=25%  Similarity=0.420  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.|+.++...+.|.+..+|...+   |+++++|...|+.|.+.|+|.....
T Consensus        21 ~~~~~~l~~l~~~~~~~t~~ela~~l---~is~~tv~~~l~~L~~~g~v~~~~~   71 (109)
T 2d1h_A           21 DTDVAVLLKMVEIEKPITSEELADIF---KLSKTTVENSLKKLIELGLVVRTKT   71 (109)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEeecc
Confidence            34456666777668899999999988   8999999999999999999988755

>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=96.55  E-value=0.15  Score=37.79  Aligned_cols=112  Identities=15%  Similarity=0.150  Sum_probs=69.9

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC--ceeEEEeecCCCCCCCHHHHHHH
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG--KQKIYIARQDQFDIPNSEELNQM   84 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G--K~kiY~~~Q~~~~~~~~ee~~~l   84 (226)
                      ..+-.||.++... .|.+..+|...+   ++++++|..+|+.|++.|+|....-+  +-.+|+.    +.   +.-...+
T Consensus        29 ~~~~~iL~~l~~~-~~~t~~~la~~l---~~s~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~~----lT---~~G~~~~   97 (144)
T 1lj9_A           29 RGQYLYLVRVCEN-PGIIQEKIAELI---KVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIY----AT---EKGKNVY   97 (144)
T ss_dssp             TTHHHHHHHHHHS-TTEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEE----EC---HHHHHHH
T ss_pred             HHHHHHHHHHHHC-cCcCHHHHHHHH---CCCHhHHHHHHHHHHHCCCEEeecCCCCCceeeeE----EC---hhHHHHH
Confidence            4456788888764 589999999988   79999999999999999999987643  2233333    22   2222111


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                       ..+..             ....-...+....+.+++..-..-|..=...++..++.++
T Consensus        98 -~~~~~-------------~~~~~~~~~~~~l~~~e~~~l~~~l~~l~~~l~~~~~~~k  142 (144)
T 1lj9_A           98 -PIIVR-------------ENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVK  142 (144)
T ss_dssp             -HHHHH-------------HHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -HHHHH-------------HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhHHHHHHhcc
Confidence             11111             1111233445567777776666666665555665555544

>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=96.49  E-value=0.16  Score=37.59  Aligned_cols=59  Identities=19%  Similarity=0.336  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee-cC-ceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE-YG-KQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~-~G-K~kiY~~   68 (226)
                      .....|+.++.-.+.|.++.+|.+.+   ++++++|...|+.|++.|+|.... -| +-.+|..
T Consensus        26 ~~~~~il~~L~~~~~~~t~~ela~~l---~~~~stvs~~l~~L~~~G~v~r~~~~~d~r~~~~~   86 (152)
T 1ku9_A           26 KSVGAVYAILYLSDKPLTISDIMEEL---KISKGNVSMSLKKLEELGFVRKVWIKGERKNYYEA   86 (152)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEE
T ss_pred             hhHHHHHHHHHHcCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEecCCCceEEEee
Confidence            45667888886567899999999988   799999999999999999998764 23 3445554

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=96.44  E-value=0.016  Score=48.18  Aligned_cols=60  Identities=10%  Similarity=0.145  Sum_probs=49.4

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce-eecCc-----eeEEEeec
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF-KEYGK-----QKIYIARQ   70 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~-K~~GK-----~kiY~~~Q   70 (226)
                      +..+-.|+.++..  .|.++.+|...+   |++.++|...|..|.+.|+|.. ...|.     ..+|..+.
T Consensus        11 ~~~R~~IL~~L~~--g~~s~~ELa~~l---glS~stVs~hL~~Le~aGLV~~~~~~gr~~GRp~~~Y~Lt~   76 (232)
T 2qlz_A           11 NKVRRDLLSHLTC--MECYFSLLSSKV---SVSSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYKISI   76 (232)
T ss_dssp             SHHHHHHHHHHTT--TTTCSSSSCTTC---CCCHHHHHHHHHHHHHTTSEEEEEECC-----CEEEEEECC
T ss_pred             CHHHHHHHHHHHh--CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEeeecCCCCCCccEEEEEcc
Confidence            5667889999973  799988877665   8999999999999999999999 67787     78887543

>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=96.43  E-value=0.022  Score=44.19  Aligned_cols=52  Identities=21%  Similarity=0.354  Sum_probs=44.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ...+-.||.++...+.|-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        52 t~~q~~vL~~L~~~~~~~t~~eLa~~l---~i~~~tvs~~l~~Le~~GlV~r~~~  103 (166)
T 3deu_A           52 TQTHWVTLHNIHQLPPDQSQIQLAKAI---GIEQPSLVRTLDQLEDKGLISRQTC  103 (166)
T ss_dssp             CHHHHHHHHHHHHSCSSEEHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEC--
T ss_pred             CHHHHHHHHHHHHcCCCCCHHHHHHHH---CCCHhhHHHHHHHHHHCCCEEeeCC
Confidence            345678999999888899999999988   7999999999999999999987753

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=96.40  E-value=0.016  Score=41.37  Aligned_cols=58  Identities=14%  Similarity=0.240  Sum_probs=50.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.|+.++.. +.|.++.+|...+   |+++++|...|..|.+. +|....-|+..+|..
T Consensus        26 ~~~Rl~IL~~l~~-~~~~~~~ela~~l---~is~stvs~hL~~L~~~-lv~~~~~gr~~~y~l   83 (99)
T 2zkz_A           26 HPMRLKIVNELYK-HKALNVTQIIQIL---KLPQSTVSQHLCKMRGK-VLKRNRQGLEIYYSI   83 (99)
T ss_dssp             SHHHHHHHHHHHH-HSCEEHHHHHHHH---TCCHHHHHHHHHHHBTT-TBEEEEETTEEEEEC
T ss_pred             CHHHHHHHHHHHH-CCCcCHHHHHHHH---CcCHHHHHHHHHHHHHH-hhhheEeCcEEEEEE
Confidence            5667788876664 4789999999988   89999999999999999 999999999887777

>1go4_E MAD1 (mitotic arrest deficient)-like 1; mitotic spindle checkpoint, cell cycle, mitosis, nuclear Pro; 2.05A {Homo sapiens} SCOP: h.1.22.1

Probab=96.38  E-value=0.012  Score=42.53  Aligned_cols=70  Identities=19%  Similarity=0.293  Sum_probs=57.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cc--C------------CH---HHHHHHHHHHHHHHHHHHH
Q 027236           77 NSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQ--SN--L------------TL---EQIREKEAQLVKEVKEMEN  137 (226)
Q Consensus        77 ~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~--~~--~------------t~---~el~~~i~~L~~e~~~l~~  137 (226)
                      |.+++..+..+|++|+.+...|..++..|+.+|....  +.  |            .+   .+....+..|+.++..|+.
T Consensus        10 ~~e~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~l~Gd~~~~~TKVlH~~~NPa~~a~~~~~~~~e~Lq~E~erLr~   89 (100)
T 1go4_E           10 SREEADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAECERLRG   89 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCSCCCTTTEEEEEESSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCccCeeeeecCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6889999999999999999999999999999998832  21  2            22   4667889999999999999


Q ss_pred             HHHHhhCCC
Q 027236          138 KLAKLRGGV  146 (226)
Q Consensus       138 kL~~l~~~~  146 (226)
                      ++..+..|.
T Consensus        90 ~v~~lEeg~   98 (100)
T 1go4_E           90 LLRAMERGG   98 (100)
T ss_dssp             HHTTCC---
T ss_pred             HHHHHhccC
Confidence            998887754

>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=96.37  E-value=0.044  Score=38.58  Aligned_cols=62  Identities=19%  Similarity=0.245  Sum_probs=48.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ...+-.||.++.. +.|.+..+|...+.. .++++++|...|+.|++.|+|....-+....|..
T Consensus         7 t~~q~~iL~~l~~-~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~~L   69 (99)
T 1tbx_A            7 FYPEAIVLAYLYD-NEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQERGEKRLYL   69 (99)
T ss_dssp             BCHHHHHHHHHTT-CTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHHH-cCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEecCCceEEEE
Confidence            3456788888875 678999999433322 3899999999999999999999887776665555

>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=96.30  E-value=0.21  Score=36.94  Aligned_cols=49  Identities=16%  Similarity=0.232  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.  +.|.+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        37 ~~~~~iL~~l~--~~~~~~~ela~~l---~~s~~tvs~~l~~Le~~glv~r~~~   85 (146)
T 2gxg_A           37 YLDFLVLRATS--DGPKTMAYLANRY---FVTQSAITASVDKLEEMGLVVRVRD   85 (146)
T ss_dssp             HHHHHHHHHHT--TSCBCHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHh--cCCcCHHHHHHHh---CCCchhHHHHHHHHHHCCCEEeecC
Confidence            45667888888  8899999998887   7999999999999999999998765

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=96.26  E-value=0.042  Score=44.65  Aligned_cols=60  Identities=18%  Similarity=0.329  Sum_probs=50.6

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec-----CceeEEEeec
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY-----GKQKIYIARQ   70 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~-----GK~kiY~~~Q   70 (226)
                      +..+-.||.++.  +.|.++.+|...+   +++.++|...|..|.+.|+|.....     |..++|....
T Consensus        14 ~~~rl~IL~~L~--~~~~s~~eLa~~l---~is~stvs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~Lt~   78 (202)
T 2p4w_A           14 NETRRRILFLLT--KRPYFVSELSREL---GVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKK   78 (202)
T ss_dssp             SHHHHHHHHHHH--HSCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECT
T ss_pred             CHHHHHHHHHHH--hCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCceEEEeeccCCCCceEEEEECh
Confidence            456778999995  5799999999988   7999999999999999999999877     6666666543

>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=96.26  E-value=0.0097  Score=43.07  Aligned_cols=60  Identities=22%  Similarity=0.381  Sum_probs=47.1

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee----ec-CceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK----EY-GKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K----~~-GK~kiY~~   68 (226)
                      ++..-.|+..+.....|.+..+|...+   ||++++|.++|..|.+.|+|...    .. |...+||.
T Consensus        17 ~~~~l~Il~~l~~~g~~~s~~eLa~~l---gvs~~tV~~~L~~L~~~GlV~~~~~~~~~~g~~v~~~~   81 (110)
T 1q1h_A           17 GDDVIDVLRILLDKGTEMTDEEIANQL---NIKVNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIYYWK   81 (110)
T ss_dssp             CSTTHHHHHHHHHHCSCBCHHHHHHTT---TSCHHHHHHHHHHHHHHTSCEEEEEC---CCCCEEEEE
T ss_pred             ChHHHHHHHHHHHcCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEecccCCCceEEEEee
Confidence            345667888888778778998888877   89999999999999999999887    44 44444455

>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=96.25  E-value=0.073  Score=40.02  Aligned_cols=47  Identities=15%  Similarity=0.312  Sum_probs=41.1

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      ..+-.||.++  .+.|.+..+|...+   ++++++|..+|+.|++.|+|...
T Consensus        38 ~~q~~iL~~l--~~~~~t~~eLa~~l---~~~~~~vs~~l~~Le~~Glv~r~   84 (151)
T 3kp7_A           38 AEQSHVLNML--SIEALTVGQITEKQ---GVNKAAVSRRVKKLLNAELVKLE   84 (151)
T ss_dssp             HHHHHHHHHH--HHSCBCHHHHHHHH---CSCSSHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHHHH--HcCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEee
Confidence            3456788888  78899999999988   79999999999999999999973

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=96.21  E-value=0.063  Score=41.00  Aligned_cols=52  Identities=19%  Similarity=0.318  Sum_probs=45.1

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ..+-.||.++...+.+-+..+|...+   +|++++|..+++.|+..|+|....-.
T Consensus        31 ~~q~~vL~~L~~~~~~~~~~eLa~~l---~~~~~tvs~~v~~Le~~GlV~R~~~~   82 (151)
T 4aik_A           31 QTHWVTLYNINRLPPEQSQIQLAKAI---GIEQPSLVRTLDQLEEKGLITRHTSA   82 (151)
T ss_dssp             HHHHHHHHHHHHSCTTSCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHH---CcCHHHHHHHHHHHHhCCCeEeecCC
Confidence            34567899998888888888998888   79999999999999999999877664

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=96.19  E-value=0.22  Score=36.78  Aligned_cols=51  Identities=14%  Similarity=0.239  Sum_probs=44.4

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++...+.|-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        37 ~~~~~iL~~l~~~~~~~t~~~la~~l---~~s~~~vs~~l~~L~~~glv~r~~~   87 (146)
T 2fbh_A           37 QARWLVLLHLARHRDSPTQRELAQSV---GVEGPTLARLLDGLESQGLVRRLAV   87 (146)
T ss_dssp             TTHHHHHHHHHHCSSCCBHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHh---CCChhhHHHHHHHHHHCCCeeecCC
Confidence            45667899995678899999999988   7999999999999999999988754

>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=96.19  E-value=0.022  Score=40.17  Aligned_cols=59  Identities=12%  Similarity=0.099  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHhcCCC---CcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRP---LNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrP---ys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ...-.||.++...+.|   .+..+|...+   ++++++|..+|+.|.+.|+|....-|..++|..
T Consensus        12 ~~~~~iL~~l~~~~~~~~~~t~~eLa~~l---~i~~~tvs~~l~~Le~~Glv~~~~d~R~~~v~L   73 (95)
T 2qvo_A           12 EKALEILMTIYYESLGGNDVYIQYIASKV---NSPHSYVWLIIKKFEEAKMVECELEGRTKIIRL   73 (95)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEHHHHHHHS---SSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             hhHHHHHHHHHHccCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCcCccCCCCCCeEEEEE
Confidence            3445567777655556   8999998877   799999999999999999997667777777776

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=96.19  E-value=0.049  Score=40.08  Aligned_cols=52  Identities=15%  Similarity=0.275  Sum_probs=44.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ...+-.||.++.. +.|.+..+|.+.+   ++++++|..+|+.|++.|+|....-+
T Consensus        28 ~~~~~~iL~~l~~-~~~~~~~ela~~l---~~s~~tvs~~l~~L~~~glv~~~~~~   79 (138)
T 3bpv_A           28 TDAQVACLLRIHR-EPGIKQDELATFF---HVDKGTIARTLRRLEESGFIEREQDP   79 (138)
T ss_dssp             CHHHHHHHHHHHH-STTCBHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CHHHHHHHHHHHH-cCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEeecCC
Confidence            3456778888887 4789999999988   79999999999999999999987543

>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=96.06  E-value=0.2  Score=37.67  Aligned_cols=50  Identities=24%  Similarity=0.325  Sum_probs=43.0

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.... |.+..+|.+.+   ++++++|..+|+.|++.|+|....-
T Consensus        44 ~~~~~iL~~l~~~~-~~t~~ela~~l---~is~~tvs~~l~~Le~~Gli~r~~~   93 (154)
T 2eth_A           44 TTELYAFLYVALFG-PKKMKEIAEFL---STTKSNVTNVVDSLEKRGLVVREMD   93 (154)
T ss_dssp             HHHHHHHHHHHHHC-CBCHHHHHHHT---TSCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEeeCC
Confidence            45667888888654 89999999887   7999999999999999999998754

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=96.04  E-value=0.045  Score=41.29  Aligned_cols=50  Identities=16%  Similarity=0.266  Sum_probs=41.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++... .|.+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        41 ~~q~~iL~~l~~~-~~~~~~eLa~~l---~~~~~~vs~~l~~L~~~Glv~r~~~   90 (149)
T 4hbl_A           41 YSQYLVMLTLWEE-NPQTLNSIGRHL---DLSSNTLTPMLKRLEQSGWVKRERQ   90 (149)
T ss_dssp             HHHHHHHHHHHHS-SSEEHHHHHHHH---TCCHHHHHHHHHHHHHHTSEEC---
T ss_pred             HHHHHHHHHHHHC-CCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEeeCCC
Confidence            4556788888764 789999999988   7999999999999999999998754

>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=95.83  E-value=0.1  Score=38.46  Aligned_cols=51  Identities=10%  Similarity=0.213  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHHhcCC-CCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNR-PLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nr-Pys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++..... |-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        34 ~~~~~iL~~l~~~~~~~~~~~ela~~l---~~~~~tvs~~l~~Le~~Gli~r~~~   85 (141)
T 3bro_A           34 GTQMTIIDYLSRNKNKEVLQRDLESEF---SIKSSTATVLLQRMEIKKLLYRKVS   85 (141)
T ss_dssp             HHHHHHHHHHHHTTTSCCBHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHH---CCCcchHHHHHHHHHHCCCEEeeCC
Confidence            456678888887654 89999999988   7999999999999999999988764

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=95.69  E-value=0.05  Score=39.65  Aligned_cols=58  Identities=17%  Similarity=0.381  Sum_probs=50.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.|+.++..  .|.++.+|...+   ++++++|...|..|.+.|+|....-|+..+|..
T Consensus        31 ~~~~~~il~~L~~--~~~s~~ela~~l---~is~stvsr~l~~Le~~Glv~~~~~~r~~~~~~   88 (119)
T 2lkp_A           31 TPSRLMILTQLRN--GPLPVTDLAEAI---GMEQSAVSHQLRVLRNLGLVVGDRAGRSIVYSL   88 (119)
T ss_dssp             CHHHHHHHHHHHH--CCCCHHHHHHHH---SSCHHHHHHHHHHHHHHCSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHHH--CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEE
Confidence            4456778888886  689999999988   799999999999999999999988888877777

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=95.66  E-value=0.19  Score=37.29  Aligned_cols=50  Identities=16%  Similarity=0.244  Sum_probs=41.2

Q ss_pred             hHHHHHHHHHHh---cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236            7 NTEAIVLNYVNE---QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus         7 ea~~~Il~y~~~---~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      .....+|.++..   .+.|.+..+|...+   +|++++|.++|+.|.+.|+|....
T Consensus        13 ~~~~~~L~~l~~l~~~~~~~s~~ela~~l---~is~~tv~~~l~~Le~~Gli~r~~   65 (139)
T 2x4h_A           13 RREFSYLLTIKRYNDSGEGAKINRIAKDL---KIAPSSVFEEVSHLEEKGLVKKKE   65 (139)
T ss_dssp             HHHHHHHHHHHHHHTTTSCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHHHHhcCCCcCHHHHHHHh---CCChHHHHHHHHHHHHCCCEEecC
Confidence            345556666553   67899999999988   799999999999999999998765

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=95.60  E-value=0.13  Score=39.82  Aligned_cols=63  Identities=11%  Similarity=0.134  Sum_probs=52.4

Q ss_pred             CCCCc----chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            1 MAPKS----DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         1 M~~kg----~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ||.|-    -+-+..||+||.  --|-+...|...|   |++=.+++-+|-.|.-+|.|..-++||..|++.
T Consensus         1 MPrk~Td~v~erk~~ILE~Lk--~G~~~t~~Iak~L---GlShg~aq~~Ly~LeREG~V~~Vk~GK~ayw~L   67 (165)
T 2vxz_A            1 MPIGHSREVLVRLRDILALLA--DGCKTTSLIQQRL---GLSHGRAKALIYVLEKEGRVTRVAFGNVALVCL   67 (165)
T ss_dssp             ----CCHHHHHHHHHHHHHHT--TCCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSCEEEEETTEEEEES
T ss_pred             CCcchhHHHHHHHHHHHHHHH--hCCccHHHHHHHh---CCcHHHHHHHHHHHHhcCceEEEEEccEEEEEe
Confidence            66553    477899999999  6788877788777   899999999999999999999999999987776

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=95.58  E-value=0.36  Score=35.76  Aligned_cols=50  Identities=18%  Similarity=0.250  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.... |-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        31 ~~q~~iL~~l~~~~-~~t~~eLa~~l---~~~~~tvs~~l~~Le~~Glv~r~~~   80 (145)
T 3g3z_A           31 YNLFAVLYTLATEG-SRTQKHIGEKW---SLPKQTVSGVCKTLAGQGLIEWQEG   80 (145)
T ss_dssp             HHHHHHHHHHHHHC-SBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEECCC
T ss_pred             HHHHHHHHHHHHCC-CCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEeeccC
Confidence            45667888887654 79999999888   7999999999999999999997544

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=95.55  E-value=0.071  Score=39.83  Aligned_cols=51  Identities=20%  Similarity=0.309  Sum_probs=41.8

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ...+-.||.++.... |.+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        39 ~~~~~~iL~~l~~~~-~~t~~ela~~l---~~~~~tvs~~l~~Le~~Glv~r~~~   89 (148)
T 3nrv_A           39 GMTEWRIISVLSSAS-DCSVQKISDIL---GLDKAAVSRTVKKLEEKKYIEVNGH   89 (148)
T ss_dssp             CHHHHHHHHHHHHSS-SBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEC---
T ss_pred             CHHHHHHHHHHHcCC-CCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEeecC
Confidence            345667888887655 99999999888   7999999999999999999987744

>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=95.54  E-value=0.48  Score=34.98  Aligned_cols=59  Identities=15%  Similarity=0.231  Sum_probs=46.5

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      ..+-.||.++...+.|.+..+|...+   ++++++|..+|+.|++.|+|.....   |...+|..
T Consensus        35 ~~~~~iL~~l~~~~~~~~~~~la~~l---~i~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~l   96 (147)
T 2hr3_A           35 FSQLVVLGAIDRLGGDVTPSELAAAE---RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSL   96 (147)
T ss_dssp             HHHHHHHHHHHHTTSCBCHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEEC------CCEEEE
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHh---CCChhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEE
Confidence            45567899998767899999999887   7999999999999999999988744   34444444

>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=95.54  E-value=0.069  Score=37.38  Aligned_cols=55  Identities=9%  Similarity=0.032  Sum_probs=42.4

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHH-HHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAG-IQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~-v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+|.++.....|.+..+|...+   ++++++ |...|+.|++.|+|.....++-.+++.
T Consensus        19 ~~L~~l~~~~~~~t~~eLa~~l---~is~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~   74 (95)
T 2pg4_A           19 PTLLEFEKKGYEPSLAEIVKAS---GVSEKTFFMGLKDRLIRAGLVKEETLSYRVKTLK   74 (95)
T ss_dssp             HHHHHHHHTTCCCCHHHHHHHH---CCCHHHHHTTHHHHHHHTTSEEEEEEETTEEEEE
T ss_pred             HHHHHHHhcCCCCCHHHHHHHH---CCCchHHHHHHHHHHHHCCCeecCCCCCCeEEEE
Confidence            4566676666689999999988   799999 999999999999999443433334433

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=95.34  E-value=0.13  Score=39.49  Aligned_cols=52  Identities=17%  Similarity=0.223  Sum_probs=43.4

Q ss_pred             hHHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            7 NTEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         7 ea~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ..+-.||.++... +.|-+..+|...+   ++++++|..+|+.|++.|+|....-.
T Consensus        46 ~~q~~vL~~l~~~~~~~~t~~eLa~~l---~~~~~tvs~~l~~Le~~Glv~r~~~~   98 (168)
T 3u2r_A           46 AQQYNTLRLLRSVHPEGMATLQIADRL---ISRAPDITRLIDRLDDRGLVLRTRKP   98 (168)
T ss_dssp             HHHHHHHHHHHHHTTSCEEHHHHHHHC------CTHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHHHHHHhcCCCCcCHHHHHHHH---CCChhhHHHHHHHHHHCCCEeecCCC
Confidence            4567799999987 6899999999887   79999999999999999999988764

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=95.33  E-value=0.4  Score=35.02  Aligned_cols=50  Identities=18%  Similarity=0.212  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.... |.+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        38 ~~~~~iL~~l~~~~-~~t~~ela~~l---~~~~~tvs~~l~~L~~~glv~r~~~   87 (140)
T 2nnn_A           38 PTQWAALVRLGETG-PCPQNQLGRLT---AMDAATIKGVVERLDKRGLIQRSAD   87 (140)
T ss_dssp             HHHHHHHHHHHHHS-SBCHHHHHHHT---TCCHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEeeCC
Confidence            45667888887654 99999998877   7999999999999999999998754

>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=95.32  E-value=0.32  Score=35.83  Aligned_cols=50  Identities=12%  Similarity=0.161  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|.+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        33 ~~~~~iL~~l~~-~~~~~~~~la~~l---~~s~~tvs~~l~~L~~~glv~r~~~   82 (145)
T 2a61_A           33 PAQFDILQKIYF-EGPKRPGELSVLL---GVAKSTVTGLVKRLEADGYLTRTPD   82 (145)
T ss_dssp             HHHHHHHHHHHH-HCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHH---CCCchhHHHHHHHHHHCCCeeecCC
Confidence            456678888876 5689999999988   7999999999999999999998764

>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=95.32  E-value=0.33  Score=35.04  Aligned_cols=58  Identities=9%  Similarity=0.190  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC---ceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG---KQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G---K~kiY~~   68 (226)
                      .-.-.||.++..  .|-+..+|...+.  +|++++|...|+.|.+.|+|.....+   ...+|..
T Consensus        22 ~~~~~IL~~L~~--~~~~~~eLa~~l~--~is~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~L   82 (112)
T 1z7u_A           22 KWKLSLMDELFQ--GTKRNGELMRALD--GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTL   82 (112)
T ss_dssp             TTHHHHHHHHHH--SCBCHHHHHHHST--TCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEE
T ss_pred             ccHHHHHHHHHh--CCCCHHHHHHHhc--cCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEE
Confidence            344568888873  6889889988774  79999999999999999999988773   4555555

>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=95.30  E-value=0.61  Score=34.62  Aligned_cols=50  Identities=16%  Similarity=0.214  Sum_probs=42.9

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++... .|.+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        40 ~~~~~iL~~l~~~-~~~t~~ela~~l---~~~~~~vs~~l~~Le~~Glv~r~~~   89 (152)
T 3bj6_A           40 VGQRAILEGLSLT-PGATAPQLGAAL---QMKRQYISRILQEVQRAGLIERRTN   89 (152)
T ss_dssp             HHHHHHHHHHHHS-TTEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHHHHHHHHHhC-CCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCeeecCC
Confidence            3566788888764 489999999988   7999999999999999999998754

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=95.28  E-value=0.56  Score=35.28  Aligned_cols=49  Identities=18%  Similarity=0.219  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .+-.||.++.. +.|.+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        50 ~~~~iL~~l~~-~~~~t~~ela~~l---~is~~tvs~~l~~Le~~glv~r~~~   98 (162)
T 2fa5_A           50 PEWRVITILAL-YPGSSASEVSDRT---AMDKVAVSRAVARLLERGFIRRETH   98 (162)
T ss_dssp             HHHHHHHHHHH-STTCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEC---
T ss_pred             HHHHHHHHHHh-CCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEeeecC
Confidence            45678888876 6799999999988   7999999999999999999987653

>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=95.26  E-value=0.59  Score=34.20  Aligned_cols=51  Identities=20%  Similarity=0.223  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHhcC-CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQN-RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~n-rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.... .|.+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        31 ~~~~~vL~~l~~~~~~~~t~~ela~~l---~~~~~tvs~~l~~Le~~Gli~r~~~   82 (139)
T 3eco_A           31 NEQGHTLGYLYAHQQDGLTQNDIAKAL---QRTGPTVSNLLRNLERKKLIYRYVD   82 (139)
T ss_dssp             HHHHHHHHHHHHSTTTCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHhcCCCCcCHHHHHHHh---CCCcccHHHHHHHHHHCCCEeecCC
Confidence            45678999998875 699999999988   7999999999999999999997754

>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=95.21  E-value=0.065  Score=39.75  Aligned_cols=58  Identities=16%  Similarity=0.231  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      ..+-.||.++.. +.|.+..+|...+   ++++++|..+|+.|++.|+|.....   +...+|..
T Consensus        37 ~~~~~iL~~l~~-~~~~~~~ela~~l---~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~l   97 (142)
T 2bv6_A           37 YPQFLVLTILWD-ESPVNVKKVVTEL---ALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHL   97 (142)
T ss_dssp             HHHHHHHHHHHH-SSEEEHHHHHHHT---TCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEE
T ss_pred             HHHHHHHHHHHH-cCCcCHHHHHHHH---CCChhhHHHHHHHHHHCCCEEeecCCCCcceEEEEE
Confidence            345678888876 4589999998887   7999999999999999999998776   44444444

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=95.07  E-value=0.43  Score=34.93  Aligned_cols=58  Identities=19%  Similarity=0.307  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      ..+-.||.++... .|.+..+|...+   ++++++|..+|+.|++.|+|....-   |...+|..
T Consensus        31 ~~~~~iL~~l~~~-~~~~~~ela~~l---~is~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~l   91 (142)
T 3bdd_A           31 LTRYSILQTLLKD-APLHQLALQERL---QIDRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWP   91 (142)
T ss_dssp             HHHHHHHHHHHHH-CSBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEE
T ss_pred             HHHHHHHHHHHhC-CCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEE
Confidence            3456788888764 589999999988   7999999999999999999998765   55555555

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=95.04  E-value=0.05  Score=40.44  Aligned_cols=56  Identities=14%  Similarity=0.253  Sum_probs=43.0

Q ss_pred             HHHHHHHHHhc--CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            9 EAIVLNYVNEQ--NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~--nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      --.|+.|+...  .+|.++.+|...+   +|+...|.++|..|...|+|.... |..--|..
T Consensus        11 al~iL~~la~~~~~~~~s~~ela~~~---~i~~~~v~~il~~L~~~Glv~~~~-g~~ggy~L   68 (129)
T 2y75_A           11 GLTIMIELAKKHGEGPTSLKSIAQTN---NLSEHYLEQLVSPLRNAGLVKSIR-GAYGGYVL   68 (129)
T ss_dssp             HHHHHHHHHHTTTSCCBCHHHHHHHT---TSCHHHHHHHHHHHHHTTSEEEC-----CCEEE
T ss_pred             HHHHHHHHHhCCCCCcCCHHHHHHHH---CcCHHHHHHHHHHHHHCCceEecC-CCCCceEe
Confidence            34577788765  5899999998877   899999999999999999998764 65545655

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=94.92  E-value=0.58  Score=34.46  Aligned_cols=51  Identities=14%  Similarity=0.144  Sum_probs=43.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ...+-.||.++... .|-+..+|...+   ++++++|...|+.|++.|+|....-
T Consensus        36 t~~~~~iL~~l~~~-~~~t~~eLa~~l---~~~~~~vs~~l~~L~~~Glv~r~~~   86 (143)
T 3oop_A           36 TPEQWSVLEGIEAN-EPISQKEIALWT---KKDTPTVNRIVDVLLRKELIVREIS   86 (143)
T ss_dssp             CHHHHHHHHHHHHH-SSEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             CHHHHHHHHHHHHc-CCcCHHHHHHHH---CCCHhhHHHHHHHHHHCCCeeccCC
Confidence            35567788888765 788999999988   7999999999999999999987654

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=94.87  E-value=0.76  Score=35.08  Aligned_cols=50  Identities=16%  Similarity=0.185  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++... .|-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        45 ~~~~~iL~~L~~~-~~~t~~eLa~~l---~is~~tvs~~l~~Le~~GlV~r~~~   94 (168)
T 2nyx_A           45 IPQFRTLVILSNH-GPINLATLATLL---GVQPSATGRMVDRLVGAELIDRLPH   94 (168)
T ss_dssp             HHHHHHHHHHHHH-CSEEHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHh---CCCHHHHHHHHHHHHHCCCEEeccC
Confidence            3456788888764 489999999988   7999999999999999999988654

>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=94.79  E-value=0.88  Score=33.82  Aligned_cols=50  Identities=16%  Similarity=0.279  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|.+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        37 ~~~~~iL~~l~~-~~~~t~~ela~~l---~~s~~tvs~~l~~Le~~glv~r~~~   86 (155)
T 1s3j_A           37 PAQLFVLASLKK-HGSLKVSEIAERM---EVKPSAVTLMADRLEQKNLIARTHN   86 (155)
T ss_dssp             HHHHHHHHHHHH-HSEEEHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEeecCC
Confidence            345678888876 4589999999988   7999999999999999999998765

>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=94.73  E-value=0.1  Score=37.53  Aligned_cols=58  Identities=14%  Similarity=0.221  Sum_probs=47.4

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      .-+-.||.++.  +.|-+..+|...+.  +++++++...|+.|.+.|+|.....   +...+|..
T Consensus        14 ~~~~~IL~~L~--~~~~~~~eLa~~l~--~is~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~L   74 (107)
T 2hzt_A           14 KWKXVILXHLT--HGKKRTSELKRLMP--NITQKMLTQQLRELEADGVINRIVYNQVPPKVEYEL   74 (107)
T ss_dssp             TTHHHHHHHHT--TCCBCHHHHHHHCT--TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             ccHHHHHHHHH--hCCCCHHHHHHHhc--CCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEE
Confidence            33456888885  67999999988774  7999999999999999999998877   45566666

>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=94.72  E-value=0.56  Score=34.92  Aligned_cols=51  Identities=24%  Similarity=0.230  Sum_probs=43.4

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.....|.+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        39 ~~q~~vL~~l~~~~~~~t~~eLa~~l---~i~~~tvs~~l~~Le~~Glv~r~~~   89 (150)
T 3fm5_A           39 VRSYSVLVLACEQAEGVNQRGVAATM---GLDPSQIVGLVDELEERGLVVRTLD   89 (150)
T ss_dssp             HHHHHHHHHHHHSTTCCCSHHHHHHH---TCCHHHHHHHHHHHHTTTSEEC---
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHH---CCCHhHHHHHHHHHHHCCCEEeeCC
Confidence            45677899998888899999999988   7999999999999999999987654

>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=94.63  E-value=0.46  Score=35.29  Aligned_cols=50  Identities=12%  Similarity=0.274  Sum_probs=39.9

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      +.-..|+.++. .+.|-+..+|...+   +|++++|.++|+.|.+.|+|.....
T Consensus         8 ~~L~~i~~l~~-~~~~~~~~ela~~l---~vs~~tvs~~l~~Le~~Glv~r~~~   57 (142)
T 1on2_A            8 MYIEQIYMLIE-EKGYARVSDIAEAL---AVHPSSVTKMVQKLDKDEYLIYEKY   57 (142)
T ss_dssp             HHHHHHHHHHH-HHSSCCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHh-hcCCCCHHHHHHHh---CCCHHHHHHHHHHHHHCCCEEEeeC
Confidence            33444555543 46689999999988   7999999999999999999988754

>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=94.59  E-value=0.091  Score=37.19  Aligned_cols=60  Identities=30%  Similarity=0.432  Sum_probs=49.0

Q ss_pred             chHHHHHHHHHHh-cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc-eeec--CceeEEEe
Q 027236            6 DNTEAIVLNYVNE-QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS-FKEY--GKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~-~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~-~K~~--GK~kiY~~   68 (226)
                      ...+-.||.++.. .|.--+..+|...+   ++.+++|.++|+.|...|+|. .+.+  -+.++|..
T Consensus        19 t~~q~~Vl~~I~~~g~~gi~qkeLa~~~---~l~~~tvt~iLk~LE~kglIkr~~~~~~~~rKvy~L   82 (91)
T 2dk5_A           19 DNQEKLVYQIIEDAGNKGIWSRDVRYKS---NLPLTEINKILKNLESKKLIKAVKSVAASKKKVYML   82 (91)
T ss_dssp             CSSHHHHHHHHHHHCTTCEEHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEEE
T ss_pred             CHHHHHHHHHHHHcCCCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEecCCCCCCcEEEEE
Confidence            4567889999997 46678888898877   789999999999999999998 4444  35688877

>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=94.58  E-value=0.79  Score=32.33  Aligned_cols=48  Identities=17%  Similarity=0.104  Sum_probs=37.3

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .||.++.   ..-+..+|...+   +++-..+.+.|+.|.+.|+|.....|    |..
T Consensus        12 ~IL~~i~---~~~~~t~La~~~---~ls~~~~~~~l~~L~~~GLI~~~~~~----~~L   59 (95)
T 1r7j_A           12 AILEACK---SGSPKTRIMYGA---NLSYALTGRYIKMLMDLEIIRQEGKQ----YML   59 (95)
T ss_dssp             HHHHHHT---TCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEETTE----EEE
T ss_pred             HHHHHHH---cCCCHHHHHHHh---CcCHHHHHHHHHHHHHCCCeEEECCe----eEE
Confidence            3455554   226777887777   89999999999999999999988554    666

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=94.55  E-value=1.1  Score=33.72  Aligned_cols=49  Identities=18%  Similarity=0.271  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .+-.||.++.. +.|-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        51 ~q~~vL~~l~~-~~~~t~~eLa~~l---~~~~~tvs~~l~~Le~~Glv~r~~~   99 (159)
T 3s2w_A           51 GQFPFLMRLYR-EDGINQESLSDYL---KIDKGTTARAIQKLVDEGYVFRQRD   99 (159)
T ss_dssp             TTHHHHHHHHH-SCSEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEecC
Confidence            44568888876 4789999999888   7999999999999999999998764

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=94.53  E-value=0.32  Score=36.44  Aligned_cols=57  Identities=11%  Similarity=0.189  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      -+-.||.++.  +.|.+..+|...+.  ||+++++...|+.|.+.|+|....+   +...+|..
T Consensus        36 w~l~IL~~L~--~g~~~~~eLa~~l~--gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~L   95 (131)
T 1yyv_A           36 WGVLILVALR--DGTHRFSDLRRXMG--GVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSL   95 (131)
T ss_dssp             HHHHHHHHGG--GCCEEHHHHHHHST--TCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEE
T ss_pred             cHHHHHHHHH--cCCCCHHHHHHHhc--cCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEE
Confidence            3456788876  67899989988774  6999999999999999999998887   45566666

>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=94.53  E-value=0.4  Score=34.66  Aligned_cols=58  Identities=9%  Similarity=0.254  Sum_probs=47.5

Q ss_pred             chHHHHHHHHHHhcCCCCc--HHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLN--SQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys--~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +.-+-.|+.++.  ..|.+  ..+|...++  ||+.+++...|+.|.+.|+|....+ ...+|..
T Consensus        26 ~~wrl~IL~~L~--~g~~~~~~~eL~~~l~--gis~~~ls~~L~~Le~~GlV~r~~~-r~~~y~L   85 (111)
T 3df8_A           26 KKYTMLIISVLG--NGSTRQNFNDIRSSIP--GISSTILSRRIKDLIDSGLVERRSG-QITTYAL   85 (111)
T ss_dssp             STTHHHHHHHHT--SSSSCBCHHHHHHTST--TCCHHHHHHHHHHHHHTTSEEEEES-SSEEEEE
T ss_pred             CccHHHHHHHHh--cCCCCCCHHHHHHHcc--CCCHHHHHHHHHHHHHCCCEEEeec-CcEEEEE
Confidence            344567888886  56777  999988774  7999999999999999999999988 5566655

>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=94.52  E-value=0.31  Score=35.82  Aligned_cols=51  Identities=24%  Similarity=0.348  Sum_probs=42.8

Q ss_pred             hHHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++... ..|.+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        37 ~~q~~vL~~l~~~~~~~~t~~eLa~~l---~~~~~tvs~~l~~Le~~Glv~r~~~   88 (127)
T 2frh_A           37 FEEFAVLTYISENKEKEYYLKDIINHL---NYKQPQVVKAVKILSQEDYFDKKRN   88 (127)
T ss_dssp             HHHHHHHHHHHHTCCSEEEHHHHHHHS---SSHHHHHHHHHHHHHHTTSSCCBCC
T ss_pred             HHHHHHHHHHHhccCCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEecCC
Confidence            4566788888864 2789999998877   7999999999999999999987544

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=94.52  E-value=0.85  Score=33.11  Aligned_cols=50  Identities=4%  Similarity=0.153  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|-+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        33 ~~~~~iL~~l~~-~~~~~~~ela~~l---~~~~~tvs~~l~~L~~~gli~r~~~   82 (139)
T 3bja_A           33 YVQFGVIQVLAK-SGKVSMSKLIENM---GCVPSNMTTMIQRMKRDGYVMTEKN   82 (139)
T ss_dssp             HHHHHHHHHHHH-SCSEEHHHHHHHC---SSCCTTHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHH-cCCcCHHHHHHHH---CCChhHHHHHHHHHHHCCCeeeccC
Confidence            456678888876 5689999998877   7999999999999999999988654

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=94.51  E-value=0.4  Score=36.06  Aligned_cols=51  Identities=10%  Similarity=0.139  Sum_probs=43.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++...+.|-+..+|...+   ++++++|...|+.|++.|+|.....
T Consensus        47 ~~~~~iL~~L~~~~~~~~~~ela~~l---~i~~~tvs~~l~~Le~~Gli~r~~~   97 (160)
T 3boq_A           47 LAKFDAMAQLARNPDGLSMGKLSGAL---KVTNGNVSGLVNRLIKDGMVVKAMS   97 (160)
T ss_dssp             HHHHHHHHHHHHCTTCEEHHHHHHHC---SSCCSCHHHHHHHHHHHTSEEEC--
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHH---CCChhhHHHHHHHHHHCCCEEeecC
Confidence            34667899997678899999998887   7999999999999999999988654

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=94.44  E-value=1.1  Score=33.17  Aligned_cols=50  Identities=14%  Similarity=0.242  Sum_probs=42.9

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++... .|-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        42 ~~~~~iL~~l~~~-~~~t~~ela~~l---~~~~~tvs~~l~~Le~~Glv~r~~~   91 (150)
T 2rdp_A           42 PPQFVALQWLLEE-GDLTVGELSNKM---YLACSTTTDLVDRMERNGLVARVRD   91 (150)
T ss_dssp             HHHHHHHHHHHHH-CSBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHH---CCCchhHHHHHHHHHHCCCeeecCC
Confidence            4566788888874 589999999888   7999999999999999999998754

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=94.42  E-value=0.32  Score=40.67  Aligned_cols=63  Identities=13%  Similarity=0.256  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCH-----HHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTL-----EQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~-----~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +..+|.+|..+...+..+..++..++.+++.+......     .++...+..++.++.....++..++
T Consensus        13 LQ~lD~~i~~l~~~~~~lp~el~~le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~   80 (256)
T 3na7_A           13 ISHLDKEIDSLEPLIREKRKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQ   80 (256)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555554444444444444444444433222     4455555555555555555555554

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=94.37  E-value=1.2  Score=33.47  Aligned_cols=50  Identities=14%  Similarity=0.173  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|.+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        52 ~~~~~iL~~l~~-~~~~t~~ela~~l---~is~~tvs~~l~~Le~~Gli~r~~~  101 (162)
T 3cjn_A           52 TAKMRALAILSA-KDGLPIGTLGIFA---VVEQSTLSRALDGLQADGLVRREVD  101 (162)
T ss_dssp             HHHHHHHHHHHH-SCSEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHH-CCCCCHHHHHHHH---CCChhHHHHHHHHHHHCCCEEecCC
Confidence            356678888876 4589999999988   7999999999999999999988653

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=94.35  E-value=0.18  Score=39.09  Aligned_cols=61  Identities=18%  Similarity=0.200  Sum_probs=49.8

Q ss_pred             chHHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC--------ceeEEEe
Q 027236            6 DNTEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG--------KQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G--------K~kiY~~   68 (226)
                      +.-+..|+.++... .++.++.+|...++  +|+.++|-..|+.|++.|+|..-.++        ..++|+.
T Consensus        28 ~~tR~~IL~~Ll~~p~~~~ta~eL~~~l~--~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~L   97 (151)
T 3u1d_A           28 HETRLDVLHQILAQPDGVLSVEELLYRNP--DETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAV   97 (151)
T ss_dssp             CHHHHHHHHHHHHSTTSCBCHHHHHHHCT--TSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEE
T ss_pred             chHHHHHHHHHHcCCCCCCCHHHHHHhcC--CCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEE
Confidence            56788999999876 46789999988763  59999999999999999999976543        3467776

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=94.32  E-value=0.89  Score=33.41  Aligned_cols=58  Identities=26%  Similarity=0.421  Sum_probs=43.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      ...+-.||.++....  .+..+|.+.+   ++++++|..+|+.|++.|+|....-   |...+|..
T Consensus        37 t~~~~~iL~~l~~~~--~t~~eLa~~l---~~s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~l   97 (146)
T 3tgn_A           37 TNTQEHILMLLSEES--LTNSELARRL---NVSQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQL   97 (146)
T ss_dssp             CHHHHHHHHHHTTCC--CCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEC----------CCEE
T ss_pred             CHHHHHHHHHHHhCC--CCHHHHHHHH---CCCHHHHHHHHHHHHHCCCeEeccCCCCCceeEEEE
Confidence            456778999998654  9999999988   7999999999999999999988763   44444444

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=94.20  E-value=0.78  Score=34.64  Aligned_cols=49  Identities=14%  Similarity=0.171  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .+-.||.++.... |-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        54 ~q~~vL~~l~~~~-~~t~~eLa~~l---~~~~~~vs~~l~~Le~~Glv~r~~~  102 (161)
T 3e6m_A           54 PKLRLLSSLSAYG-ELTVGQLATLG---VMEQSTTSRTVDQLVDEGLAARSIS  102 (161)
T ss_dssp             HHHHHHHHHHHHS-EEEHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEECC-
T ss_pred             HHHHHHHHHHhCC-CCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEeeCC
Confidence            4556888887754 89999998877   7999999999999999999998755

>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=94.10  E-value=0.87  Score=33.50  Aligned_cols=50  Identities=24%  Similarity=0.316  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++... .|.+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        37 ~~~~~vL~~l~~~-~~~t~~eLa~~l---~~~~~tvs~~l~~L~~~Glv~r~~~   86 (142)
T 3ech_A           37 PPDVHVLKLIDEQ-RGLNLQDLGRQM---CRDKALITRKIRELEGRNLVRRERN   86 (142)
T ss_dssp             HHHHHHHHHHHHT-TTCCHHHHHHHH---C---CHHHHHHHHHHHTTSEEC---
T ss_pred             HHHHHHHHHHHhC-CCcCHHHHHHHh---CCCHHHHHHHHHHHHHCCCEeeccC
Confidence            4567789999875 489999999988   7999999999999999999988655

>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=94.03  E-value=0.13  Score=38.29  Aligned_cols=50  Identities=18%  Similarity=0.280  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.... |.+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        40 ~~~~~iL~~l~~~~-~~~~~~la~~l---~~~~~tvs~~l~~L~~~glv~r~~~   89 (147)
T 1z91_A           40 YPQYLALLLLWEHE-TLTVKKMGEQL---YLDSGTLTPMLKRMEQQGLITRKRS   89 (147)
T ss_dssp             HHHHHHHHHHHHHS-EEEHHHHHHTT---TCCHHHHHHHHHHHHHHTSEECCBC
T ss_pred             HHHHHHHHHHHHCC-CCCHHHHHHHH---CCCcCcHHHHHHHHHHCCCEEeccC
Confidence            45667888888754 88999998877   7999999999999999999988755

>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=94.02  E-value=1.8  Score=34.44  Aligned_cols=52  Identities=17%  Similarity=0.366  Sum_probs=45.1

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee---ecCc
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK---EYGK   62 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K---~~GK   62 (226)
                      +..+..|+.++.  +.|.+..+|...+   |++.++|...|+.|.+.|+|...   .-|.
T Consensus        19 d~~~~~IL~~L~--~~~~s~~eLA~~l---glS~stv~~~l~~Le~~GlI~~~~~~~~~~   73 (192)
T 1uly_A           19 EDTRRKILKLLR--NKEMTISQLSEIL---GKTPQTIYHHIEKLKEAGLVEVKRTEMKGN   73 (192)
T ss_dssp             SHHHHHHHHHHT--TCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEEEEETT
T ss_pred             CHHHHHHHHHHH--cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEecccccc
Confidence            566778999997  4689999999988   79999999999999999999886   4565

>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=93.97  E-value=0.15  Score=36.49  Aligned_cols=56  Identities=18%  Similarity=0.275  Sum_probs=45.5

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC---ceeEEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG---KQKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G---K~kiY~~   68 (226)
                      +-.||.++.  +.|-+..+|...++  |++.++|...|+.|.+.|+|.....+   ...+|..
T Consensus        27 ~~~IL~~L~--~~~~~~~eL~~~l~--gis~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~L   85 (107)
T 2fsw_A           27 TLLIIFQIN--RRIIRYGELKRAIP--GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSL   85 (107)
T ss_dssp             HHHHHHHHT--TSCEEHHHHHHHST--TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             HHHHHHHHH--hCCcCHHHHHHHcc--cCCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEE
Confidence            446788885  67899989988773  69999999999999999999988773   4456665

>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=93.90  E-value=1.8  Score=33.80  Aligned_cols=52  Identities=13%  Similarity=0.201  Sum_probs=44.9

Q ss_pred             hHHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            7 NTEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         7 ea~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ..+-.||.++... +.|-+..+|...+   ++++++|..+|+.|++.|+|......
T Consensus        41 ~~q~~vL~~L~~~~~~~~t~~eLa~~l---~is~~tvs~~l~~Le~~GlV~r~~~~   93 (189)
T 3nqo_A           41 SRQYMTILSILHLPEEETTLNNIARKM---GTSKQNINRLVANLEKNGYVDVIPSP   93 (189)
T ss_dssp             HHHHHHHHHHHHSCGGGCCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHHhccCCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            3566788999874 5799999999988   79999999999999999999987663

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=93.88  E-value=0.86  Score=33.88  Aligned_cols=47  Identities=11%  Similarity=0.173  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      ..+-.||.++... .|-+..+|...+   ++++++|..+|+.|++.|+|..
T Consensus        41 ~~~~~iL~~l~~~-~~~t~~eLa~~l---~~~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           41 IQQLAMINVIYST-PGISVADLTKRL---IITGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             HHHHHHHHHHHHS-TTEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHC-CCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEe
Confidence            3456788888864 689999999988   7999999999999999999988

>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=93.84  E-value=0.097  Score=43.40  Aligned_cols=56  Identities=18%  Similarity=0.328  Sum_probs=46.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +.--.||++|....+|.++.+|...+   ++++++|-..|..|++.|.|...   ...-|..
T Consensus         8 ~r~l~iL~~l~~~~~~~~~~ela~~~---gl~~stv~r~l~~L~~~G~v~~~---~~~~Y~l   63 (249)
T 1mkm_A            8 KKAFEILDFIVKNPGDVSVSEIAEKF---NMSVSNAYKYMVVLEEKGFVLRK---KDKRYVP   63 (249)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEC---TTSCEEE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCcEEEC---CCCcEEE
Confidence            34457899998888899999999887   89999999999999999999876   2334655

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=93.53  E-value=0.5  Score=36.00  Aligned_cols=56  Identities=23%  Similarity=0.312  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      ..++..|..++..+..++..+..+|..+.-  -.+++..++..|+.++.+|+.++..|
T Consensus        74 ~~~~~~L~~~l~~~~kE~~~lK~el~~~~~--k~e~~~~e~~~l~~~~~~l~~~~~~l  129 (138)
T 3hnw_A           74 KKMADSLSLDIENKDKEIYDLKHELIAAQI--KAESSAKEIKELKSEINKYQKNIVKL  129 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444333331  12333334444444444444444333

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=93.52  E-value=0.76  Score=31.74  Aligned_cols=66  Identities=12%  Similarity=0.251  Sum_probs=36.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC-----CHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           77 NSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL-----TLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        77 ~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~-----t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      |-+=+..+..+|..+-+.+..|+-++.+|+.+-..|....     ..+.|..++.+|+++...-+++|..|
T Consensus         4 S~ElleqLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~~L   74 (81)
T 2jee_A            4 SLEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQAL   74 (81)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455677777777777766666666666655544443221     11334555555555555555555443

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=93.19  E-value=0.54  Score=34.30  Aligned_cols=60  Identities=23%  Similarity=0.339  Sum_probs=45.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcc---c--ccH-HHHHHHHHHHHHcCCcceeec---Cce-eEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKY---N--LKK-AGIQKALDSLADNGKISFKEY---GKQ-KIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~---~--v~K-~~v~k~L~~Lv~~g~i~~K~~---GK~-kiY~~   68 (226)
                      --+-.||.++..  .|-+..+|...+...   .  ++. .++-.+|+.|.++|+|.....   |.. ++|..
T Consensus        13 ~~~~~IL~~L~~--~~~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~L   82 (118)
T 2esh_A           13 WLASTILLLVAE--KPSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRI   82 (118)
T ss_dssp             HHHHHHHHHHHH--SCBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEE
T ss_pred             hHHHHHHHHHHc--CCCCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEEE
Confidence            455678888865  688877888877532   3  888 999999999999999998864   444 55655

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=93.17  E-value=0.22  Score=36.50  Aligned_cols=58  Identities=16%  Similarity=0.287  Sum_probs=47.2

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +.....||++|... -|.++.+|...+. .+++.++|.+.|..|.+.|+|...  |.. +|..
T Consensus        12 d~~d~~IL~~L~~~-g~~s~~eLA~~l~-~giS~~aVs~rL~~Le~~GLV~~~--~rg-~Y~L   69 (111)
T 3b73_A           12 TIWDDRILEIIHEE-GNGSPKELEDRDE-IRISKSSVSRRLKKLADHDLLQPL--ANG-VYVI   69 (111)
T ss_dssp             CHHHHHHHHHHHHH-SCBCHHHHHTSTT-CCSCHHHHHHHHHHHHHTTSEEEC--STT-CEEE
T ss_pred             CHHHHHHHHHHHHc-CCCCHHHHHHHHh-cCCCHHHHHHHHHHHHHCCCEEec--CCc-eEEE
Confidence            56778999999764 4999988887652 278999999999999999999885  444 7766

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=93.15  E-value=0.11  Score=43.93  Aligned_cols=56  Identities=16%  Similarity=0.215  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +.--.||++|-...+|.++.+|...+   |++|++|-..|.+|++.|.|....-|   -|..
T Consensus        30 ~Ral~IL~~l~~~~~~ltl~eia~~l---gl~ksTv~RlL~tL~~~G~v~~~~~~---~Y~L   85 (275)
T 3mq0_A           30 RRAVRILDLVAGSPRDLTAAELTRFL---DLPKSSAHGLLAVMTELDLLARSADG---TLRI   85 (275)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHH---TCC--CHHHHHHHHHHTTSEEECTTS---EEEE
T ss_pred             HHHHHHHHHHhhCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEECCCC---cEEe
Confidence            44456999999999999999999988   89999999999999999999876422   4666

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=92.99  E-value=0.15  Score=42.06  Aligned_cols=55  Identities=11%  Similarity=0.165  Sum_probs=46.0

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      --.||++|.....|.++.+|...+   |++|++|-..|..|++.|.|....-  ..-|..
T Consensus         8 ~l~iL~~l~~~~~~~s~~ela~~~---gl~~stv~r~l~~L~~~G~v~~~~~--~~~Y~l   62 (241)
T 2xrn_A            8 AASIMRALGSHPHGLSLAAIAQLV---GLPRSTVQRIINALEEEFLVEALGP--AGGFRL   62 (241)
T ss_dssp             HHHHHHHHHTCTTCEEHHHHHHHT---TSCHHHHHHHHHHHHTTTSEEECGG--GCEEEE
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEeCC--CCeEEE
Confidence            346899998888899999999888   8999999999999999999987533  334666

>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=92.89  E-value=0.18  Score=40.16  Aligned_cols=46  Identities=17%  Similarity=0.316  Sum_probs=38.6

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      +.|++|+.+...|-|..+|...+   |+++++|...|..|..+|.|...
T Consensus        12 ~~I~~~~~~~g~~~s~~eia~~l---gl~~~tv~~~l~~Le~~G~i~~~   57 (196)
T 3k2z_A           12 LFIEEFIEKNGYPPSVREIARRF---RITPRGALLHLIALEKKGYIERK   57 (196)
T ss_dssp             HHHHHHHHHHSSCCCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHc---CCCcHHHHHHHHHHHHCCCEEec
Confidence            33444555678899999999988   79999999999999999999775

>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=92.82  E-value=1.2  Score=33.03  Aligned_cols=51  Identities=18%  Similarity=0.302  Sum_probs=37.2

Q ss_pred             hHHHHHHHHHHhcC-CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQN-RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~n-rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.... .|.+..+|...+   ++++++|..+|+.|+++|+|....-
T Consensus        41 ~~q~~vL~~l~~~~~~~~t~~eLa~~l---~~~~~~vs~~l~~L~~~Glv~r~~~   92 (148)
T 3jw4_A           41 SQQGRMIGYIYENQESGIIQKDLAQFF---GRRGASITSMLQGLEKKGYIERRIP   92 (148)
T ss_dssp             HHHHHHHHHHHHHTTTCCCHHHHHHC---------CHHHHHHHHHHTTSBCCC--
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHH---CCChhHHHHHHHHHHHCCCEEeeCC
Confidence            45567888988754 799999998877   7999999999999999999987754

>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens}

Probab=92.82  E-value=0.18  Score=32.13  Aligned_cols=37  Identities=22%  Similarity=0.369  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027236           75 IPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRT  111 (226)
Q Consensus        75 ~~~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~  111 (226)
                      .++..+...|..++.+|+.++..|..++.++.++|.+
T Consensus        15 ~p~~~d~eaLk~E~~eLk~k~~~L~~~~~el~~~l~~   51 (53)
T 2yy0_A           15 TPENPEIELLRLELAEMKEKYEAIVEENKKLKAKLAQ   51 (53)
T ss_dssp             -CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5678999999999999999999999999988887753

>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=92.80  E-value=0.42  Score=36.31  Aligned_cols=58  Identities=14%  Similarity=0.130  Sum_probs=46.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC--ceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG--KQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G--K~kiY~~   68 (226)
                      +.-.-.||.++.  +.|-+..+|...+   +|+++++...|+.|++.|+|....+.  ....|..
T Consensus        23 ~~w~l~IL~~L~--~g~~~~~eLa~~l---gis~~tls~~L~~Le~~GlI~r~~~~~d~~~~y~L   82 (146)
T 2f2e_A           23 DGWSMLIVRDAF--EGLTRFGEFQKSL---GLAKNILAARLRNLVEHGVMVAVPAESGSHQEYRL   82 (146)
T ss_dssp             SSSHHHHHHHHH--TTCCSHHHHHHHH---CCCHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEE
T ss_pred             CchHHHHHHHHH--hCCCCHHHHHHHh---CCCHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEE
Confidence            334556888885  5688988998888   79999999999999999999998873  2455555

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=92.78  E-value=0.24  Score=37.07  Aligned_cols=50  Identities=16%  Similarity=0.204  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|.+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        47 ~~~~~iL~~l~~-~~~~t~~ela~~l---~~s~~tvs~~l~~Le~~glv~r~~~   96 (153)
T 2pex_A           47 YPQYLVMLVLWE-TDERSVSEIGERL---YLDSATLTPLLKRLQAAGLVTRTRA   96 (153)
T ss_dssp             HHHHHHHHHHHH-SCSEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             HHHHHHHHHHHh-CCCcCHHHHHHHh---CCCcccHHHHHHHHHHCCCEeecCC
Confidence            456678888876 5689999999988   7999999999999999999988654

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=92.76  E-value=1.9  Score=32.04  Aligned_cols=34  Identities=15%  Similarity=0.150  Sum_probs=29.2

Q ss_pred             cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236           24 NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus        24 s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      |..++...+   ||+.+.|.+||..|..+|+|.....
T Consensus        40 ser~La~~~---gVSr~tVReAl~~L~~eGlv~~~~g   73 (134)
T 4ham_A           40 SIREFASRI---GVNPNTVSKAYQELERQEVIITVKG   73 (134)
T ss_dssp             CHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             cHHHHHHHH---CCCHHHHHHHHHHHHHCCcEEEEcC
Confidence            666777666   8999999999999999999987754

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=92.69  E-value=1.8  Score=31.76  Aligned_cols=49  Identities=16%  Similarity=0.199  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .+-.||.++.... | +..+|...+   ++++++|...|+.|++.|+|....-.
T Consensus        38 ~~~~iL~~l~~~~-~-~~~~la~~l---~~~~~tvs~~l~~Le~~Glv~r~~~~   86 (144)
T 3f3x_A           38 LDFSILKATSEEP-R-SMVYLANRY---FVTQSAITAAVDKLEAKGLVRRIRDS   86 (144)
T ss_dssp             HHHHHHHHHHHSC-E-EHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHHHHHHCC-C-CHHHHHHHH---CCChhHHHHHHHHHHHCCCEEeccCC
Confidence            4567888887654 4 999999888   79999999999999999999988654

>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=92.67  E-value=0.59  Score=38.32  Aligned_cols=60  Identities=15%  Similarity=0.134  Sum_probs=50.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      +.-...|++++.. +.+-++.++..++   |++...++.+|+.++.+|++..+.-+-..+||+|
T Consensus       153 ~~~~~~il~~~~~-~g~vt~~~la~~l---~ws~~~a~e~L~~~e~~G~l~~D~~~eg~~y~pn  212 (218)
T 3cuq_B          153 EEMVASALETVSE-KGSLTSEEFAKLV---GMSVLLAKERLLLAEKMGHLCRDDSVEGLRFYPN  212 (218)
T ss_dssp             GGGHHHHHHHHHH-TSCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEESSSCEEEEEC
T ss_pred             HHHHHHHHHHHHH-CCCcCHHHHHHHh---CCCHHHHHHHHHHHHHcCCEEEECCCCceEEehh
Confidence            4677889998864 6788999998888   8999999999999999999999986656556663

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=92.62  E-value=0.09  Score=43.98  Aligned_cols=55  Identities=9%  Similarity=0.192  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .--.||++|...++|.++.+|...+   |++|++|-..|..|++.|.|....-|   -|..
T Consensus        24 r~l~iL~~l~~~~~~~~~~eia~~~---gl~kstv~r~l~tL~~~G~v~~~~~~---~Y~l   78 (260)
T 2o0y_A           24 RVIDLLELFDAAHPTRSLKELVEGT---KLPKTTVVRLVATMCARSVLTSRADG---SYSL   78 (260)
T ss_dssp             HHHHHHTTCBTTBSSBCHHHHHHHH---CCCHHHHHHHHHHHHHTTSEEECTTS---CEEE
T ss_pred             HHHHHHHHHhhCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEECCCC---eEEe
Confidence            3446788887778899999999988   89999999999999999999887544   4655

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=92.60  E-value=0.14  Score=42.67  Aligned_cols=55  Identities=16%  Similarity=0.168  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +.--.||++|.....|.++.+|...+   |++|++|-..|..|++.|.|...  +  .-|..
T Consensus        14 ~r~l~iL~~l~~~~~~~~~~eia~~~---gl~~stv~r~l~~L~~~G~v~~~--~--~~Y~L   68 (257)
T 2g7u_A           14 ERGFAVLLAFDAQRPNPTLAELATEA---GLSRPAVRRILLTLQKLGYVAGS--G--GRWSL   68 (257)
T ss_dssp             HHHHHHHHTCSSSCSSCBHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEE--T--TEEEE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEeC--C--CEEEE
Confidence            34456888888778899999999988   89999999999999999999875  3  45665

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=92.60  E-value=0.59  Score=29.74  Aligned_cols=55  Identities=11%  Similarity=0.163  Sum_probs=37.6

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCceeEE
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGKQKIY   66 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY   66 (226)
                      +..++..+..++.|+|+.+|.+.|...  +|+.++|-..|+.   -|+|....-|....|
T Consensus         6 R~~~i~~ll~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~~---lg~v~~~~~~~~~~Y   62 (64)
T 2p5k_A            6 RHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKE---LHLVKVPTNNGSYKY   62 (64)
T ss_dssp             HHHHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHHH---HTCEEEEETTTEEEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHHH---cCCEEEecCCCceee
Confidence            344444455678999999999999653  7999999999994   477722222344444

>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=92.59  E-value=2.5  Score=31.75  Aligned_cols=50  Identities=20%  Similarity=0.191  Sum_probs=43.0

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++... .|-+..+|...+   ++++++|..+|+.|++.|+|....-
T Consensus        46 ~~q~~iL~~l~~~-~~~t~~eLa~~l---~~~~~tvs~~l~~Le~~Glv~r~~~   95 (162)
T 3k0l_A           46 LPQFTALSVLAAK-PNLSNAKLAERS---FIKPQSANKILQDLLANGWIEKAPD   95 (162)
T ss_dssp             HHHHHHHHHHHHC-TTCCHHHHHHHH---TSCGGGHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHHC-CCCCHHHHHHHH---CCCHHHHHHHHHHHHHCcCeEecCC
Confidence            3456788888765 599999999988   7999999999999999999998764

>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=92.47  E-value=0.46  Score=32.90  Aligned_cols=63  Identities=10%  Similarity=0.220  Sum_probs=53.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeec
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQ   70 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q   70 (226)
                      .+.++.||++++..-..-+=.++...++  +|+......++..|...|+|..-.-|.+-||=...
T Consensus        13 ~~ie~~IL~l~~~~P~GItd~~L~~~~p--~~~~~~r~~aIN~LL~~gkiel~K~~~~liYr~k~   75 (81)
T 2dk8_A           13 VEIENRIIELCHQFPHGITDQVIQNEMP--HIEAQQRAVAINRLLSMGQLDLLRSNTGLLYRIKD   75 (81)
T ss_dssp             HHHHHHHHHHHHHCSSCEEHHHHHHHCT--TSCHHHHHHHHHHHHHHTSEEEEECSSSEEEEECC
T ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHCC--CCCHHHHHHHHHHHHHcCCeEEEecCCeEEEEecc
Confidence            4668999999998888888888888886  69999999999999999999988888667775533

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=92.36  E-value=0.25  Score=33.90  Aligned_cols=45  Identities=18%  Similarity=0.200  Sum_probs=38.4

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      ..|++|+.+ +.+-++.+|...|   +|+..+|-.-|+.|.+.|+|.--
T Consensus         5 ~~Il~~L~~-~g~vsv~eLa~~l---~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            5 IQVRDLLAL-RGRMEAAQISQTL---NTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHH-SCSBCHHHHHHHT---TCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHH-cCCCcHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEe
Confidence            578999975 5578988998887   79999999999999999988543

>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=92.34  E-value=0.26  Score=38.99  Aligned_cols=49  Identities=14%  Similarity=0.274  Sum_probs=43.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCC-cce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGK-ISF   57 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~-i~~   57 (226)
                      .+-...|+.+|.+.++|.|+.++...+   +|+..+|.+-|+.|.+.|. |..
T Consensus        20 ~~R~~~Il~~L~~~~~~~s~~eLa~~l---~vS~~Ti~rdi~~L~~~G~~I~~   69 (187)
T 1j5y_A           20 QERLKSIVRILERSKEPVSGAQLAEEL---SVSRQVIVQDIAYLRSLGYNIVA   69 (187)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHH---TSCHHHHHHHHHHHHHHTCCCEE
T ss_pred             HHHHHHHHHHHHHcCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEE
Confidence            345678999999888999999999988   8999999999999999999 655

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=92.30  E-value=0.37  Score=36.97  Aligned_cols=48  Identities=21%  Similarity=0.356  Sum_probs=42.0

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      ++....|+.++... -|.+..+|...+   |++.++|.+.|..|.+.|.|..
T Consensus         9 d~~~~~il~~L~~~-~~~s~~ela~~l---g~s~~tv~~~l~~L~~~G~i~~   56 (162)
T 2p5v_A            9 DKTDIKILQVLQEN-GRLTNVELSERV---ALSPSPCLRRLKQLEDAGIVRQ   56 (162)
T ss_dssp             CHHHHHHHHHHHHC-TTCCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHHc-CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEee
Confidence            67778999998764 457999999988   7999999999999999999974

>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=92.12  E-value=0.38  Score=35.16  Aligned_cols=50  Identities=14%  Similarity=0.156  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|-+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        34 ~~~~~iL~~l~~-~~~~~~~~la~~l---~~~~~tvs~~l~~L~~~gli~r~~~   83 (138)
T 1jgs_A           34 AAQFKVLCSIRC-AACITPVELKKVL---SVDLGALTRMLDRLVCKGWVERLPN   83 (138)
T ss_dssp             HHHHHHHHHHHH-HSSBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHh-cCCCCHHHHHHHH---CCChHHHHHHHHHHHHCCCEEecCC
Confidence            456678888875 4588999998877   7999999999999999999998755

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=92.11  E-value=2.5  Score=30.60  Aligned_cols=50  Identities=12%  Similarity=0.190  Sum_probs=42.4

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|-+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        36 ~~~~~iL~~l~~-~~~~t~~ela~~l---~~s~~~vs~~l~~Le~~glv~r~~~   85 (142)
T 2fbi_A           36 EQQWRVIRILRQ-QGEMESYQLANQA---CILRPSMTGVLARLERDGIVRRWKA   85 (142)
T ss_dssp             HHHHHHHHHHHH-HCSEEHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHH---CCCHhHHHHHHHHHHHCCCEEeecC
Confidence            356678888876 4589999998877   7999999999999999999988755

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=92.04  E-value=0.23  Score=34.87  Aligned_cols=46  Identities=13%  Similarity=0.175  Sum_probs=39.6

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      ..|++|+.+ +.+-++.+|...|   +|+..+|-.-|+.|.+.|+|.--.
T Consensus         5 ~~Il~~L~~-~g~vsv~eLA~~l---~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            5 MEVRDMLAL-QGRMEAKQLSARL---QTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHH-SCSEEHHHHHHHT---TCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHH-cCCCcHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            468999975 5678989998887   899999999999999999987653

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=92.00  E-value=3.3  Score=31.91  Aligned_cols=71  Identities=20%  Similarity=0.272  Sum_probs=45.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHH
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEK  164 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~  164 (226)
                      ...|..|+.++..++..++.+..++..-.+.  .+.+.+++..|.-+...++.++               .+++++....
T Consensus        67 ~~~I~~L~~El~~l~~ki~dLeeel~eK~K~--~e~l~DEl~aLqlq~n~lE~kl---------------~kLq~EN~~L  129 (152)
T 3a7p_A           67 LNTLAILQKELKSKEQEIRRLKEVIALKNKN--TERLNAALISGTIENNVLQQKL---------------SDLKKEHSQL  129 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHH
Confidence            4577778888888888888887776654432  2334445555555544444444               4566777777


Q ss_pred             HHHHHHHH
Q 027236          165 LSQWRKRK  172 (226)
Q Consensus       165 ~~~w~kRk  172 (226)
                      ..+|-+|+
T Consensus       130 V~RWM~rk  137 (152)
T 3a7p_A          130 VARWLKKT  137 (152)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88898886

>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=91.98  E-value=0.96  Score=33.27  Aligned_cols=50  Identities=18%  Similarity=0.222  Sum_probs=42.4

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|-+..+|...+   ++++++|..+++.|++.|+|....-
T Consensus        36 ~~q~~vL~~l~~-~~~~t~~eLa~~l---~~~~~tvs~~l~~L~~~Glv~r~~~   85 (140)
T 3hsr_A           36 YTGYIVLMAIEN-DEKLNIKKLGERV---FLDSGTLTPLLKKLEKKDYVVRTRE   85 (140)
T ss_dssp             HHHHHHHHHSCT-TCEEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             HHHHHHHHHHHH-cCCcCHHHHHHHH---CCChhhHHHHHHHHHHCCCeEecCC
Confidence            455678888875 6799999999988   7999999999999999999998754

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=91.96  E-value=0.29  Score=40.76  Aligned_cols=57  Identities=19%  Similarity=0.250  Sum_probs=47.6

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ....-.||.++.. +.|-++.+|...+   ++++++|.+.|+.|.+.|+|...  |....|..
T Consensus       151 ~~~~~~IL~~L~~-~~~~s~~eLA~~l---glsksTv~r~L~~Le~~GlV~r~--~r~~~~~L  207 (244)
T 2wte_A          151 SREEMKLLNVLYE-TKGTGITELAKML---DKSEKTLINKIAELKKFGILTQK--GKDRKVEL  207 (244)
T ss_dssp             CHHHHHHHHHHHH-HTCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEE--TTTTEEEE
T ss_pred             CHHHHHHHHHHHH-cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEe--CCccEEEE
Confidence            4456788998874 5689999999988   79999999999999999999886  66666666

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=91.94  E-value=1.3  Score=31.77  Aligned_cols=60  Identities=18%  Similarity=0.295  Sum_probs=45.8

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeec---Cce-eEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEY---GKQ-KIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~-kiY~~   68 (226)
                      --+-.||.++..  .|..--+|...+.. .+++.++|-.+|..|.++|+|.....   |.. ++|..
T Consensus         9 ~l~~~IL~~L~~--~~~~gyel~~~l~~~~~i~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~L   73 (108)
T 3l7w_A            9 LIEYLILAIVSK--HDSYGYDISQTIKLIASIKESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYHL   73 (108)
T ss_dssp             HHHHHHHHHHHH--SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEEE
T ss_pred             HHHHHHHHHHHc--CCCcHHHHHHHHHHHhCCCcChHHHHHHHHHHCCCeEEEeecCCCCcceEEEE
Confidence            345678888875  57776677777754 47999999999999999999998753   554 55555

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=91.84  E-value=1.2  Score=33.92  Aligned_cols=61  Identities=5%  Similarity=0.186  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAK  141 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~  141 (226)
                      .+...+..++.++..++..|+.++..++.++..+...  .+++..++..|+.++..|+..|..
T Consensus        75 ~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e--~~~l~~~~~~l~~~~~~le~~~~~  135 (138)
T 3hnw_A           75 KMADSLSLDIENKDKEIYDLKHELIAAQIKAESSAKE--IKELKSEINKYQKNIVKLETELND  135 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5566777888888888888888888888777777754  467788888888888888887754

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=91.62  E-value=0.082  Score=44.28  Aligned_cols=55  Identities=16%  Similarity=0.282  Sum_probs=46.2

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      --.||++|...+.|.++.+|...+   |++|++|-..|..|++.|.|....  .+.-|..
T Consensus         8 al~IL~~l~~~~~~lsl~eia~~l---gl~ksT~~RlL~tL~~~G~v~~~~--~~~~Y~l   62 (260)
T 3r4k_A            8 ALTLLTYFNHGRLEIGLSDLTRLS---GMNKATVYRLMSELQEAGFVEQVE--GARSYRL   62 (260)
T ss_dssp             HHHHHTTCBTTBSEEEHHHHHHHH---CSCHHHHHHHHHHHHHTTSEEECS--SSSEEEE
T ss_pred             HHHHHHHHhhCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEcC--CCCcEEc
Confidence            346889998888999999999988   899999999999999999998643  3234666

>2hgc_A YJCQ protein; SR346, structure, autostructure, NESG, PSI-2, northeast structural genomics consortium, protein structure initiative; NMR {Bacillus subtilis} SCOP: a.4.5.77

Probab=91.60  E-value=0.54  Score=34.00  Aligned_cols=65  Identities=17%  Similarity=0.186  Sum_probs=46.1

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHHHHH
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQM   84 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~~~l   84 (226)
                      +||.|+...+.|+|.    .+|   ||+....-.+|+.|+++|+|.+-.|.... +... ...+..|.+-++-+
T Consensus         9 kIL~~L~~~~~~is~----e~l---~Ise~~~~~il~~L~d~GyI~Gv~~~~~~-~~i~-~~~~~IT~~GleYL   73 (102)
T 2hgc_A            9 AILKEIFEGNTPLSE----NDI---GVTEDQFDDAVNFLKREGYIIGVHYSDDR-PHLY-KLGPELTEKGENYL   73 (102)
T ss_dssp             HHHHHHHHHCSCCCH----HHH---TSCHHHHHHHHHHHHHHTSEECCEESSSS-EECC-SSCCEECHHHHHHH
T ss_pred             HHHHHHHhCCCcCCH----Hhc---CCCHHHHHHHHHHHHHCCCccceEEEeCc-ceee-ccCceECHHHHHHH
Confidence            689999998878773    334   89999999999999999999999875441 2211 00144566665543

>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=91.45  E-value=1.2  Score=38.56  Aligned_cols=68  Identities=21%  Similarity=0.177  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHH
Q 027236            8 TEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEEL   81 (226)
Q Consensus         8 a~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~   81 (226)
                      -+..||++|.++ +.|.|..+|.+.|   +|+.++|-|.++.|-+.|.++.-.-|+  -|..... .+.++++++
T Consensus         4 ~~~~iL~~L~~~~g~~~Sg~eLa~~l---gvSr~aV~k~i~~L~~~G~~i~~~~~~--GY~L~~~-~~~l~~~~i   72 (323)
T 3rkx_A            4 YSQDVLQLLYKNKPNYISGQSIAESL---NISRTAVKKVIDQLKLEGCKIDSVNHK--GHLLQQL-PDIWYQGII   72 (323)
T ss_dssp             HHHHHHHHHHHHTTSCBCHHHHHHHH---TSCHHHHHHHHHHHHHTTCEEEEETTT--EEEEEEC-CSSCCHHHH
T ss_pred             HHHHHHHHHHhCCCCccCHHHHHHHH---CCCHHHHHHHHHHHHhcCCeEEEeCCC--eEEEecC-cccCCHHHH
Confidence            467899999864 5799999999988   899999999999999999988776675  4544332 233456655

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=91.34  E-value=0.31  Score=36.51  Aligned_cols=50  Identities=14%  Similarity=0.177  Sum_probs=41.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.. +.|-+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        43 ~~~~~iL~~l~~-~~~~t~~ela~~l---~i~~~tvs~~l~~Le~~Glv~r~~~   92 (155)
T 3cdh_A           43 VPEWRVLACLVD-NDAMMITRLAKLS---LMEQSRMTRIVDQMDARGLVTRVAD   92 (155)
T ss_dssp             HHHHHHHHHHSS-CSCBCHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEECC-
T ss_pred             HHHHHHHHHHHH-CCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEeccC
Confidence            345678888864 5689999998877   7999999999999999999987543

>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=91.31  E-value=0.91  Score=34.27  Aligned_cols=59  Identities=14%  Similarity=0.262  Sum_probs=47.7

Q ss_pred             CCCCcchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce-------eecCce
Q 027236            1 MAPKSDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF-------KEYGKQ   63 (226)
Q Consensus         1 M~~kg~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~-------K~~GK~   63 (226)
                      |+..=++....|+.++... -+-+..+|...+   |++.++|.+.|..|.+.|.|..       ...|..
T Consensus         1 m~~~ld~~~~~il~~L~~~-~~~s~~ela~~l---g~s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~G~~   66 (151)
T 2cyy_A            1 MRVPLDEIDKKIIKILQND-GKAPLREISKIT---GLAESTIHERIRKLRESGVIKKFTAIIDPEALGYS   66 (151)
T ss_dssp             CCCCCCHHHHHHHHHHHHC-TTCCHHHHHHHH---CSCHHHHHHHHHHHHHHTSSCCCCCCCCGGGGTCC
T ss_pred             CCCCcCHHHHHHHHHHHHc-CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEEEEEECHHHCCcc
Confidence            4444467777899988764 568988999888   7999999999999999999975       556764

>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=91.29  E-value=0.16  Score=36.51  Aligned_cols=42  Identities=26%  Similarity=0.433  Sum_probs=34.7

Q ss_pred             cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           24 NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        24 s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      |..++...+   +|+.+.|.++|..|.++|+|....-|..-+|+.
T Consensus        45 s~~eLa~~l---gVSr~tVr~al~~L~~~GlI~~~~gG~~G~~V~   86 (102)
T 2b0l_A           45 VASKIADRV---GITRSVIVNALRKLESAGVIESRSLGMKGTYIK   86 (102)
T ss_dssp             CHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEECSSSCEEEE
T ss_pred             CHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEeCCCCcEEEe
Confidence            888888877   899999999999999999998887553344554

>2oa5_A Hypothetical protein BQLF2; MHR28B, NESG, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; HET: PE5; 2.10A {Murid herpesvirus 4} SCOP: d.362.1.1 PDB: 2h3r_A*

Probab=90.95  E-value=3.4  Score=29.99  Aligned_cols=49  Identities=14%  Similarity=0.160  Sum_probs=36.5

Q ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHHHHHh---hCCCCCCCHHHHHHHHHHHH
Q 027236          114 SNLTLEQIREKEAQLVKEVKEMENKLAKL---RGGVTLVKPEDRMAVEEMFL  162 (226)
Q Consensus       114 ~~~t~~el~~~i~~L~~e~~~l~~kL~~l---~~~~~~vs~ee~~~~~~~~~  162 (226)
                      ..+|.+||.+++..|+-|++.|+.+|..-   ..+..++||.+.+.+...+.
T Consensus         6 ~~~t~EeLaaeL~kLqmENK~LKkkl~~~g~~~p~d~~LTp~qKea~I~s~~   57 (110)
T 2oa5_A            6 PDKTYEEMVKEVERLKLENKTLKQKVKSSGAVSSDDSILTAAKRESIIVSSS   57 (110)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHTC---------CCBCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCccCCHHHHHHHHHHHH
Confidence            46899999999999999999999998641   12346789998887665543

>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=90.84  E-value=1.4  Score=37.95  Aligned_cols=68  Identities=18%  Similarity=0.309  Sum_probs=53.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHH
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEEL   81 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~   81 (226)
                      +-...|++++. .+.+.|..++.+.+   +|+.++|.+-|+.|.+.|.+....-|+  -|..... ++.++++++
T Consensus         5 ~r~~~Il~~L~-~~~~~s~~eLa~~l---~vS~~ti~r~l~~L~~~G~~i~~~~g~--GY~l~~~-~~~L~~~eI   72 (321)
T 1bia_A            5 TVPLKLIALLA-NGEFHSGEQLGETL---GMSRAAINKHIQTLRDWGVDVFTVPGK--GYSLPEP-IQLLNAKQI   72 (321)
T ss_dssp             HHHHHHHHHHT-TSSCBCHHHHHHHH---TSCHHHHHHHHHHHHHTTCCCEEETTT--EEECSSC-CCCCCHHHH
T ss_pred             hHHHHHHHHHH-cCCCcCHHHHHHHH---CCCHHHHHHHHHHHHhCCCcEEEecCC--CcEEeec-cccCCHHHH
Confidence            45678999995 67899999999988   799999999999999999999887787  4555332 234455554

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=90.84  E-value=0.19  Score=42.02  Aligned_cols=54  Identities=20%  Similarity=0.301  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .--.||++|....+|.++.+|...+   |++|++|-..|..|++.|.|...  +  .-|..
T Consensus        22 r~l~iL~~l~~~~~~~~~~eia~~~---gl~~stv~r~l~tL~~~G~v~~~--~--~~Y~L   75 (265)
T 2ia2_A           22 RGLAVIRCFDHRNQRRTLSDVARAT---DLTRATARRFLLTLVELGYVATD--G--SAFWL   75 (265)
T ss_dssp             HHHHHHHTCCSSCSSEEHHHHHHHH---TCCHHHHHHHHHHHHHHTSEEES--S--SEEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEec--C--CEEEE
Confidence            3446888887778999999999988   89999999999999999999875  3  45665

>3lay_A Zinc resistance-associated protein; salmonella typhimurium L structural genomics, center for structural genomics of INFE diseases; 2.70A {Salmonella enterica subsp}

Probab=90.82  E-value=2.3  Score=33.61  Aligned_cols=64  Identities=16%  Similarity=0.144  Sum_probs=44.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHH
Q 027236           74 DIPNSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKL  139 (226)
Q Consensus        74 ~~~~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL  139 (226)
                      -.+|++.-.+++.-..+.+.+...+.+++.....+|..|...++.+  .+.|.+|.+++.+++.+|
T Consensus        66 LnLT~EQq~ql~~I~~e~r~~~~~Lr~ql~akr~EL~aL~~a~~~D--eakI~aL~~Ei~~Lr~qL  129 (175)
T 3lay_A           66 SPLTTEQQATAQKIYDDYYTQTSALRQQLISKRYEYNALLTASSPD--TAKINAVAKEMESLGQKL  129 (175)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCC--HHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC--HHHHHHHHHHHHHHHHHH
Confidence            3467899999999999999999999999999999999987653321  123334444444444444

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=90.80  E-value=1.6  Score=32.63  Aligned_cols=61  Identities=16%  Similarity=0.271  Sum_probs=33.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           77 NSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        77 ~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      +..++..+...+..|+.++..++.....|+..|+.+....     ...+..++..+..++..|..+
T Consensus        34 ~k~Ei~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~~~-----~~~l~~~q~~i~~lE~eL~~~   94 (129)
T 3tnu_B           34 TKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQRG-----ELALKDARNKLAELEEALQKA   94 (129)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHhHHHH
Confidence            3456666666666676777766666666666666555432     223334444444444444443

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=90.75  E-value=3.1  Score=31.14  Aligned_cols=46  Identities=20%  Similarity=0.299  Sum_probs=36.3

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      ..|+.++.. +.+.+..++...+   +|++++|.++|+.|.+.|+|....
T Consensus        43 ~~i~~~l~~-~~~~~~~~la~~l---~vs~~tvs~~l~~Le~~Glv~r~~   88 (155)
T 2h09_A           43 ELISDLIRE-VGEARQVDMAARL---GVSQPTVAKMLKRLATMGLIEMIP   88 (155)
T ss_dssp             HHHHHHHHH-HSCCCHHHHHHHH---TSCHHHHHHHHHHHHHTTCEEEET
T ss_pred             HHHHHHHHh-CCCcCHHHHHHHh---CcCHHHHHHHHHHHHHCCCEEEec
Confidence            344445543 4678988888887   799999999999999999987654

>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=90.63  E-value=0.57  Score=35.18  Aligned_cols=48  Identities=13%  Similarity=0.284  Sum_probs=41.2

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      ++....|+.++.. |.+-+..+|...+   |++.++|.+.|+.|.+.|.|..
T Consensus         4 d~~d~~il~~L~~-~~~~s~~ela~~l---g~s~~tv~~~l~~L~~~G~i~~   51 (144)
T 2cfx_A            4 DQIDLNIIEELKK-DSRLSMRELGRKI---KLSPPSVTERVRQLESFGIIKQ   51 (144)
T ss_dssp             CHHHHHHHHHHHH-CSCCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHH-cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEE
Confidence            4556689998875 5668989999988   7999999999999999999974

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=90.62  E-value=0.95  Score=34.98  Aligned_cols=51  Identities=14%  Similarity=0.154  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHhcCCC--CcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRP--LNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrP--ys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++.....|  -+..+|...+   ++++++|...|+.|++.|+|....-
T Consensus        69 ~~~~~iL~~L~~~~~~~~~t~~eLa~~l---~is~~tvs~~l~~Le~~GlV~r~~~  121 (181)
T 2fbk_A           69 AAGWDLLLTLYRSAPPEGLRPTELSALA---AISGPSTSNRIVRLLEKGLIERRED  121 (181)
T ss_dssp             HHHHHHHHHHHHHCCSSCBCHHHHHHHC---SCCSGGGSSHHHHHHHHTSEECCC-
T ss_pred             HHHHHHHHHHHHcCCCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCcCEEecCC
Confidence            4567899999988776  8999998877   7999999999999999999987654

>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=90.46  E-value=0.87  Score=34.21  Aligned_cols=48  Identities=19%  Similarity=0.304  Sum_probs=41.1

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      ++....|+.++.. +-+.+..+|...+   |++.++|...|+.|.+.|.|..
T Consensus         2 d~~~~~il~~L~~-~~~~~~~ela~~l---g~s~~tv~~~l~~L~~~G~i~~   49 (150)
T 2pn6_A            2 DEIDLRILKILQY-NAKYSLDEIAREI---RIPKATLSYRIKKLEKDGVIKG   49 (150)
T ss_dssp             CHHHHHHHHHHTT-CTTSCHHHHHHHH---TSCHHHHHHHHHHHHHTTSSCC
T ss_pred             ChHHHHHHHHHHH-cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCcEEE
Confidence            3456789998864 5578999999988   8999999999999999999975

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=90.44  E-value=2.5  Score=31.51  Aligned_cols=51  Identities=12%  Similarity=0.201  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHh-cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            8 TEAIVLNYVNE-QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         8 a~~~Il~y~~~-~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .+-.||.++.. .+.|-+..+|...+   ++++++|..+++.|++.|+|....-.
T Consensus        36 ~q~~vL~~L~~~~~~~~t~~eLa~~l---~~~~~tvs~~v~~Le~~Glv~r~~~~   87 (147)
T 4b8x_A           36 ARYEALVLLTFSKSGELPMSKIGERL---MVHPTSVTNTVDRLVRSGLVAKRPNP   87 (147)
T ss_dssp             HHHHHHHHHHTSGGGEEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHH---CCCHHHHHHHHHHHHhCCCEEEeecC
Confidence            34457777764 45688999999888   79999999999999999999988764

>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis, CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA synthetase family; 2.00A {Candida albicans} PDB: 3qo7_A* 3qo8_A* 3qo5_A

Probab=90.40  E-value=1.4  Score=40.35  Aligned_cols=65  Identities=23%  Similarity=0.256  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL-TLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~-t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      -+++..++.+..+++.++..++.+...+..++..+.+.. ..++|.++..+|..++.++++++..+
T Consensus        32 ~~~~~~ld~~~r~~~~~~~~l~~~rn~~sk~i~~~k~~~~~~~~l~~~~~~l~~~i~~le~~~~~~   97 (485)
T 3qne_A           32 VDEIIAEYKEWVKLRFDLDEHNKKLNSVQKEIGKRFKAKEDAKDLIAEKEKLSNEKKEIIEKEAEA   97 (485)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            366788899999999999999999999999998877643 33556666555555555555544433

>1u5t_B Defective in vacuolar protein sorting; VPS36P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54

Probab=90.39  E-value=0.37  Score=37.99  Aligned_cols=60  Identities=12%  Similarity=0.133  Sum_probs=44.1

Q ss_pred             chHHHHHHHHHHhcCCCC-----cHH-H-HHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            6 DNTEAIVLNYVNEQNRPL-----NSQ-N-VADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPy-----s~~-d-i~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      ++-...|++++... .||     |+. + +   ..+.+++...++.+|+.++.+|++..+.-.....||.|
T Consensus        98 d~~~~~il~~~~~~-~g~d~~~vt~~~~~l---a~~~~ws~~~a~e~L~~~e~~G~l~~D~~~~G~~y~~N  164 (169)
T 1u5t_B           98 DVVKEKLVDLIGDN-PGSDLLRLTQILSSN---NSKSNWTLGILMEVLQNCVDEGDLLIDKQLSGIYYYKN  164 (169)
T ss_dssp             HHHHHHHHHHHHHS-CSBCHHHHHHHHHTS---CTTCCCCHHHHHHHHHHHHHHTSEEEEECSSCEEEEEC
T ss_pred             hHHHHHHHHHHHhc-CCCCcccccHHHHHH---HHHhCCCHHHHHHHHHHHHHcCCEEEECCCCcceEEee
Confidence            44557889998744 466     433 3 3   33348999999999999999999999964333678886

>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=90.37  E-value=0.64  Score=34.49  Aligned_cols=47  Identities=17%  Similarity=0.367  Sum_probs=39.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      +....|+.++.. +.+.+..+|...+   |++.++|.+.|+.|.+.|.|..
T Consensus         4 ~~~~~il~~L~~-~~~~~~~ela~~l---g~s~~tv~~~l~~L~~~G~i~~   50 (141)
T 1i1g_A            4 ERDKIILEILEK-DARTPFTEIAKKL---GISETAVRKRVKALEEKGIIEG   50 (141)
T ss_dssp             SHHHHHHHHHHH-CTTCCHHHHHHHH---TSCHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEec
Confidence            456678998875 4567888999888   7999999999999999999964

>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=90.25  E-value=0.48  Score=36.07  Aligned_cols=53  Identities=17%  Similarity=0.183  Sum_probs=40.1

Q ss_pred             HHHHHHHh-cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNE-QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~-~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .++-||-. .++|.++.+|...+   +|+...|.++|..|+..|+|.+.. | .--|..
T Consensus        18 ~~L~~La~~~~~~~~~~~iA~~~---~i~~~~l~kil~~L~~~Glv~s~r-G-~GGy~L   71 (149)
T 1ylf_A           18 HILSILKNNPSSLCTSDYMAESV---NTNPVVIRKIMSYLKQAGFVYVNR-G-PGGAGL   71 (149)
T ss_dssp             HHHHHHHHSCGGGCCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEC-----CCEEE
T ss_pred             HHHHHHHhCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCcEEEcc-C-CCceEe
Confidence            45556654 45799999998877   799999999999999999998765 4 334544

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=90.24  E-value=0.92  Score=34.06  Aligned_cols=56  Identities=11%  Similarity=0.144  Sum_probs=45.7

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCc---eeEEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGK---QKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK---~kiY~~   68 (226)
                      .-.||..+.  +.|.+..++...++  +|+..++...|+.|.++|+|....+..   ...|..
T Consensus        28 ~l~IL~~L~--~g~~rf~eL~~~l~--gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~L   86 (131)
T 4a5n_A           28 KGILFYHMI--DGKKRFNEFRRICP--SITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSL   86 (131)
T ss_dssp             HHHHHHHHT--TSCBCHHHHHHHCT--TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             HHHHHHHHh--cCCcCHHHHHHHhc--ccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEE
Confidence            456777776  67888889988885  799999999999999999999988853   455555

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=90.12  E-value=0.93  Score=30.59  Aligned_cols=26  Identities=19%  Similarity=0.298  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhC
Q 027236          119 EQIREKEAQLVKEVKEMENKLAKLRG  144 (226)
Q Consensus       119 ~el~~~i~~L~~e~~~l~~kL~~l~~  144 (226)
                      .++...|.+...+|..|+..|.+|++
T Consensus        43 ~eLEk~L~ekd~eI~~LqseLDKfrS   68 (72)
T 3nmd_A           43 DELELELDQKDELIQMLQNELDKYRS   68 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            34556667777777777777777765

>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: SSA; 2.60A {Pyrococcus horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A* 2zr3_A

Probab=90.10  E-value=1.8  Score=39.21  Aligned_cols=64  Identities=20%  Similarity=0.355  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSN-LTLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~-~t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      +++..++.+..+++.++..++.+.+.+..++..+++. ...++|.++..+|..+++++++++..+
T Consensus        31 ~~~~~l~~~~r~~~~~~~~l~~~~n~~sk~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   95 (455)
T 2dq0_A           31 DEILKLDTEWRTKLKEINRLRHERNKIAVEIGKRRKKGEPVDELLAKSREIVKRIGELENEVEEL   95 (455)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6677889999999999999999999999999987665 444666666666666666666655544

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=89.79  E-value=1.6  Score=30.88  Aligned_cols=38  Identities=18%  Similarity=0.265  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSN  115 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~  115 (226)
                      .+++..+...++..-+.+..|+++.+.|+.++..+...
T Consensus         8 Ke~mq~LNdRlAsyIdKVR~LEqqN~~Le~~i~~l~~~   45 (93)
T 3s4r_A            8 KVELQELNDRFANLIDKVRFLEQQNKILLAELEQLKGQ   45 (93)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            35688889999999999999999999999999888764

>3eyi_A Z-DNA-binding protein 1; alternative splicing, DNA-binding, polymorphism, DNA binding protein/Z-DNA complex, DNA binding protein/DNA complex; 1.45A {Homo sapiens} PDB: 2l4m_A

Probab=89.66  E-value=0.45  Score=31.89  Aligned_cols=59  Identities=20%  Similarity=0.334  Sum_probs=47.1

Q ss_pred             cchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCce-eEE
Q 027236            5 SDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ-KIY   66 (226)
Q Consensus         5 g~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~-kiY   66 (226)
                      ++..++.|+.||. .+-|-.|-.|+.+|.-  -+...|.-.|=+|-.+|+|.+..-.+. .||
T Consensus         8 s~~~ee~I~~fL~-~~Gp~~AL~IAK~LGl--ktAK~VNp~LY~m~~~~lL~~Dek~~~W~iy   67 (72)
T 3eyi_A            8 SQQREEDIYRFLK-DNGPQRALVIAQALGM--RTAKDVNRDLYRMKSRHLLDMDEQSKAWTIY   67 (72)
T ss_dssp             SSHHHHHHHHHHH-HHCSEEHHHHHHHTTC--CSGGGTHHHHHHHHHTTSEEECTTTCEEEEC
T ss_pred             hhhhHHHHHHHHH-HcCCchHHHHHHHhCc--chhhhcCHHHHHHHHccCcCCCCCCCceeEE
Confidence            3566899999999 7889999999999942  234459999999999999987766666 565

>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=89.30  E-value=0.16  Score=44.68  Aligned_cols=48  Identities=15%  Similarity=0.283  Sum_probs=40.8

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      +.-+..||+++.  +.|.|-.+|...+   ++++++|.+.++.|.++|+|..-
T Consensus        19 ~~~~~~il~~l~--~~~~sr~~la~~~---gls~~tv~~~v~~L~~~gli~~~   66 (380)
T 2hoe_A           19 AENISRILKRIM--KSPVSRVELAEEL---GLTKTTVGEIAKIFLEKGIVVEE   66 (380)
T ss_dssp             ---CCCSHHHHH--HSCBCHHHHHHHH---TCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHH--cCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEee
Confidence            444456999999  8999999999888   89999999999999999999774

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=89.30  E-value=0.81  Score=34.67  Aligned_cols=46  Identities=13%  Similarity=0.213  Sum_probs=38.2

Q ss_pred             HHHHHHHhc--CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           11 IVLNYVNEQ--NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        11 ~Il~y~~~~--nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      .+|-||-..  ++|.|+.+|...+   +|+...|.++|..|...|+|.+..
T Consensus        15 ~~L~~La~~~~~~~~s~~~IA~~~---~i~~~~l~kil~~L~~aGlv~s~r   62 (143)
T 3t8r_A           15 TLMISLAKKEGQGCISLKSIAEEN---NLSDLYLEQLVGPLRNAGLIRSVR   62 (143)
T ss_dssp             HHHHHHHTTTTSCCEEHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHhCCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCEEEecC
Confidence            456666543  4699999998877   899999999999999999988764

>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=89.09  E-value=0.96  Score=34.05  Aligned_cols=47  Identities=15%  Similarity=0.286  Sum_probs=41.0

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      ++....||.++.. +.|.+..+|...+   |++.++|.+.|+.|.+.|.|.
T Consensus         6 d~~~~~iL~~L~~-~~~~s~~ela~~l---g~s~~tv~~~l~~L~~~G~i~   52 (150)
T 2w25_A            6 DDIDRILVRELAA-DGRATLSELATRA---GLSVSAVQSRVRRLESRGVVQ   52 (150)
T ss_dssp             CHHHHHHHHHHHH-CTTCCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHHHHH-cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEE
Confidence            4566789999864 5678999999988   899999999999999999995

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=88.85  E-value=1.1  Score=34.85  Aligned_cols=48  Identities=17%  Similarity=0.326  Sum_probs=41.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      ++....|+.++.. |-+-|..+|...+   |++.++|...|+.|.+.|.|..
T Consensus        16 d~~d~~IL~~L~~-~~~~s~~eLA~~l---glS~~tv~~~l~~L~~~G~I~~   63 (171)
T 2ia0_A           16 DDLDRNILRLLKK-DARLTISELSEQL---KKPESTIHFRIKKLQERGVIER   63 (171)
T ss_dssp             CHHHHHHHHHHHH-CTTCCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHH-cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEe
Confidence            6677789999875 5568988999988   8999999999999999999963

>3eqx_A FIC domain containing transcriptional regulator; FIC family protein, structural genomics, joint center for ST genomics, JCSG; HET: MSE PGE; 1.60A {Shewanella oneidensis}

Probab=88.74  E-value=0.5  Score=41.81  Aligned_cols=54  Identities=22%  Similarity=0.258  Sum_probs=39.9

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+++++..+ -.+++.++...+   +++.+++.+.|..|++.|.|..-.-|+.++|..
T Consensus       301 ~ll~~l~~~-p~~t~~~~~~~~---~~S~~TA~r~L~~L~e~GiL~~~~~gR~~~y~~  354 (373)
T 3eqx_A          301 ELVQVIFEQ-PYCRIQNLVESG---LAKRQTASVYLKQLCDIGVLEEVQSGKEKLFVH  354 (373)
T ss_dssp             HHHHHHHHC-SEEEHHHHHHTS---SSCHHHHHHHHHHHHHTTSCEEC--CCSCEEEC
T ss_pred             HHHHHHHHC-CCccHHHHHHHh---CcCHHHHHHHHHHHHHCCcEEEeCCCCceEeeh
Confidence            355555542 235666665544   899999999999999999999888899998876

>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=88.67  E-value=0.58  Score=36.37  Aligned_cols=54  Identities=22%  Similarity=0.340  Sum_probs=41.2

Q ss_pred             HHHHHHHh-cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNE-QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~-~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+|-||-. .++|.|..+|...+   +|+...|.++|..|...|+|.+.. |+.==|..
T Consensus        16 r~l~~La~~~~~~~s~~~IA~~~---~is~~~l~kil~~L~~aGlv~s~r-G~~GGy~L   70 (162)
T 3k69_A           16 HSILYLDAHRDSKVASRELAQSL---HLNPVMIRNILSVLHKHGYLTGTV-GKNGGYQL   70 (162)
T ss_dssp             HHHHHHHTTTTSCBCHHHHHHHH---TSCGGGTHHHHHHHHHTTSSEEEC-STTCEEEC
T ss_pred             HHHHHHHhCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEeec-CCCCCeEe
Confidence            45566654 47899999998877   799999999999999999987653 44323443

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=88.65  E-value=0.87  Score=35.68  Aligned_cols=56  Identities=18%  Similarity=0.318  Sum_probs=43.4

Q ss_pred             hHHHHHHHHHHhcCC-------CCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNR-------PLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nr-------Pys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .++++|..|+.....       |++-++|.+.+   |++..+|-++|..|.++|+|...   ..+|...
T Consensus       147 ~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~l---g~sr~tvsR~l~~L~~~g~I~~~---~~~i~i~  209 (220)
T 3dv8_A          147 SLDKRVASFLLEETSIEGTNELKITHETIANHL---GSHREVITRMLRYFQVEGLVKLS---RGKITIL  209 (220)
T ss_dssp             CHHHHHHHHHHHHHHHHTSSEECCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEE---TTEEEES
T ss_pred             CHHHHHHHHHHHhhhhcCCceecCCHHHHHHHh---CCCHHHHHHHHHHHHHCCCEEeC---CCEEEEe
Confidence            456777777766433       89999999988   89999999999999999999643   3345444

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=88.50  E-value=1.6  Score=33.82  Aligned_cols=54  Identities=15%  Similarity=0.288  Sum_probs=41.5

Q ss_pred             HHHHHHHh--cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNE--QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~--~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .++-||-.  .++|.++.+|...+   +|+...|.++|..|...|+|.+.. |..==|+.
T Consensus        31 r~L~~LA~~~~~~~~s~~eIA~~~---~i~~~~l~kil~~L~~aGlv~s~r-G~~GGy~L   86 (159)
T 3lwf_A           31 TITLELAKRIGDGPISLRSIAQDK---NLSEHYLEQLIGPLRNAGIVKSIR-GAHGGYVL   86 (159)
T ss_dssp             HHHHHHHHTTTSCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEC-STTCEEEE
T ss_pred             HHHHHHHhcCCCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCeEEEec-CCCCceEe
Confidence            34555543  35799999998887   799999999999999999999875 33323444

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=88.47  E-value=1.6  Score=32.71  Aligned_cols=60  Identities=20%  Similarity=0.319  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      ..++..+...+..|+.++..++.....|+..|+.+....     ...+..++..+..++..|..+
T Consensus        37 k~Ei~elrr~iq~L~~el~~l~~~~~sLE~~l~e~e~~~-----~~~l~~~q~~i~~lE~eL~~~   96 (131)
T 3tnu_A           37 KSEISELRRTMQNLEIELQSQLSMKASLENSLEETKGRY-----CMQLAQIQEMIGSVEEQLAQL   96 (131)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHH
Confidence            344555566666666666666666666666665555432     223334444444444444443

>3dfg_A Xcrecx, regulatory protein RECX; RECX RECA, homologous recombination, tandem repeats, three-helix bundle, cytoplasm; 1.50A {Xanthomonas campestris PV}

Probab=88.46  E-value=0.83  Score=35.47  Aligned_cols=54  Identities=17%  Similarity=0.216  Sum_probs=47.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      ..+....+.||-  .|++|-.+|..-|...|++...|..+|+.|.+.|.|.-..|.
T Consensus        17 ~~a~~~Al~~Ls--~r~~s~~EL~~KL~~kg~~~e~Ie~vl~~l~~~g~ldD~rfA   70 (162)
T 3dfg_A           17 QTPVQRALGLLV--HREHSKKELNRKLQARGIEPEAAQAAVERLAGEGWQDDVRFA   70 (162)
T ss_dssp             CCHHHHHHHHHH--HSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCCHHHHH
T ss_pred             HHHHHHHHHHhh--chhhhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHH
Confidence            688889999997  679999999999988899999999999999999987655553

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=88.24  E-value=1  Score=33.88  Aligned_cols=47  Identities=28%  Similarity=0.440  Sum_probs=40.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      ++....|+.++.. |-+-|..+|...+   |++.++|.+.|..|.+.|.|.
T Consensus         8 d~~d~~il~~L~~-~~~~s~~ela~~l---g~s~~tv~~~l~~L~~~G~i~   54 (151)
T 2dbb_A            8 DRVDMQLVKILSE-NSRLTYRELADIL---NTTRQRIARRIDKLKKLGIIR   54 (151)
T ss_dssp             CHHHHHHHHHHHH-CTTCCHHHHHHHT---TSCHHHHHHHHHHHHHHTSEE
T ss_pred             CHHHHHHHHHHHH-cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEE
Confidence            5666789998875 5668988998877   899999999999999999997

>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=88.19  E-value=1.2  Score=33.55  Aligned_cols=48  Identities=15%  Similarity=0.198  Sum_probs=41.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      ++....|+.++... .+-+..+|...+   |++.++|...|+.|.+.|.|..
T Consensus         7 d~~d~~il~~L~~~-~~~s~~ela~~l---g~s~~tv~~~l~~L~~~G~i~~   54 (152)
T 2cg4_A            7 DNLDRGILEALMGN-ARTAYAELAKQF---GVSPETIHVRVEKMKQAGIITG   54 (152)
T ss_dssp             CHHHHHHHHHHHHC-TTSCHHHHHHHH---TSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CHHHHHHHHHHHHc-CCCCHHHHHHHH---CcCHHHHHHHHHHHHHcCCcce
Confidence            56677899988764 567888999888   8999999999999999999985

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=88.05  E-value=1  Score=33.32  Aligned_cols=51  Identities=16%  Similarity=0.183  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHHhc----CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQ----NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~----nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.|+-|+...    +.+.|..+|.+.+   +++.++|..+|+.|++.|+|..+..
T Consensus        32 ~~e~~vll~L~~~~~~~~~~ps~~~LA~~l---~~s~~~V~~~l~~Le~kGlI~~~~~   86 (128)
T 2vn2_A           32 EGELVLLLHMQSFFEEGVLFPTPAELAERM---TVSAAECMEMVRRLLQKGMIAIEEH   86 (128)
T ss_dssp             HHHHHHHHHHHHHHTTTCSSCCHHHHHHTS---SSCHHHHHHHHHHHHHTTSSEECC-
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEeE
Confidence            3444566666653    3335877777766   8999999999999999999988644

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=88.04  E-value=2.1  Score=30.79  Aligned_cols=51  Identities=12%  Similarity=0.192  Sum_probs=37.2

Q ss_pred             chHHHHHHHHHHhc-CCC----CcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236            6 DNTEAIVLNYVNEQ-NRP----LNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus         6 ~ea~~~Il~y~~~~-nrP----ys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      +...+.|.+.+... ..|    -|..++...+   ||+.+.|.++|..|+++|+|....
T Consensus        12 ~~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~---~vSr~tvr~al~~L~~~Gli~~~~   67 (113)
T 3tqn_A           12 QQLRDKIVEAIIDGSYVEGEMIPSIRKISTEY---QINPLTVSKAYQSLLDDNVIEKRR   67 (113)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEECCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEec
Confidence            44445555555542 333    2877887777   899999999999999999987664

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=87.95  E-value=0.71  Score=37.34  Aligned_cols=49  Identities=4%  Similarity=0.164  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      -..|+.. ...+.|-+..+|...|   +|++++|.++|+.|.++|+|....++
T Consensus         8 L~~I~~l-~~~~~~~~~~~lA~~l---~vs~~tvs~~l~~Le~~GlV~r~~~~   56 (214)
T 3hrs_A            8 LKCLYEL-GTRHNKITNKEIAQLM---QVSPPAVTEMMKKLLAEELLIKDKKA   56 (214)
T ss_dssp             HHHHHHT-TSSCSCCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEETTT
T ss_pred             HHHHHHH-HhcCCCcCHHHHHHHH---CCChhHHHHHHHHHHHCCCEEEecCC
Confidence            3444443 3467899999999988   79999999999999999999998874

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61

Probab=87.93  E-value=1.8  Score=32.86  Aligned_cols=61  Identities=21%  Similarity=0.305  Sum_probs=45.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-----ccccHHHHHHHHHHHHHcCCcceeec----Cce-eEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-----YNLKKAGIQKALDSLADNGKISFKEY----GKQ-KIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-----~~v~K~~v~k~L~~Lv~~g~i~~K~~----GK~-kiY~~   68 (226)
                      .--+-.||.++..  .|.+.-+|...+..     .+++..+|-.+|+.|.++|+|.....    |.. ++|..
T Consensus        40 g~~~~~IL~~L~~--~~~~gyeI~~~l~~~~~~~~~is~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~L  110 (145)
T 1xma_A           40 GYVDTIILSLLIE--GDSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRI  110 (145)
T ss_dssp             GTHHHHHHHHHHH--CCEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEE
T ss_pred             CcHHHHHHHHHHh--CCCCHHHHHHHHHHhhCCccCcChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEE
Confidence            4457788998864  67777777777743     15999999999999999999988754    444 55544

>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=87.73  E-value=0.82  Score=36.60  Aligned_cols=50  Identities=12%  Similarity=0.073  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++... .|-+..+|...+   ++++++|..+|+.|++.|+|.....
T Consensus        48 ~~q~~iL~~L~~~-~~~t~~eLa~~l---~i~~stvs~~l~~Le~~GlV~r~~~   97 (207)
T 2fxa_A           48 INEHHILWIAYQL-NGASISEIAKFG---VMHVSTAFNFSKKLEERGYLRFSKR   97 (207)
T ss_dssp             HHHHHHHHHHHHH-TSEEHHHHHHHT---TCCHHHHHHHHHHHHHHTSEEEECC
T ss_pred             HHHHHHHHHHHHC-CCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEecC
Confidence            4456788888765 589999998887   7999999999999999999998765

>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...

Probab=87.71  E-value=1.2  Score=34.45  Aligned_cols=48  Identities=13%  Similarity=0.191  Sum_probs=39.6

Q ss_pred             hHHHHHHHHHHhcC-------------CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            7 NTEAIVLNYVNEQN-------------RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         7 ea~~~Il~y~~~~n-------------rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      .++++|..|+....             -|++-++|.+.+   |++..+|.++|..|.++|.|..
T Consensus       139 ~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~iA~~l---g~sr~tvsR~l~~L~~~g~I~~  199 (210)
T 3ryp_A          139 DVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIV---GCSRETVGRILKMLEDQNLISA  199 (210)
T ss_dssp             CHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHHHHhcCcCCCCCceEeccCHHHHHHHh---CCcHHHHHHHHHHHHHCCcEEe
Confidence            46677777776532             178889999888   8999999999999999999975

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=87.47  E-value=2.7  Score=28.25  Aligned_cols=36  Identities=25%  Similarity=0.330  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 027236           80 ELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSN  115 (226)
Q Consensus        80 e~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~  115 (226)
                      ++...+..|.++..++.+....+..|+.+|..+++.
T Consensus        34 ELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfrSV   69 (72)
T 3nmd_A           34 ELRQRDALIDELELELDQKDELIQMLQNELDKYRSV   69 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            344455566666666666666666666666666554

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=87.47  E-value=1.4  Score=34.69  Aligned_cols=65  Identities=12%  Similarity=0.205  Sum_probs=53.0

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC-----ceeEEEeecCCCC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG-----KQKIYIARQDQFD   74 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G-----K~kiY~~~Q~~~~   74 (226)
                      +-.+-.|+.+|.  .+|.++.+|...|.  +++.++|-.-|..|.+-|+|....-|     ..++|-+....+.
T Consensus        22 ~P~Rl~il~~L~--~~~~~~~~l~~~l~--~~~~~~~s~Hl~~L~~aglv~~~~e~~~~g~~er~y~~~~~~~~   91 (182)
T 4g6q_A           22 HPLRWRITQLLI--GRSLTTRELAELLP--DVATTTLYRQVGILVKAGVLMVTAEHQVRGAVERTYTLNTQAGD   91 (182)
T ss_dssp             SHHHHHHHHHTT--TSCEEHHHHHHHCT--TBCHHHHHHHHHHHHHHTSEEEEEEEEETTEEEEEEEECTTTTT
T ss_pred             CHHHHHHHHHHH--hCCCCHHHHHHHhc--CCCHHHHHHHHHHHHHCCCeEEEEeecccCcceeEEEecccccc
Confidence            567788999985  58999999998883  58999999999999999999865443     3588888777653

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=87.25  E-value=2.3  Score=30.33  Aligned_cols=59  Identities=24%  Similarity=0.411  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHH
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKL  139 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL  139 (226)
                      .++..+..++..|..++.....++..|...|..-+..  ..++......++.++.+|...|
T Consensus         5 ~~~e~lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~--R~~aE~~~~~ie~ElEeLTasL   63 (97)
T 2eqb_B            5 SNYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENEL--RTKAEEEADKLNKEVEDLTASL   63 (97)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555666666666666555555555555444322  1233444555555555555555

>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}

Probab=87.15  E-value=2.2  Score=39.24  Aligned_cols=65  Identities=18%  Similarity=0.240  Sum_probs=47.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC---------CHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL---------TLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~---------t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      -+++..++.+..+++.++..++.+.+.+..++..+.+..         ..++|.++..+|.++++++++++..+
T Consensus        69 ~~~~~~ld~~~r~~~~~~~~l~~~rn~~sk~i~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~~  142 (501)
T 1wle_A           69 LPGIISTWQELRQLREQIRSLEEEKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQL  142 (501)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTGGGCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467888899999999999999999999999998876432         23466666666666666655554443

>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=86.45  E-value=2.5  Score=28.74  Aligned_cols=49  Identities=16%  Similarity=0.198  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHHhcC--CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            7 NTEAIVLNYVNEQN--RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         7 ea~~~Il~y~~~~n--rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      +.-++|+.++..-.  .-+++.+|..-|   |++|+.|.++|=+|..+|.|.+-
T Consensus        12 ~~~~~v~~~i~~L~~~~~~Ta~~IAkkL---g~sK~~vNr~LY~L~kkG~V~~~   62 (75)
T 1sfu_A           12 EIFSLVKKEVLSLNTNDYTTAISLSNRL---KINKKKINQQLYKLQKEDTVKMV   62 (75)
T ss_dssp             HHHHHHHHHHHTSCTTCEECHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhCCCCcchHHHHHHHHH---CCCHHHHHHHHHHHHHCCCEecC
Confidence            45566666666433  346888888777   89999999999999999999775

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=86.10  E-value=2.3  Score=31.53  Aligned_cols=51  Identities=12%  Similarity=0.197  Sum_probs=36.4

Q ss_pred             chHHHHHHHHHHhc-CC---CC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236            6 DNTEAIVLNYVNEQ-NR---PL-NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus         6 ~ea~~~Il~y~~~~-nr---Py-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      +..-+.|.+.+... ..   +. |..++...+   ||+.+.|.++|..|..+|+|....
T Consensus         7 ~~i~~~i~~~I~~g~l~~G~~LPse~~La~~~---gvSr~tVr~Al~~L~~~Gli~~~~   62 (129)
T 2ek5_A            7 KQIASLIEDSIVDGTLSIDQRVPSTNELAAFH---RINPATARNGLTLLVEAGILYKKR   62 (129)
T ss_dssp             HHHHHHHHHHHHTTSSCTTSCBCCHHHHHHHT---TCCHHHHHHHHHHHHTTTSEEEET
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCcEEEec
Confidence            44444555554432 22   23 777777766   899999999999999999997654

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=86.06  E-value=2.9  Score=31.40  Aligned_cols=59  Identities=15%  Similarity=0.233  Sum_probs=40.9

Q ss_pred             hHHHHHHHHHHh---c-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec----Cce-eEEEe
Q 027236            7 NTEAIVLNYVNE---Q-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY----GKQ-KIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~---~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~----GK~-kiY~~   68 (226)
                      +.+-.|+=++..   + +.+-|..+|.+.+   +++.+.|.++|++|+++|.|.-+..    |+. .+|..
T Consensus        32 ~~E~~lLl~L~~~~~~g~~~ps~~~LA~~~---~~s~~~v~~~L~~L~~KGlI~i~~~~d~~g~~~~~ydL   99 (135)
T 2v79_A           32 ETELILLLKIKMHLEKGSYFPTPNQLQEGM---SISVEECTNRLRMFIQKGFLFIEECEDQNGIKFEKYSL   99 (135)
T ss_dssp             HHHHHHHHHHHHHHTTTCCSCCHHHHHTTS---SSCHHHHHHHHHHHHHHTSCEEEEEECTTCCEEEEEEC
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEEeEecCCCceEEEeeH
Confidence            344455544444   2 4555777766655   8999999999999999999998544    555 44444

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=85.90  E-value=1.1  Score=33.66  Aligned_cols=47  Identities=13%  Similarity=0.287  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHhcC----CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            8 TEAIVLNYVNEQN----RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         8 a~~~Il~y~~~~n----rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      .+-.||.++....    .|.+..+|...+   ++++++|..+++.|+..|+|..
T Consensus        34 ~q~~vL~~l~~~~~~~~~~~t~~eLa~~l---~~~~~tvsr~v~~Le~~glVr~   84 (148)
T 4fx0_A           34 TQFSTLAVISLSEGSAGIDLTMSELAARI---GVERTTLTRNLEVMRRDGLVRV   84 (148)
T ss_dssp             HHHHHHHHHHC---------CHHHHHHHH---TCCHHHHHHHHHHHHHTTSBC-
T ss_pred             HHHHHHHHHHHhcCCCCCCcCHHHHHHHH---CCChhhHHHHHHHHHHCCCEEe
Confidence            3456777776543    468999998888   7999999999999999999854

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=85.87  E-value=3.8  Score=41.15  Aligned_cols=23  Identities=9%  Similarity=0.163  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Q 027236          120 QIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus       120 el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      +|...+..|++++..|+..+..+
T Consensus      1020 ~L~~kv~~L~~e~~~L~qq~~~l 1042 (1080)
T 2dfs_A         1020 ETEQLVSELKEQNTLLKTEKEEL 1042 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444333

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=85.86  E-value=1.2  Score=31.77  Aligned_cols=51  Identities=16%  Similarity=0.294  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHH-HHhcccccHHHHHHHHHHHHHcCCcceeecCce
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVAD-ALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ   63 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~-~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~   63 (226)
                      ..+--||-++.... |-|+.+|.+ .+   ++.+++|-..|+.|..+|+|.  .-|.-
T Consensus        16 ~~QfsiL~~L~~~~-~~t~~~Lae~~l---~~drstvsrnl~~L~r~GlVe--~~~~D   67 (95)
T 1bja_A           16 EKTATILITIAKKD-FITAAEVREVHP---DLGNAVVNSNIGVLIKKGLVE--KSGDG   67 (95)
T ss_dssp             HHHHHHHHHHHHST-TBCHHHHHHTCT---TSCHHHHHHHHHHHHTTTSEE--EETTE
T ss_pred             HHHHHHHHHHHHCC-CCCHHHHHHHHh---cccHHHHHHHHHHHHHCCCee--cCCCC
Confidence            45667888898777 999999999 44   799999999999999999998  33444

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=85.60  E-value=3.1  Score=30.51  Aligned_cols=52  Identities=13%  Similarity=0.146  Sum_probs=36.9

Q ss_pred             chHHHHHHHHHHh-cCC---CC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            6 DNTEAIVLNYVNE-QNR---PL-NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         6 ~ea~~~Il~y~~~-~nr---Py-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      +...+.|.+.+.. ...   ++ |..++...+   ||+.+.|.++|..|+++|+|.....
T Consensus        16 ~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~---~vSr~tvr~Al~~L~~~G~i~~~~g   72 (125)
T 3neu_A           16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKL---AVNPNTVSRAYQELERAGYIYAKRG   72 (125)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCeEEEecC
Confidence            3444445555443 222   22 777887777   8999999999999999999977644

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=85.53  E-value=5.4  Score=28.83  Aligned_cols=60  Identities=17%  Similarity=0.161  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhc---ccccHHHHHHHHHHHHHcCCcceeec----Cce-eEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQK---YNLKKAGIQKALDSLADNGKISFKEY----GKQ-KIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~---~~v~K~~v~k~L~~Lv~~g~i~~K~~----GK~-kiY~~   68 (226)
                      --+-.||..+.  ..|..--+|...+..   ..++-.++-.+|..|.++|+|.....    |.. ++|..
T Consensus         9 ~l~~~IL~~L~--~~~~~Gyei~~~l~~~~~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~L   76 (115)
T 4esb_A            9 VLEGCILYIIS--QEEVYGYELSTKLNKHGFTFVSEGSIYPLLLRMQKEKLIEGTLKASSLGPKRKYYHI   76 (115)
T ss_dssp             THHHHHHHHHH--HSCEEHHHHHHHHHHTTCTTCCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEE
T ss_pred             HHHHHHHHHHH--cCCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCeEEEeeecCCCCCcEEEEE
Confidence            34567888887  367777788777753   25899999999999999999998753    555 55555

>1g6u_A Domain swapped dimer; designed three helix bundle, de novo protein; 1.48A {Synthetic} SCOP: k.9.1.1

Probab=85.49  E-value=4  Score=24.13  Aligned_cols=41  Identities=22%  Similarity=0.443  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHhcc-CCHHHHH---HHHHHHHHHHHHHHHHHHHhh
Q 027236          103 SKLEGEIRTLQSN-LTLEQIR---EKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus       103 k~l~~el~~l~~~-~t~~el~---~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      ..+.++|..+++. -+.+|+.   .++..|++++..+.++|..++
T Consensus         3 aalkselqalkkegfspeelaaleselqalekklaalksklqalk   47 (48)
T 1g6u_A            3 AALKSELQALKKEGFSPEELAALESELQALEKKLAALKSKLQALK   47 (48)
T ss_dssp             HHHHHHHHHHHHTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3455666666665 4444433   345555666666666665543

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=85.34  E-value=8  Score=28.63  Aligned_cols=22  Identities=23%  Similarity=0.522  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHh
Q 027236           92 QEQLEEQRKAISKLEGEIRTLQ  113 (226)
Q Consensus        92 ~~~l~~l~~~~k~l~~el~~l~  113 (226)
                      +.++.+++..+..|+.+|..+.
T Consensus        35 k~Ei~elrr~iq~L~~el~~l~   56 (129)
T 3tnu_B           35 KHEISEMNRMIQRLRAEIDNVK   56 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444443

>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=85.34  E-value=1.3  Score=38.92  Aligned_cols=46  Identities=15%  Similarity=0.246  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      -+..||++++ .+.|.|-.+|...+   ++++++|.+.++.|.+.|+|..
T Consensus        17 n~~~il~~l~-~~~~~sr~~la~~~---~ls~~tv~~~v~~L~~~g~i~~   62 (406)
T 1z6r_A           17 NAGAVYRLID-QLGPVSRIDLSRLA---QLAPASITKIVHEMLEAHLVQE   62 (406)
T ss_dssp             HHHHHHHHHH-SSCSCCHHHHHHHT---TCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHH-HcCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCcEEe
Confidence            3457999998 47899999998877   8999999999999999999977

>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting, protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54

Probab=85.26  E-value=2.4  Score=39.58  Aligned_cols=62  Identities=15%  Similarity=0.192  Sum_probs=50.1

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHh----cccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQ----KYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~----~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +.....|++++. .+..-++.++...+.    +.+++...++.+|+.++.+|++..+.-....+||+
T Consensus       493 ~~~~~~il~l~~-~~g~vT~~~la~~lg~~~~~~~Ws~~~A~e~L~~~e~eG~l~rDd~~~G~~yyp  558 (566)
T 1w7p_D          493 DVVKEKLVDLIG-DNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQLSGIYYYK  558 (566)
T ss_dssp             HHHHHHHHHHHT-TSTTCCHHHHHHHHSCSSSCCCBCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             hHHHHHHHHHHH-hcCCcCHHHHHHHhCCccccCcccHHHHHHHHHHHHHcCCEEEECCCCceEEeh
Confidence            456788889876 478889999999884    12499999999999999999999997544566666

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=85.21  E-value=15  Score=33.48  Aligned_cols=65  Identities=17%  Similarity=0.188  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC---------HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLT---------LEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t---------~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +++..++.++..++++.......+.....++........         .+.+.+.+..+++..+.++.++..++
T Consensus       456 ~e~~~~~~~i~~l~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  529 (597)
T 3oja_B          456 AEVNELRAEVQQLTNEQIQQEQLLQGLHAEIDTNLRRYRLPKDGLARSSDNLNKVFTHLKERQAFKLRETQARR  529 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCccccccCCHHHHHHHHHHHHHhhhhhhHHHHHHHH
Confidence            356666777777777777777777777777766554322         15566666666666666666665554

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*

Probab=84.78  E-value=6.1  Score=28.50  Aligned_cols=59  Identities=22%  Similarity=0.284  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhc-----ccccHHHHHHHHHHHHHcCCcceee----cCce-eEEEe
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQK-----YNLKKAGIQKALDSLADNGKISFKE----YGKQ-KIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~-----~~v~K~~v~k~L~~Lv~~g~i~~K~----~GK~-kiY~~   68 (226)
                      -+-.||..+.+  +|..--+|...+..     .+++..++-.+|..|.++|+|....    -|.. ++|..
T Consensus        13 l~~~IL~~L~~--~~~~Gyei~~~l~~~~~~~~~i~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~L   81 (116)
T 3f8b_A           13 TNVILLNVLKQ--GDNYVYGIIKQVKEASNGEMELNEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYRL   81 (116)
T ss_dssp             HHHHHHHHHHH--CCBCHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEEE
Confidence            34568888874  67666677766643     2699999999999999999999874    3444 55555

>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=84.69  E-value=1.3  Score=39.30  Aligned_cols=48  Identities=19%  Similarity=0.266  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      -+..||+++.. +.|.|-.+|...+   ++++++|.+.++.|.++|+|..-.
T Consensus        40 n~~~il~~l~~-~~~~sr~ela~~~---gls~~tv~~~v~~L~~~gli~~~~   87 (429)
T 1z05_A           40 NAGRVYKLIDQ-KGPISRIDLSKES---ELAPASITKITRELIDAHLIHETT   87 (429)
T ss_dssp             HHHHHHHHHHH-HCSBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHH-cCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEecc
Confidence            34569999986 5799999998877   899999999999999999997754

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=84.06  E-value=0.15  Score=36.28  Aligned_cols=38  Identities=16%  Similarity=0.307  Sum_probs=31.5

Q ss_pred             cCCCC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           19 QNRPL-NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        19 ~nrPy-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      .+.++ |..++...+   +|+.++|.++|..|.+.|+|....
T Consensus        31 ~g~~lps~~eLa~~~---~vSr~tvr~al~~L~~~Gli~~~~   69 (102)
T 1v4r_A           31 PGDTLPSVADIRAQF---GVAAKTVSRALAVLKSEGLVSSRG   69 (102)
T ss_dssp             TTSBCCCHHHHHHHS---SSCTTHHHHHTTTTTTSSCCEEET
T ss_pred             CcCCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEeC
Confidence            34455 888887776   899999999999999999997654

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=83.94  E-value=6.3  Score=31.50  Aligned_cols=25  Identities=8%  Similarity=0.130  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236          119 EQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus       119 ~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      ..|...+..|...+..+..+|..|.
T Consensus        91 ~~Lq~el~~l~~~~~~l~~~ireLE  115 (189)
T 2v71_A           91 SVLEDDLSQTRAIKEQLHKYVRELE  115 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555555555555555555553

>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=83.72  E-value=1.5  Score=36.45  Aligned_cols=58  Identities=21%  Similarity=0.293  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHhcC-CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC--ceeEEEe
Q 027236            8 TEAIVLNYVNEQN-RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG--KQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~n-rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G--K~kiY~~   68 (226)
                      .+-.||.++.... .|-+..+|...+   ++++++|..+++.|...|+|.-..-.  +=.++..
T Consensus       159 ~q~~vL~~L~~~~~~~~t~~eLa~~l---~i~~~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~  219 (250)
T 1p4x_A          159 VEFTILAIITSQNKNIVLLKDLIETI---HHKYPQTVRALNNLKKQGYLIKERSTEDERKILIH  219 (250)
T ss_dssp             HHHHHHHHHHTTTTCCEEHHHHHHHS---SSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEE
T ss_pred             HHHHHHHHHHhCCCCCcCHHHHHHHH---CCChhhHHHHHHHHHHCCCEEeeCCCCCCCeEEEE
Confidence            4567899998765 469999998877   79999999999999999999987653  2344544

>3kn1_A Golgi phosphoprotein 3; beta hairpin, phosphoinositide binding domain, cell membrane, cytoplasm, endosome, golgi apparatus, membrane, mitochondrion; HET: MSE; 2.90A {Homo sapiens}

Probab=83.48  E-value=6  Score=32.96  Aligned_cols=77  Identities=16%  Similarity=0.193  Sum_probs=53.6

Q ss_pred             CcchHHHHHHHHHHhcCCCCcHHHHHHHHhcc-------ccc-HHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCC
Q 027236            4 KSDNTEAIVLNYVNEQNRPLNSQNVADALQKY-------NLK-KAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDI   75 (226)
Q Consensus         4 kg~ea~~~Il~y~~~~nrPys~~di~~~l~~~-------~v~-K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~   75 (226)
                      -|+---+.+++.|..+.+|.++++...-+++.       ++. +..-..++++|++.|.|....   +++....-..+|.
T Consensus        79 tgD~lLd~aL~~i~~~~~p~~v~~Wi~~l~~~twn~~~~~~ql~~vre~v~~~Lv~~GvLr~e~---~~~llf~~~~~p~  155 (249)
T 3kn1_A           79 TGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVLTTEK---QNFLLFDMTTHPL  155 (249)
T ss_dssp             CSCHHHHHHHHHHHHSCSCCBHHHHHHHHHTCCCCHHHHTTCCCCHHHHHHHHHHHTTSBCCEE---EEETTEEEEECCB
T ss_pred             CCCHHHHHHHHHHHhcCCCCCHHHHHHHhccccccccchhhhhhhHHHHHHHHHHHCCeeEecc---cceeecCCcccCC
Confidence            35667788999999988899999988877631       112 566779999999999999885   4443223333555


Q ss_pred             CCHHHHHH
Q 027236           76 PNSEELNQ   83 (226)
Q Consensus        76 ~~~ee~~~   83 (226)
                      .++..-..
T Consensus       156 ~D~~~~~~  163 (249)
T 3kn1_A          156 TNNNIKQR  163 (249)
T ss_dssp             CCHHHHHH
T ss_pred             CCchHHHH
Confidence            55554433

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=83.24  E-value=7.8  Score=28.80  Aligned_cols=21  Identities=24%  Similarity=0.490  Sum_probs=7.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 027236           92 QEQLEEQRKAISKLEGEIRTL  112 (226)
Q Consensus        92 ~~~l~~l~~~~k~l~~el~~l  112 (226)
                      +.++.+++..+..|+.+|..+
T Consensus        37 k~Ei~elrr~iq~L~~el~~l   57 (131)
T 3tnu_A           37 KSEISELRRTMQNLEIELQSQ   57 (131)
T ss_dssp             ----CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444433

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=83.21  E-value=1.2  Score=32.92  Aligned_cols=33  Identities=15%  Similarity=0.102  Sum_probs=29.2

Q ss_pred             cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           24 NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        24 s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      |..++...+   ||+.+.|.++|..|..+|+|....
T Consensus        37 se~~La~~~---~vSr~tvr~Al~~L~~~Gli~~~~   69 (126)
T 3by6_A           37 SVRETALQE---KINPNTVAKAYKELEAQKVIRTIP   69 (126)
T ss_dssp             CHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEEec
Confidence            877887777   899999999999999999997654

>1xd7_A YWNA; structural genomics, protein structure initiative, winged HE binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} SCOP: a.4.5.55

Probab=83.19  E-value=2.3  Score=31.98  Aligned_cols=52  Identities=13%  Similarity=0.230  Sum_probs=40.2

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+|-||-....+ ++.+|...+   +|+...+.++|..|+..|+|.+.. | .-=|..
T Consensus        13 ~~L~~La~~~~~-s~~~IA~~~---~i~~~~l~kIl~~L~~aGlv~s~r-G-~GGy~L   64 (145)
T 1xd7_A           13 HILSLISMDEKT-SSEIIADSV---NTNPVVVRRMISLLKKADILTSRA-G-VPGASL   64 (145)
T ss_dssp             HHHHHHHTCSCC-CHHHHHHHH---TSCHHHHHHHHHHHHHTTSEECCS-S-SSSCEE
T ss_pred             HHHHHHHhCCCC-CHHHHHHHH---CcCHHHHHHHHHHHHHCCceEeec-C-CCCcee
Confidence            456666654446 988888877   899999999999999999998876 4 333544

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=83.11  E-value=2.2  Score=33.44  Aligned_cols=57  Identities=11%  Similarity=0.205  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHHhc--------------CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQ--------------NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~--------------nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .++++|..||...              .-|++-++|.+.+   |++..+|.++|..|.++|.|.....|  .|...
T Consensus       138 ~~~~Rl~~~L~~l~~~~g~~~~~~~~~~~~~t~~~lA~~l---g~sr~tvsR~l~~l~~~g~I~~~~~~--~i~i~  208 (220)
T 2fmy_A          138 DARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALML---GTTRQTVSVLLNDFKKMGILERVNQR--TLLLK  208 (220)
T ss_dssp             HHHHHHHHHHHHHHHHHCEEETTEEEEECSSCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEESSSS--EEEES
T ss_pred             CHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHh---CCcHHHHHHHHHHHHHCCCEEEcCCC--EEEEc
Confidence            4566677776543              2488999999988   89999999999999999998653234  45544

>1ses_A Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A {Thermus thermophilus} SCOP: a.2.7.1 d.104.1.1 PDB: 1ser_A* 1set_A* 1sry_A

Probab=82.92  E-value=2.2  Score=38.21  Aligned_cols=64  Identities=19%  Similarity=0.249  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      -+++..++.+..+++.++..++.+.+.+..++.. .+....++|.++..++..+++++++++..+
T Consensus        27 ~~~~~~~~~~~r~~~~~~~~l~~~~n~~sk~i~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   90 (421)
T 1ses_A           27 LEALLALDREVQELKKRLQEVQTERNQVAKRVPK-APPEEKEALIARGKALGEEAKRLEEALREK   90 (421)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5778888999999999999999999999888876 222233455555555555555555544443

>2dq3_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, nationa on protein structural and functional analyses; HET: SSA; 3.00A {Aquifex aeolicus}

Probab=82.88  E-value=1.8  Score=38.81  Aligned_cols=64  Identities=20%  Similarity=0.373  Sum_probs=47.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC-CH-------HHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           79 EELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL-TL-------EQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        79 ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~-t~-------~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      +++..++.+..+++.++..++.+.+.+..++..+++.. ..       .++.++|.+++.+..+++++|..+
T Consensus        30 ~~~~~~~~~~r~~~~~~~~l~~~~n~~sk~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (425)
T 2dq3_A           30 DKVLELDKRRREIIKRLEALRSERNKLSKEIGKLKREGKDTTEIQNRVKELKEEIDRLEEELRKVEEELKNT  101 (425)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSSCSCTTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56777888999999999999999999999998876542 22       455566666666666666666554

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=82.80  E-value=9.8  Score=27.51  Aligned_cols=58  Identities=17%  Similarity=0.274  Sum_probs=42.5

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhc---ccccHHHHHHHHHHHHHcCCcceeec----Cce-eEEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQK---YNLKKAGIQKALDSLADNGKISFKEY----GKQ-KIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~---~~v~K~~v~k~L~~Lv~~g~i~~K~~----GK~-kiY~~   68 (226)
                      +-.||..+..  +|...-+|...+..   .+++-.++-.+|..|.++|+|.....    |.. ++|..
T Consensus        13 ~~~IL~lL~~--~p~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~L   78 (117)
T 4esf_A           13 EGCVLEIISR--RETYGYEITRHLNDLGFTEVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSL   78 (117)
T ss_dssp             HHHHHHHHHH--SCBCHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEEE
T ss_pred             HHHHHHHHHc--CCCCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEE
Confidence            4568888874  67777777776643   26899999999999999999998853    444 55555

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=82.62  E-value=4.1  Score=32.57  Aligned_cols=57  Identities=19%  Similarity=0.352  Sum_probs=44.2

Q ss_pred             hHHHHHHHHHHhc--------------CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            7 NTEAIVLNYVNEQ--------------NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         7 ea~~~Il~y~~~~--------------nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      .++++|..||...              .-|++-++|.+.+   |++..+|-++|..|.++|+|...   ...|...+
T Consensus       164 ~~~~Rla~~L~~l~~~~g~~~~~~~~i~~~lt~~~lA~~l---G~sr~tvsR~l~~L~~~GlI~~~---~~~i~I~d  234 (243)
T 3la7_A          164 DMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAI---GSTRVTVTRLLGDLREKKMISIH---KKKITVHK  234 (243)
T ss_dssp             SHHHHHHHHHHHHHHHHEEECSSSEEECSCCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEE---TTEEEECC
T ss_pred             CHHHHHHHHHHHHHHHhCCCCCCCeEEeccCCHHHHHHHH---CCcHHHHHHHHHHHHHCCCEEEc---CCEEEECC
Confidence            4567777777652              2478999999988   89999999999999999999854   34555553

>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=82.35  E-value=4  Score=32.84  Aligned_cols=52  Identities=12%  Similarity=0.303  Sum_probs=38.3

Q ss_pred             chHHHHHHHHHHhc----CCCC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            6 DNTEAIVLNYVNEQ----NRPL-NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         6 ~ea~~~Il~y~~~~----nrPy-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      +...+.|.+.+...    +.+. |-.++...+   ||+++.|-+||..|+.+|+|.....
T Consensus        10 ~~v~~~l~~~I~~g~l~pG~~LPsE~eLa~~~---gVSR~tVReAL~~L~~eGlv~~~~g   66 (239)
T 1hw1_A           10 GFAEEYIIESIWNNRFPPGTILPAERELSELI---GVTRTTLREVLQRLARDGWLTIQHG   66 (239)
T ss_dssp             HHHHHHHHHHHHTTSSCTTSBCCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCcEEEecC
Confidence            44555555555432    3345 777777766   8999999999999999999988754

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=82.27  E-value=5.1  Score=29.11  Aligned_cols=54  Identities=13%  Similarity=0.113  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+.|+..|..  .|+++.|+...+   +++...+..+|..|+..|.|+--.-|   +|+.
T Consensus         7 ~l~~~i~~~~~~--~p~~~~~la~~~---~~~~~~~~~~l~~l~~~G~l~~i~~~---~~~~   60 (121)
T 2pjp_A            7 AIWQKAEPLFGD--EPWWVRDLAKET---GTDEQAMRLTLRQAAQQGIITAIVKD---RYYR   60 (121)
T ss_dssp             HHHHHHGGGCSS--SCEEHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEEETT---EEEE
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHh---CCCHHHHHHHHHHHHHCCCEEEecCC---ceEC
Confidence            456677777743  799988887766   79999999999999999999886543   5554

>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli}

Probab=81.87  E-value=2.7  Score=34.22  Aligned_cols=56  Identities=13%  Similarity=0.162  Sum_probs=42.2

Q ss_pred             hHHHHHHHHHHhcC-------------CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQN-------------RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~n-------------rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .++++|..||....             -|++-++|.+.+   |++..+|.++|..|.++|+|...   ..+|+..
T Consensus       189 ~~~~Rla~~Ll~l~~~~~~~~~~~~~~l~lt~~~lA~~l---G~sr~tvsR~l~~L~~~GlI~~~---~~~i~I~  257 (260)
T 3kcc_A          189 LVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIV---GCSRETVGRILKMLEDQNLISAH---GKTIVVY  257 (260)
T ss_dssp             CHHHHHHHHHHHHHTSTTCEEETTEEEEECCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEC---SSEEEEC
T ss_pred             CHHHHHHHHHHHHHHhcCCCCCCCceeecCCHHHHHHHh---CCCHHHHHHHHHHHHHCCCEEEc---CCEEEEE
Confidence            45677777765421             178889999888   89999999999999999999753   3345444

>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum SENS binding, transcription; 2.30A {Xanthomonas campestris PV}

Probab=81.79  E-value=3  Score=32.72  Aligned_cols=49  Identities=10%  Similarity=0.221  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHHhcC-------------CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            7 NTEAIVLNYVNEQN-------------RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         7 ea~~~Il~y~~~~n-------------rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      .++++|..||....             -|++-++|.+.+   |++..+|.++|..|.++|+|...
T Consensus       159 ~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~lt~~~lA~~l---g~sr~tvsR~l~~L~~~g~I~~~  220 (230)
T 3iwz_A          159 DVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLV---GCSREMAGRVLKKLQADGLLHAR  220 (230)
T ss_dssp             CHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHHHHhhCCCCCCCceecCCCHHHHHHHh---CCcHHHHHHHHHHHHHCCCEEEC
Confidence            46778888887532             257888998888   89999999999999999999753

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=81.70  E-value=3.8  Score=32.01  Aligned_cols=61  Identities=23%  Similarity=0.404  Sum_probs=45.4

Q ss_pred             hHHHHHHHHHHh-c----------CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCC
Q 027236            7 NTEAIVLNYVNE-Q----------NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQF   73 (226)
Q Consensus         7 ea~~~Il~y~~~-~----------nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~   73 (226)
                      .++++|..||.. .          .-|++-++|.+.+   |++..+|-++|..|.++|+|...   ...|...+-+.+
T Consensus       152 ~~~~Rl~~~L~~~~~~~~~~~~~~~~~~t~~~lA~~l---g~sr~tvsR~l~~l~~~g~I~~~---~~~i~i~d~~~L  223 (227)
T 3dkw_A          152 NATHRVVRYLLTLAAHAPGENCRVEIPVAKQLVAGHL---SIQPETFSRIMHRLGDEGIIHLD---GREISILDRERL  223 (227)
T ss_dssp             HHHHHHHHHHHHHHCSSSSSCCCCCCCSCTHHHHHHT---TSCHHHHHHHHHHHHHHTSEEES---SSCEEESCSTTT
T ss_pred             CHHHHHHHHHHHhhhhcCCCCeEEEecCCHHHHHHHh---CCCHHHHHHHHHHHHHCCcEEec---CCEEEEeCHHHH
Confidence            456778887754 2          2367888998877   89999999999999999999653   345666654433

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=81.55  E-value=4.4  Score=33.86  Aligned_cols=33  Identities=9%  Similarity=0.148  Sum_probs=28.5

Q ss_pred             cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           24 NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        24 s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      |-.++...+   ||++++|.+||+.|+++|+|....
T Consensus        55 se~~La~~~---~vSr~tvr~Al~~L~~~G~i~~~~   87 (272)
T 3eet_A           55 SQARIREEY---GVSDTVALEARKVLMAEGLVEGRS   87 (272)
T ss_dssp             CHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             CHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEec
Confidence            777777766   899999999999999999987654

>2co5_A Viral protein F93; viral protein-winged helix complex, winged helix, DNA-bindin WHTH, disulfide bond, STIV; 2.2A {Sulfolobus turreted icosahedral virus} SCOP: a.4.5.48

Probab=81.44  E-value=10  Score=26.77  Aligned_cols=59  Identities=17%  Similarity=0.240  Sum_probs=45.2

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhc---ccccHHHHHHHHHHHHHcCCcceeecCc-eeEEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQK---YNLKKAGIQKALDSLADNGKISFKEYGK-QKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~---~~v~K~~v~k~L~~Lv~~g~i~~K~~GK-~kiY~~   68 (226)
                      .-.||.++.....|+.-.++...+..   ..++-.++--+|..|.++|+|.+.. |. .++|-.
T Consensus        11 ~~~IL~lL~~~~~~~~g~~i~~ei~~~~~~~is~GtlYp~L~rLe~~GlI~~~~-~~~rk~Y~i   73 (99)
T 2co5_A           11 YYIILKVLVINGSRLEKKRLRSEILKRFDIDISDGVLYPLIDSLIDDKILREEE-APDGKVLFL   73 (99)
T ss_dssp             HHHHHHHHHHTTTEEEGGGHHHHHHHHHCCBCCHHHHHHHHHHHHHTTSEEEEC-CTTSCEEEE
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHCCCEEEee-CCCcEEEEE
Confidence            34588888877788876566555443   2588999999999999999999988 55 466666

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=81.21  E-value=21  Score=29.30  Aligned_cols=59  Identities=14%  Similarity=0.281  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           84 MKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        84 l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      ++.++..+..++..+...++..+..+...++.-.-..|..+|..++.++..++..+..+
T Consensus        58 ~~~~~~~~e~~i~~~~~ri~~~~~~l~~v~~~kE~~aL~kEie~~~~~i~~lE~eile~  116 (256)
T 3na7_A           58 LKLQVSKNEQTLQDTNAKIASIQKKMSEIKSERELRSLNIEEDIAKERSNQANREIENL  116 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444444444444444444444333322333556666666666666666655444

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=80.96  E-value=8.3  Score=27.99  Aligned_cols=56  Identities=18%  Similarity=0.217  Sum_probs=37.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHH
Q 027236           77 NSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENK  138 (226)
Q Consensus        77 ~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~k  138 (226)
                      +..+++.+...+....+.+.....++..++.++......      ...|.-|++++....+.
T Consensus        22 ~~~ei~~L~~~L~~AEeaL~~Kq~~idelk~ei~q~~~~------lE~I~vLkaQv~IY~~D   77 (110)
T 2v4h_A           22 ASMQLEDLRQQLQQAEEALVAKQELIDKLKEEAEQHKIV------METVPVLKAQADIYKAD   77 (110)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HTHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHH
Confidence            445777888888888888888888888888877775433      23445555555444443

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=80.88  E-value=3.4  Score=31.55  Aligned_cols=48  Identities=17%  Similarity=0.337  Sum_probs=40.3

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      |+....|+..+.. |-|-|..+|...+   |++.++|..-|+.|.+.|.|..
T Consensus         2 D~~d~~il~~L~~-~~~~s~~~la~~l---g~s~~tv~~rl~~L~~~g~i~~   49 (162)
T 3i4p_A            2 DRLDRKILRILQE-DSTLAVADLAKKV---GLSTTPCWRRIQKMEEDGVIRR   49 (162)
T ss_dssp             CHHHHHHHHHHTT-CSCSCHHHHHHHH---TCCHHHHHHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHHHHHH-CCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeee
Confidence            3455678888875 5667989999888   8999999999999999999873

>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2

Probab=80.61  E-value=3.6  Score=31.63  Aligned_cols=49  Identities=14%  Similarity=0.238  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHhcC-------------CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            7 NTEAIVLNYVNEQN-------------RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         7 ea~~~Il~y~~~~n-------------rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      .+.++|..||....             -|++-++|.+.+   |++..+|-++|..|.++|+|...
T Consensus       136 ~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~l---g~sr~tvsR~l~~l~~~g~I~~~  197 (207)
T 2oz6_A          136 DVTGRVARTLLDLCQQPDAMTHPDGMQIKITRQEIGRIV---GCSREMVGRVLKSLEEQGLVHVK  197 (207)
T ss_dssp             CHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHHHHhcCCCCCCCceecccCHHHHHHHh---CCCHHHHHHHHHHHHHCCCEEec
Confidence            45667777765321             267888998888   89999999999999999999654

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=80.54  E-value=3.8  Score=33.05  Aligned_cols=37  Identities=22%  Similarity=0.407  Sum_probs=33.6

Q ss_pred             CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           20 NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        20 nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      +.|-+..+|...|   +|+.++|..+|+.|.++|+|....
T Consensus        28 ~~~V~~~~LA~~L---gvS~~SV~~~lkkL~e~GLV~~~~   64 (200)
T 2p8t_A           28 KEPLGRKQISERL---ELGEGSVRTLLRKLSHLDIIRSKQ   64 (200)
T ss_dssp             TSCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             cCCccHHHHHHHh---CCCHHHHHHHHHHHHHCCCEEEeC
Confidence            5899999999988   799999999999999999998877

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=80.49  E-value=5.1  Score=31.70  Aligned_cols=58  Identities=21%  Similarity=0.338  Sum_probs=45.5

Q ss_pred             chHHHHHHHHHHhcC--------CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            6 DNTEAIVLNYVNEQN--------RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         6 ~ea~~~Il~y~~~~n--------rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      ..++++|..||....        -|++-++|.+.+   |++..+|.++|..|.++|+|... .|  .|...+
T Consensus       162 ~~~~~Rl~~~L~~l~~~~~~~~~~~~t~~~lA~~l---G~sr~tvsR~l~~l~~~glI~~~-~~--~i~I~d  227 (232)
T 1zyb_A          162 LDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCL---DDTRLNISKTLNELQDNGLIELH-RK--EILIPD  227 (232)
T ss_dssp             CSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHH---TSCHHHHHHHHHHHHHTTSCEEE-TT--EEEESC
T ss_pred             cCHHHHHHHHHHHHHhhcCCeEEecCCHHHHHHHh---CCChhHHHHHHHHHHHCCCEEec-CC--EEEEeC
Confidence            357788999988632        257899999888   89999999999999999999754 33  455543

>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A*

Probab=80.41  E-value=3.5  Score=32.58  Aligned_cols=56  Identities=18%  Similarity=0.303  Sum_probs=42.9

Q ss_pred             chHHHHHHHHHHhcC----------CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQN----------RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~n----------rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ..+.++|..||....          -|++-++|.+.+   |++..+|-++|..|.++| |.   ++...|...
T Consensus       152 ~~~~~Rl~~~L~~~~~~~~~~~~~~l~~t~~~iA~~l---g~sr~tvsR~l~~L~~~g-i~---~~~~~i~I~  217 (237)
T 3fx3_A          152 QTGAQRVAEFLLELCDCDTGACEVTLPYDKMLIAGRL---GMKPESLSRAFSRLKAAG-VT---VKRNHAEIE  217 (237)
T ss_dssp             CCHHHHHHHHHHHHCCC-----EEECCSCTHHHHHHT---TCCHHHHHHHHHHHGGGT-EE---CCTTEEEES
T ss_pred             CCHHHHHHHHHHHHhhhcCCCeEEEecCCHHHHHHHh---CCCHHHHHHHHHHHHHCC-eE---eeCCEEEEc
Confidence            356788888888742          377888888877   899999999999999999 52   233456555

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=80.18  E-value=14  Score=26.37  Aligned_cols=36  Identities=8%  Similarity=0.151  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 027236           81 LNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNL  116 (226)
Q Consensus        81 ~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~  116 (226)
                      +..+..++..+..++..++.++..+..-+..|...+
T Consensus        15 ~~~l~~~~~~l~~q~~~l~~~~~e~~~~~~eL~~l~   50 (117)
T 2zqm_A           15 LESYQQQLQLVVQQKQKVQLELTEAKKALDEIESLP   50 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            344455555555566666666666655555555543

>3lss_A Seryl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, serrs, translation, ATP-binding, nucleotide-binding, structural genomics; HET: ATP; 1.95A {Trypanosoma brucei} PDB: 3lsq_A*

Probab=80.01  E-value=8.8  Score=35.08  Aligned_cols=37  Identities=11%  Similarity=0.091  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 027236           78 SEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQS  114 (226)
Q Consensus        78 ~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~  114 (226)
                      -+++..++.+..+++.++..++.+.+.+..++..+.+
T Consensus        36 ~d~~~~ld~~~r~~~~~~~~l~~~rN~~sk~i~~~~~   72 (484)
T 3lss_A           36 VDAIIEADKKWRRTQFLTEASKKLINICSKAVGAKKK   72 (484)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4677888899999999999999999999988877665

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	226
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	97.97
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	97.76
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	97.63
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	97.42
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	97.42
d1okra_	120	Methicillin resistance regulatory protein MecI {St	97.3
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	97.27
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	97.22
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	97.12
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	96.98
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	96.98
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	96.89
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	96.89
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.61
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	96.6
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	96.56
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.4
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	96.28
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	96.06
d1ucra_	74	Dissimilatory sulfite reductase DsvD {Desulfovibri	96.03
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	95.88
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	95.88
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	95.87
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	95.5
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	95.49
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	95.28
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	95.17
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	94.79
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	94.75
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	94.58
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	94.56
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	94.2
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	94.14
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	93.66
d1zyba1	73	Probable transcription regulator BT4300, C-termina	93.63
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	93.62
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	93.01
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	92.95
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	92.85
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	92.8
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	92.77
d1q46a1	87	Eukaryotic initiation factor 2alpha, eIF2alpha, do	92.72
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	92.43
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	92.03
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	91.93
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	91.86
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	91.5
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	90.97
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	90.48
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	90.06
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	90.02
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	89.95
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	89.91
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	89.89
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	89.64
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	89.53
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	89.38
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	89.13
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	89.07
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	88.84
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	88.42
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.91
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	87.87
d1ivsa1	66	Valyl-tRNA synthetase (ValRS) C-terminal domain {T	87.69
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	87.67
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	87.63
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	87.5
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	87.0
d2oa5a1	96	Uncharacterized protein BQLF2 {Murid herpesvirus 4	86.16
d1j1ja_	217	Translin {Human (Homo sapiens) [TaxId: 9606]}	85.49
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	85.37
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	81.94
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	81.87
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	80.89

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.97  E-value=8.4e-06  Score=59.75  Aligned_cols=63  Identities=17%  Similarity=0.241  Sum_probs=56.4

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+.+..|++++-..+.|.++.+|.+.|+. ++++.++|..+|..|+++|.|..+..|...+|.+
T Consensus         6 ~~~E~~IM~~lW~~g~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~~gr~~~Y~~   69 (122)
T d2g9wa1           6 GDLERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDDRAHRYAP   69 (122)
T ss_dssp             CHHHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC---CCEEEE
T ss_pred             CHHHHHHHHHHHcCCCCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEeecCCeEEEEe
Confidence            57889999999999999999999999975 5789999999999999999999999999999998

>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.76  E-value=6.3e-05  Score=54.91  Aligned_cols=61  Identities=15%  Similarity=0.178  Sum_probs=56.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +++..|++++-+.. |-++.+|.+.+.. ++.+.++|...|..|+++|.|.....|+..+|.+
T Consensus         6 ~~E~~VM~~lW~~~-~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~~~~gr~~~Y~~   67 (122)
T d1sd4a_           6 MAEWDVMNIIWDKK-SVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSENIYFYSS   67 (122)
T ss_dssp             HHHHHHHHHHHHSS-SEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             HHHHHHHHHHHcCC-CCCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceeeeccCCeEEEee
Confidence            67889999999865 9999999999976 5789999999999999999999999999999998

>d1p6ra_ a.4.5.39 (A:) Penicillinase repressor BlaI {Bacillus licheniformis [TaxId: 1402]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Bacillus licheniformis [TaxId: 1402]

Probab=97.63  E-value=0.00014  Score=49.47  Aligned_cols=65  Identities=22%  Similarity=0.333  Sum_probs=58.9

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQD   71 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~   71 (226)
                      .+++-.|++++=+ +.|-++.+|.+.+.. .+.+.++|...|..|+++|.|..+..|+..+|.+..+
T Consensus         8 s~~E~~IM~~lW~-~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~k~gr~~~Y~p~is   73 (82)
T d1p6ra_           8 SDAELEVMKVIWK-HSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKEGRVFVYTPNID   73 (82)
T ss_dssp             CHHHHHHHHHHHT-SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESCS
T ss_pred             CHHHHHHHHHHHh-CCCCCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEEEecCCeEEEEecCC
Confidence            6899999999997 559999999998876 5789999999999999999999999999999988544

>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=97.42  E-value=0.00032  Score=49.03  Aligned_cols=60  Identities=18%  Similarity=0.356  Sum_probs=54.5

Q ss_pred             cchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            5 SDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         5 g~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      |+..+-.|+.++.  +.|.++.+|.+.+   |++.++|..-|..|.+.|+|..+.-|+..+|..+
T Consensus        21 ~~p~Rl~Il~~L~--~~~~~v~ela~~l---~is~stvS~HL~~L~~aglV~~~r~G~~~~Y~l~   80 (98)
T d1r1ta_          21 ADPNRLRLLSLLA--RSELCVGDLAQAI---GVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQ   80 (98)
T ss_dssp             CCHHHHHHHHHHT--TCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEES
T ss_pred             CCHHHHHHHHHHH--cCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCceEEEEECCEEEEEEC
Confidence            4677888999885  5799999999988   7999999999999999999999999999999884

>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=97.42  E-value=0.00033  Score=48.63  Aligned_cols=60  Identities=17%  Similarity=0.275  Sum_probs=54.2

Q ss_pred             cchHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236            5 SDNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus         5 g~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      |+..+-.|+.++..  +|+++.+|.+.+   |++.++|..-|..|.+.|+|..+.-|+..+|..+
T Consensus        16 ~d~~Rl~Il~~L~~--~~~~v~el~~~l---~~s~~~vS~HL~~L~~~glv~~~r~G~~~~Y~l~   75 (94)
T d1r1ua_          16 GDYNRIRIMELLSV--SEASVGHISHQL---NLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLD   75 (94)
T ss_dssp             CSHHHHHHHHHHHH--CCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEES
T ss_pred             CCHHHHHHHHHHHc--CCccHHHHHHHH---CCCHHHHHHHHHHHHHCCceEEEEECCEEEEEEC
Confidence            46678889999874  689999999988   7999999999999999999999999999999883

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.30  E-value=0.0016  Score=46.68  Aligned_cols=62  Identities=19%  Similarity=0.207  Sum_probs=56.2

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhc-ccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQK-YNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~-~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      -+++-.|+.++-+.. |-++.+|.+.+.. .++..++|..+|+.|+++|+|..+.-|+..+|.+
T Consensus         6 t~~E~~VM~~lW~~~-~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~~~gr~~~Y~~   68 (120)
T d1okra_           6 SSAEWEVMNIIWMKK-YASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYS   68 (120)
T ss_dssp             CHHHHHHHHHHHHHS-SEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEETTEEEEEE
T ss_pred             CHHHHHHHHHHHcCC-CCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEEecCCceEEee
Confidence            468889999999864 9999999998864 5799999999999999999999999999999988

>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=97.27  E-value=0.014  Score=42.56  Aligned_cols=59  Identities=19%  Similarity=0.336  Sum_probs=49.6

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec-Cce-eEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY-GKQ-KIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~-GK~-kiY~~   68 (226)
                      .....|+.++.-++.|-++.+|...+   |+++++|..+|+.|++.|+|....- |.. .+|.+
T Consensus        26 ~~~~~i~~~L~~~~~plt~~ela~~l---~vsk~~vs~~l~~L~~~GlV~r~~~~~drr~~~~~   86 (151)
T d1ku9a_          26 KSVGAVYAILYLSDKPLTISDIMEEL---KISKGNVSMSLKKLEELGFVRKVWIKGERKNYYEA   86 (151)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEE
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHh---CCCcchHHHHHHHHHHCCCEEEEEcCCCCceeEEe
Confidence            45678999999999999999999988   7999999999999999999987654 333 35555

>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=97.22  E-value=0.00033  Score=51.45  Aligned_cols=63  Identities=13%  Similarity=0.266  Sum_probs=52.9

Q ss_pred             chHHHHHHHHHHhc-CCCCcHHHHHHHHhcc--cccHHHHHHHHHHHHHcCCcceeecCce-eEEEe
Q 027236            6 DNTEAIVLNYVNEQ-NRPLNSQNVADALQKY--NLKKAGIQKALDSLADNGKISFKEYGKQ-KIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~-nrPys~~di~~~l~~~--~v~K~~v~k~L~~Lv~~g~i~~K~~GK~-kiY~~   68 (226)
                      -..+..||++|.+. ++|+|+.+|.+.+...  .|+.++|=.+|+.|++.|+|..=.++.. .+|..
T Consensus        15 T~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~~~~~~~~~~~y~~   81 (134)
T d1mzba_          15 TLPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDGGHAVFEL   81 (134)
T ss_dssp             CHHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSSSSCEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEEEEeecCCceEEEe
Confidence            46789999999875 7899999999999774  5899999999999999999997777554 44443

>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=97.12  E-value=0.0018  Score=45.51  Aligned_cols=51  Identities=25%  Similarity=0.420  Sum_probs=45.8

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+-.||.++..++.|.++.+|.+.+   ++++++|...|+.|++.|+|....-
T Consensus        21 ~~~~~iL~~L~~~~~~~t~~eLa~~~---~i~~~tvs~~l~~L~~~GlV~r~~~   71 (109)
T d2d1ha1          21 DTDVAVLLKMVEIEKPITSEELADIF---KLSKTTVENSLKKLIELGLVVRTKT   71 (109)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHH---CccHhHHHHHHHHHHHCCCEEEeec
Confidence            56678999999899999999999988   7999999999999999999986654

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {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: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.98  E-value=0.00083  Score=47.71  Aligned_cols=59  Identities=22%  Similarity=0.361  Sum_probs=49.5

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +..+-.|+.++.. +.|+++.+|.+.+   |++.++|..-|..|.+.|+|.++.-|+..+|..
T Consensus        30 dp~Rl~Il~~L~~-~~~~~v~ela~~l---~~s~s~vS~HL~~L~~aGlv~~~r~G~~~~Y~l   88 (108)
T d1u2wa1          30 DENRAKITYALCQ-DEELCVCDIANIL---GVTIANASHHLRTLYKQGVVNFRKEGKLALYSL   88 (108)
T ss_dssp             SHHHHHHHHHHHH-SSCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEC----CCEEEE
T ss_pred             CHHHHHHHHHHHh-CCCccHHHHHHHH---ccChhHHHHHHHHHHHCCeeEEEEECCEEEEEE
Confidence            6677889988853 5899999999988   799999999999999999999999999998888

>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=96.98  E-value=0.0046  Score=43.42  Aligned_cols=59  Identities=15%  Similarity=0.182  Sum_probs=49.2

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      ...+..|+.++. .+.|-++.+|...+   |++++.|..+|+.|.+.|+|.....   |...+|.+
T Consensus        19 t~~e~~v~~~L~-~~g~~t~~eia~~~---~i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a   80 (109)
T d1sfxa_          19 KPSDVRIYSLLL-ERGGMRVSEIAREL---DLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSA   80 (109)
T ss_dssp             CHHHHHHHHHHH-HHCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEE
T ss_pred             CHHHHHHHHHHH-hcCCCCHHHHHHHh---CCCcchHHHHHHHHHhCCCEEEEeccCCCccccccC
Confidence            567889999998 56799999999988   8999999999999999999975543   45556666

>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=96.89  E-value=0.0013  Score=43.39  Aligned_cols=54  Identities=15%  Similarity=0.305  Sum_probs=46.9

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      --.|++++-.+.+|.++.+|...+   |++++++-+.|..|++.|.|....-|.   |..
T Consensus         7 ~l~IL~~~a~~~~~~s~~eia~~~---~~~~st~~rll~tL~~~g~l~~~~~g~---y~l   60 (75)
T d1mkma1           7 AFEILDFIVKNPGDVSVSEIAEKF---NMSVSNAYKYMVVLEEKGFVLRKKDKR---YVP   60 (75)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEECTTSC---EEE
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEECCCCC---Eee
Confidence            346899999999999999998877   899999999999999999999865443   655

>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=96.89  E-value=0.0043  Score=42.70  Aligned_cols=59  Identities=10%  Similarity=0.177  Sum_probs=48.0

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      +..+-.||.|+.. +.|.++.+|.+.+   ++++++|...|..|.+.|+|.....   +...+|..
T Consensus        15 ~p~r~~IL~~L~~-~~~~~~~eLa~~l---~is~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~L   76 (100)
T d1ub9a_          15 NPVRLGIMIFLLP-RRKAPFSQIQKVL---DLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEI   76 (100)
T ss_dssp             SHHHHHHHHHHHH-HSEEEHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             CHHHHHHHHHhcc-CCCeeHHHHHHHH---hhccccccHHHHHHhhhceeEEEEcCcCCccccccC
Confidence            4457789999964 4689999999988   7999999999999999999998765   34455554

>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=96.61  E-value=0.0022  Score=41.70  Aligned_cols=49  Identities=16%  Similarity=0.226  Sum_probs=41.4

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      +..|+.++. ++.|.|-.+|...+   |+++++|..+++.|++.|+|.....+
T Consensus         7 ~~~Il~~i~-~~g~~sr~eLa~~~---gLS~~Tvs~iv~~L~~~glv~e~g~~   55 (70)
T d1z6ra1           7 AGAVYRLID-QLGPVSRIDLSRLA---QLAPASITKIVHEMLEAHLVQELEIK   55 (70)
T ss_dssp             HHHHHHHHH-SSCSCCHHHHHHHT---TCCHHHHHHHHHHHHHHTSEEEC---
T ss_pred             HHHHHHHHH-HcCCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEeeCCc
Confidence            457899998 69999999998877   89999999999999999999765443

>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=96.60  E-value=0.0076  Score=43.68  Aligned_cols=59  Identities=20%  Similarity=0.303  Sum_probs=46.8

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      .++-.||.++...+.|-+..+|...+   ++++++|.++|+.|+++|+|....-   |..+++..
T Consensus        31 ~~~~~~L~~l~~~~~~~t~~~la~~l---~i~~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~l   92 (140)
T d3deua1          31 QTHWVTLHNIHQLPPDQSQIQLAKAI---GIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKL   92 (140)
T ss_dssp             HHHHHHHHHHHHSCSSEEHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEC--------CEEEE
T ss_pred             HHHHHHHHHHHHcCCCccHHHHHHHH---CCCHhHHHHHHHHHHhCCCEEecccCCCCCceeeEE
Confidence            45668999999878789999999988   7999999999999999999987766   45555555

>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=96.56  E-value=0.0024  Score=49.16  Aligned_cols=62  Identities=18%  Similarity=0.322  Sum_probs=52.1

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCc-----eeEEEeecCC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGK-----QKIYIARQDQ   72 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK-----~kiY~~~Q~~   72 (226)
                      +..+-.||.++.  +.|.|+.+|.+.+   |++.++|-..|+.|.+.|+|.+..-|+     .++|..+.+.
T Consensus        18 ~p~R~~Il~~L~--~~~~s~~ela~~l---g~s~~~v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~~~~~   84 (190)
T d1ulya_          18 EDTRRKILKLLR--NKEMTISQLSEIL---GKTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRTADV   84 (190)
T ss_dssp             SHHHHHHHHHHT--TCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEESSSE
T ss_pred             CHHHHHHHHHHH--hCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEEEeeccCCcceEEEEEcccc
Confidence            556788999984  6799999999999   899999999999999999998765553     6888776553

>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=96.40  E-value=0.0032  Score=40.83  Aligned_cols=46  Identities=20%  Similarity=0.274  Sum_probs=40.9

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCccee
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFK   58 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K   58 (226)
                      +..||.++.. +-|.|..+|...+   |++.++|...|+.|+++|+|...
T Consensus         8 ~~~Il~~l~~-~g~~sr~eLa~~~---glS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           8 AGRVYKLIDQ-KGPISRIDLSKES---ELAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHH-HCSBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHH-cCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEe
Confidence            4689999986 6799999999988   89999999999999999999743

>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=96.28  E-value=0.0023  Score=41.01  Aligned_cols=49  Identities=14%  Similarity=0.274  Sum_probs=43.8

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCC-cce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGK-ISF   57 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~-i~~   57 (226)
                      .+-...|+.+|.+++.|.++.++.+.|   +|+..+|.+-|+.|.+.|. |..
T Consensus         6 ~eR~~~Il~~L~~~~~~vs~~~La~~l---~VS~~TI~rdi~~L~~~G~~I~~   55 (65)
T d1j5ya1           6 QERLKSIVRILERSKEPVSGAQLAEEL---SVSRQVIVQDIAYLRSLGYNIVA   55 (65)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHH---TSCHHHHHHHHHHHHHHTCCCEE
T ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHH---CCCHHHHHHHHHHHHHCCCeEEE
Confidence            456778999999999999999999998   8999999999999999997 443

>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=96.06  E-value=0.009  Score=37.75  Aligned_cols=53  Identities=13%  Similarity=0.288  Sum_probs=39.8

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCce
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ   63 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~   63 (226)
                      +=-..|+....+.. |-+..+|...|   ||++++|.+++..|.++|+|....||..
T Consensus         7 dYLk~I~~l~~~~~-~v~~~~iA~~L---~vs~~SVs~mikrL~~~GlV~~~~Y~~i   59 (61)
T d2ev0a1           7 DYIEQIYMLIEEKG-YARVSDIAEAL---AVHPSSVTKMVQKLDKDEYLIYEKYRGL   59 (61)
T ss_dssp             HHHHHHHHHHHHHS-SCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEC----CC
T ss_pred             HHHHHHHHHHhcCC-CccHHHHHHHh---CCCchhHHHHHHHHHHCCCEEEccCCCe
Confidence            33456777665554 66778999988   8999999999999999999999999864

>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=96.03  E-value=0.013  Score=37.98  Aligned_cols=61  Identities=15%  Similarity=0.378  Sum_probs=52.6

Q ss_pred             chHHHHHHHHHHh---cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNE---QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~---~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      +++..+|++||..   ...-|=.+|+.+.++  ..+--.|+|++..||.+|.+..=--|++..|-.
T Consensus         2 ee~k~~Ive~l~~k~~~KsKfYfkDf~k~~P--d~k~R~vKK~~~~lV~e~~L~ywSSGSTTMYgl   65 (74)
T d1ucra_           2 EEAKQKVVDFLNSKSGSKSKFYFNDFTDLFP--DMKQREVKKILTALVNDEVLEYWSSGSTTMYGL   65 (74)
T ss_dssp             CHHHHHHHHHHSSHHHHSSCEEHHHHHHHCT--TSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             cHHHHHHHHHHHhccCCcCceeHHHHHHHCC--CccHHHHHHHHHHHhccceEEEEcCCCcEEecc
Confidence            6889999999943   556688899999887  457789999999999999999999999999966

>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=95.88  E-value=0.015  Score=36.87  Aligned_cols=51  Identities=8%  Similarity=0.162  Sum_probs=42.4

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCce
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ   63 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~   63 (226)
                      -..|+.. .+.+.+-...+|...|   +|++++|.+++..|.++|+|..+.||.-
T Consensus        11 L~~I~~L-~~~~~~v~~~~iA~~L---~vs~~SVt~mvkrL~~~Glv~~~~y~~i   61 (63)
T d2isya1          11 LRTIYDL-EEEGVTPLRARIAERL---DQSGPTVSQTVSRMERDGLLRVAGDRHL   61 (63)
T ss_dssp             HHHHHHH-HHTTCCCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEECTTSCE
T ss_pred             HHHHHHH-HhcCCCCcHHHHHHHh---CCCchhHHHHHHHHHHCCCEEEcCCCce
Confidence            3455554 4556778888999988   8999999999999999999999999864

>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=95.88  E-value=0.15  Score=36.14  Aligned_cols=105  Identities=10%  Similarity=0.144  Sum_probs=67.4

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEeecCCCCCCCHHHHHH
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIARQDQFDIPNSEELNQ   83 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~~Q~~~~~~~~ee~~~   83 (226)
                      .++-.||.++.....+-+..+|...+   ++++++|.++++.|+..|+|....-   |...+...    .+  ...++- 
T Consensus        28 ~~q~~iL~~l~~~~~~~t~~~la~~~---~~~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~l----T~--~G~~~~-   97 (137)
T d2fbha1          28 QARWLVLLHLARHRDSPTQRELAQSV---GVEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVL----TP--KADVLI-   97 (137)
T ss_dssp             TTHHHHHHHHHHCSSCCBHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEE----CT--THHHHH-
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHH---CCCHHHHHHHHHHHHHcCCccccCCCCCCCchhhhc----CH--HHHHHH-
Confidence            45567888887766567989998888   7999999999999999999998877   44444444    22  122221 


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHH
Q 027236           84 MKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEME  136 (226)
Q Consensus        84 l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~  136 (226)
                        .+             -......-...+-+..+.+|+..-+.-|.+=...++
T Consensus        98 --~~-------------~~~~~~~~~~~~~~~l~~~e~~~l~~~l~~l~~~l~  135 (137)
T d2fbha1          98 --AD-------------IEAIAASVRNDVLTGIDESEQALCQQVLLRILANLE  135 (137)
T ss_dssp             --HH-------------HHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             --HH-------------HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence              11             111223334445566777777766665555444433

>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=95.87  E-value=0.018  Score=36.41  Aligned_cols=53  Identities=19%  Similarity=0.305  Sum_probs=45.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCce
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ   63 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~   63 (226)
                      +-.-.||.+|. .+.+.|..++.+.|   +|++++|-+.++.|.+.|.++...-|..
T Consensus         5 ~~~~~iL~~L~-~~~~~s~~eLa~~l---~vS~~ti~r~i~~L~~~G~~I~~~~g~G   57 (63)
T d1biaa1           5 TVPLKLIALLA-NGEFHSGEQLGETL---GMSRAAINKHIQTLRDWGVDVFTVPGKG   57 (63)
T ss_dssp             HHHHHHHHHHT-TSSCBCHHHHHHHH---TSCHHHHHHHHHHHHHTTCCCEEETTTE
T ss_pred             HHHHHHHHHHH-HCCcCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCcEEEeCCCe
Confidence            45567999884 68899999999988   8999999999999999999777766664

>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=95.50  E-value=0.0099  Score=37.59  Aligned_cols=44  Identities=16%  Similarity=0.324  Sum_probs=38.5

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      +||..+++  .|.|-.+|.+.+   |+++++|...++.|.+.|+|..-.
T Consensus         3 ~Il~~i~~--~pisr~eLa~~~---gls~~TVs~~v~~L~~~GlV~e~~   46 (62)
T d2hoea1           3 RILKRIMK--SPVSRVELAEEL---GLTKTTVGEIAKIFLEKGIVVEEK   46 (62)
T ss_dssp             CSHHHHHH--SCBCHHHHHHHH---TCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHH--CCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCEEECC
Confidence            47888874  399999999988   899999999999999999997653

>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=95.49  E-value=0.04  Score=36.77  Aligned_cols=47  Identities=21%  Similarity=0.263  Sum_probs=42.4

Q ss_pred             cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           19 QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        19 ~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+.|.|..+|...+   ++++++|..+|+.|.++|+|....-|...+|+.
T Consensus        18 ~~~~lt~~eLa~~l---~i~~~~vs~~l~~Le~~GlV~r~~D~R~~~i~L   64 (85)
T d3ctaa1          18 NRAYLTSSKLADML---GISQQSASRIIIDLEKNGYITRTVTKRGQILNI   64 (85)
T ss_dssp             SEEECCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred             CCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCeeeecccccccceE
Confidence            34488999999888   899999999999999999999999899888877

>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=95.28  E-value=0.024  Score=36.67  Aligned_cols=48  Identities=29%  Similarity=0.477  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHhcCCCC--cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            7 NTEAIVLNYVNEQNRPL--NSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPy--s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      -+..+|+.+++...+|.  +..+|..-|+  +++...|.++++.|+++|.|=
T Consensus         6 ~~q~~V~~~i~s~~~~eGi~~~el~~~l~--~~~~~~i~~aid~L~~eG~IY   55 (69)
T d1dpua_           6 VAQNQVLNLIKACPRPEGLNFQDLKNQLK--HMSVSSIKQAVDFLSNEGHIY   55 (69)
T ss_dssp             HHHHHHHHHHHHCCCTTTEEHHHHHHHST--TSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhCCCccCcCHHHHHHHcc--CCCHHHHHHHHHHHHhCCcee
Confidence            46789999999988875  6777877774  799999999999999999874

>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=95.17  E-value=0.11  Score=36.79  Aligned_cols=59  Identities=14%  Similarity=0.241  Sum_probs=47.5

Q ss_pred             hHHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            7 NTEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      ..+-.||.|+... +.|-|..+|.+-+   ++++++|..+|+.|++.|+|....-   +.++.+..
T Consensus        29 ~~q~~vL~~l~~~~~~~it~~ela~~~---~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~l   91 (135)
T d3broa1          29 GTQMTIIDYLSRNKNKEVLQRDLESEF---SIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKL   91 (135)
T ss_dssp             HHHHHHHHHHHHTTTSCCBHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEE
T ss_pred             HHHHHHHHHHHHcCCCCCCHHHHHHHH---CcCHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcc
Confidence            4556788888875 5789999999988   7999999999999999999987765   44444444

>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=94.79  E-value=0.034  Score=42.66  Aligned_cols=61  Identities=20%  Similarity=0.384  Sum_probs=49.6

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec----Cc-eeEEEeecC
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY----GK-QKIYIARQD   71 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~----GK-~kiY~~~Q~   71 (226)
                      +..+-.||.++.  +.|.++.+|...|   |++.++|-.-|+.|.+.|+|.+..-    |. .++|...+.
T Consensus        14 ~~~R~~Il~~L~--~~~~~~~ela~~l---~~s~~~v~~HL~~L~~~Glv~~~~~~~~~G~~~~~y~l~~~   79 (194)
T d2p4wa1          14 NETRRRILFLLT--KRPYFVSELSREL---GVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKG   79 (194)
T ss_dssp             SHHHHHHHHHHH--HSCEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTT
T ss_pred             CHHHHHHHHHHH--hCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEEEEeecCCCCceEEEEeccc
Confidence            556788999886  4799999999988   8999999999999999999987654    33 356665554

>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=94.75  E-value=0.067  Score=34.76  Aligned_cols=58  Identities=16%  Similarity=0.211  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHH-HHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKA-GIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~-~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      |-+++|++||.... |-++-+|..+|   |++|+ .|-.+|=+|..+|.|.--.--.-.++.+
T Consensus         5 d~eekI~~~L~~~g-~~~Al~iak~l---Gl~kakeVN~~LY~L~k~g~v~k~~~tPP~W~L~   63 (73)
T d1xmka1           5 EIKEKICDYLFNVS-DSSALNLAKNI---GLTKARDINAVLIDMERQGDVYRQGTTPPIWHLT   63 (73)
T ss_dssp             HHHHHHHHHHHHTC-CEEHHHHHHHH---CGGGHHHHHHHHHHHHHTTSEEEECSSSCEEEEC
T ss_pred             HHHHHHHHHHHHcC-CchHHHHHHHh---CCCcHHHHhHHHHHHHHCCCeecCCCCCCceeee
Confidence            45789999997766 89999999999   89995 6999999999999998643222245544

>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=94.58  E-value=0.48  Score=33.64  Aligned_cols=58  Identities=17%  Similarity=0.230  Sum_probs=46.8

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      -.+-.||.++. .+.|-+..+|...+   ++++++|.++++.|++.|+|....-   |....+..
T Consensus        36 ~~q~~vL~~l~-~~~~~t~~~la~~l---~~~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~l   96 (141)
T d1lnwa_          36 PPDVHVLKLID-EQRGLNLQDLGRQM---CRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFL   96 (141)
T ss_dssp             HHHHHHHHHHH-SSTTCBHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEE
T ss_pred             HHHHHHHHHHH-HCCCCCHHHHHHHH---CccHhHHHHHHHHHHHhhceeeeccCCCCcchhhcc
Confidence            45667887886 57788999998877   7999999999999999999998877   44444444

>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=94.56  E-value=0.044  Score=35.36  Aligned_cols=51  Identities=18%  Similarity=0.320  Sum_probs=41.3

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccc-cHHHHHHHHHHHHHcCCcceeecCce
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNL-KKAGIQKALDSLADNGKISFKEYGKQ   63 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v-~K~~v~k~L~~Lv~~g~i~~K~~GK~   63 (226)
                      -+-|.+|+.+.+.|=|..+|.+.+   |+ +.++|...|..|.+.|.|... .|+.
T Consensus        11 L~~I~~~~~~~G~~Ps~rei~~~~---g~~S~stv~~~l~~Le~kG~I~r~-~~~~   62 (71)
T d1jhfa1          11 FDLIRDHISQTGMPPTRAEIAQRL---GFRSPNAAEEHLKALARKGVIEIV-SGAS   62 (71)
T ss_dssp             HHHHHHHHHHHSSCCCHHHHHHHT---TCSSHHHHHHHHHHHHHTTSEEEC-SSSS
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHc---CCCCHHHHHHHHHHHHHCcCeecC-CCCC
Confidence            345556667788899999999888   66 689999999999999999885 3443

>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=94.20  E-value=0.33  Score=34.64  Aligned_cols=51  Identities=16%  Similarity=0.238  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      -.+-.||.++...+.|-++.+|.+.+   ++++++|..+++.|+..|+|.....
T Consensus        34 ~~q~~vL~~L~~~~g~~t~~~La~~~---~~~~~~vs~~i~~L~~~glv~r~~~   84 (145)
T d2hr3a1          34 FSQLVVLGAIDRLGGDVTPSELAAAE---RMRSSNLAALLRELERGGLIVRHAD   84 (145)
T ss_dssp             HHHHHHHHHHHHTTSCBCHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHH---CCCHHHHHHHHHHHHHcCCeEeeeC
Confidence            45678899998888899999999988   7999999999999999999987765

>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=94.14  E-value=0.63  Score=33.17  Aligned_cols=51  Identities=20%  Similarity=0.290  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCc
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGK   62 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK   62 (226)
                      .+-.||.++.. |.|-+..+|...+   ++++++|..+++.|++.|+|....-..
T Consensus        30 ~q~~iL~~i~~-~~~~t~~~la~~l---~i~~~tvs~~l~~L~~~glI~r~~~~~   80 (144)
T d1lj9a_          30 GQYLYLVRVCE-NPGIIQEKIAELI---KVDRTTAARAIKRLEEQGFIYRQEDAS   80 (144)
T ss_dssp             THHHHHHHHHH-STTEEHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             HHHHHHHHHHh-CCCCCHHHHHHHH---CccHhhHHHHHHHHHhhhcccccCCCC
Confidence            45567777765 5689999999988   799999999999999999999887753

>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=93.66  E-value=0.74  Score=32.40  Aligned_cols=57  Identities=11%  Similarity=0.163  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC---ceeEEEe
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG---KQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G---K~kiY~~   68 (226)
                      .+-.||.++... -|-+..+|...+   ++++++|..+|+.|+..|+|....-.   ..+++..
T Consensus        31 ~q~~iL~~i~~~-~~~t~~~la~~l---~i~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~L   90 (139)
T d2a61a1          31 AQFDILQKIYFE-GPKRPGELSVLL---GVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVI   90 (139)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHh---CCCcccchHHHHHHHhcCeeeeeeccCCCCeEEEEE
Confidence            455788888765 488999998877   89999999999999999999888764   4555555

>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=93.63  E-value=0.15  Score=32.75  Aligned_cols=57  Identities=21%  Similarity=0.341  Sum_probs=44.8

Q ss_pred             chHHHHHHHHHHhcCC--------CCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            6 DNTEAIVLNYVNEQNR--------PLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nr--------Pys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+.+.+|..||.....        |++-.+|.+.+   |++..+|.++|..|.++|.|. ..+|+  |...
T Consensus         3 ~dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~l---g~sr~tvsr~l~~l~~~g~I~-~~~~~--i~I~   67 (73)
T d1zyba1           3 LDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCL---DDTRLNISKTLNELQDNGLIE-LHRKE--ILIP   67 (73)
T ss_dssp             CSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHH---TSCHHHHHHHHHHHHHTTSCE-EETTE--EEES
T ss_pred             CCHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEE-ecCCE--EEEc
Confidence            3678899999875432        46888888877   899999999999999999996 45554  4444

>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=93.62  E-value=0.13  Score=33.43  Aligned_cols=52  Identities=17%  Similarity=0.303  Sum_probs=41.9

Q ss_pred             hHHHHHHHHHHhcC--------------CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            7 NTEAIVLNYVNEQN--------------RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         7 ea~~~Il~y~~~~n--------------rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      |++++|..||....              -|+|-++|.+.+   |++..+|-++|..|.++|+|....-|
T Consensus         1 dv~~Rla~~Ll~l~~~~g~~~~~~~~i~~~~t~~eiA~~l---G~sretvsr~l~~l~~~g~I~~~~~~   66 (80)
T d1ft9a1           1 DIKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLI---GSSRQTTSTALNSLIKEGYISRQGRG   66 (80)
T ss_dssp             HHHHHHHHHHHHTCBCCCSCC--CCCCEECCCHHHHHHHH---CSCHHHHHHHHHHHHHTTSSEECSTT
T ss_pred             CHHHHHHHHHHHHHHHhCCCCCCCeEEecCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEECCCC
Confidence            45677777776421              289999999988   89999999999999999999866433

>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Seryl-tRNA synthetase (SerRS)
domain: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=93.01  E-value=0.23  Score=34.33  Aligned_cols=66  Identities=18%  Similarity=0.271  Sum_probs=50.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027236           77 NSEELNQMKEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLR  143 (226)
Q Consensus        77 ~~ee~~~l~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~  143 (226)
                      +-+.+..++.+..+++.++..++.+.+.+..++....+. ..+++.++...|..++..++..+..+.
T Consensus        26 ~ld~i~~ld~~rr~l~~~~e~l~~~rN~~sk~i~k~~~~-~~~~l~~~~k~lk~~i~~le~~~~~~~   91 (110)
T d1seta1          26 DLEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPE-EKEALIARGKALGEEAKRLEEALREKE   91 (110)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-chHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            357788899999999999999999999999888754432 235667777777777777777765543

>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=92.95  E-value=0.51  Score=33.25  Aligned_cols=50  Identities=18%  Similarity=0.281  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .+-.||.++.. +.|-+..+|...+   +++++++..+++.|++.|+|..+.-+
T Consensus        35 ~q~~vL~~i~~-~~~~t~~~la~~l---~~~~~~~s~~l~~L~~~Gli~r~~~~   84 (136)
T d2bv6a1          35 PQFLVLTILWD-ESPVNVKKVVTEL---ALDTGTVSPLLKRMEQVDLIKRERSE   84 (136)
T ss_dssp             HHHHHHHHHHH-SSEEEHHHHHHHT---TCCTTTHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHc-CCCCCHHHHHHHH---CCCHhHHHHHHHHHHHCCCEEEeecC
Confidence            44567777775 5688999998887   89999999999999999999987664

>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=92.85  E-value=1  Score=31.54  Aligned_cols=58  Identities=14%  Similarity=0.272  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCce--eEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQ--KIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~--kiY~~   68 (226)
                      ..+-.||.++.. +.|-+..+|.+.+   ++++++|..+++.|+++|+|....-..-  .+|++
T Consensus        30 ~~q~~vL~~l~~-~~~~t~~~la~~~---~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~   89 (136)
T d2fbia1          30 EQQWRVIRILRQ-QGEMESYQLANQA---CILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVN   89 (136)
T ss_dssp             HHHHHHHHHHHH-HCSEEHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEE
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEeecCccCchhhhc
Confidence            345678888876 4578999998877   7999999999999999999988877653  35555

>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=92.80  E-value=0.17  Score=35.88  Aligned_cols=58  Identities=19%  Similarity=0.276  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC--ceeEEEe
Q 027236            8 TEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG--KQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G--K~kiY~~   68 (226)
                      .+=.||.++... +.+.++.+|...+   ++++++|..+++.|++.|+|.-..-.  +-.+|+.
T Consensus        34 ~q~~vL~~l~~~~~~~~~~~~ia~~l---~~~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~   94 (125)
T d1p4xa2          34 VEFTILAIITSQNKNIVLLKDLIETI---HHKYPQTVRALNNLKKQGYLIKERSTEDERKILIH   94 (125)
T ss_dssp             HHHHHHHHHHTTTTCCEEHHHHHHHS---SSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEE
T ss_pred             HHHHHHHHHHHccCCCccHHHHHHHH---CCCcchHHHHHHHHHhccCEeeeecCCCCCeEEEE
Confidence            445688888754 4678999998888   79999999999999999999877654  3355555

>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=92.77  E-value=0.09  Score=33.29  Aligned_cols=41  Identities=17%  Similarity=0.276  Sum_probs=34.5

Q ss_pred             CCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEE
Q 027236           22 PLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIY   66 (226)
Q Consensus        22 Pys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY   66 (226)
                      |+|-+||.+.+   |++..+|.++|..|.++|+|... +++-.||
T Consensus        29 ~lt~~~lA~~~---G~sRetvsr~L~~l~~~glI~~~-~~~I~I~   69 (69)
T d1i5za1          29 KITRQEIGQIV---GCSRETVGRILKMLEDQNLISAH-GKTIVVY   69 (69)
T ss_dssp             ECCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEE-TTEEEEC
T ss_pred             CCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEEc-CCEEEEC
Confidence            68889998888   89999999999999999999753 5555554

>d1q46a1 a.60.14.1 (A:89-175) Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: eIF2alpha middle domain-like
family: eIF2alpha middle domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.72  E-value=0.068  Score=35.94  Aligned_cols=60  Identities=22%  Similarity=0.284  Sum_probs=48.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCcccccccccchhhchhhh
Q 027236          149 VKPEDRMAVEEMFLEKLSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSLQSFSDLL  216 (226)
Q Consensus       149 vs~ee~~~~~~~~~~~~~~w~kRkri~~~i~~~i~e~~~~~~k~l~e~lGie~Ded~~v~~~~~~~~~  216 (226)
                      |||+++.+=+..|.       +-| ....|+..+++.++.+.++|++.+|+.-+.-||-.+..|...+
T Consensus         1 VS~edi~kCeery~-------K~K-~V~sIlrhvAekl~~~lEeLy~~iaWpL~~kyG~aydaFk~av   60 (87)
T d1q46a1           1 VSSEDIIKCEEKYQ-------KSK-TVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSI   60 (87)
T ss_dssp             CCHHHHHHHHHHHH-------HHH-HHHHHHHHHHHHTTCCHHHHHHHTHHHHHHHHSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH-------HHH-HHHHHHHHHHHHHCCCHHHHHHHHhhhhHhhcchHHHHHHHHh
Confidence            68898887776654       444 5589999999999999999999999998888887676665543

>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=92.43  E-value=0.38  Score=33.80  Aligned_cols=58  Identities=22%  Similarity=0.343  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC--ceeEEEe
Q 027236            8 TEAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG--KQKIYIA   68 (226)
Q Consensus         8 a~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G--K~kiY~~   68 (226)
                      .+-.||.++... +.|.+.++|...+   ++++++|..+++.|.+.|+|....-.  +=.+|+.
T Consensus        35 ~q~~iL~~l~~~~~~~~t~~eia~~~---~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~   95 (125)
T d1p4xa1          35 KEFILLTYLFHQQENTLPFKKIVSDL---CYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYIS   95 (125)
T ss_dssp             HHHHHHHHHHSCSCSEEEHHHHHHHS---SSCGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEE
T ss_pred             HHHHHHHHHHHhccCCcCHHHHHHHh---CCCcchHHHHHHHHHHCCCceeecccCCCCeEEEE
Confidence            456788888764 3589999998877   79999999999999999999988764  3356665

>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=92.03  E-value=0.38  Score=33.27  Aligned_cols=50  Identities=24%  Similarity=0.371  Sum_probs=41.2

Q ss_pred             HHHHHHHHHhc-CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            9 EAIVLNYVNEQ-NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         9 ~~~Il~y~~~~-nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      +-.||.++... +.|.++.+|.+.+   ++++++|.++++.|++.|+|....-.
T Consensus        35 q~~vL~~l~~~~~~~~t~~~la~~l---~~~~~tvs~~i~~Le~~gli~r~~~~   85 (115)
T d2frha1          35 EFAVLTYISENKEKEYYLKDIINHL---NYKQPQVVKAVKILSQEDYFDKKRNE   85 (115)
T ss_dssp             HHHHHHHHHHTCCSEEEHHHHHHHS---SSHHHHHHHHHHHHHHTTSSCCBCCS
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHH---CCCHhHHHHHHHHHHhhhhheeeecc
Confidence            44567667654 5689999999988   79999999999999999999888653

>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=91.93  E-value=0.071  Score=37.30  Aligned_cols=50  Identities=26%  Similarity=0.298  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHh-cCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            8 TEAIVLNYVNE-QNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         8 a~~~Il~y~~~-~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .+-.||.++.. .+.|.+..+|.+.+   ++++++|..+++.|++.|+|.-..-
T Consensus        33 ~q~~vL~~l~~~~~~~~t~~ela~~l---~~~~~~vs~~i~~Le~~gli~r~~~   83 (115)
T d1hsja1          33 EEIYILNHILRSESNEISSKEIAKCS---EFKPYYLTKALQKLKDLKLLSKKRS   83 (115)
T ss_dssp             HHHHHHHHHHTCSCSEEEHHHHHHSS---CCCHHHHHHHHHHHHTTTTSCCEEC
T ss_pred             HHHHHHHHHHccCCCCcCHHHHHHHH---CCChhhHHHHHHHHHHcCCeEEEee
Confidence            45568888875 45689999998877   7999999999999999999987655

>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=91.86  E-value=1.4  Score=30.96  Aligned_cols=50  Identities=16%  Similarity=0.278  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .+-.||.++.. +.|-++.+|...+   ++++++|..+++.|+..|+|....-.
T Consensus        36 ~q~~iL~~l~~-~~~~t~~~la~~~---~i~~~~vs~~l~~L~~~glv~r~~~~   85 (143)
T d1s3ja_          36 AQLFVLASLKK-HGSLKVSEIAERM---EVKPSAVTLMADRLEQKNLIARTHNT   85 (143)
T ss_dssp             HHHHHHHHHHH-HSEEEHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHH---CcCHHHHHHHHHHHHHhhhheeeeec
Confidence            45568888875 5588999998888   79999999999999999999987764

>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=91.50  E-value=0.19  Score=35.68  Aligned_cols=49  Identities=18%  Similarity=0.292  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ++-.||.++.. +.|-+..+|.+.+   ++++++|.++++.|+..|+|....-
T Consensus        34 ~q~~vL~~l~~-~~~~t~~~La~~~---~i~~~~vsr~i~~L~~~glv~r~~~   82 (137)
T d1z91a1          34 PQYLALLLLWE-HETLTVKKMGEQL---YLDSGTLTPMLKRMEQQGLITRKRS   82 (137)
T ss_dssp             HHHHHHHHHHH-HSEEEHHHHHHTT---TCCHHHHHHHHHHHHHHTSEECCBC
T ss_pred             HHHHHHHHHHc-CCCCCHHHHHHHH---CcCHHHHHHHHHHHhhccceEEeec
Confidence            45668888876 4578988888877   7999999999999999999998866

>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=90.97  E-value=0.31  Score=30.45  Aligned_cols=47  Identities=17%  Similarity=0.229  Sum_probs=40.6

Q ss_pred             hHHHHHHHHHHhcC-CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            7 NTEAIVLNYVNEQN-RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         7 ea~~~Il~y~~~~n-rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      .-.+.|...|.+.+ .|-++.||.+.+   |++-..+...|.-|+..|.|+
T Consensus         7 ~l~~~I~~~~~~~g~~PP~vrdl~~~l---~~~e~~~~~lL~~l~~~G~lv   54 (64)
T d1lvaa3           7 KLLKDLEDKYRVSRWQPPSFKEVAGSF---NLDPSELEELLHYLVREGVLV   54 (64)
T ss_dssp             HHHHHHHHHHHHHTTSCCBHHHHHHHT---TCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHHcCCCCCcHHHHHHHh---CCCHHHHHHHHHHHHHCCCEE
Confidence            34567888887765 999999998888   799999999999999999886

>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=90.48  E-value=0.18  Score=32.60  Aligned_cols=42  Identities=19%  Similarity=0.366  Sum_probs=33.3

Q ss_pred             CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           21 RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        21 rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      -|+|-++|.+.+   |++..+|.++|..|.++|+|.   ++...|+..
T Consensus        29 ~~lt~~elA~~~---g~sretvsr~l~~l~~~glI~---~~~~~i~I~   70 (80)
T d3e5ua1          29 MPLSQKSIGEIT---GVHHVTVSRVLASLKRENILD---KKKNKIIVY   70 (80)
T ss_dssp             SCCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEE---C----CEES
T ss_pred             eCCCHHHHHHHH---CCCHHHHHHHHHHHHHCCcEE---ecCCEEEEc
Confidence            488989999888   899999999999999999985   455566665

>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=90.06  E-value=0.27  Score=34.64  Aligned_cols=53  Identities=13%  Similarity=0.255  Sum_probs=43.2

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      .+|-|+.. |.|.|..+|...+   +++...|.|+|..|...|+|.+.. |..=.|.+
T Consensus         8 ~~L~~la~-~~~~ss~~IA~~~---~~~~~~v~kIl~~L~~aglV~s~r-G~~GGyLa   60 (127)
T d1xd7a_           8 HILSLISM-DEKTSSEIIADSV---NTNPVVVRRMISLLKKADILTSRA-GVPGASLK   60 (127)
T ss_dssp             HHHHHHHT-CSCCCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEECCS-SSSSCEES
T ss_pred             HHHHHHhc-CCCCCHHHHHHHh---CcCHHHHHHHHHHHHHhCcccccC-CCCCcccc
Confidence            35777764 7899999998887   799999999999999999998764 45555744

>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=90.02  E-value=0.22  Score=35.65  Aligned_cols=54  Identities=15%  Similarity=0.120  Sum_probs=41.5

Q ss_pred             HHHHHHH-hcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEee
Q 027236           11 IVLNYVN-EQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIAR   69 (226)
Q Consensus        11 ~Il~y~~-~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~   69 (226)
                      .||-||- ..++|.|..+|...+   +++...+.|+|..|+..|+|.+..- +.= |+..
T Consensus        11 ~~L~~la~~~~~~vss~~IA~~~---~i~~~~l~kil~~L~~aGlv~S~rG-~GG-~~L~   65 (138)
T d1ylfa1          11 HILSILKNNPSSLCTSDYMAESV---NTNPVVIRKIMSYLKQAGFVYVNRG-PGG-AGLL   65 (138)
T ss_dssp             HHHHHHHHSCGGGCCHHHHHHHH---TSCHHHHHHHHHHHHHTTSEEEC----CC-EEES
T ss_pred             HHHHHHHhCCCCcCcHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEeecC-CCC-ceec
Confidence            4667775 357799999998877   8999999999999999999988765 444 4453

>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Seryl-tRNA synthetase (SerRS)
domain: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=89.95  E-value=1.3  Score=30.12  Aligned_cols=91  Identities=14%  Similarity=0.186  Sum_probs=60.2

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHHHHHHHHHH
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENA   89 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~~~l~~~i~   89 (226)
                      +.|.+-+...+-++.+..|...-.    ..-.++.-++.|-.+.--.++.+|+.             .+++...+..+..
T Consensus        12 e~v~~~l~~R~~~~~ld~i~~ld~----~rr~l~~~~e~l~~~rN~~sk~i~k~-------------~~~~~~~l~~~~k   74 (110)
T d1seta1          12 EVFHRAIREKGVALDLEALLALDR----EVQELKKRLQEVQTERNQVAKRVPKA-------------PPEEKEALIARGK   74 (110)
T ss_dssp             HHHHHHHHHTTCCCCHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHGGGC-------------CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCccCHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHh-------------hccchHHHHHHHH
Confidence            455666667777777655544332    24566667777777766677778752             1455556667777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 027236           90 KLQEQLEEQRKAISKLEGEIRTLQSNLT  117 (226)
Q Consensus        90 ~l~~~l~~l~~~~k~l~~el~~l~~~~t  117 (226)
                      .+.+++..++.+...++.++..+...++
T Consensus        75 ~lk~~i~~le~~~~~~~~~l~~~ll~iP  102 (110)
T d1seta1          75 ALGEEAKRLEEALREKEARLEALLLQVP  102 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            7777777777777777777777766544

>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=89.91  E-value=0.58  Score=28.89  Aligned_cols=47  Identities=13%  Similarity=0.308  Sum_probs=39.7

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      ++.-..|+..+.. |-+-+..+|...+   |++.++|..-++.|.++|.|.
T Consensus         4 D~~D~~IL~~L~~-n~r~s~~~iA~~l---gis~~tv~~Ri~~L~~~giI~   50 (63)
T d2cfxa1           4 DQIDLNIIEELKK-DSRLSMRELGRKI---KLSPPSVTERVRQLESFGIIK   50 (63)
T ss_dssp             CHHHHHHHHHHHH-CSCCCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHHHHH-cCCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCee
Confidence            4455678888885 6666888999888   899999999999999999995

>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=89.89  E-value=0.11  Score=35.44  Aligned_cols=63  Identities=16%  Similarity=0.175  Sum_probs=42.0

Q ss_pred             CCCCc--chHHHHHHHHHHh--------cCCCC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236            1 MAPKS--DNTEAIVLNYVNE--------QNRPL-NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus         1 M~~kg--~ea~~~Il~y~~~--------~nrPy-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      ||.++  .-.=..|.+.|..        ..... |..++...+   +|+.++|.++|+.|+++|+|... -|+. +|+.
T Consensus         1 mp~~~p~~~~y~qi~~~i~~~I~~g~l~~G~~LPs~r~La~~~---~vSr~tvr~Al~~L~~~Gli~~~-~g~G-~~V~   74 (100)
T d1v4ra1           1 MPYKAPEGKGYADVATHFRTLIKSGELAPGDTLPSVADIRAQF---GVAAKTVSRALAVLKSEGLVSSR-GALG-TVVE   74 (100)
T ss_dssp             CCCCCCSSCCHHHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHS---SSCTTHHHHHTTTTTTSSCCEEE-TTTE-EESC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHcCCCCCcCCCccHHHHHHHH---CCCHHHHHHHHHHHHHCCcEEEe-cCCE-EEEC
Confidence            77664  1223344444443        23344 877777766   89999999999999999998866 3443 3554

>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=89.64  E-value=2.3  Score=29.63  Aligned_cols=50  Identities=24%  Similarity=0.302  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecC
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYG   61 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~G   61 (226)
                      .+-.||.++... .|-++.+|...+   ++++++|..+++.|+++|+|.-..-.
T Consensus        33 ~q~~iL~~l~~~-~~~t~~~La~~l---~i~~~~vs~~v~~L~~~gli~r~~~~   82 (140)
T d2etha1          33 TELYAFLYVALF-GPKKMKEIAEFL---STTKSNVTNVVDSLEKRGLVVREMDP   82 (140)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHT---TSCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeeeeecc
Confidence            456788888766 467988888877   79999999999999999999988764

>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=89.53  E-value=0.37  Score=30.61  Aligned_cols=56  Identities=16%  Similarity=0.199  Sum_probs=45.5

Q ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec-CceeEEEe
Q 027236            9 EAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY-GKQKIYIA   68 (226)
Q Consensus         9 ~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~-GK~kiY~~   68 (226)
                      ...||+.-... -.-|...+.++|   |-++.-++.+|+.|+.+|++=.+.- |.-..||.
T Consensus         5 qt~vLe~a~~~-G~Vt~s~l~~~l---gW~~~Ra~~aLd~lv~eGl~WvD~Q~~~e~~YWf   61 (68)
T d1u5ta2           5 QTKILEICSIL-GYSSISLLKANL---GWEAVRSKSALDEMVANGLLWIDYQGGAEALYWD   61 (68)
T ss_dssp             HHHHHHTTTTT-SCCBHHHHHHHH---CCCSHHHHHHHHHHHHTTSSEEECSSSSSCEEEC
T ss_pred             HHHHHHHHHHc-CceeHHHHHHHh---CCCHHHHHHHHHHHHhcCcEEEecCCCCCceeeC
Confidence            45677766544 566888888888   7899999999999999999999987 55678886

>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=89.38  E-value=2  Score=28.51  Aligned_cols=82  Identities=16%  Similarity=0.183  Sum_probs=47.0

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCceeEEEeecCCCCCCCHHHHHHHHHHHH
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGKQKIYIARQDQFDIPNSEELNQMKEENA   89 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~~Q~~~~~~~~ee~~~l~~~i~   89 (226)
                      +.|.+.+.-....-+.+.|   +.+.+++=..+++.|+.|++.|+|..    ..+.|+.    -+  .+.++-..-.++.
T Consensus         6 eIi~DIL~~~~~g~~kT~i---~~~aNLs~~~~~kyl~~L~~~GLI~~----~~~~Y~i----T~--kG~~~L~~~~~~~   72 (90)
T d1r7ja_           6 EIIQAILEACKSGSPKTRI---MYGANLSYALTGRYIKMLMDLEIIRQ----EGKQYML----TK--KGEELLEDIRKFN   72 (90)
T ss_dssp             HHHHHHHHHHTTCBCHHHH---HHHHTCCHHHHHHHHHHHHHTTSEEE----ETTEEEE----CH--HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCccHH---HHHcCCCHHHHHHHHHHHHHCCCeee----cCCEEEE----Cc--cHHHHHHHHHHHH
Confidence            3455555543333343344   33346788999999999999999963    2357888    22  1233333334455


Q ss_pred             HHHHHHHHHHHHHHH
Q 027236           90 KLQEQLEEQRKAISK  104 (226)
Q Consensus        90 ~l~~~l~~l~~~~k~  104 (226)
                      ++.+.+..+..++..
T Consensus        73 ~~~~~l~~l~~~i~~   87 (90)
T d1r7ja_          73 EMRKNMDQLKEKINS   87 (90)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            555555555554443

>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=89.13  E-value=0.34  Score=31.24  Aligned_cols=37  Identities=22%  Similarity=0.251  Sum_probs=30.7

Q ss_pred             CCC-cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236           21 RPL-NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus        21 rPy-s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .+. |..++...+   +|+.++|.+||..|+.+|+|....-
T Consensus        20 ~~LPse~~La~~~---~vSr~tvr~Al~~L~~~Gli~~~~g   57 (78)
T d3bwga1          20 DKLPVLETLMAQF---EVSKSTITKSLELLEQKGAIFQVRG   57 (78)
T ss_dssp             CBCCCHHHHHHHT---TCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CCCcCHHHHHHHH---CCCHHHHHHHHHHHHHCCcEEEEcC
Confidence            344 777777666   8999999999999999999998744

>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=89.07  E-value=0.26  Score=31.80  Aligned_cols=34  Identities=12%  Similarity=0.225  Sum_probs=30.6

Q ss_pred             CCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236           21 RPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus        21 rPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      -|+|-+||.+.+   |++..+|.++|..|.++|+|..
T Consensus        28 ~~lt~~eLA~~~---G~sretvsr~L~~l~~~glI~~   61 (81)
T d2gaua1          28 IYLSREELATLS---NMTVSNAIRTLSTFVSERMLAL   61 (81)
T ss_dssp             CCCCHHHHHHHT---TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             ecCCHHHHHHHH---CCCHHHHHHHHHHHHHCCCEEe
Confidence            488999998877   8999999999999999999863

>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=88.84  E-value=0.24  Score=31.89  Aligned_cols=33  Identities=12%  Similarity=0.435  Sum_probs=29.5

Q ss_pred             cHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceee
Q 027236           24 NSQNVADALQKYNLKKAGIQKALDSLADNGKISFKE   59 (226)
Q Consensus        24 s~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~   59 (226)
                      |..++...+   +|+.+.|.++|+.|+++|+|....
T Consensus        29 s~~eLa~~~---~vSr~tvr~Al~~L~~~G~i~~~~   61 (74)
T d1hw1a1          29 AERELSELI---GVTRTTLREVLQRLARDGWLTIQH   61 (74)
T ss_dssp             CHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cHHHHHHHH---CCCHHHHHHHHHHHHHCCcEEEEe
Confidence            777887777   899999999999999999998874

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=88.42  E-value=2.8  Score=29.14  Aligned_cols=58  Identities=12%  Similarity=0.119  Sum_probs=45.8

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec---CceeEEEe
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY---GKQKIYIA   68 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~---GK~kiY~~   68 (226)
                      -.+-.||.++.. +.|-+..+|...+   ++++++|..+++.|+++|+|....-   |..+.+..
T Consensus        34 ~~q~~vL~~l~~-~~~~t~~ela~~~---~i~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~l   94 (138)
T d1jgsa_          34 AAQFKVLCSIRC-AACITPVELKKVL---SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKL   94 (138)
T ss_dssp             HHHHHHHHHHHH-HSSBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEE
T ss_pred             HHHHHHHHhHHh-CcCCCHHHHHHHH---CCCHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEE
Confidence            355678888865 4588999998888   7999999999999999999987766   34444444

>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=87.91  E-value=0.85  Score=27.77  Aligned_cols=46  Identities=17%  Similarity=0.403  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      +....|+.+|.+. -.-|..+|...+   |++.++|..-++.|.++|.|.
T Consensus         3 ~~D~kIl~~L~~n-~r~s~~~lA~~~---gls~~~v~~Ri~~L~~~giI~   48 (60)
T d1i1ga1           3 ERDKIILEILEKD-ARTPFTEIAKKL---GISETAVRKRVKALEEKGIIE   48 (60)
T ss_dssp             SHHHHHHHHHHHC-TTCCHHHHHHHH---TSCHHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeE
Confidence            4556889988864 444666888877   899999999999999999985

>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=87.87  E-value=0.37  Score=30.33  Aligned_cols=38  Identities=13%  Similarity=0.322  Sum_probs=30.9

Q ss_pred             CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236           20 NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus        20 nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      ..+.+..++...+   +|+.+.|.++|..|+++|+|.....
T Consensus        23 G~~l~~~~La~~~---~vSr~tvr~Al~~L~~~Gli~~~~~   60 (69)
T d2hs5a1          23 GARLSEPDICAAL---DVSRNTVREAFQILIEDRLVAHELN   60 (69)
T ss_dssp             TCEECHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             cCccCHHHHHHHH---CCCHHHHHHHHHHHHHCCcEEEEcC
Confidence            3445666666665   8999999999999999999998854

>d1ivsa1 a.2.7.3 (A:797-862) Valyl-tRNA synthetase (ValRS) C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Valyl-tRNA synthetase (ValRS) C-terminal domain
domain: Valyl-tRNA synthetase (ValRS) C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=87.69  E-value=1.5  Score=27.14  Aligned_cols=58  Identities=9%  Similarity=0.160  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH---HhccCCH--HHHHHHHHHHHHHHHHHHHHHHHh
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRT---LQSNLTL--EQIREKEAQLVKEVKEMENKLAKL  142 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~---l~~~~t~--~el~~~i~~L~~e~~~l~~kL~~l  142 (226)
                      +.++..|..++..++.++..+...|.+   +...|..  ++-...+.++..++..++..|..|
T Consensus         3 ~~E~~RL~K~l~kl~~~i~~~~~kL~N~~F~~kAP~~Vv~~~k~kl~~~~~~~~~l~~~l~~L   65 (66)
T d1ivsa1           3 EEWRRRQEKRLKELLALAERSQRKLASPGFREKAPKEVVEAEEARLKENLEQAERIREALSQI   65 (66)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSTTHHHHSCTTHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCChHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            456667777777777777777776654   3334544  566677788888888888877654

>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=87.67  E-value=0.37  Score=35.56  Aligned_cols=49  Identities=12%  Similarity=0.084  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeec
Q 027236            8 TEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEY   60 (226)
Q Consensus         8 a~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~   60 (226)
                      .+-.||.++.. +.|-+..+|.+.+   ++++++|..+++.|.+.|+|....-
T Consensus        42 ~q~~vL~~l~~-~~~~t~~~la~~~---~l~~~tvs~~i~rL~~~gli~r~~~   90 (162)
T d2fxaa1          42 NEHHILWIAYQ-LNGASISEIAKFG---VMHVSTAFNFSKKLEERGYLRFSKR   90 (162)
T ss_dssp             HHHHHHHHHHH-HTSEEHHHHHHHT---TCCHHHHHHHHHHHHHHTSEEEECC
T ss_pred             HHHHHHhhhcc-CCCcCHHHHHHHH---cCCchhhHHHHHHHHHCCCceeecc
Confidence            34567877775 4477988888877   8999999999999999999987755

>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=87.63  E-value=0.96  Score=27.64  Aligned_cols=46  Identities=26%  Similarity=0.443  Sum_probs=39.4

Q ss_pred             HHHHHHHHHhc--CCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            9 EAIVLNYVNEQ--NRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         9 ~~~Il~y~~~~--nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      ++.||.+|.+.  ..-+++.++..-|   +|+|..|.++|=+|...|+++-
T Consensus         1 Eq~vl~~l~~lg~~~~~tA~~LA~kl---~vpKk~iNr~LYsL~~kgkl~k   48 (59)
T d2gxba1           1 EQRILKFLEELGEGKATTAHDLSGKL---GTPKKEINRVLYSLAKKGKLQK   48 (59)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHH---TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ChHHHHHHHhcCCccchhHHHHHHHh---CCcHHHHHHHHHHHHHccchhh
Confidence            46789999884  4678999988877   7999999999999999999864

>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=87.50  E-value=0.91  Score=27.86  Aligned_cols=48  Identities=15%  Similarity=0.198  Sum_probs=39.2

Q ss_pred             chHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236            6 DNTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus         6 ~ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      |+.-..|+..|... -.-|..+|...+   |++.++|..-++.|.++|.|..
T Consensus         4 D~~D~~IL~~L~~~-~r~s~~eiA~~l---~ls~~~v~~Ri~rL~~~GiI~~   51 (63)
T d2cg4a1           4 DNLDRGILEALMGN-ARTAYAELAKQF---GVSPETIHVRVEKMKQAGIITG   51 (63)
T ss_dssp             CHHHHHHHHHHHHC-TTSCHHHHHHHH---TSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CHHHHHHHHHHHHc-CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeEe
Confidence            34556788888865 445777898888   8999999999999999999973

>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=87.00  E-value=1.1  Score=27.17  Aligned_cols=46  Identities=11%  Similarity=0.289  Sum_probs=37.4

Q ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcc
Q 027236            7 NTEAIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKIS   56 (226)
Q Consensus         7 ea~~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~   56 (226)
                      +--..|+..|.+. -+-|..+|...+   |++.++|..-++.|.++|.|.
T Consensus         3 ~~D~~Il~~L~~n-~r~s~~eiA~~l---~ls~~~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1           3 EIDKKIIKILQND-GKAPLREISKIT---GLAESTIHERIRKLRESGVIK   48 (60)
T ss_dssp             HHHHHHHHHHHHC-TTCCHHHHHHHH---CSCHHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHH---CcCHHHHHHHHHHHHHCCCeE
Confidence            3445788888864 444666888888   899999999999999999986

>d2oa5a1 d.362.1.1 (A:7-102) Uncharacterized protein BQLF2 {Murid herpesvirus 4 [TaxId: 33708]}

class: Alpha and beta proteins (a+b)
fold: BLRF2-like
superfamily: BLRF2-like
family: BLRF2-like
domain: Uncharacterized protein BQLF2
species: Murid herpesvirus 4 [TaxId: 33708]

Probab=86.16  E-value=1.5  Score=29.41  Aligned_cols=46  Identities=15%  Similarity=0.167  Sum_probs=33.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHh---hCCCCCCCHHHHHHHHHHH
Q 027236          116 LTLEQIREKEAQLVKEVKEMENKLAKL---RGGVTLVKPEDRMAVEEMF  161 (226)
Q Consensus       116 ~t~~el~~~i~~L~~e~~~l~~kL~~l---~~~~~~vs~ee~~~~~~~~  161 (226)
                      .|.+||.+++..|+-|++.|+.+|..-   ...+.+.||.+.+.+...|
T Consensus         2 ~t~EeLaaeL~rL~~ENk~LKkkl~~~~~~~~~d~~LT~~qke~~I~s~   50 (96)
T d2oa5a1           2 KTYEEMVKEVERLKLENKTLKQKVKSSGAVSSDDSILTAAKRESIIVSS   50 (96)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHHTC---------CCBCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCccCCHHHHHHHHHHH
Confidence            477999999999999999999998652   2345678998887666554

>d1j1ja_ a.118.16.1 (A:) Translin {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Translin
family: Translin
domain: Translin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.49  E-value=6.1  Score=29.96  Aligned_cols=119  Identities=12%  Similarity=0.153  Sum_probs=67.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHH
Q 027236           85 KEENAKLQEQLEEQRKAISKLEGEIRTLQSNLTLEQIREKEAQLVKEVKEMENKLAKLRGGVTLVKPEDRMAVEEMFLEK  164 (226)
Q Consensus        85 ~~~i~~l~~~l~~l~~~~k~l~~el~~l~~~~t~~el~~~i~~L~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~  164 (226)
                      +...+.+.+-...+....+....-|....+.++.......+.+....+..+.+.+..+..--+   ....-+....|...
T Consensus        18 ~d~RE~lik~sRdI~~~sk~~I~~Lhr~~~~~~~~~~~~~~~~~~~~l~~i~~~~~~l~~~~~---~~~~y~y~~~~~~~   94 (217)
T d1j1ja_          18 QDIREEIRKVVQSLEQTAREILTLLQGVHQGAGFQDIPKRCLKAREHFGTVKTHLTSLKTKFP---AEQYYRFHEHWRFV   94 (217)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHGGGGSSSSSTTHHHHHHHHHHHHHHHHHHHHHHHHTSC---GGGHHHHGGGTHHH
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHcc---cCcHHHHHhHhHHH
Confidence            333333444444444444444444444445566666666677777777777777766654321   12222223333333


Q ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCcccccccccchh
Q 027236          165 LSQWRKRKRMLRDIWDPIMENSPKNLKEFKEELGIEYDEDVGVSLQ  210 (226)
Q Consensus       165 ~~~w~kRkri~~~i~~~i~e~~~~~~k~l~e~lGie~Ded~~v~~~  210 (226)
                      ..+|..=    -.+..|+..+.-.+.+++.+.+|++.+.+.++.++
T Consensus        95 lQE~vEA----~~f~~~l~~~~l~s~eev~~~l~~~~~~~~~~~v~  136 (217)
T d1j1ja_          95 LQRLVFL----AAFVVYLETETLVTREAVTEILGIEPDREKGFHLD  136 (217)
T ss_dssp             HHHHHHH----HHHHHHHHHSSCCCHHHHHHHHTCCCSSSSSSCCC
T ss_pred             HHHHHHH----HHHHHHHhCCCCCCHHHHHHHhCCCCCccccCCCC
Confidence            3444332    34557777887678999999999998877665543

>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=81.94  E-value=1.5  Score=28.93  Aligned_cols=47  Identities=21%  Similarity=0.268  Sum_probs=39.1

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcce
Q 027236           10 AIVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISF   57 (226)
Q Consensus        10 ~~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~   57 (226)
                      ..|.+++.++..|=+..+|...+. .+++.++|-..|..|.+.|+|..
T Consensus        11 ~~Ive~y~~~g~Pv~s~~i~~~~~-l~~S~aTIRn~m~~LE~~G~l~~   57 (87)
T d1stza1          11 YCIVREYIENKKPVSSQRVLEVSN-IEFSSATIRNDMKKLEYLGYIYQ   57 (87)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHHSC-CCSCHHHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHHcCCccCHHHHHHHhC-CCCCHHHHHHHHHHHHHCCcccC
Confidence            345556677899999999999863 36789999999999999999865

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=81.87  E-value=1.3  Score=29.94  Aligned_cols=41  Identities=12%  Similarity=0.304  Sum_probs=33.5

Q ss_pred             CCcHHHHHHHHhccccc-HHHHHHHHHHHHHcCCcceeecCceeEEEe
Q 027236           22 PLNSQNVADALQKYNLK-KAGIQKALDSLADNGKISFKEYGKQKIYIA   68 (226)
Q Consensus        22 Pys~~di~~~l~~~~v~-K~~v~k~L~~Lv~~g~i~~K~~GK~kiY~~   68 (226)
                      |+|-+||.+.+   |++ ..+|.++|..|.++|+|.. ..|+  |+..
T Consensus        31 ~lTqeeLA~~l---G~s~ReTVsR~L~~L~~~GlI~~-~~~~--i~I~   72 (100)
T d2bgca1          31 NLTMQELGYSS---GIAHSSAVSRIISKLKQEKVIVY-KNSC--FYVQ   72 (100)
T ss_dssp             CCCHHHHHHHT---TCCCHHHHHHHHHHHHHTTSEEE-ETTE--EEES
T ss_pred             ccCHHHHHHHh---CCchHHHHHHHHHHHHHCCCEEE-cCCE--EEEe
Confidence            68999999877   785 8999999999999999985 3443  5555

>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=80.89  E-value=3.3  Score=27.38  Aligned_cols=54  Identities=15%  Similarity=0.266  Sum_probs=42.3

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHHhcccccHHHHHHHHHHHHHcCCcceeecCc---eeEEEe
Q 027236           11 IVLNYVNEQNRPLNSQNVADALQKYNLKKAGIQKALDSLADNGKISFKEYGK---QKIYIA   68 (226)
Q Consensus        11 ~Il~y~~~~nrPys~~di~~~l~~~~v~K~~v~k~L~~Lv~~g~i~~K~~GK---~kiY~~   68 (226)
                      .|+..+.  +.|....++...+.  ||+...+.+-|..|++.|+|.-..|..   ...|..
T Consensus        15 ~Il~~L~--~g~~rF~el~~~l~--gis~~~Ls~rLk~Le~~glv~r~~~~~~p~~veY~L   71 (95)
T d2hzta1          15 VILCHLT--HGKKRTSELKRLMP--NITQKMLTQQLRELEADGVINRIVYNQVPPKVEYEL   71 (95)
T ss_dssp             HHHHHHT--TCCBCHHHHHHHCT--TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             HHHHHHH--cCCCCHHHHHHHhh--cCChhHHHHHHHHHHHhHHHhheeccccccchhhhh
Confidence            4666764  45666668888775  899999999999999999999887753   355766