Psyllid ID: psy672

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310----
Protein Sequence
MPLWTEQEALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAEDEVEEEVEEDVVVNDGVGRNGAGAVIRRAFINEHFA
Secondary Structure (PSIPRED)
ccHHHHHHHccccHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHcccccccEEEEEccEEEEccccccccccccccccccEEEEEEEEcccccEEEEEccccccccHHHHHHccHHHHHccccccccEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHcccccccccHHHHHHHHHHHHHHHHHcccccccccccHHccccccccccccccccHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHHHHHccccHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccccccccEEEEEccEEEEEccccccccccccccccEEEEEEEEEccccEEEEEEEcccccccHHHHHHHcHHHHHHcccccccEEEEcccccccccEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MPLWTEQEALRFSKDVVLNIIFPLARnvletntmqgvkqppMTRLLAVIQFYATgnfqiftgdshgvsqptMCRLVKEVSKALAQAHVNYvkfpeqlaptKVAFqgignfpgvvgcvdcthvpiqlpsvengenfrnrkgtfslnvqviggpnleiwdvvsgwpgsvhdsriftnsrvchrfergevrgillgdsgyaqntflytpllnpttpqeqrynkahiktrNSVERLFGIWKRRFACLRRklanspvtCTHIVTACAVLHNIAVqtrqelpaedeveeeVEEDVvvndgvgrngagAVIRRAFINEHFA
Flexible Loop (DISEMBL)
MPLWTEQEALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEqrynkahiktrnsvERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQelpaedeveeeveedvvvndgvgrngagAVIRRAFINEHFA
Low Complexity Region (SEG)
MPLWTEQEALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELPaedeveeeveedvvvndgvgrngagavIRRAFINEHFA
Disordered region (IsUnstruct)
*******EALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPTT****RYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQ********************************************
Disordered Region (DISOPRED)
MPLWTEQEALRFSKDVVLNIIFPLARNVL**********PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAEDEVEEEVEEDV************AVIRRAFINEHFA
Disordered Region (DISEMBL)
MPLWTEQEALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTR***************DVVVNDGVGRNGAGAVIRRAFINEHFA
Disordered Region (DISPRO)
*PLWTEQEALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQE****************************VIRRAFINEHFA
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPLWTEQEALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAEDEVEEEVEEDVVVNDGVGRNGAGAVIRRAFINEHFA
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	314	2.2.26 [Sep-21-2011]
Q17QR8	349	Putative nuclease HARBI1	yes	N/A	0.850	0.765	0.361	3e-42
Q96MB7	349	Putative nuclease HARBI1	yes	N/A	0.850	0.765	0.361	3e-42
B0BN95	349	Putative nuclease HARBI1	yes	N/A	0.850	0.765	0.361	1e-41
Q8BR93	349	Putative nuclease HARBI1	yes	N/A	0.729	0.656	0.388	2e-40
Q6AZB8	349	Putative nuclease HARBI1	no	N/A	0.958	0.862	0.321	5e-40
Q5U538	347	Putative nuclease HARBI1	N/A	N/A	0.863	0.780	0.319	5e-32

>sp|Q17QR8|HARB1_BOVIN Putative nuclease HARBI1 OS=Bos taurus GN=HARBI1 PE=2 SV=1

 Score =  172 bits (436), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 104/288 (36%), Positives = 150/288 (52%), Gaps = 21/288 (7%)

Query: 41  PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
           P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    ++ FP   A  
Sbjct: 69  PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPADEASV 128

Query: 101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
              K  F G+   PGV+G VDC HV I+ P+ E+  ++ NRKG  SLN  ++      + 
Sbjct: 129 QALKDEFYGLAGIPGVIGVVDCMHVAIKAPNAED-LSYVNRKGLHSLNCLMVCDIRGALM 187

Query: 158 DVVSGWPGSVHDSRIFTNSRVCHRFERG-EVRGILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
            V + WPGS+ D  +   S +  +FE G      LLGDS +   T+L TPL  P TP E 
Sbjct: 188 TVETSWPGSLQDCVVLQQSSLSSQFEAGMHKESWLLGDSSFFLRTWLMTPLHIPETPAEY 247

Query: 217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQTRQ 273
           RYN AH  T + +E+ F     RF CL   +  L  SP   +HI+ AC VLHNI+++   
Sbjct: 248 RYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKSSHIILACCVLHNISLEHGM 307

Query: 274 EL-------PAEDEVEEEVEEDVVVNDGVGRNGAGAVIRRAFINEHFA 314
           ++       P E   EEE E    ++    R      IR+  +  HF+
Sbjct: 308 DVWSSPVTGPVEQPPEEEYEHMESLDLEADR------IRQELMLTHFS 349

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.
Bos taurus (taxid: 9913)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp|Q96MB7|HARB1_HUMAN Putative nuclease HARBI1 OS=Homo sapiens GN=HARBI1 PE=1 SV=1

 Score =  172 bits (436), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 104/288 (36%), Positives = 152/288 (52%), Gaps = 21/288 (7%)

Query: 41  PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
           P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    +++FP   A  
Sbjct: 69  PETQVLAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIRFPADEASI 128

Query: 101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
              K  F G+   PGV+G VDC HV I+ P+ E+  ++ NRKG  SLN  ++      + 
Sbjct: 129 QALKDEFYGLAGMPGVMGVVDCIHVAIKAPNAED-LSYVNRKGLHSLNCLMVCDIRGTLM 187

Query: 158 DVVSGWPGSVHDSRIFTNSRVCHRFERGEVR-GILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
            V + WPGS+ D  +   S +  +FE G  +   LLGDS +   T+L TPL  P TP E 
Sbjct: 188 TVETNWPGSLQDCAVLQQSSLSSQFEAGMHKDSWLLGDSSFFLRTWLMTPLHIPETPAEY 247

Query: 217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQTRQ 273
           RYN AH  T + +E+ F     RF CL   +  L  SP   +HI+ AC VLHNI+++   
Sbjct: 248 RYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKSSHIILACCVLHNISLEHGM 307

Query: 274 EL-------PAEDEVEEEVEEDVVVNDGVGRNGAGAVIRRAFINEHFA 314
           ++       P E   EEE E    ++    R      IR+  +  HF+
Sbjct: 308 DVWSSPMTGPMEQPPEEEYEHMESLDLEADR------IRQELMLTHFS 349

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B0BN95|HARB1_RAT Putative nuclease HARBI1 OS=Rattus norvegicus GN=Harbi1 PE=2 SV=1

 Score =  170 bits (431), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 104/288 (36%), Positives = 152/288 (52%), Gaps = 21/288 (7%)

Query: 41  PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
           P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    ++ FP   A  
Sbjct: 69  PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPADEAAI 128

Query: 101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
              K  F G+   PGV+G VDC HV I+ P+ E+  ++ NRKG  SLN  V+      + 
Sbjct: 129 QSLKDEFYGLAGMPGVIGAVDCIHVAIKAPNAED-LSYVNRKGLHSLNCLVVCDIRGALM 187

Query: 158 DVVSGWPGSVHDSRIFTNSRVCHRFERGEVR-GILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
            V + WPGS+ D  +   S +  +FE G  +   LLGDS +  +T+L TPL  P TP E 
Sbjct: 188 TVETSWPGSLQDCAVLQQSSLSSQFETGMPKDSWLLGDSSFFLHTWLLTPLHIPETPAEY 247

Query: 217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQTRQ 273
           RYN+AH  T + +E+       RF CL   +  L  SP   +HI+ AC VLHNI+++   
Sbjct: 248 RYNRAHSATHSVIEKTLRTLCCRFRCLDGSKGALQYSPEKSSHIILACCVLHNISLEHGM 307

Query: 274 EL-------PAEDEVEEEVEEDVVVNDGVGRNGAGAVIRRAFINEHFA 314
           ++       P E   E E E+   ++    R      IR+  I  HF+
Sbjct: 308 DVWSSPVTGPIEQPPEGEDEQMESLDLEADR------IRQELILTHFS 349

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q8BR93|HARB1_MOUSE Putative nuclease HARBI1 OS=Mus musculus GN=Harbi1 PE=2 SV=1

 Score =  166 bits (421), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 92/237 (38%), Positives = 131/237 (55%), Gaps = 8/237 (3%)

Query: 41  PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
           P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    ++ FP   A  
Sbjct: 69  PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPVDEAAV 128

Query: 101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
              K  F G+   PGV+G  DC HV I+ P+ E+  ++ NRKG  SLN  V+      + 
Sbjct: 129 QSLKDEFYGLAGMPGVIGVADCIHVAIKAPNAED-LSYVNRKGLHSLNCLVVCDIRGALM 187

Query: 158 DVVSGWPGSVHDSRIFTNSRVCHRFERGEVR-GILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
            V + WPGS+ D  +   S +  +FE G  +   LLGDS +   ++L TPL  P T  E 
Sbjct: 188 TVETSWPGSLQDCAVLQRSSLTSQFETGMPKDSWLLGDSSFFLRSWLLTPLPIPETAAEY 247

Query: 217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQ 270
           RYN+AH  T + +ER       RF CL   +  L  SP  C+HI+ AC VLHNI++ 
Sbjct: 248 RYNRAHSATHSVIERTLQTLCCRFRCLDGSKGALQYSPEKCSHIILACCVLHNISLD 304

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q6AZB8|HARB1_DANRE Putative nuclease HARBI1 OS=Danio rerio GN=harbi1 PE=2 SV=1

 Score =  165 bits (417), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 103/320 (32%), Positives = 157/320 (49%), Gaps = 19/320 (5%)

Query: 13  SKDVVLNII-FP---------LARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTG 62
           S D +LN   FP         L ++ L   T +     P  ++LA + FY +G+FQ   G
Sbjct: 31  SDDFLLNTFGFPREFIYYLVELLKDSLLRRTQRSRAISPDVQILAALGFYTSGSFQSKMG 90

Query: 63  DSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT---KVAFQGIGNFPGVVGCVDC 119
           D+ G+SQ +M R V  V+KAL +    ++ F    A     K  F  I   P V G VDC
Sbjct: 91  DAIGISQASMSRCVSNVTKALIEKAPEFIGFTRDEATKQQFKDEFYRIAGIPNVTGVVDC 150

Query: 120 THVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVC 179
            H+ I+ P+ ++  ++ N+KG  S+N Q++      +    + WPGS+ D  +F  S V 
Sbjct: 151 AHIAIKAPNADDS-SYVNKKGFHSINCQLVCDARGLLLSAETHWPGSLTDRAVFKQSNVA 209

Query: 180 HRFERGE--VRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWK 237
             FE  E    G LLGD+ Y    +L TP+ +P +P + RYN AH  T   V+R F   +
Sbjct: 210 KLFEEQENDDEGWLLGDNRYPLKKWLMTPVQSPESPADYRYNLAHTTTHEIVDRTFRAIQ 269

Query: 238 RRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAEDEVEEEVEEDVVVNDG 294
            RF CL   +  L  SP  C+HI+ AC VLHNI++Q+  +    +  E   +    ++  
Sbjct: 270 TRFRCLDGAKGYLQYSPEKCSHIIQACCVLHNISLQSGLDAWTFERTEATDQSGEDIDPS 329

Query: 295 VGRNGAGAVIRRAFINEHFA 314
              +     +R+  I  HF+
Sbjct: 330 DTDDPEALRVRQELIQNHFS 349

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q5U538|HARB1_XENLA Putative nuclease HARBI1 OS=Xenopus laevis GN=harbi1 PE=2 SV=1

 Score =  138 bits (348), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 90/282 (31%), Positives = 143/282 (50%), Gaps = 11/282 (3%)

Query: 41  PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQ---L 97
           P T+++A + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    ++ FP     +
Sbjct: 69  PETQIMAALGFYTSGSFQTRMGDTIGISQASMSRCVTNVTEALVERASQFISFPRDERSV 128

Query: 98  APTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
              K  F  +   PGV+G VDCT V I+ P+ E+  ++ N +G  SLN  ++      + 
Sbjct: 129 QGLKDEFYNLAGVPGVLGVVDCTQVNIKAPNSED-LSYVNSRGLHSLNCLLVCDARGSLL 187

Query: 158 DVVSGWPGSVHDSRIFTNSRVCHRFE-RGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
              +   GS+ D+ +   S +   FE +   +G LL D+ +    +L TP+  P +P + 
Sbjct: 188 WAETSRLGSMQDNAVLHQSELSGLFETKMHKQGWLLADNAFILRPWLMTPVQIPESPSDY 247

Query: 217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQTRQ 273
           RYN AH  T + +ER     + RF CL   R  L  SP     IV AC +LHNIA+Q   
Sbjct: 248 RYNMAHTATHSVMERTQRSLRLRFRCLDGSRATLQYSPEKSAQIVLACCILHNIALQHDL 307

Query: 274 ELPAEDEVEE-EVEEDVVVNDGVGRNGAGAVIRRAFINEHFA 314
           ++ +E      E EE+ V  + +        +R+  I  HF+
Sbjct: 308 DIVSESGATSLEPEEECVHMEPL--ESEAYRMRQELILTHFS 347

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

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	314
332374146	353	unknown [Dendroctonus ponderosae]	0.971	0.864	0.406	2e-64
328704555	370	PREDICTED: putative nuclease HARBI1-like	0.942	0.8	0.436	6e-60
328705831	326	PREDICTED: putative nuclease HARBI1-like	0.872	0.840	0.452	1e-59
328711563	335	PREDICTED: putative nuclease HARBI1-like	0.866	0.811	0.444	9e-59
270012680	358	hypothetical protein TcasGA2_TC015989 [T	0.955	0.837	0.424	5e-58
328697485	681	PREDICTED: hypothetical protein LOC10057	0.885	0.408	0.405	5e-56
328696997	356	PREDICTED: putative nuclease HARBI1-like	0.977	0.862	0.387	1e-54
326320058	369	nuclease HARBI1-like [Acyrthosiphon pisu	0.888	0.756	0.405	8e-54
328700311	287	PREDICTED: putative nuclease HARBI1-like	0.859	0.940	0.414	8e-54
270015185	561	hypothetical protein TcasGA2_TC000011 [T	0.968	0.541	0.387	3e-52

>gi|332374146|gb|AEE62214.1| unknown [Dendroctonus ponderosae]

 Score =  251 bits (642), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 126/310 (40%), Positives = 189/310 (60%), Gaps = 5/310 (1%)

Query: 7   QEALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG 66
           ++  RFSK++V N++ PL  +  E  T +G+  P +  LL  +QFY +G+ +I  G+  G
Sbjct: 45  RKRFRFSKEIVQNVLLPLVGHQREQITNRGLPVPLIIGLLLTLQFYGSGSLRIICGELKG 104

Query: 67  VSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQL 126
             Q T+ R++ +V++++ +   NY+KFPE L   +  FQ I NFP V+GC+ C  +PI  
Sbjct: 105 FHQSTVSRVITKVTRSIYEQSRNYIKFPENLNTVQTQFQTIRNFPNVIGCIGCAQIPIMS 164

Query: 127 PSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGE 186
           P   N E FRN K +FSLNVQ++ GP+LEI+D+V+  PGS  +  +F  S V  RFE+ +
Sbjct: 165 PGGPNAELFRNGKRSFSLNVQIVAGPDLEIYDIVATNPGSYRNDHVFNKSAVKTRFEKKQ 224

Query: 187 VRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRK 246
           + G LLGDSGY   T+L TP  +P T +E+RYN+AH + RN V+R FG+ + RF+CLRR 
Sbjct: 225 LPGYLLGDSGYPSLTYLLTPFRDPCTNEEKRYNEAHAQIRNIVDRTFGVLRHRFSCLRRL 284

Query: 247 LANSPVTCTHIVTACAVLHNIAVQTRQ--ELPAEDEVEEEVEEDVVVNDGVGRNGAGAVI 304
           L +   T   I+ ACAVLHNI++  R+  E   ED VE+              + +G ++
Sbjct: 285 LRHKHETICCIIVACAVLHNISIAHREVVEPDGEDGVEDLAAAASDA---TTDSQSGQLV 341

Query: 305 RRAFINEHFA 314
           R   +  HF+
Sbjct: 342 RATILRNHFS 351

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328704555|ref|XP_001947392.2| PREDICTED: putative nuclease HARBI1-like [Acyrthosiphon pisum]

 Score =  237 bits (604), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 135/309 (43%), Positives = 180/309 (58%), Gaps = 13/309 (4%)

Query: 15  DVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCR 74
           D VLN I     + L+ +T +     PMT+LL  ++FYATGNF I  GD  G+S  +  +
Sbjct: 64  DKVLNEI----DDQLKYSTDRNNSIAPMTQLLITLRFYATGNFLITVGDFGGISVASAGK 119

Query: 75  LVKEVSKALAQAHVNYVKFPE---QLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVEN 131
           +VK VS ALA     Y++ PE   +    KV F G+  FP V+G +DCTH+ +Q PS E 
Sbjct: 120 IVKRVSYALAFLSSRYIRLPETPEEKMELKVQFYGLARFPKVIGAIDCTHIKLQCPSKEY 179

Query: 132 GENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRG-I 190
           GE +RNRKG FSLNVQ +   NLE  DVV  WPGS HDS IF NSR+  R E  E    I
Sbjct: 180 GELYRNRKGYFSLNVQALVNANLEFMDVVVRWPGSAHDSNIFANSRLKARIELPEFSDCI 239

Query: 191 LLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANS 250
           +LGDSGYA + +L TPL + TT  E+ YN++ I+TRN VER FG+WKRRF  L   L   
Sbjct: 240 ILGDSGYALSHYLLTPLAHTTTNAERLYNESQIRTRNVVERSFGVWKRRFPVLFFGLRLK 299

Query: 251 PVTCTHIVTACAVLHNIAVQTRQELPAED--EVEEEVEEDVVVNDGVGR---NGAGAVIR 305
             T   ++ ACAVLHN+A       P +D   +++ +  ++   +   +   N     +R
Sbjct: 300 METTMAVIQACAVLHNMARLQNDPQPPDDIENIKQLLSAEISEIEAATQPQINSPAQALR 359

Query: 306 RAFINEHFA 314
            A I EHF+
Sbjct: 360 TALIMEHFS 368

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328705831|ref|XP_003242919.1| PREDICTED: putative nuclease HARBI1-like [Acyrthosiphon pisum]

 Score =  236 bits (602), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 128/283 (45%), Positives = 169/283 (59%), Gaps = 9/283 (3%)

Query: 41  PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPE---QL 97
           PMT+LL  ++FYATGNF I  GD  G+S  +  ++VK VS ALA     Y++ PE   + 
Sbjct: 42  PMTQLLITLRFYATGNFLITVGDFGGISVASAGKIVKRVSYALAFLSSRYIRLPETPEEK 101

Query: 98  APTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
              KV F G+  FP V+G +DCTH+ +Q PS E GE +RNRKG FSLNVQ +   NLE  
Sbjct: 102 MELKVQFYGLARFPKVIGAIDCTHIKLQCPSKEYGELYRNRKGYFSLNVQALVNANLEFM 161

Query: 158 DVVSGWPGSVHDSRIFTNSRVCHRFERGEVRG-ILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
           DVV  WPGS HDS IF NSR+  R E  E    I+LGDSGYA + +L TPL   TT  E+
Sbjct: 162 DVVVRWPGSAHDSNIFANSRLKARIELPEFSDCIILGDSGYALSHYLLTPLARTTTNAER 221

Query: 217 RYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELP 276
            YN++ I+TRN VER FG+WKRRF  L   L     T   ++ ACAVLHN+A       P
Sbjct: 222 LYNESQIRTRNVVERSFGVWKRRFPVLFFGLRLKMETTMAVIQACAVLHNMARLQNDPQP 281

Query: 277 AEDE--VEEEVEEDVVVNDGVGR---NGAGAVIRRAFINEHFA 314
            +D+  +++ +  ++   +   +   N     +R A I EHF+
Sbjct: 282 PDDKENIKQLLSAEISEIEAATQPQINSPAQALRTALIMEHFS 324

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328711563|ref|XP_003244572.1| PREDICTED: putative nuclease HARBI1-like [Acyrthosiphon pisum]

 Score =  233 bits (594), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 125/281 (44%), Positives = 166/281 (59%), Gaps = 9/281 (3%)

Query: 41  PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPE---QL 97
           PMT+LL  ++F+ATGNF I  GD  GVS     ++VK VS  LA     Y+K P+   ++
Sbjct: 53  PMTQLLLTLRFFATGNFLITAGDFSGVSVAAAGQIVKRVSYVLATKSDKYIKMPKTTAEI 112

Query: 98  APTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
              KV F G+  F  V+G +DCTH+ +Q PS E GE +RNR G FSLN+Q +   NLE  
Sbjct: 113 MELKVKFYGLARFLKVIGAIDCTHIKLQSPSREYGEQYRNRNGYFSLNLQALVNANLEFL 172

Query: 158 DVVSGWPGSVHDSRIFTNSRVCHRFERGEVRG-ILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
           DVV+ WPGS HDS +F NSR+  R E  E +  ++LGD GYA + +L TP+ NPTT  E+
Sbjct: 173 DVVARWPGSAHDSNVFANSRLRARMELHEFKDCVILGDPGYALSHYLLTPIANPTTKAER 232

Query: 217 RYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELP 276
            YN++ I+TRN VER FG+WKRRF  L   L     T   ++ +CA+LHNIA       P
Sbjct: 233 LYNESQIRTRNVVERTFGVWKRRFPVLFFGLRLKMETSMAVIQSCAILHNIARLANDPQP 292

Query: 277 AEDEVEEEVE----EDVVVNDGVGRNGAGAVIRRAFINEHF 313
             DEVE   +    E + + D +        +R A I EHF
Sbjct: 293 P-DEVENITDLLTNELMDIEDVIQPEHNNCGLRNALIAEHF 332

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270012680|gb|EFA09128.1| hypothetical protein TcasGA2_TC015989 [Tribolium castaneum]

 Score =  230 bits (587), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 132/311 (42%), Positives = 180/311 (57%), Gaps = 11/311 (3%)

Query: 10  LRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQ 69
            RFSK  +L  +  L  + LE  T +      + ++L  +++ ATG+FQ   GD+  V +
Sbjct: 51  FRFSKATIL-WLHELIGHDLEPTTRRRKSISAINKILITMRYLATGSFQQLVGDTVAVHK 109

Query: 70  PTMCRLVKEVSKALAQAHVNYVKFP--EQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLP 127
            T+C ++K V + +AQ    ++K P  E+L   ++ F      P V+G +DC+HV I+ P
Sbjct: 110 STVCVVIKSVIQKIAQLKPQFIKMPNREELHNVQLKFYRKRRMPRVIGAIDCSHVRIESP 169

Query: 128 SVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEV 187
              N E FRNRKG FS+NVQ +   +L+I ++V+ WPGSVHDS IF +S +C   ERGE 
Sbjct: 170 GGPNAEIFRNRKGFFSINVQAVCDADLQIRNIVARWPGSVHDSTIFNDSSLCAHLERGEY 229

Query: 188 R-GILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRK 246
             G LLGDSGYA   FL TP+LNP T  E+ YN +H  TRN++ER FG+ KRRF CL   
Sbjct: 230 ENGFLLGDSGYACRPFLLTPVLNPRTAAEEAYNLSHRTTRNAIERCFGVLKRRFPCLSLG 289

Query: 247 LANSPVTCTHIVTACAVLHNIAVQTRQELPAED---EVEEEVE-EDVVVNDGVGRNGAGA 302
           L     T    + ACAVLHNIA+ T    P  D   EV +E+E E V  N+ +  N A  
Sbjct: 290 LRTKMNTTLATIVACAVLHNIAIFTNDNEPPRDPDVEVPQELEIEPVHRNNNINENTAA- 348

Query: 303 VIRRAFINEHF 313
             R A I  HF
Sbjct: 349 --RTALIRTHF 357

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328697485|ref|XP_003240353.1| PREDICTED: hypothetical protein LOC100574226 [Acyrthosiphon pisum]

 Score =  224 bits (570), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 116/286 (40%), Positives = 170/286 (59%), Gaps = 8/286 (2%)

Query: 1   MPLWTEQE---ALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNF 57
           + +W + E     R  K  V  ++F +  + L++ T +     P+T+LL  ++FYA G  
Sbjct: 35  LEMWDDDEFFMRFRLKKTTVKELLFKIEFH-LKSKTNRNRAILPITKLLLTLRFYALGTI 93

Query: 58  QIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQ---LAPTKVAFQGIGNFPGVV 114
            +  GD  GVS+ + C +V+ V++A+A     Y+K PE    +  T++ F  I  FP ++
Sbjct: 94  LLANGDFVGVSKTSACNIVRTVTEAIASLRPLYIKMPEHHCNIQETRLKFYNIARFPRII 153

Query: 115 GCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFT 174
           G +DCTHV +Q P     E +RNRKG FSLNVQV+GG +LEI D+V+ WPGS HD  IF 
Sbjct: 154 GAIDCTHVKLQSPGGNIAEVYRNRKGYFSLNVQVVGGRSLEILDIVARWPGSTHDQVIFN 213

Query: 175 NSRVCHRFERGEV-RGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLF 233
           NS +  +FE  E+   ILLGD GY    ++  PL++P T  E  YN++ I+TRN++ERLF
Sbjct: 214 NSTIHFKFETNEMGDNILLGDGGYECRPYILVPLISPNTNAELLYNESQIRTRNTIERLF 273

Query: 234 GIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAED 279
           G+WKRRF  L   +  +P     I+ A AVLHN+A    + +P  D
Sbjct: 274 GVWKRRFPILSLGIRTTPDRAQAIIVATAVLHNLASVLGESIPPID 319

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328696997|ref|XP_003240200.1| PREDICTED: putative nuclease HARBI1-like [Acyrthosiphon pisum]

 Score =  219 bits (558), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 124/320 (38%), Positives = 181/320 (56%), Gaps = 13/320 (4%)

Query: 4   WTEQE---ALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIF 60
           W E +     R SK+ VL +I  L    + +NT +        +LL  ++FYATG+F I 
Sbjct: 39  WDEHDFKTRFRLSKETVL-MILDLIGPSISSNTDRNNAVTTTQKLLLALRFYATGSFLIS 97

Query: 61  TGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPE---QLAPTKVAFQGIGNFPGVVGCV 117
            GD  GVS+ T C +V++VS ALAQ    ++K PE   ++   +  F GI  FP V+G +
Sbjct: 98  AGDVVGVSKSTACVIVRDVSVALAQLRPQFIKMPETNDEIKELQKQFYGIAKFPLVIGAI 157

Query: 118 DCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSR 177
           DCTH+ IQ P   N E FRNRKG FSLNVQ +    L+I D+V  WPGS HDS IF+ S+
Sbjct: 158 DCTHIKIQSPGGPNAEYFRNRKGWFSLNVQTVVSAKLKIMDIVVRWPGSTHDSTIFSRSK 217

Query: 178 VCHRF--ERGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGI 235
           + +    E+     +++ DSGYA    + TP LNP    E  YN++ I+TRN VER +G+
Sbjct: 218 INNDLHVEQKWGNSLIVADSGYANTKHIVTPFLNPQAGPENLYNESQIRTRNPVERCYGV 277

Query: 236 WKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAED-EVEEEVEEDVVVNDG 294
            KRRF  L   +        +++ AC+VLHNIA+     +P +D ++ +E+ E  ++N+ 
Sbjct: 278 LKRRFPVLSLGMRLQISNIQNVIIACSVLHNIAIDCNDVMPMDDVQLPDELTE--LINEP 335

Query: 295 VGRNGAGAVIRRAFINEHFA 314
              N      R   +NE+F+
Sbjct: 336 TIENRQNNA-RTRLVNEYFS 354

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|326320058|ref|NP_001191896.1| nuclease HARBI1-like [Acyrthosiphon pisum] gi|239790602|dbj|BAH71852.1| ACYPI004890 [Acyrthosiphon pisum]

 Score =  216 bits (551), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 120/296 (40%), Positives = 165/296 (55%), Gaps = 17/296 (5%)

Query: 32  NTMQGVKQ----PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87
           NT+   K+     PM +LL  ++FYATGNF I  G+  G+S+P+ CR+V++V+ ALA+  
Sbjct: 68  NTLSTAKRMTSITPMQKLLVALRFYATGNFLITAGELVGISEPSACRIVQQVTHALAELR 127

Query: 88  VNYVKFP---EQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSL 144
            +YVK P   E++      F  I   P V+G +DCTH+ I  P  EN E FRNRKG FS+
Sbjct: 128 PDYVKMPQNVEEIRQVSYHFYKIAKMPRVIGAIDCTHIRIHSPGGENAEYFRNRKGYFSM 187

Query: 145 NVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEV-RGILLGDSGYAQNTFL 203
           NVQ +   NL+I D+V  WPGSVHD  IF NS++    E G     +L+ DSGYA +  +
Sbjct: 188 NVQTVADANLQILDIVVRWPGSVHDQTIFLNSKLKTDLENGRFGNNLLVADSGYANSQHV 247

Query: 204 YTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAV 263
            TPLL      E+ YN++ I+TRN VER +G+WKRRF  L         T    + ACAV
Sbjct: 248 ITPLLQTNNRVEELYNESLIRTRNVVERQYGVWKRRFPILSFGFRIKLETTMAAIVACAV 307

Query: 264 LHNIAVQTRQELPAEDEVEEEVEEDVVVNDGVGRNGAGAVIRRAF------INEHF 313
           L NI      E P +D    E    +VV +   +    A I + F      +N++F
Sbjct: 308 LFNITRSLDGEEPPDD---HEARNFIVVQEAPSQTPVHANINQQFTARNRLLNDYF 360

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328700311|ref|XP_003241214.1| PREDICTED: putative nuclease HARBI1-like [Acyrthosiphon pisum]

 Score =  216 bits (551), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 118/285 (41%), Positives = 160/285 (56%), Gaps = 15/285 (5%)

Query: 41  PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFP-EQLAP 99
           P+ ++L  ++FYA G   I   D  GVS  +  R +K VS A+A     ++K P   L  
Sbjct: 5   PINQVLLTLRFYALGTMLISVADMFGVSVSSASRTIKNVSYAIAGFSGLFLKIPTNDLVE 64

Query: 100 TKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDV 159
           TK+    I  FP V G +DCTHV IQ P  E  E+FRNRKG FSLNVQ +   +L+  D+
Sbjct: 65  TKMKMFKIARFPLVFGAIDCTHVRIQSPGGEFAESFRNRKGYFSLNVQALVNSDLKFMDI 124

Query: 160 VSGWPGSVHDSRIFTNSRVCHRFERGEV-RGILLGDSGYAQNTFLYTPLLNPTTPQEQRY 218
           V+ WPGS HDS IF NSR+  R E GE     +LGDSGYA   ++ TP+LNP    E  Y
Sbjct: 125 VAIWPGSAHDSNIFRNSRLYARLESGEFNNNAILGDSGYALKPYMLTPILNPVGRIEMLY 184

Query: 219 NKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAE 278
           N++ I+TRN +ER FG+WKRRF  L   +     T   I+ A A+LHNI     ++LP +
Sbjct: 185 NESQIRTRNIIERCFGVWKRRFPVLSLGMRLQLKTVQAIIVATAILHNICRDMNEDLPED 244

Query: 279 ---------DEVEEEVEEDVVVNDGVGRNGAGAVIRRAFINEHFA 314
                    +E E+  E D   +D    NG  ++ R + +N +FA
Sbjct: 245 SSDDVLHQLNEAEDMTETDHRHDD----NGEDSITRNSLLNNYFA 285

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270015185|gb|EFA11633.1| hypothetical protein TcasGA2_TC000011 [Tribolium castaneum]

 Score =  211 bits (538), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 121/312 (38%), Positives = 173/312 (55%), Gaps = 8/312 (2%)

Query: 7   QEALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG 66
           ++  R +K  V++++  +   V    T +       T++L  ++FYATG F    GD   
Sbjct: 253 KKRFRLNKATVMHLVDIIGDRV-APKTQRNKSLSAQTQMLIALRFYATGGFLELLGDWIH 311

Query: 67  VSQPTMCRLVKEVSKALAQAHVNYVKFP---EQLAPTKVAFQGIGNFPGVVGCVDCTHVP 123
           V +  +CR+++ V+  +A+   +Y+K P   E+L  TK  F  I  FP VVG +DCTHV 
Sbjct: 312 VHKSNICRVIQRVTHEIARLSPHYIKMPRTAEELMATKRKFFRICGFPRVVGAIDCTHVG 371

Query: 124 IQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFE 183
           IQ P   N E +RNRKG FS+NVQ I   +L++  ++S WPGSVHDS IF NS +   F 
Sbjct: 372 IQSPGGANAELYRNRKGYFSINVQTICDADLKLLHIISRWPGSVHDSTIFNNSPLPVDFR 431

Query: 184 RGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACL 243
            G  RG LLGD GY    +L  P+ NP    ++ YN+A+IKTRN++ER FGI KRRF  L
Sbjct: 432 LG--RGYLLGDGGYPCQQYLLIPVRNPNNASQEAYNRAYIKTRNTIERFFGILKRRFPLL 489

Query: 244 RRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAE-DEVEEEVEEDVVVNDGVGRNGAGA 302
           +  L     T   ++ AC VL+NI  +    +    DEV E  EED +  +    N    
Sbjct: 490 KSGLRLKIDTIVQVIVACGVLYNICKERNDHIEEYFDEVMENDEEDFIYQEN-NINNVNF 548

Query: 303 VIRRAFINEHFA 314
            +R + I+  FA
Sbjct: 549 AVRNSLIDTIFA 560

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

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	314
UNIPROTKB|E1BQ99	348	HARBI1 "Uncharacterized protei	0.729	0.658	0.400	6.8e-40
UNIPROTKB|F1SIA2	349	HARBI1 "Uncharacterized protei	0.729	0.656	0.392	8.7e-40
UNIPROTKB|Q96MB7	349	HARBI1 "Putative nuclease HARB	0.818	0.736	0.368	2.9e-39
UNIPROTKB|E2RCW9	349	HARBI1 "Uncharacterized protei	0.729	0.656	0.392	6.1e-39
RGD|1584007	349	Harbi1 "harbinger transposase	0.729	0.656	0.392	6.1e-39
UNIPROTKB|Q17QR8	349	HARBI1 "Putative nuclease HARB	0.729	0.656	0.392	7.8e-39
MGI|MGI:2443194	349	Harbi1 "harbinger transposase	0.726	0.653	0.389	3.4e-38
ZFIN|ZDB-GENE-040608-1	349	harbi1 "harbinger transposase	0.821	0.739	0.347	1.9e-37
TAIR|locus:2143104	502	AT5G12010 [Arabidopsis thalian	0.850	0.531	0.267	6.8e-20
TAIR|locus:2123874	540	AT4G29780 "AT4G29780" [Arabido	0.843	0.490	0.277	7.8e-19

UNIPROTKB|E1BQ99 HARBI1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 425 (154.7 bits), Expect = 6.8e-40, P = 6.8e-40
 Identities = 95/237 (40%), Positives = 134/237 (56%)

Query:    41 PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
             P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    ++ FPE  A  
Sbjct:    69 PETQVLAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERAPQFIHFPEDEAAV 128

Query:   101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
                K  F  +   PGV+G VDCTHV I+ P+ E+  ++ NRKG  SLN  ++      + 
Sbjct:   129 QSLKDDFYALAGMPGVLGVVDCTHVAIKAPNAED-LSYVNRKGLHSLNCLMVCDARGALL 187

Query:   158 DVVSGWPGSVHDSRIFTNSRVCHRFERGEVR-GILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
                + WPGS+ D  +   + +  +FE    + G LLGDS +   T+L TPL  P TP E 
Sbjct:   188 SAETHWPGSMPDCNVLQQAALTSQFENELYKDGWLLGDSSFFLRTWLMTPLHIPETPAEY 247

Query:   217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQ 270
             RYN AH  T N +ER F   + RF CL   +  L  SP   +HI+ AC VLHNI++Q
Sbjct:   248 RYNMAHSATHNVIERTFRTIRSRFRCLDGSKGTLQYSPEKSSHIILACCVLHNISLQ 304

GO:0005737 "cytoplasm" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

UNIPROTKB|F1SIA2 HARBI1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 424 (154.3 bits), Expect = 8.7e-40, P = 8.7e-40
 Identities = 93/237 (39%), Positives = 134/237 (56%)

Query:    41 PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
             P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    +++FP   A  
Sbjct:    69 PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVTNVTEALVERASQFIRFPADEASV 128

Query:   101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
                K  F G+   PGV+G VDC HV I+ P+ E+  ++ NRKG  SLN  ++      + 
Sbjct:   129 QALKDEFYGLAGMPGVIGVVDCIHVAIKAPNAED-LSYVNRKGLHSLNCLMVCDIRGTLM 187

Query:   158 DVVSGWPGSVHDSRIFTNSRVCHRFERG-EVRGILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
              V + WPGS+ D  +   S +  +FE G      LLGDS +   ++L TPL  P TP E 
Sbjct:   188 TVETNWPGSLQDCVVLQQSSLSSQFEAGMHKESWLLGDSSFFLRSWLMTPLHIPETPAEY 247

Query:   217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQ 270
             RYN AH  T + +E+ F     RF CL   +  L  SP  C+HI+ AC VLHNI+++
Sbjct:   248 RYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKCSHIILACCVLHNISLE 304

GO:0005813 "centrosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|Q96MB7 HARBI1 "Putative nuclease HARBI1" [Homo sapiens (taxid:9606)]

 Score = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 98/266 (36%), Positives = 144/266 (54%)

Query:    12 FSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPT 71
             F +  +  ++  L  N L   T +     P T++LA + FY +G+FQ   GD+ G+SQ +
Sbjct:    41 FPRQFIYYLVELLGAN-LSRPTQRSRAISPETQVLAALGFYTSGSFQTRMGDAIGISQAS 99

Query:    72 MCRLVKEVSKALAQAHVNYVKFPEQLAPT---KVAFQGIGNFPGVVGCVDCTHVPIQLPS 128
             M R V  V++AL +    +++FP   A     K  F G+   PGV+G VDC HV I+ P+
Sbjct:   100 MSRCVANVTEALVERASQFIRFPADEASIQALKDEFYGLAGMPGVMGVVDCIHVAIKAPN 159

Query:   129 VENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVR 188
              E+  ++ NRKG  SLN  ++      +  V + WPGS+ D  +   S +  +FE G  +
Sbjct:   160 AED-LSYVNRKGLHSLNCLMVCDIRGTLMTVETNWPGSLQDCAVLQQSSLSSQFEAGMHK 218

Query:   189 GI-LLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACL---R 244
                LLGDS +   T+L TPL  P TP E RYN AH  T + +E+ F     RF CL   +
Sbjct:   219 DSWLLGDSSFFLRTWLMTPLHIPETPAEYRYNMAHSATHSVIEKTFRTLCSRFRCLDGSK 278

Query:   245 RKLANSPVTCTHIVTACAVLHNIAVQ 270
               L  SP   +HI+ AC VLHNI+++
Sbjct:   279 GALQYSPEKSSHIILACCVLHNISLE 304

GO:0004518 "nuclease activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005813 "centrosome" evidence=IDA

UNIPROTKB|E2RCW9 HARBI1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 93/237 (39%), Positives = 133/237 (56%)

Query:    41 PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
             P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    +++FP   A  
Sbjct:    69 PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERATQFIRFPADEASM 128

Query:   101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
                K  F G+   PGV+G VDC HV I+ P+ E+  ++ NRKG  SLN  ++      + 
Sbjct:   129 QALKDEFYGLAGMPGVIGVVDCIHVAIKAPNAED-LSYVNRKGLHSLNCLMVCDIRGALM 187

Query:   158 DVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGI-LLGDSGYAQNTFLYTPLLNPTTPQEQ 216
              V + WPGS+ D  +   S +   FE G  +   LLGDS +   T+L TPL  P TP E 
Sbjct:   188 TVETNWPGSLQDYAVLQQSSLNSHFEAGMHKDSWLLGDSSFFLRTWLMTPLHIPETPAEY 247

Query:   217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQ 270
             RYN AH  T + +E+ F     RF CL   +  L  SP   +HI+ AC VLHNI+++
Sbjct:   248 RYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKSSHIILACCVLHNISLE 304

GO:0005813 "centrosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

RGD|1584007 Harbi1 "harbinger transposase derived 1" [Rattus norvegicus (taxid:10116)]

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 93/237 (39%), Positives = 134/237 (56%)

Query:    41 PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
             P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    ++ FP   A  
Sbjct:    69 PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPADEAAI 128

Query:   101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
                K  F G+   PGV+G VDC HV I+ P+ E+  ++ NRKG  SLN  V+      + 
Sbjct:   129 QSLKDEFYGLAGMPGVIGAVDCIHVAIKAPNAED-LSYVNRKGLHSLNCLVVCDIRGALM 187

Query:   158 DVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGI-LLGDSGYAQNTFLYTPLLNPTTPQEQ 216
              V + WPGS+ D  +   S +  +FE G  +   LLGDS +  +T+L TPL  P TP E 
Sbjct:   188 TVETSWPGSLQDCAVLQQSSLSSQFETGMPKDSWLLGDSSFFLHTWLLTPLHIPETPAEY 247

Query:   217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQ 270
             RYN+AH  T + +E+       RF CL   +  L  SP   +HI+ AC VLHNI+++
Sbjct:   248 RYNRAHSATHSVIEKTLRTLCCRFRCLDGSKGALQYSPEKSSHIILACCVLHNISLE 304

GO:0004518 "nuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0005813 "centrosome" evidence=IEA;ISO

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q17QR8 HARBI1 "Putative nuclease HARBI1" [Bos taurus (taxid:9913)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 93/237 (39%), Positives = 132/237 (55%)

Query:    41 PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
             P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    ++ FP   A  
Sbjct:    69 PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPADEASV 128

Query:   101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
                K  F G+   PGV+G VDC HV I+ P+ E+  ++ NRKG  SLN  ++      + 
Sbjct:   129 QALKDEFYGLAGIPGVIGVVDCMHVAIKAPNAED-LSYVNRKGLHSLNCLMVCDIRGALM 187

Query:   158 DVVSGWPGSVHDSRIFTNSRVCHRFERG-EVRGILLGDSGYAQNTFLYTPLLNPTTPQEQ 216
              V + WPGS+ D  +   S +  +FE G      LLGDS +   T+L TPL  P TP E 
Sbjct:   188 TVETSWPGSLQDCVVLQQSSLSSQFEAGMHKESWLLGDSSFFLRTWLMTPLHIPETPAEY 247

Query:   217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAVQ 270
             RYN AH  T + +E+ F     RF CL   +  L  SP   +HI+ AC VLHNI+++
Sbjct:   248 RYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKSSHIILACCVLHNISLE 304

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

MGI|MGI:2443194 Harbi1 "harbinger transposase derived 1" [Mus musculus (taxid:10090)]

 Score = 409 (149.0 bits), Expect = 3.4e-38, P = 3.4e-38
 Identities = 92/236 (38%), Positives = 131/236 (55%)

Query:    41 PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPT 100
             P T++LA + FY +G+FQ   GD+ G+SQ +M R V  V++AL +    ++ FP   A  
Sbjct:    69 PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPVDEAAV 128

Query:   101 ---KVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIW 157
                K  F G+   PGV+G  DC HV I+ P+ E+  ++ NRKG  SLN  V+      + 
Sbjct:   129 QSLKDEFYGLAGMPGVIGVADCIHVAIKAPNAED-LSYVNRKGLHSLNCLVVCDIRGALM 187

Query:   158 DVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGI-LLGDSGYAQNTFLYTPLLNPTTPQEQ 216
              V + WPGS+ D  +   S +  +FE G  +   LLGDS +   ++L TPL  P T  E 
Sbjct:   188 TVETSWPGSLQDCAVLQRSSLTSQFETGMPKDSWLLGDSSFFLRSWLLTPLPIPETAAEY 247

Query:   217 RYNKAHIKTRNSVERLFGIWKRRFACL---RRKLANSPVTCTHIVTACAVLHNIAV 269
             RYN+AH  T + +ER       RF CL   +  L  SP  C+HI+ AC VLHNI++
Sbjct:   248 RYNRAHSATHSVIERTLQTLCCRFRCLDGSKGALQYSPEKCSHIILACCVLHNISL 303

GO:0003674 "molecular_function" evidence=ND

GO:0004518 "nuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

ZFIN|ZDB-GENE-040608-1 harbi1 "harbinger transposase derived 1" [Danio rerio (taxid:7955)]

 Score = 402 (146.6 bits), Expect = 1.9e-37, P = 1.9e-37
 Identities = 93/268 (34%), Positives = 142/268 (52%)

Query:    12 FSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPT 71
             F ++ +  ++  L ++ L   T +     P  ++LA + FY +G+FQ   GD+ G+SQ +
Sbjct:    41 FPREFIYYLV-ELLKDSLLRRTQRSRAISPDVQILAALGFYTSGSFQSKMGDAIGISQAS 99

Query:    72 MCRLVKEVSKALAQAHVNYVKFPEQLAPT---KVAFQGIGNFPGVVGCVDCTHVPIQLPS 128
             M R V  V+KAL +    ++ F    A     K  F  I   P V G VDC H+ I+ P+
Sbjct:   100 MSRCVSNVTKALIEKAPEFIGFTRDEATKQQFKDEFYRIAGIPNVTGVVDCAHIAIKAPN 159

Query:   129 VENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEV- 187
              ++  ++ N+KG  S+N Q++      +    + WPGS+ D  +F  S V   FE  E  
Sbjct:   160 ADDS-SYVNKKGFHSINCQLVCDARGLLLSAETHWPGSLTDRAVFKQSNVAKLFEEQEND 218

Query:   188 -RGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACL--- 243
               G LLGD+ Y    +L TP+ +P +P + RYN AH  T   V+R F   + RF CL   
Sbjct:   219 DEGWLLGDNRYPLKKWLMTPVQSPESPADYRYNLAHTTTHEIVDRTFRAIQTRFRCLDGA 278

Query:   244 RRKLANSPVTCTHIVTACAVLHNIAVQT 271
             +  L  SP  C+HI+ AC VLHNI++Q+
Sbjct:   279 KGYLQYSPEKCSHIIQACCVLHNISLQS 306

GO:0004518 "nuclease activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

TAIR|locus:2143104 AT5G12010 [Arabidopsis thaliana (taxid:3702)]

 Score = 243 (90.6 bits), Expect = 6.8e-20, P = 6.8e-20
 Identities = 75/280 (26%), Positives = 125/280 (44%)

Query:     7 QEALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG 66
             ++A R SK     I   L   V + +T      P   R+   I   ATG          G
Sbjct:   176 KKAFRMSKSTFELICDELNSAVAKEDTALRNAIPVRQRVAVCIWRLATGEPLRLVSKKFG 235

Query:    67 VSQPTMCRLVKEVSKALAQAHV-NYVKFP--EQLAPTKVAFQGIGNFPGVVGCVDCTHVP 123
             +   T  +LV EV KA+    +  Y+++P  E L   +  F+ +   P VVG +  TH+P
Sbjct:   236 LGISTCHKLVLEVCKAIKDVLMPKYLQWPDDESLRNIRERFESVSGIPNVVGSMYTTHIP 295

Query:   124 IQLPSVENGENF------RNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSR 177
             I  P +     F      RN+K ++S+ +Q +  P     D+  GWPGS+ D ++   S 
Sbjct:   296 IIAPKISVASYFNKRHTERNQKTSYSITIQAVVNPKGVFTDLCIGWPGSMPDDKVLEKSL 355

Query:   178 VCHRFERGEV-RGI-LLGDSGYAQNTFLYTPLLNPT-TPQEQRYNKAHIKTRNSVERLFG 234
             +  R   G + +G+ + G  G+    ++  P      T  +  +N+   + +   +  FG
Sbjct:   356 LYQRANNGGLLKGMWVAGGPGHPLLDWVLVPYTQQNLTWTQHAFNEKMSEVQGVAKEAFG 415

Query:   235 IWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQE 274
               K R+ACL+++          ++ AC VLHNI  + R+E
Sbjct:   416 RLKGRWACLQKRTEVKLQDLPTVLGACCVLHNIC-EMREE 454

GO:0005634 "nucleus" evidence=ISM

GO:0005886 "plasma membrane" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0015824 "proline transport" evidence=RCA

TAIR|locus:2123874 AT4G29780 "AT4G29780" [Arabidopsis thaliana (taxid:3702)]

 Score = 234 (87.4 bits), Expect = 7.8e-19, P = 7.8e-19
 Identities = 77/277 (27%), Positives = 125/277 (45%)

Query:    11 RFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQP 70
             R SK     I   L   V + NTM     P   R+   +   ATG       +  G+   
Sbjct:   218 RMSKSTFNLICEELDTTVTKKNTMLRDAIPAPKRVGVCVWRLATGAPLRHVSERFGLGIS 277

Query:    71 TMCRLVKEVSKALAQAHV-NYVKFPE--QLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLP 127
             T  +LV EV +A+    +  Y+ +P   ++  TK  F+ +   P VVG +  TH+PI  P
Sbjct:   278 TCHKLVIEVCRAIYDVLMPKYLLWPSDSEINSTKAKFESVHKIPNVVGSIYTTHIPIIAP 337

Query:   128 SVENGENF------RNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCH- 180
              V     F      RN+K ++S+ VQ +   +    DV  G PGS+ D +I   S +   
Sbjct:   338 KVHVAAYFNKRHTERNQKTSYSITVQGVVNADGIFTDVCIGNPGSLTDDQILEKSSLSRQ 397

Query:   181 RFERGEVRGI-LLGDSGYAQNTFLYTPLLNPT-TPQEQRYNKAHIKTRNSVERLFGIWKR 238
             R  RG +R   ++G+SG+    +L  P      T  +  +N++  + +      F   K 
Sbjct:   398 RAARGMLRDSWIVGNSGFPLTDYLLVPYTRQNLTWTQHAFNESIGEIQGIATAAFERLKG 457

Query:   239 RFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQEL 275
             R+ACL+++         +++ AC VLHNI    ++E+
Sbjct:   458 RWACLQKRTEVKLQDLPYVLGACCVLHNICEMRKEEM 494

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

---

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)
Q17QR8	HARB1_BOVIN	3, ., 1, ., -, ., -	0.3611	0.8503	0.7650	yes	N/A
Q96MB7	HARB1_HUMAN	3, ., 1, ., -, ., -	0.3611	0.8503	0.7650	yes	N/A
B0BN95	HARB1_RAT	3, ., 1, ., -, ., -	0.3611	0.8503	0.7650	yes	N/A
Q8BR93	HARB1_MOUSE	3, ., 1, ., -, ., -	0.3881	0.7292	0.6561	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	314
pfam13359	155	pfam13359, DDE_4, DDE superfamily endonuclease	5e-45
pfam04827	205	pfam04827, Plant_tran, Plant transposon protein	4e-10

>gnl|CDD|222071 pfam13359, DDE_4, DDE superfamily endonuclease

 Score =  150 bits (380), Expect = 5e-45
 Identities = 51/158 (32%), Positives = 72/158 (45%), Gaps = 11/158 (6%)

Query: 117 VDCTHVPIQLPS--VENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFT 174
           +D T +PI+ P    E  + +   K   +L V ++  P+  I  V  GWPGSV D RI  
Sbjct: 1   IDGTEIPIERPKSLEEQAQTYSGYKKHNTLKVLIVVDPDGRIIFVSVGWPGSVSDKRILE 60

Query: 175 NSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLL-----NPTTPQEQRYNKAHIKTRNSV 229
           NS +  +   G+    +L D G+  +  L  P          T +E  +N+     R  V
Sbjct: 61  NSGLLEKLPPGDY---VLADRGFPLSDSLLAPPAKKPGGAQLTEEEVEFNRRIASARIHV 117

Query: 230 ERLFGIWKRRFACLRRKLANSPVT-CTHIVTACAVLHN 266
           ER+ G  K RF  LR +L  S +T    IV  C  LHN
Sbjct: 118 ERVIGRLKGRFRILRGRLRISKLTTLDKIVLVCCALHN 155

This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Length = 155

>gnl|CDD|203098 pfam04827, Plant_tran, Plant transposon protein

 Score = 58.1 bits (140), Expect = 4e-10
 Identities = 43/181 (23%), Positives = 76/181 (41%), Gaps = 15/181 (8%)

Query: 110 FPGVVGCVDCTHVPIQ-LPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVH 168
           FPG++G +DC H   +  P+   G+  R    + ++ ++ +   +L IW    G PGS +
Sbjct: 24  FPGMLGSLDCMHWKWKNCPTAWKGQYTRGDSKSPTIILEAVASYDLWIWHAFFGCPGSNN 83

Query: 169 DSRIFTNSRVCHRFERGE-------VRGI------LLGDSGYAQNTFLYTPLLNPTTPQE 215
           D  +   S +     +G        V G        L D  Y +       +  P   + 
Sbjct: 84  DINVLNQSPIFDDILQGTAPRVRYTVNGRQYNMGYYLADGIYPEWATFVKSIRLPQLEKH 143

Query: 216 QRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTH-IVTACAVLHNIAVQTRQE 274
           + + +     R  VER FG+ + RF  +         +    I+TAC +LHN+ V+  ++
Sbjct: 144 KLFAQQQEACRKDVERAFGVLQARFKIVATPARLWNQSDLSNIMTACIILHNMIVEDERD 203

Query: 275 L 275
           L
Sbjct: 204 L 204

This family contains plant transposases which are putative members of the PIF / Ping-Pong family. Length = 205

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	314
PF13359	158	DDE_Tnp_4: DDE superfamily endonuclease	100.0
KOG4585|consensus	326		100.0
PF04827	205	Plant_tran: Plant transposon protein; InterPro: IP	100.0
PF13612	155	DDE_Tnp_1_3: Transposase DDE domain	99.2
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	99.17
PF13586	88	DDE_Tnp_1_2: Transposase DDE domain	98.24
PF01609	213	DDE_Tnp_1: Transposase DDE domain; InterPro: IPR00	98.08
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	96.74
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	96.44
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.24
PF13340	75	DUF4096: Putative transposase of IS4/5 family (DUF	95.95
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	95.79
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	95.43
PF13518	52	HTH_28: Helix-turn-helix domain	95.29
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.16
smart00351	125	PAX Paired Box domain.	95.08
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	94.68
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	94.57
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	94.36
cd00131	128	PAX Paired Box domain	94.36
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	94.18
COG3415	138	Transposase and inactivated derivatives [DNA repli	93.99
PRK09413	121	IS2 repressor TnpA; Reviewed	93.69
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	93.68
PRK00118	104	putative DNA-binding protein; Validated	93.37
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	93.14
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	92.93
PRK04217	110	hypothetical protein; Provisional	92.75
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	92.18
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	92.12
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	92.04
PRK12529	178	RNA polymerase sigma factor; Provisional	91.4
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	91.14
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	90.99
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	90.91
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	90.89
PRK08301	234	sporulation sigma factor SigE; Reviewed	90.08
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	89.54
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	89.53
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	89.47
PRK12547	164	RNA polymerase sigma factor; Provisional	89.43
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	89.42
PRK12519	194	RNA polymerase sigma factor; Provisional	89.31
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	89.3
PRK12511	182	RNA polymerase sigma factor; Provisional	89.15
PRK06030	124	hypothetical protein; Provisional	89.11
PRK12530	189	RNA polymerase sigma factor; Provisional	88.99
PHA00542	82	putative Cro-like protein	88.97
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	88.81
PRK09415	179	RNA polymerase factor sigma C; Reviewed	88.76
PRK12514	179	RNA polymerase sigma factor; Provisional	88.67
PRK12516	187	RNA polymerase sigma factor; Provisional	88.54
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	88.51
TIGR02844	80	spore_III_D sporulation transcriptional regulator	88.43
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	88.26
PRK03975	141	tfx putative transcriptional regulator; Provisiona	88.15
PRK12533	216	RNA polymerase sigma factor; Provisional	88.01
PRK15320	251	transcriptional activator SprB; Provisional	87.98
PRK12524	196	RNA polymerase sigma factor; Provisional	87.96
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	87.96
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	87.91
COG3293	124	Transposase and inactivated derivatives [DNA repli	87.86
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	87.84
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	87.84
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	87.84
PRK09047	161	RNA polymerase factor sigma-70; Validated	87.82
PRK12531	194	RNA polymerase sigma factor; Provisional	87.81
PF13751	125	DDE_Tnp_1_6: Transposase DDE domain	87.81
PRK05803	233	sporulation sigma factor SigK; Reviewed	87.76
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	87.58
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	87.46
PRK12537	182	RNA polymerase sigma factor; Provisional	87.32
PRK12515	189	RNA polymerase sigma factor; Provisional	87.28
PRK05602	186	RNA polymerase sigma factor; Reviewed	87.16
PRK11924	179	RNA polymerase sigma factor; Provisional	87.14
COG3316	215	Transposase and inactivated derivatives [DNA repli	87.08
PRK12512	184	RNA polymerase sigma factor; Provisional	87.05
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	87.0
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	86.91
PHA00675	78	hypothetical protein	86.89
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	86.79
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	86.7
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	86.63
PF13551	112	HTH_29: Winged helix-turn helix	86.51
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	86.47
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	86.45
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	86.45
PF13730	55	HTH_36: Helix-turn-helix domain	86.4
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	86.32
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	86.23
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	86.02
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	85.99
PRK12534	187	RNA polymerase sigma factor; Provisional	85.98
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	85.96
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	85.84
PRK12546	188	RNA polymerase sigma factor; Provisional	85.75
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	85.63
PRK12540	182	RNA polymerase sigma factor; Provisional	85.57
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	85.57
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	85.57
PRK12532	195	RNA polymerase sigma factor; Provisional	85.5
PRK05572	252	sporulation sigma factor SigF; Validated	85.49
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	85.49
PF13309	64	HTH_22: HTH domain	85.47
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	85.41
PRK06811	189	RNA polymerase factor sigma-70; Validated	85.36
PF13610	140	DDE_Tnp_IS240: DDE domain	85.24
PF00872	381	Transposase_mut: Transposase, Mutator family; Inte	85.17
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	85.07
COG2963	116	Transposase and inactivated derivatives [DNA repli	85.06
PF08299	70	Bac_DnaA_C: Bacterial dnaA protein helix-turn-heli	85.02
PRK12539	184	RNA polymerase sigma factor; Provisional	84.85
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	84.84
PRK12544	206	RNA polymerase sigma factor; Provisional	84.78
PRK12520	191	RNA polymerase sigma factor; Provisional	84.76
PRK06759	154	RNA polymerase factor sigma-70; Validated	84.69
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	84.64
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	84.46
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	84.4
PRK12523	172	RNA polymerase sigma factor; Reviewed	84.12
PRK08583	257	RNA polymerase sigma factor SigB; Validated	84.03
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	83.98
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	83.69
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	83.43
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	83.07
PRK12525	168	RNA polymerase sigma factor; Provisional	82.87
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	82.83
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	82.67
PRK08215	258	sporulation sigma factor SigG; Reviewed	82.61
PRK06704	228	RNA polymerase factor sigma-70; Validated	82.35
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	82.21
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	82.17
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	82.11
PRK13919	186	putative RNA polymerase sigma E protein; Provision	81.62
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	81.61
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	81.51
PRK12522	173	RNA polymerase sigma factor; Provisional	81.39
PRK08295	208	RNA polymerase factor sigma-70; Validated	81.27
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	81.23
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	81.23
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	81.03
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	80.84
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	80.79
PRK07670	251	RNA polymerase sigma factor SigD; Validated	80.62
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	80.55
PRK12527	159	RNA polymerase sigma factor; Reviewed	80.54
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	80.14
PF05344	65	DUF746: Domain of Unknown Function (DUF746); Inter	80.11
PRK06930	170	positive control sigma-like factor; Validated	80.11

>PF13359 DDE_Tnp_4: DDE superfamily endonuclease

Probab=100.00  E-value=3.1e-39  Score=265.96  Aligned_cols=150  Identities=46%  Similarity=0.708  Sum_probs=138.4

Q ss_pred             eeceEEEEecCCC--CCCCcccCCCCceeeeeeeecCCcccEEEeecCCCCCcChhhhhccCcchhhhh-cCCcceEEEe
Q psy672          117 VDCTHVPIQLPSV--ENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFE-RGEVRGILLG  193 (314)
Q Consensus       117 iDgt~i~i~~P~~--~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~-~~~~~~~llg  193 (314)
                      ||||+|++++|..  .+...|+++|+.|++|+|++||++|+|++++.++||++||+.+|++|++...++ ..+.++++||
T Consensus         1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~~~~~~~~l~   80 (158)
T PF13359_consen    1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQAFPPGEYLLG   80 (158)
T ss_pred             CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeecccccCccccc
Confidence            7999999999943  268899999999999999999999999999999999999999999999888765 2334799999


Q ss_pred             CCCCCCcccccccCCC----CCCchhhhhhhhhhhhHHHHHHHHHHHHhhhhhccccccCC-hhhHHHHHHHHHHHhh
Q psy672          194 DSGYAQNTFLYTPLLN----PTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANS-PVTCTHIVTACAVLHN  266 (314)
Q Consensus       194 D~gY~~~~~l~~P~~~----~~~~~~~~fN~~~s~~R~~vE~~fg~lK~rf~~L~~~~~~~-~~~~~~~i~a~~~LhN  266 (314)
                      |+||++.+++++|+++    +.+++|+.||+.|++.|.+||++||+||+||++|+.+++.+ .+.+..+|.|||+|||
T Consensus        81 D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ii~~~~~LhN  158 (158)
T PF13359_consen   81 DSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQIILACCVLHN  158 (158)
T ss_pred             cccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHHHHheeEEEEC
Confidence            9999999999999973    34799999999999999999999999999999998889988 9999999999999999

>KOG4585|consensus

Probab=100.00  E-value=5.2e-38  Score=283.18  Aligned_cols=293  Identities=25%  Similarity=0.370  Sum_probs=228.9

Q ss_pred             ccccCHHHHHHhhHHhhhhhhcccCC--CCCC-CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672            9 ALRFSKDVVLNIIFPLARNVLETNTM--QGVK-QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus         9 ~frmsr~~f~~~L~~~l~~~~~~~~~--~~~~-~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .|++++.+|. .|+............  .... +++..++++.|+.++++.+.+.++..||...+|+     .+......
T Consensus         7 ~~~~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~   80 (326)
T KOG4585|consen    7 EFRKSYTTFD-KICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKED   80 (326)
T ss_pred             HHHHHHHHHH-HHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhc
Confidence            6899999999 999886544221111  1111 2288899999999999999999999999999988     55666667


Q ss_pred             hccccccCCCc--hhhhHHHhhhcCCCCCceeeeeceEEEEecCCCCCCCcccCCCCceeeeeeeecCCcccEEEeecCC
Q psy672           86 AHVNYVKFPEQ--LAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGW  163 (314)
Q Consensus        86 ~~~~~i~~P~~--~~~~~~~f~~~~~~p~~~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~  163 (314)
                      +++.++.||..  ...+.+.++.   +|+|+|++|+||+++..| ......|.++  .++.|+|+|||.+++|+++.+|+
T Consensus        81 ~~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~-~~~~~~~~n~--~~~~Nvlav~n~d~~f~~v~vg~  154 (326)
T KOG4585|consen   81 LAPHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVP-PKSGSVYFNK--EQSKNLLAVCNFDMRFIYVDVGW  154 (326)
T ss_pred             ccchhhcCchhhhhhhhcccccc---ccchhccccccccceecC-cccccccccc--ccchhhhheecCCceEEEEEccC
Confidence            89999999987  6667666665   999999999999999988 6667777777  78899999999999999999999


Q ss_pred             CCCcChhhhhccCcchhhhhcCCcceEEEeCCCCCC------------cccccccCCCCC-CchhhhhhhhhhhhHHHHH
Q psy672          164 PGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQ------------NTFLYTPLLNPT-TPQEQRYNKAHIKTRNSVE  230 (314)
Q Consensus       164 pGs~~D~~i~~~s~~~~~l~~~~~~~~llgD~gY~~------------~~~l~~P~~~~~-~~~~~~fN~~~s~~R~~vE  230 (314)
                      ||+.||+.|+..+.........+...|.|.|.||+.            .+++++|+..+. +..++.||.+|+..|.++|
T Consensus       155 ~Gs~~D~kvl~~~~~~~~~~~~~~~k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~elFN~rh~~~r~v~e  234 (326)
T KOG4585|consen  155 PGSAHDTKVLQDSLLYKRNFPHPPLKYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQPTNSQELFNKRHSSLRSVAE  234 (326)
T ss_pred             CCCccHHHHHHhhcccccccccCCccccccccCcccccccccccccccchhhhcccCCCCCCchHHHHhhhhhhHHHHHH
Confidence            999999999999887765444432245555555554            455556665553 5788899999999999999


Q ss_pred             HHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhhccccCCCCCCCccchh--hhh-ccccccCCCCCCchHHHHHHH
Q psy672          231 RLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAEDEVEE--EVE-EDVVVNDGVGRNGAGAVIRRA  307 (314)
Q Consensus       231 ~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~~~~~~~~~~~~~~~~~--~~~-~~~~~~~~~~~~~~~~~~R~~  307 (314)
                      ++||.||+||++|.+.......+...+|.|||+|||++++..+.++++...+.  +.+ .........+....+...|++
T Consensus       235 ~~fg~lk~rw~il~~~~~~~~~~~~~iV~a~caLHN~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~~~~~~~~~r~~  314 (326)
T KOG4585|consen  235 RAFGVLKAKWRILQRREKYDLKKLPKIVTACCALHNIIRDSDEEDPDDPKWEKFDDYGENVAHLRYAPQQRDYMEKIRDN  314 (326)
T ss_pred             HHHHHhhhhhHHHhhcccccccchHHHHHHHHHHHHHHHhhcccccccccccccccccccchhcccchhHHHHHHHHHHH
Confidence            99999999999999876677889999999999999999999987766553321  111 111122223457778899999


Q ss_pred             HHHhhc
Q psy672          308 FINEHF  313 (314)
Q Consensus       308 ~~~~~f  313 (314)
                      |+.+.+
T Consensus       315 l~~~l~  320 (326)
T KOG4585|consen  315 LLSELW  320 (326)
T ss_pred             HHHHHH
Confidence            988765

>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity

Probab=100.00  E-value=5.7e-36  Score=243.44  Aligned_cols=185  Identities=25%  Similarity=0.494  Sum_probs=165.2

Q ss_pred             ccccCCCc--hhhhHHHhhhcCCCCCceeeeeceEEEEe-cCCCCCCCcccCCCCceeeeeeeecCCcccEEEeecCCCC
Q psy672           89 NYVKFPEQ--LAPTKVAFQGIGNFPGVVGCVDCTHVPIQ-LPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPG  165 (314)
Q Consensus        89 ~~i~~P~~--~~~~~~~f~~~~~~p~~~g~iDgt~i~i~-~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pG  165 (314)
                      +|++-|+.  .+++. .+.+..||||.+|.|||+|+.++ +|....+.+.++++|.+|+.+++|++++++|++++.|.||
T Consensus         2 ~YLr~P~~~d~~rll-~~~e~rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G   80 (205)
T PF04827_consen    2 EYLRRPTNEDLERLL-QIGEARGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG   80 (205)
T ss_pred             cccCCCChhHHHHHH-HhhhhcCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence            57777887  55665 44556799999999999999999 7744445555699999999999999999999999999999


Q ss_pred             CcChhhhhccCcchhhhhcCCc-------------ceEEEeCCCCCCcccccccCCCCCCchhhhhhhhhhhhHHHHHHH
Q psy672          166 SVHDSRIFTNSRVCHRFERGEV-------------RGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERL  232 (314)
Q Consensus       166 s~~D~~i~~~s~~~~~l~~~~~-------------~~~llgD~gY~~~~~l~~P~~~~~~~~~~~fN~~~s~~R~~vE~~  232 (314)
                      |.||..|+..|++...+..|..             -.|.|+|..||.+..+++.++.|.+.+++.|.....++|..||+|
T Consensus        81 S~NDiNVL~~Splf~~~~~G~ap~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p~~~k~k~fa~~QE~~RKDVErA  160 (205)
T PF04827_consen   81 SNNDINVLDRSPLFDDLLQGQAPRVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLPQGEKRKLFAKHQESARKDVERA  160 (205)
T ss_pred             cccccccccccHHHHHHhcCcCCceEEEecCeecccceeeccCcCcchHhHhhhcchhhchhhHHHHHhCHHHHHHHHHH
Confidence            9999999999999998877731             569999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhhhcccccc-CChhhHHHHHHHHHHHhhhccccCCC
Q psy672          233 FGIWKRRFACLRRKLA-NSPVTCTHIVTACAVLHNIAVQTRQE  274 (314)
Q Consensus       233 fg~lK~rf~~L~~~~~-~~~~~~~~~i~a~~~LhN~~~~~~~~  274 (314)
                      ||.|++||+|++.+-+ ++.+.+..|+.||++||||+++++.+
T Consensus       161 FGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr~  203 (205)
T PF04827_consen  161 FGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDERD  203 (205)
T ss_pred             HHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEecccc
Confidence            9999999999998665 68899999999999999999987643

However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds

>PF13612 DDE_Tnp_1_3: Transposase DDE domain

Probab=99.20  E-value=1e-11  Score=100.75  Aligned_cols=128  Identities=18%  Similarity=0.260  Sum_probs=97.0

Q ss_pred             CCCCceeeeeceEEEEecCCCCC---------CCcccCCCCceeeeeeeecCCcccEEEeecCCCCCcChhhhhccCcch
Q psy672          109 NFPGVVGCVDCTHVPIQLPSVEN---------GENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVC  179 (314)
Q Consensus       109 ~~p~~~g~iDgt~i~i~~P~~~~---------~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~  179 (314)
                      |-+..+.+||.|.||+..+....         ...|+..+-+|++|++++|+.+|.++.+... ||++||..++..-  .
T Consensus         2 ~~~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~lT-~an~~D~~~~~~l--~   78 (155)
T PF13612_consen    2 GQCTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTLT-PANVHDRKVLEEL--S   78 (155)
T ss_pred             CCccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEEc-ccccccccccccc--c
Confidence            34567889999999998663221         1234455567899999999999999999887 9999999887331  1


Q ss_pred             hhhhcCCcceEEEeCCCCCCcc----------cccccCCCCCC-chhhhhhhhhhhhHHHHHHHHHHHHhhhhhcc
Q psy672          180 HRFERGEVRGILLGDSGYAQNT----------FLYTPLLNPTT-PQEQRYNKAHIKTRNSVERLFGIWKRRFACLR  244 (314)
Q Consensus       180 ~~l~~~~~~~~llgD~gY~~~~----------~l~~P~~~~~~-~~~~~fN~~~s~~R~~vE~~fg~lK~rf~~L~  244 (314)
                          ... ...++||+||-...          .++||.++... .....+++.+.+.|..||.+|+.||+.|.+=+
T Consensus        79 ----~~~-~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk~~~~~~~~~~l~~~R~~IETvfs~Lk~~~~ie~  149 (155)
T PF13612_consen   79 ----ENL-KGKLFGDKGYISKELKDELKEQGIKLITPRRKNMKNKLMPLFDKLLLRKRRIIETVFSQLKNQFNIEH  149 (155)
T ss_pred             ----ccc-ccceecchhhhcchHHhhhhhceEEEeccccccccccccchhhhhhhheeeEeehHHHHHHHhhceEe
Confidence                111 34799999996532          47889886653 33456788999999999999999999888765

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=99.17  E-value=5e-11  Score=79.01  Aligned_cols=50  Identities=22%  Similarity=0.141  Sum_probs=47.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      ++++++|++++|.||++|.++.++|..||||+|||++++++++++|+...
T Consensus         2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l   51 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL   51 (53)
T ss_pred             CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence            57999999999999999999999999999999999999999999998743

>PF13586 DDE_Tnp_1_2: Transposase DDE domain

Probab=98.24  E-value=1e-06  Score=64.89  Aligned_cols=76  Identities=20%  Similarity=0.259  Sum_probs=55.9

Q ss_pred             EEeCCCCCCcc--------cccc---cCCCCCCchhhhhhhhhhhhHHHHHHHHHHHHhhhhhccccccCChhhHHHHHH
Q psy672          191 LLGDSGYAQNT--------FLYT---PLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVT  259 (314)
Q Consensus       191 llgD~gY~~~~--------~l~~---P~~~~~~~~~~~fN~~~s~~R~~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~  259 (314)
                      ++||+||....        .+.+   +-+++....+..+...+.+.|.+||++|+.||. |+.|...+.........++.
T Consensus         1 v~aDkgYd~~~~r~~l~~~gi~~~i~~~~~~~~~~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek~~~s~~~~v~   79 (88)
T PF13586_consen    1 VLADKGYDSRALREYLRERGIRPVIPKRGRRKKRRPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEKLASSFLAFVH   79 (88)
T ss_pred             CcccCCcCCHHHHHHHHHCCCEEecCCCCCccccccCccchhhhccceehhhhhHHHHH-cCccccccccCHHHHHHHHH
Confidence            57999998631        2222   222222233678889999999999999999999 99999888888887777887


Q ss_pred             HHHHHhhh
Q psy672          260 ACAVLHNI  267 (314)
Q Consensus       260 a~~~LhN~  267 (314)
                      .+|++-++
T Consensus        80 la~~~i~l   87 (88)
T PF13586_consen   80 LACIVIWL   87 (88)
T ss_pred             HHHHHHHh
Confidence            77776554

>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element

Probab=98.08  E-value=3.4e-07  Score=77.75  Aligned_cols=149  Identities=19%  Similarity=0.250  Sum_probs=85.2

Q ss_pred             ceeeeeceEEEEecCCCCCCCcccCCCCceeeeeeeec-CCcccEEEeecCCCCCcChhhhhccCcchhhhhcCCcceEE
Q psy672          113 VVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIG-GPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGIL  191 (314)
Q Consensus       113 ~~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~v~-d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~~~~~~l  191 (314)
                      .+-+||+|.|+.. +.......+.+++...++++++++ +..|.++.+... +|+.+|...+.+  +.+. ..+..+..+
T Consensus         5 ~~~~iD~T~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~-~~~~~~~~v   79 (213)
T PF01609_consen    5 RVVAIDGTTIRTP-HDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER-KPGRKPDLV   79 (213)
T ss_dssp             EEEEEETTT--EE-EEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT------EEEE
T ss_pred             eEEEEECcEEEee-cchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc-cccccccce
Confidence            4569999999988 101112334455566778999999 557778888887 999999988776  2222 223448899


Q ss_pred             EeCCCCCCcc----------cccccCCCCCC-----------------------------------chhhhhhhh-----
Q psy672          192 LGDSGYAQNT----------FLYTPLLNPTT-----------------------------------PQEQRYNKA-----  221 (314)
Q Consensus       192 lgD~gY~~~~----------~l~~P~~~~~~-----------------------------------~~~~~fN~~-----  221 (314)
                      ++|+||....          ..+.|.+....                                   ..+......     
T Consensus        80 v~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (213)
T PF01609_consen   80 VADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKKGYFLVTNI  159 (213)
T ss_dssp             EE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--TTS---EE
T ss_pred             eecccccceeccccccccccccccccccccccccccchhhcccccccccccccccccccccccccccccccccccccccc
Confidence            9999998643          11233332110                                   001111122     


Q ss_pred             ---------hhhhHHHHHHHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhh
Q psy672          222 ---------HIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNI  267 (314)
Q Consensus       222 ---------~s~~R~~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~  267 (314)
                               ..+.|..||+.|..||+.|. +......+.+.+...+.++++-.|+
T Consensus       160 ~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~~~~~~~~~~~~~~~~la~nl  213 (213)
T PF01609_consen  160 TTLPRDTAALYRRRWQIERFFRELKQFLG-LERLRVRSPERIEAHLFLTLLAYNL  213 (213)
T ss_dssp             EEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS--SSHHHHHHHHHHHHHH---
T ss_pred             cccccccceeecccchhhHHHHHHHhcCC-CchhcccCHHHHHHHHHHHHhhCcC
Confidence                     89999999999999999544 3322334677788888888877775

Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=96.74  E-value=0.00072  Score=42.89  Aligned_cols=42  Identities=21%  Similarity=0.274  Sum_probs=31.1

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672           35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK   77 (314)
Q Consensus        35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~   77 (314)
                      |++.++.+ ++.-++..+..|.+..++|..||||++||.+++.
T Consensus         2 Rp~~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen    2 RPPKLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             SSSSSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             cCCCCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            34445544 5666777889999999999999999999999875

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=96.44  E-value=0.004  Score=40.28  Aligned_cols=45  Identities=24%  Similarity=0.359  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL   83 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l   83 (314)
                      .+|++++-.+.++| ..+.++.++|..+|+|.+||+++.++.+.-|
T Consensus         4 ~L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL   48 (50)
T PF04545_consen    4 QLPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL   48 (50)
T ss_dssp             TS-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence            57889999998888 7788899999999999999999999887655

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=96.24  E-value=0.002  Score=40.62  Aligned_cols=41  Identities=20%  Similarity=0.111  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      +.++++++..+.- ++..|.+.+.+|..+|+|+|||++.+++
T Consensus         3 ~~Lt~~eR~~I~~-l~~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEA-LLEQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHH-HHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHH-HHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            3567777777664 4689999999999999999999999875

>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)

Probab=95.95  E-value=0.0093  Score=42.24  Aligned_cols=62  Identities=16%  Similarity=0.068  Sum_probs=49.2

Q ss_pred             hhHHhhhhhhcccC--CCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           20 IIFPLARNVLETNT--MQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        20 ~L~~~l~~~~~~~~--~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      ...+.|++.+....  +++...+..+-+-..|+.+.+|++++.+...|| +.+||++.+.++...
T Consensus         4 ~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~~   67 (75)
T PF13340_consen    4 EEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSRS   67 (75)
T ss_pred             HHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHHc
Confidence            44556666665432  334567888889999999999999999999999 888999999988764

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=95.79  E-value=0.014  Score=42.10  Aligned_cols=49  Identities=18%  Similarity=0.188  Sum_probs=44.5

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           34 MQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        34 ~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      ..+..+++..++.++-..+..|.+...++..||||..|+++|+.++-..
T Consensus         4 H~nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~   52 (85)
T PF13011_consen    4 HKNARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAE   52 (85)
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence            3566799999999999999999999999999999999999999988754

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=95.43  E-value=0.0052  Score=39.65  Aligned_cols=39  Identities=21%  Similarity=0.145  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +.++.+...+. .|.+..++|..+|||++||++|++++..
T Consensus         5 ~~R~~ii~l~~-~G~s~~~ia~~lgvs~~Tv~~w~kr~~~   43 (50)
T PF13384_consen    5 ERRAQIIRLLR-EGWSIREIAKRLGVSRSTVYRWIKRYRE   43 (50)
T ss_dssp             -----HHHHHH-HT--HHHHHHHHTS-HHHHHHHHT----
T ss_pred             hHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence            34444444444 4999999999999999999999988753

>PF13518 HTH_28: Helix-turn-helix domain

Probab=95.29  E-value=0.013  Score=37.98  Aligned_cols=37  Identities=24%  Similarity=0.317  Sum_probs=31.4

Q ss_pred             HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ++.+...++ .|.+...+|..||||.+|+.+|+.++-.
T Consensus         2 r~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~   38 (52)
T PF13518_consen    2 RLQIVELYL-EGESVREIAREFGISRSTVYRWIKRYRE   38 (52)
T ss_pred             HHHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence            455666667 6779999999999999999999998876

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=95.16  E-value=0.01  Score=38.95  Aligned_cols=42  Identities=17%  Similarity=0.174  Sum_probs=30.8

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      +..+++++++-+. ..+-.|.+..++|..|||++||++.++..
T Consensus         4 R~~LTl~eK~~iI-~~~e~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    4 RKSLTLEEKLEII-KRLEEGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             SSS--HHHHHHHH-HHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             CccCCHHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            4568889998774 45788889999999999999999998864

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>smart00351 PAX Paired Box domain

Probab=95.08  E-value=0.028  Score=44.07  Aligned_cols=45  Identities=16%  Similarity=0.042  Sum_probs=38.8

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +..+|.+.+.-+.+.+. .|.+..++|..||||++||++|++++-+
T Consensus        15 ~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~   59 (125)
T smart00351       15 GRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE   59 (125)
T ss_pred             CCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34588888888877765 8999999999999999999999999855

>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []

Probab=94.68  E-value=0.027  Score=35.62  Aligned_cols=37  Identities=19%  Similarity=0.157  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHhhcC-CcccccCCcccccHHHHHHHHHH
Q psy672           42 MTRLLAVIQFYATG-NFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        42 ~~~l~~~L~~L~~g-~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      ++.+..+|..+.+| .+++.+|..|||+++|+++.++.
T Consensus         2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g   39 (45)
T PF05225_consen    2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG   39 (45)
T ss_dssp             HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            57788888888888 99999999999999999987653

In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=94.57  E-value=0.085  Score=38.72  Aligned_cols=53  Identities=13%  Similarity=0.112  Sum_probs=47.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCcccccCCccc-ccHHHHHHHHHHHHHHHHH
Q psy672           33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG-VSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fg-is~stv~~~~~~v~~~l~~   85 (314)
                      ..+...++..-++++.|..-..|.++.++|..|| .+.|||+..++++-..+.+
T Consensus        22 ~~R~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~   75 (90)
T cd06571          22 KSRKKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE   75 (90)
T ss_pred             CCCCcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence            3455678899999999999999999999999999 9999999999999988764

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D

Probab=94.36  E-value=0.023  Score=40.03  Aligned_cols=44  Identities=18%  Similarity=0.082  Sum_probs=30.6

Q ss_pred             HHH-HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           42 MTR-LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        42 ~~~-l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      +++ +-++=+.+.+..+.+.+|..||||+|||++=+.+=+..|..
T Consensus         5 eeR~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~   49 (82)
T PF12116_consen    5 EERVIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINP   49 (82)
T ss_dssp             HHHHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-H
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCH
Confidence            344 44677778899999999999999999999887765655553

It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.

>cd00131 PAX Paired Box domain

Probab=94.36  E-value=0.051  Score=42.76  Aligned_cols=46  Identities=15%  Similarity=0.081  Sum_probs=39.5

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      ..++|.+.+.-+.+.+ ..|.+...+|.+||||++||.+|++++-+.
T Consensus        15 ~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~   60 (128)
T cd00131          15 GRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYET   60 (128)
T ss_pred             CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            3568888888777665 689999999999999999999999988764

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=94.18  E-value=0.044  Score=32.03  Aligned_cols=41  Identities=24%  Similarity=0.179  Sum_probs=29.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHH
Q psy672           35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLV   76 (314)
Q Consensus        35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~   76 (314)
                      +...++.+++..+.. .+..+.+...++..+|+|.+|+++++
T Consensus         2 r~~~~~~~~~~~i~~-~~~~~~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           2 RPPKLTPEQIEEARR-LLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCCcCCHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence            344456655544444 45677899999999999999999863

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=93.99  E-value=0.047  Score=43.36  Aligned_cols=45  Identities=20%  Similarity=0.071  Sum_probs=40.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      ..+.+.+.+++..++..|.+.+++|.+||||.+|+.+++++.-+-
T Consensus         4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~   48 (138)
T COG3415           4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRET   48 (138)
T ss_pred             hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccc
Confidence            345678888999999999999999999999999999999988763

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=93.69  E-value=0.076  Score=41.32  Aligned_cols=46  Identities=15%  Similarity=0.229  Sum_probs=42.2

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +...+.+.++.++...+.+|.+..++|..||||.+|+++|.+++..
T Consensus        10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~   55 (121)
T PRK09413         10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE   55 (121)
T ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence            4568999999999999999999999999999999999999998754

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=93.68  E-value=0.038  Score=38.89  Aligned_cols=45  Identities=20%  Similarity=0.242  Sum_probs=37.9

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVS   80 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~   80 (314)
                      +...|++.++-++-.++..|.+..+++..+||+.+|+++|.....
T Consensus         4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    4 RRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             S----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence            456899999999999999999999999999999999999999987

This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.

>PRK00118 putative DNA-binding protein; Validated

Probab=93.37  E-value=0.11  Score=39.12  Aligned_cols=48  Identities=15%  Similarity=0.061  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      +.+|..++-++.|+ +-.|.++..+|+.+|+|++||.+++.+....+-+
T Consensus        16 ~~L~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~   63 (104)
T PRK00118         16 SLLTEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED   63 (104)
T ss_pred             ccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            44667766666444 5569999999999999999999999988877765

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=93.14  E-value=0.14  Score=33.25  Aligned_cols=45  Identities=18%  Similarity=0.245  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .++..++-++  .++..|.+..++|..+|+|.+||.+++.+....|.
T Consensus         3 ~l~~~e~~i~--~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~   47 (58)
T smart00421        3 SLTPREREVL--RLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG   47 (58)
T ss_pred             CCCHHHHHHH--HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            3566555533  33578999999999999999999999998876654

lux regulon (activates the bioluminescence operon

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=92.93  E-value=0.12  Score=33.02  Aligned_cols=43  Identities=19%  Similarity=0.200  Sum_probs=34.0

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      +++.++-++.+.|+ .|.++.+++..+|+|.+|+.+++++....
T Consensus        11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            55666666655554 77899999999999999999999887543

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>PRK04217 hypothetical protein; Provisional

Probab=92.75  E-value=0.18  Score=38.49  Aligned_cols=49  Identities=22%  Similarity=0.068  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ..++.+++-++ ..+.-.|.++.++|+.+|||.+||.+++.+....|.+.
T Consensus        41 ~~Lt~eereai-~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~   89 (110)
T PRK04217         41 IFMTYEEFEAL-RLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQM   89 (110)
T ss_pred             ccCCHHHHHHH-HHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            34677776443 44445888999999999999999999999988888763

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=92.18  E-value=0.18  Score=41.14  Aligned_cols=48  Identities=13%  Similarity=0.220  Sum_probs=43.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++-++.|.+  .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l  159 (166)
T PRK09639        112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY  159 (166)
T ss_pred             cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            48888998888877  9999999999999999999999999998887654

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=92.12  E-value=0.11  Score=33.57  Aligned_cols=32  Identities=16%  Similarity=0.159  Sum_probs=26.2

Q ss_pred             HHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672           48 VIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV   79 (314)
Q Consensus        48 ~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v   79 (314)
                      .+..+....++..+|..+|+|.+||.+++++.
T Consensus        20 i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   20 ILKLLRESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            34445555799999999999999999999874

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=92.04  E-value=0.14  Score=35.85  Aligned_cols=41  Identities=12%  Similarity=0.069  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      .+|...+.+..|.+.-.|.++.++|+.+|+|.+||..+++.
T Consensus        15 ~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879        15 WVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             cCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            57788888888888889999999999999999999998875

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=91.40  E-value=0.27  Score=40.79  Aligned_cols=48  Identities=10%  Similarity=0.095  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++|++++.++.|.++ .|.++.++|..+|+|.+||...+++....+.+.
T Consensus       127 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~  174 (178)
T PRK12529        127 TLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL  174 (178)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence            478888888888877 889999999999999999999999887777653

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=91.14  E-value=0.3  Score=31.68  Aligned_cols=43  Identities=21%  Similarity=0.299  Sum_probs=33.1

Q ss_pred             CHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           40 PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        40 s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      +..++-++.+  +..|.+..++|..+|+|.+|+..++++....+.
T Consensus         2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~   44 (57)
T cd06170           2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG   44 (57)
T ss_pred             CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence            3444443333  468899999999999999999999998876554

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=90.99  E-value=0.27  Score=31.98  Aligned_cols=44  Identities=18%  Similarity=0.331  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      ++|+.++-++.|.|+ .|.++.++|+.+|+|.+||...+.+....
T Consensus        10 ~L~~~~r~i~~l~~~-~g~s~~eIa~~l~~s~~~v~~~l~ra~~~   53 (54)
T PF08281_consen   10 QLPERQREIFLLRYF-QGMSYAEIAEILGISESTVKRRLRRARKK   53 (54)
T ss_dssp             CS-HHHHHHHHHHHT-S---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH-HCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            467777777766554 67889999999999999999998887654

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=90.91  E-value=0.27  Score=40.44  Aligned_cols=49  Identities=14%  Similarity=0.022  Sum_probs=41.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++.++.|.++ .|.++.++|..+|+|.+||...+++...-|-+.+
T Consensus       128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l  176 (182)
T PRK09652        128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL  176 (182)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            477888887777776 6889999999999999999999998888777644

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=90.89  E-value=0.17  Score=36.92  Aligned_cols=32  Identities=22%  Similarity=0.276  Sum_probs=27.4

Q ss_pred             HHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672           46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK   77 (314)
Q Consensus        46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~   77 (314)
                      ...+.++..|.+..++|+.+|||++|++++.+
T Consensus        41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        41 LQVAKMLKQGKTYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            55566789999999999999999999999553

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=90.08  E-value=0.34  Score=42.06  Aligned_cols=50  Identities=24%  Similarity=0.254  Sum_probs=42.8

Q ss_pred             CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++-++.|.|+   -.|.++.++|+.+|||.+||....++....|-+..
T Consensus       178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l  230 (234)
T PRK08301        178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEI  230 (234)
T ss_pred             hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            477888888888774   58999999999999999999999999988887644

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=89.54  E-value=0.44  Score=42.21  Aligned_cols=50  Identities=14%  Similarity=0.139  Sum_probs=42.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHV   88 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~   88 (314)
                      .+|+.++.++.|+|+ .+.++.++|..+|+|.++|..+.++...-|-....
T Consensus       205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~  254 (257)
T PRK05911        205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATLS  254 (257)
T ss_pred             cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            478888888888875 68899999999999999999999998888876543

>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family

Probab=89.53  E-value=0.46  Score=38.72  Aligned_cols=47  Identities=15%  Similarity=0.046  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      ++|+.++.++.|.|+ .|.++.++|..+|+|.+||....++....|-+
T Consensus       122 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~  168 (170)
T TIGR02952       122 ILTPKQQHVIALRFG-QNLPIAEVARILGKTEGAVKILQFRAIKKLAR  168 (170)
T ss_pred             hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            578888888888766 58999999999999999999999998877754

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=89.47  E-value=0.28  Score=36.12  Aligned_cols=41  Identities=17%  Similarity=-0.037  Sum_probs=32.9

Q ss_pred             CCHHHHHHHHHHH------hhcCCcccccCCcccccHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQF------YATGNFQIFTGDSHGVSQPTMCRLVKEV   79 (314)
Q Consensus        39 ~s~~~~l~~~L~~------L~~g~~~~~l~~~fgis~stv~~~~~~v   79 (314)
                      +++.++-.+.++|      +..+.+++.++...|||.+||+|+-+..
T Consensus        33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~l   79 (94)
T TIGR01321        33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNL   79 (94)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhc
Confidence            6778887777775      3457899999999999999999876543

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=89.43  E-value=0.49  Score=38.59  Aligned_cols=48  Identities=13%  Similarity=-0.038  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+.
T Consensus       112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~  159 (164)
T PRK12547        112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL  159 (164)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            467777777777777 888999999999999999999999998888763

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=89.42  E-value=0.39  Score=35.93  Aligned_cols=43  Identities=21%  Similarity=0.240  Sum_probs=37.1

Q ss_pred             CHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672           40 PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL   83 (314)
Q Consensus        40 s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l   83 (314)
                      .++++.++.++|+ ++.++.++++.+++|++|++++-++.+..|
T Consensus        57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L   99 (100)
T PF07374_consen   57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKEL   99 (100)
T ss_pred             ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            4788899999888 678899999999999999999988876644

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=89.31  E-value=0.33  Score=40.75  Aligned_cols=48  Identities=17%  Similarity=0.151  Sum_probs=39.4

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      +|++++-++.|.++. |.++.++|+.+|+|.+||...+.+....|-+..
T Consensus       142 L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l  189 (194)
T PRK12519        142 LPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLRELL  189 (194)
T ss_pred             CCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            566666666666655 899999999999999999999999888887643

>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1

Probab=89.30  E-value=0.49  Score=37.92  Aligned_cols=47  Identities=19%  Similarity=0.241  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||....++....|-+
T Consensus       113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~  159 (161)
T TIGR02985       113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELRK  159 (161)
T ss_pred             HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            367788888888666 68899999999999999999999988776653

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=89.15  E-value=0.48  Score=39.51  Aligned_cols=50  Identities=14%  Similarity=0.034  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHV   88 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~   88 (314)
                      ++|+..+-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+...
T Consensus       111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~  160 (182)
T PRK12511        111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE  160 (182)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence            477777777777777 58999999999999999999999999988876543

>PRK06030 hypothetical protein; Provisional

Probab=89.11  E-value=0.88  Score=35.48  Aligned_cols=47  Identities=9%  Similarity=0.008  Sum_probs=43.0

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL   83 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l   83 (314)
                      ..+...-|++|.|.+--++.++..+|..||.+.|||..-++.+-+.+
T Consensus        51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~   97 (124)
T PRK06030         51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR   97 (124)
T ss_pred             cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence            57889999999999999999999999999999999999999777655

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=88.99  E-value=0.45  Score=39.89  Aligned_cols=48  Identities=10%  Similarity=0.058  Sum_probs=41.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++|+..+-++.|.++. |.++.++|..+|+|.+||...+++....|-+.
T Consensus       134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~  181 (189)
T PRK12530        134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQAC  181 (189)
T ss_pred             hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            4677788888887766 89999999999999999999999988888763

>PHA00542 putative Cro-like protein

Probab=88.97  E-value=0.3  Score=35.11  Aligned_cols=33  Identities=33%  Similarity=0.411  Sum_probs=27.5

Q ss_pred             HHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672           46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      -+...+...|.+..++|+..|||++|++++.+.
T Consensus        22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g   54 (82)
T PHA00542         22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSG   54 (82)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            334456788999999999999999999998753

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=88.81  E-value=0.55  Score=38.06  Aligned_cols=47  Identities=17%  Similarity=0.123  Sum_probs=37.7

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+...-|-+.
T Consensus       110 L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~  156 (163)
T PRK07037        110 LPARTRYAFEMYRL-HGETQKDIARELGVSPTLVNFMIRDALVHCRKC  156 (163)
T ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            56666666666654 488999999999999999999988888877763

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=88.76  E-value=0.48  Score=39.25  Aligned_cols=49  Identities=16%  Similarity=0.156  Sum_probs=41.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|-+..
T Consensus       127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l  175 (179)
T PRK09415        127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL  175 (179)
T ss_pred             hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            4777777777777765 889999999999999999999999988887643

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=88.67  E-value=0.56  Score=38.74  Aligned_cols=48  Identities=13%  Similarity=0.027  Sum_probs=40.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|++.+-.+.|.++ .|.++.++|+.+|+|.+||...+++....|-+.
T Consensus       129 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~  176 (179)
T PRK12514        129 ELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC  176 (179)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence            367777777777765 788999999999999999999999988887653

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=88.54  E-value=0.57  Score=39.25  Aligned_cols=49  Identities=14%  Similarity=0.059  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-+.+
T Consensus       116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l  164 (187)
T PRK12516        116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL  164 (187)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            366777777777666 8999999999999999999999999998888643

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=88.51  E-value=0.55  Score=37.29  Aligned_cols=46  Identities=7%  Similarity=-0.021  Sum_probs=38.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      -++..++-.+.|  +..|.++.++|+.+|+|++||+.+.++...-|-.
T Consensus         6 ~Lte~qr~VL~L--r~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~   51 (137)
T TIGR00721         6 FLTERQIKVLEL--REKGLSQKEIAKELKTTRANVSAIEKRAMENIEK   51 (137)
T ss_pred             CCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence            467777777777  3799999999999999999999999988877763

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=88.43  E-value=0.34  Score=34.67  Aligned_cols=37  Identities=22%  Similarity=0.186  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHhhcC-CcccccCCcccccHHHHHHHHH
Q psy672           41 PMTRLLAVIQFYATG-NFQIFTGDSHGVSQPTMCRLVK   77 (314)
Q Consensus        41 ~~~~l~~~L~~L~~g-~~~~~l~~~fgis~stv~~~~~   77 (314)
                      +++++...+-+|..| .+..++|+.||+|.+||++.++
T Consensus         4 ~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~   41 (80)
T TIGR02844         4 IEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT   41 (80)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence            355666666676663 4567899999999999999775

Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=88.26  E-value=0.67  Score=35.86  Aligned_cols=69  Identities=17%  Similarity=0.097  Sum_probs=43.0

Q ss_pred             cccccCHHHHHHhhHHhhhhh-hcccCCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672            8 EALRFSKDVVLNIIFPLARNV-LETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV   79 (314)
Q Consensus         8 ~~frmsr~~f~~~L~~~l~~~-~~~~~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v   79 (314)
                      ..|.+|+.++. ..+..-+.. +......+..+.  ...+..+.--....+..+++..||||.+|+++.+++.
T Consensus        26 ~~F~VS~~Tv~-~W~k~~~~G~~~~k~r~~~Kid--~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl   95 (119)
T PF01710_consen   26 KRFGVSRNTVY-RWLKRKETGDLEPKPRGRKKID--RDELKALVEENPDATLRELAERLGVSPSTIWRALKRL   95 (119)
T ss_pred             HHhCcHHHHHH-HHHHhccccccccccccccccc--HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence            57999999999 666643332 222111111443  3333333333455677899999999999999887764

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=88.15  E-value=0.62  Score=37.16  Aligned_cols=47  Identities=13%  Similarity=0.056  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      ..+++.++-.+.|  ...|.++.++|+.+|+|++||+.+.++...-|-+
T Consensus         5 ~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~   51 (141)
T PRK03975          5 SFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIEK   51 (141)
T ss_pred             cCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            4577888877777  3699999999999999999999999987776654

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=88.01  E-value=0.6  Score=40.18  Aligned_cols=49  Identities=16%  Similarity=0.018  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++-++.|+|+ .|.++.++|+.+|||.+||...+++....|-+..
T Consensus       134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l  182 (216)
T PRK12533        134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALL  182 (216)
T ss_pred             cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            467777777777777 6999999999999999999999999888888643

>PRK15320 transcriptional activator SprB; Provisional

Probab=87.98  E-value=0.58  Score=39.32  Aligned_cols=45  Identities=18%  Similarity=0.183  Sum_probs=37.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .+|..+.  -.|.+|+.|.+.+++|+.+++|.+||+.+..+...-+.
T Consensus       164 ~LSdREI--EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg  208 (251)
T PRK15320        164 GVTQAKY--ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG  208 (251)
T ss_pred             CCCHHHH--HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence            3444443  67888999999999999999999999999999888766

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=87.96  E-value=0.66  Score=39.05  Aligned_cols=48  Identities=17%  Similarity=0.128  Sum_probs=41.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+++....|-..
T Consensus       136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~  183 (196)
T PRK12524        136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAAL  183 (196)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            467777777777777 789999999999999999999999998888763

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=87.96  E-value=0.3  Score=40.21  Aligned_cols=48  Identities=19%  Similarity=0.146  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       126 ~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~  173 (176)
T PRK09638        126 KLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE  173 (176)
T ss_pred             cCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence            477888888888776 699999999999999999999999988887763

>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family

Probab=87.91  E-value=0.63  Score=37.46  Aligned_cols=47  Identities=15%  Similarity=0.199  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+
T Consensus       111 ~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~  157 (159)
T TIGR02989       111 KLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD  157 (159)
T ss_pred             HCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence            488888888888665 78999999999999999999999988877754

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).

>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=87.86  E-value=0.19  Score=39.08  Aligned_cols=93  Identities=16%  Similarity=0.125  Sum_probs=62.0

Q ss_pred             eeeeecCCcccEEEeecCCCCCcChhhhhccCcchhhhhcCCcceEEEeCCCCCCcccccccCCCCC-------Cchhhh
Q psy672          145 NVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPT-------TPQEQR  217 (314)
Q Consensus       145 ~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~~~~~~llgD~gY~~~~~l~~P~~~~~-------~~~~~~  217 (314)
                      +.+.++|..|+++....+ +|..+ ...-. ..+-+     ..-.-+|+|.+|...+|...|-..+.       ...+..
T Consensus         2 ~~~~l~D~~~~~i~~~lp-~~~~~-~~~~~-~~~~~-----~~v~~~i~~~~~~g~~wr~~p~~~~~~~~~~~~~~~~~~   73 (124)
T COG3293           2 KLHALVDAEWRPVEPLLP-PAKYG-GPPGV-TLLRD-----REVLNGIADLLYTGCAWRALPADFPPATTVIPYRRFRRW   73 (124)
T ss_pred             CcccccccccceeeccCC-CcccC-CCCCC-ccccc-----HHHHHHHHHHhccchHHHHhHHHhCCCceEeCCCcchhh
Confidence            467899999999999886 54433 21110 00000     01224678899988777665544321       123577


Q ss_pred             hhhhhhhhHHHHHHHHHHHHhhhhhcccc
Q psy672          218 YNKAHIKTRNSVERLFGIWKRRFACLRRK  246 (314)
Q Consensus       218 fN~~~s~~R~~vE~~fg~lK~rf~~L~~~  246 (314)
                      ++..+...|..+|+.|+.+|. |+.+...
T Consensus        74 ~~~g~~~~~~~~~~~f~~~~~-~r~~~~~  101 (124)
T COG3293          74 FKRGLWKRRNLVERTFGRLKQ-FRRTATR  101 (124)
T ss_pred             HHHHHHHHHHHHHHHHHHHhc-ccceecc
Confidence            889999999999999999998 8888754

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=87.84  E-value=0.3  Score=31.95  Aligned_cols=29  Identities=14%  Similarity=0.165  Sum_probs=24.5

Q ss_pred             CcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           56 NFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        56 ~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .+..++|+.+|||++|++..+++...-|.
T Consensus        24 ~tl~elA~~lgis~st~~~~LRrae~kli   52 (53)
T PF04967_consen   24 ITLEELAEELGISKSTVSEHLRRAERKLI   52 (53)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence            45578999999999999999998877654

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=87.84  E-value=0.62  Score=38.64  Aligned_cols=48  Identities=13%  Similarity=0.090  Sum_probs=41.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|..++-++.|.|+ .|.++.++|+.+|||.+||...+++....|-..
T Consensus       136 ~L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  183 (187)
T PRK09641        136 QLPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ  183 (187)
T ss_pred             hCCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            467788888878776 799999999999999999999999988877753

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=87.84  E-value=0.63  Score=36.60  Aligned_cols=47  Identities=26%  Similarity=0.285  Sum_probs=38.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.+.++ .|.++.++|..+|+|.+||.+...++...|-+
T Consensus       110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~  156 (158)
T TIGR02937       110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE  156 (158)
T ss_pred             hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            467777777666555 68999999999999999999999998776653

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=87.82  E-value=0.72  Score=37.21  Aligned_cols=48  Identities=21%  Similarity=0.235  Sum_probs=40.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~  153 (161)
T PRK09047        106 KLPARQREAFLLRYW-EDMDVAETAAAMGCSEGSVKTHCSRATHALAKA  153 (161)
T ss_pred             hCCHHHHHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            477777777777665 588899999999999999999999999888763

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=87.81  E-value=0.7  Score=38.84  Aligned_cols=47  Identities=9%  Similarity=0.035  Sum_probs=38.2

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|+..+-++.|.++ .|.++.++|..+|||.+||...+++....|-..
T Consensus       142 Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~  188 (194)
T PRK12531        142 LPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS  188 (194)
T ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence            55566666666655 889999999999999999999999888887753

>PF13751 DDE_Tnp_1_6: Transposase DDE domain

Probab=87.81  E-value=0.22  Score=38.69  Aligned_cols=50  Identities=28%  Similarity=0.218  Sum_probs=37.3

Q ss_pred             hhhhhhhHH-HHHHHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhhcc
Q psy672          219 NKAHIKTRN-SVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAV  269 (314)
Q Consensus       219 N~~~s~~R~-~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~~~  269 (314)
                      ...+.+.|. .||++||.||. +--|..........+..-+...|+.|||..
T Consensus        73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~r  123 (125)
T PF13751_consen   73 GKELYKQRSIKVEGVFGTIKR-NHGLRRFRYRGLEKVRIEFLLAAIAYNLKR  123 (125)
T ss_pred             hhhhhheeecccccccccchh-ccCCccccccchhhhHHHHHHHHHHHHHHH
Confidence            356777888 99999999999 455543333456788888888888999853

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=87.76  E-value=0.58  Score=40.69  Aligned_cols=49  Identities=14%  Similarity=0.129  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++.++.|.|+   -.|.++.++|..+|+|.+||.+..++....|-..
T Consensus       175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~  226 (233)
T PRK05803        175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE  226 (233)
T ss_pred             hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            588899999999886   4678999999999999999999988887777653

>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=87.58  E-value=0.59  Score=31.15  Aligned_cols=26  Identities=31%  Similarity=0.377  Sum_probs=22.3

Q ss_pred             CcccccCCcccccHHHHHHHHHHHHH
Q psy672           56 NFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        56 ~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      .+..+|++.++++++|+++.+++...
T Consensus        22 ~t~~~la~~l~~~~~~vs~~v~~L~~   47 (62)
T PF12802_consen   22 LTQSELAERLGISKSTVSRIVKRLEK   47 (62)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            58899999999999999999887765

...

>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=87.46  E-value=0.56  Score=29.68  Aligned_cols=28  Identities=21%  Similarity=0.253  Sum_probs=22.8

Q ss_pred             cCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           54 TGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        54 ~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      .+.+..++|+.+|+|.+||++++++..+
T Consensus        16 ~~~t~~ela~~~~is~~tv~~~l~~L~~   43 (48)
T PF13412_consen   16 PRITQKELAEKLGISRSTVNRYLKKLEE   43 (48)
T ss_dssp             TTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4478899999999999999999998764

...

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=87.32  E-value=0.75  Score=38.16  Aligned_cols=46  Identities=22%  Similarity=0.195  Sum_probs=37.5

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      +|+..+.++.|. +-.|.++.++|+.+|||.+||....++....|-+
T Consensus       134 L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~  179 (182)
T PRK12537        134 LEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE  179 (182)
T ss_pred             CCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence            555666555554 5788999999999999999999999999888765

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=87.28  E-value=0.75  Score=38.39  Aligned_cols=48  Identities=21%  Similarity=0.241  Sum_probs=41.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++|++++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-..
T Consensus       131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~  178 (189)
T PRK12515        131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL  178 (189)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            477777777777776 889999999999999999999999988888764

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=87.16  E-value=0.7  Score=38.44  Aligned_cols=48  Identities=23%  Similarity=0.261  Sum_probs=41.0

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      +|+.++-++.|.++. |.++.++|+.+|+|..||...+++....|-+..
T Consensus       129 L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  176 (186)
T PRK05602        129 LPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQL  176 (186)
T ss_pred             CCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence            677777777777764 999999999999999999999999988887643

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=87.14  E-value=0.71  Score=37.76  Aligned_cols=48  Identities=15%  Similarity=0.158  Sum_probs=39.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||.+.+++....|-+.
T Consensus       125 ~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~  172 (179)
T PRK11924        125 ALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLREC  172 (179)
T ss_pred             hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            366777777767666 689999999999999999999999988877653

>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=87.08  E-value=5.2  Score=34.19  Aligned_cols=187  Identities=14%  Similarity=0.064  Sum_probs=108.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCc-----ccccHHHHHHHHHHHHHHHHHhccccccCCCchhhhHHHhhhcCCCCC
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDS-----HGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPG  112 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~-----fgis~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~~~~~p~  112 (314)
                      .++-.-+...+=+||+.+.+++++.+.     ..++.+|+++++.+....+.......-+                . ++
T Consensus         8 ~f~~~vi~~~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~~~~~r~~----------------~-~~   70 (215)
T COG3316           8 QFPRNIIAVAVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLARRLKRRKR----------------K-AG   70 (215)
T ss_pred             hcchhhHHHHHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHHHhhhhcc----------------c-cc
Confidence            455555555666677778999887664     3567889999999999988874422211                1 11


Q ss_pred             ceeeeeceEEEEecCCCCCCCcccCCCCceeeeeeeecCCcccEEEeecCCCCCcChhhhhccCcchhhhhcCCcceEEE
Q psy672          113 VVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILL  192 (314)
Q Consensus       113 ~~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~~~~~~ll  192 (314)
                      -.=.||-|.|+|.--   .   +         -+-..||.+|..+++...--=+...+..|    +...++....+.-++
T Consensus        71 ~~w~vDEt~ikv~gk---w---~---------ylyrAid~~g~~Ld~~L~~rRn~~aAk~F----l~kllk~~g~p~v~v  131 (215)
T COG3316          71 DSWRVDETYIKVNGK---W---H---------YLYRAIDADGLTLDVWLSKRRNALAAKAF----LKKLLKKHGEPRVFV  131 (215)
T ss_pred             cceeeeeeEEeeccE---e---e---------ehhhhhccCCCeEEEEEEcccCcHHHHHH----HHHHHHhcCCCceEE
Confidence            111689888887311   0   0         11246788899999888644445555443    333344433367888


Q ss_pred             eCCCCCCcccccccCCCCCCchhhhhhhhhhhh-HHHHHHHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhhccc
Q psy672          193 GDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKT-RNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQ  270 (314)
Q Consensus       193 gD~gY~~~~~l~~P~~~~~~~~~~~fN~~~s~~-R~~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~~~~  270 (314)
                      .|++=-....+-.--.        .+-++-++. .+.+|+-+..+|.|=+-+. .+. ++..+..++...-.+|++-..
T Consensus       132 tDka~s~~~A~~~l~~--------~~ehr~~~ylnN~iE~dh~~iKrr~~~~~-~f~-~~~sa~~~~~gie~i~~~~~~  200 (215)
T COG3316         132 TDKAPSYTAALRKLGS--------EVEHRTSKYLNNRIEQDHRPIKRRTRPMK-RFK-SLSSAASTISGIESIHMLYKR  200 (215)
T ss_pred             ecCccchHHHHHhcCc--------chheecccccccchhhcchhHHHHhcccc-cCC-ChHHHHHHHHhHHHHHHHHhh
Confidence            8876433211110000        111222222 4778999999998766552 222 344566666666677776544

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=87.05  E-value=0.79  Score=38.01  Aligned_cols=48  Identities=19%  Similarity=0.060  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++|+.++-++.|.|+. |.++.++|..+|+|.+||...+++....|-+.
T Consensus       131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~  178 (184)
T PRK12512        131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAK  178 (184)
T ss_pred             hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            3677777777776665 89999999999999999999999999888764

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=87.00  E-value=0.69  Score=38.72  Aligned_cols=52  Identities=12%  Similarity=0.008  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcccc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNY   90 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~   90 (314)
                      .+|++++-++.|.++ .|.++.++|+.+|+|..||...+.+....|-+....+
T Consensus       138 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~  189 (193)
T PRK11923        138 QLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPL  189 (193)
T ss_pred             hCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            366777777777765 7889999999999999999999999988887755443

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=86.91  E-value=0.49  Score=31.38  Aligned_cols=44  Identities=18%  Similarity=0.175  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      ++..+.-  +|.+++.|.+..++|...|||.+||..+..++..-+.
T Consensus         4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~   47 (58)
T PF00196_consen    4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG   47 (58)
T ss_dssp             S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred             cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence            4444433  5778999999999999999999999999998877654

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>PHA00675 hypothetical protein

Probab=86.89  E-value=0.49  Score=33.17  Aligned_cols=40  Identities=8%  Similarity=-0.031  Sum_probs=28.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK   77 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~   77 (314)
                      .+...+--.+-..+-+.|.++..||..||||++||..|.+
T Consensus        22 KLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         22 KLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             ccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence            3444333333333337888999999999999999987765

>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1

Probab=86.79  E-value=0.78  Score=40.28  Aligned_cols=47  Identities=21%  Similarity=0.190  Sum_probs=39.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      ++|..++-++.|.++ .|.++.++|..+|||.+||...+.+....|-+
T Consensus       161 ~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~  207 (244)
T TIGR03001       161 ALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLE  207 (244)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            356666777777665 78899999999999999999999999998876

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=86.70  E-value=0.84  Score=40.35  Aligned_cols=48  Identities=23%  Similarity=0.162  Sum_probs=41.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+++.++.++.|+|+ .|.++.++|..+|+|.++|++..++...-|-..
T Consensus       203 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~  250 (256)
T PRK07408        203 QLEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL  250 (256)
T ss_pred             cCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            477888888888876 588999999999999999999999998887763

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=86.63  E-value=0.78  Score=40.89  Aligned_cols=48  Identities=15%  Similarity=0.077  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHHHHHhh-cCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYA-TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~-~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|..++..+.|+|+. .+.++.++|..+|||.++|+++.++.+.-|-.
T Consensus       218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~  266 (270)
T TIGR02392       218 SLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA  266 (270)
T ss_pred             cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            4888999999999974 47899999999999999999999988877764

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.

>PF13551 HTH_29: Winged helix-turn helix

Probab=86.51  E-value=0.51  Score=35.54  Aligned_cols=36  Identities=19%  Similarity=0.211  Sum_probs=31.0

Q ss_pred             HHHHhhcCCc-ccccCCcccccHHHHHHHHHHHHHHH
Q psy672           48 VIQFYATGNF-QIFTGDSHGVSQPTMCRLVKEVSKAL   83 (314)
Q Consensus        48 ~L~~L~~g~~-~~~l~~~fgis~stv~~~~~~v~~~l   83 (314)
                      +|..+..|.+ ...+|..+|+|.+||+++++++...-
T Consensus         4 ~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G   40 (112)
T PF13551_consen    4 ILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGG   40 (112)
T ss_pred             HHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence            5666888985 99999999999999999999987543

>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family

Probab=86.47  E-value=0.86  Score=36.86  Aligned_cols=47  Identities=15%  Similarity=0.189  Sum_probs=39.6

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|+.++.++.|.+ -.|.++.++|+.+|+|.+||...+.+....|-+.
T Consensus       111 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  157 (162)
T TIGR02983       111 LPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLREL  157 (162)
T ss_pred             CCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            5667777766666 5699999999999999999999999999888764

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=86.45  E-value=0.85  Score=39.66  Aligned_cols=49  Identities=27%  Similarity=0.277  Sum_probs=43.0

Q ss_pred             CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++.++.|.++   ..|.++.++|+..|+|.+||....++....|-+.
T Consensus       178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~  229 (234)
T TIGR02835       178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE  229 (234)
T ss_pred             hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            588999999999886   3789999999999999999999998888877653

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=86.45  E-value=0.85  Score=38.28  Aligned_cols=49  Identities=18%  Similarity=0.044  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-+..
T Consensus       134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l  182 (192)
T PRK09643        134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAELL  182 (192)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            377778877777666 7899999999999999999999988888777643

>PF13730 HTH_36: Helix-turn-helix domain

Probab=86.40  E-value=0.71  Score=30.10  Aligned_cols=43  Identities=26%  Similarity=0.281  Sum_probs=30.7

Q ss_pred             CCHH-HHHHHHHHHhhcC-----CcccccCCcccccHHHHHHHHHHHHH
Q psy672           39 QPPM-TRLLAVIQFYATG-----NFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        39 ~s~~-~~l~~~L~~L~~g-----~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +++. ..|.+.|..+++.     .+.+.+++..|+|+.||.+++++..+
T Consensus         3 Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~   51 (55)
T PF13730_consen    3 LSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEE   51 (55)
T ss_pred             CCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4443 3455666666522     25678999999999999999987654

>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1

Probab=86.32  E-value=1  Score=37.37  Aligned_cols=48  Identities=17%  Similarity=0.057  Sum_probs=40.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|.++ .|.++.++|..+|||.+||...+++....|-+.
T Consensus       140 ~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~  187 (189)
T TIGR02984       140 KLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI  187 (189)
T ss_pred             cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            477887777777666 889999999999999999999999988877653

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).

>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=86.23  E-value=0.76  Score=30.35  Aligned_cols=39  Identities=23%  Similarity=0.285  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +-.++...+=..+.+..++++.++++++++++++++...
T Consensus         5 q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~   43 (59)
T PF01047_consen    5 QFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEK   43 (59)
T ss_dssp             HHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence            333333333345578899999999999999998887654

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 ....

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=86.02  E-value=1.1  Score=33.17  Aligned_cols=44  Identities=14%  Similarity=0.098  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      ..|....=.|+....|...+|+.|+||++.|+..++++...|..
T Consensus        20 ~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~   63 (105)
T COG2739          20 KKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED   63 (105)
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence            34444444455667788999999999999999999999998874

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=85.99  E-value=0.34  Score=38.81  Aligned_cols=47  Identities=11%  Similarity=0.024  Sum_probs=38.5

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+.
T Consensus       106 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~  152 (154)
T TIGR02950       106 LPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL  152 (154)
T ss_pred             CCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            56666666666656 799999999999999999999999988877653

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=85.98  E-value=0.98  Score=37.54  Aligned_cols=47  Identities=13%  Similarity=-0.012  Sum_probs=37.7

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|+.++-++.|.+ -.|.++.++|..+|+|.+||...+++....|-..
T Consensus       138 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  184 (187)
T PRK12534        138 LEPPRSELIRTAF-FEGITYEELAARTDTPIGTVKSWIRRGLAKLKAC  184 (187)
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence            5555555555554 4899999999999999999999999998887764

>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=85.96  E-value=0.78  Score=29.89  Aligned_cols=30  Identities=23%  Similarity=0.094  Sum_probs=24.0

Q ss_pred             cCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672           54 TGNFQIFTGDSHGVSQPTMCRLVKEVSKAL   83 (314)
Q Consensus        54 ~g~~~~~l~~~fgis~stv~~~~~~v~~~l   83 (314)
                      .+.+..++|+.+|||+.||.+.+...-+.+
T Consensus        14 ~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   14 EPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             TSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            336778999999999999999998876554

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 ....

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=85.84  E-value=1.2  Score=40.68  Aligned_cols=52  Identities=15%  Similarity=0.153  Sum_probs=43.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcccc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNY   90 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~   90 (314)
                      ++|+.++.++.|.++ .|.++.++|+.+|+|.+||...+.+....|-+.....
T Consensus       142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  193 (324)
T TIGR02960       142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSA  193 (324)
T ss_pred             hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccc
Confidence            467777777777665 7889999999999999999999999999998755543

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=85.75  E-value=0.97  Score=37.90  Aligned_cols=49  Identities=16%  Similarity=0.060  Sum_probs=42.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++-++.|.++ .|.++.++|..+|||.+||...+.+....|-+..
T Consensus       113 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l  161 (188)
T PRK12546        113 QLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELL  161 (188)
T ss_pred             hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            477888888888777 8999999999999999999999999999888644

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=85.63  E-value=0.86  Score=37.87  Aligned_cols=49  Identities=12%  Similarity=-0.050  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-+..
T Consensus       138 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l  186 (190)
T TIGR02939       138 ALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL  186 (190)
T ss_pred             cCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            356666666666655 8899999999999999999999999998888644

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=85.57  E-value=1  Score=37.48  Aligned_cols=49  Identities=16%  Similarity=0.029  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      ++|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+.+
T Consensus       111 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l  159 (182)
T PRK12540        111 KLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL  159 (182)
T ss_pred             hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            366677777767665 8899999999999999999999999999988744

>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family

Probab=85.57  E-value=1  Score=36.71  Aligned_cols=48  Identities=8%  Similarity=0.051  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|-+.
T Consensus       119 ~L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~  166 (169)
T TIGR02954       119 TLNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR  166 (169)
T ss_pred             hCCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3666666666565555 89999999999999999999999998888764

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.

>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=85.57  E-value=0.58  Score=29.59  Aligned_cols=38  Identities=18%  Similarity=0.130  Sum_probs=26.9

Q ss_pred             HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ++-+.........+..++++.+|+|++|++++++...+
T Consensus         4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~   41 (47)
T PF01022_consen    4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE   41 (47)
T ss_dssp             HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence            34443333445567789999999999999999887654

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 ....

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=85.50  E-value=0.94  Score=38.02  Aligned_cols=48  Identities=15%  Similarity=0.119  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+.
T Consensus       136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~  183 (195)
T PRK12532        136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQC  183 (195)
T ss_pred             hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            467777777777666 788899999999999999999999999888864

>PRK05572 sporulation sigma factor SigF; Validated

Probab=85.49  E-value=1.1  Score=39.48  Aligned_cols=48  Identities=21%  Similarity=0.347  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++.++.|+|+ .|.++.++|..+|+|.++|+++.++...-|-..
T Consensus       202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~  249 (252)
T PRK05572        202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK  249 (252)
T ss_pred             cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            588888888888775 678999999999999999999999998887753

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=85.49  E-value=1.1  Score=36.66  Aligned_cols=47  Identities=19%  Similarity=0.167  Sum_probs=38.3

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|+.++-++.|.+ -.|.++.++|+.+|+|.+||...+++....|-+.
T Consensus       119 L~~~~r~vl~L~~-~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~  165 (173)
T PRK09645        119 LSPEHRAVLVRSY-YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLA  165 (173)
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            5666666665555 4588999999999999999999999988888764

>PF13309 HTH_22: HTH domain

Probab=85.47  E-value=0.66  Score=31.66  Aligned_cols=41  Identities=22%  Similarity=0.391  Sum_probs=32.3

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcc-----cccCCcccccHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQ-----IFTGDSHGVSQPTMCRLVK   77 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~-----~~l~~~fgis~stv~~~~~   77 (314)
                      ..++.++++-+.-.....|...     ..+|+.+|||+.||++|++
T Consensus        19 ~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr   64 (64)
T PF13309_consen   19 SRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR   64 (64)
T ss_pred             hhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence            4577888888877777777433     5789999999999999863

>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=85.41  E-value=1.1  Score=30.16  Aligned_cols=41  Identities=20%  Similarity=0.188  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHhh---cCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           41 PMTRLLAVIQFYA---TGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        41 ~~~~l~~~L~~L~---~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ..+.-+-+++.|.   ...+..++|+.+|+|.+||+..+++...
T Consensus         5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~   48 (60)
T PF01325_consen    5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE   48 (60)
T ss_dssp             HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence            4556667777777   4456678999999999999999888764

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 ....

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=85.36  E-value=0.99  Score=37.72  Aligned_cols=47  Identities=11%  Similarity=0.144  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-.
T Consensus       131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~  177 (189)
T PRK06811        131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK  177 (189)
T ss_pred             hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            478888888888776 68999999999999999999999998888765

>PF13610 DDE_Tnp_IS240: DDE domain

Probab=85.24  E-value=1.5  Score=34.84  Aligned_cols=131  Identities=15%  Similarity=0.086  Sum_probs=75.9

Q ss_pred             eeeceEEEEecCCCCCCCcccCCCCceeeeeeeecCCcccEEEeecCCCCCcChhhhhccCcchhhhhcC-CcceEEEeC
Q psy672          116 CVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERG-EVRGILLGD  194 (314)
Q Consensus       116 ~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~-~~~~~llgD  194 (314)
                      .||-|.|+|.-           ++    .=+-.++|++|+++++.+.---...++.-|    +...+... ..+..++.|
T Consensus         5 ~~DEt~iki~G-----------~~----~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~F----l~~~l~~~~~~p~~ivtD   65 (140)
T PF13610_consen    5 HVDETYIKIKG-----------KW----HYLWRAIDAEGNILDFYLSKRRDTAAAKRF----LKRALKRHRGEPRVIVTD   65 (140)
T ss_pred             EEeeEEEEECC-----------EE----EEEEEeecccccchhhhhhhhcccccceee----ccccceeeccccceeecc
Confidence            68888888741           10    112468999999998888633333333222    22233332 235677778


Q ss_pred             CC--CCCcccccccC-CCCCCchhhhhhhhhhhhHHHHHHHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhhcccc
Q psy672          195 SG--YAQNTFLYTPL-LNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQT  271 (314)
Q Consensus       195 ~g--Y~~~~~l~~P~-~~~~~~~~~~fN~~~s~~R~~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~~~~~  271 (314)
                      ++  |+.--.-+.+- ..+.    ...-....-.++.||+-+..+|.|.+... ++ .+.+.+..++.+-.+.||+....
T Consensus        66 k~~aY~~A~~~l~~~~~~~~----~v~~~~~k~~nN~iE~~h~~~K~r~r~~~-gF-ks~~~A~~~l~~~~~~~n~~r~~  139 (140)
T PF13610_consen   66 KLPAYPAAIKELNPEGRLHD----KVEHRQRKYLNNRIERDHRTIKRRTRPMN-GF-KSFRSAQRTLSGFEAYHNFRRPH  139 (140)
T ss_pred             cCCccchhhhhccccccccc----ccceeechhhhChhhHhhhhhhhhccccc-Cc-CCHHHHHHHHHHHHHHHHHhCCC
Confidence            65  43211111111 0000    00001112246789999999999887665 34 36788999999999999997643

>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element

Probab=85.17  E-value=1.4  Score=41.45  Aligned_cols=130  Identities=15%  Similarity=0.091  Sum_probs=73.4

Q ss_pred             HHHhhcCCcccccCCc----cc---ccHHHHHHHHHHHHHHHHHhccccccCCCchhhhHHHhhhcCCCCCceeeeeceE
Q psy672           49 IQFYATGNFQIFTGDS----HG---VSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTH  121 (314)
Q Consensus        49 L~~L~~g~~~~~l~~~----fg---is~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~~~~~p~~~g~iDgt~  121 (314)
                      +..+..|.+.+++...    +|   +|++||++++.++.+.+.....+-+                .+.|-.+-.|||++
T Consensus       108 ~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R~L----------------~~~~y~~l~iD~~~  171 (381)
T PF00872_consen  108 ISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNRPL----------------ESEPYPYLWIDGTY  171 (381)
T ss_pred             hhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhhcc----------------ccccccceeeeeee
Confidence            3446777777766654    46   8999999999998887775432221                12223455899999


Q ss_pred             EEEecCCCCCCCcccCCCCceeeeeeeecCCccc--EEEeecCCCCCcChhhhhccCcchhhhhcCCc-ceEEEeCCCCC
Q psy672          122 VPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLE--IWDVVSGWPGSVHDSRIFTNSRVCHRFERGEV-RGILLGDSGYA  198 (314)
Q Consensus       122 i~i~~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~--i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~~~-~~~llgD~gY~  198 (314)
                      +++..- .        .-..-++-+-+.+|.+|+  ++.+..+ ++  -+...|.+ -+.+.-++|.. ...+++|.+=.
T Consensus       172 ~kvr~~-~--------~~~~~~~~v~iGi~~dG~r~vLg~~~~-~~--Es~~~W~~-~l~~L~~RGl~~~~lvv~Dg~~g  238 (381)
T PF00872_consen  172 FKVRED-G--------RVVKKAVYVAIGIDEDGRREVLGFWVG-DR--ESAASWRE-FLQDLKERGLKDILLVVSDGHKG  238 (381)
T ss_pred             cccccc-c--------ccccchhhhhhhhhcccccceeeeecc-cC--CccCEeee-cchhhhhccccccceeecccccc
Confidence            988632 1        111223445566777775  7777766 22  22223321 12222233332 56778887655


Q ss_pred             CcccccccC
Q psy672          199 QNTFLYTPL  207 (314)
Q Consensus       199 ~~~~l~~P~  207 (314)
                      +..-+-.-|
T Consensus       239 l~~ai~~~f  247 (381)
T PF00872_consen  239 LKEAIREVF  247 (381)
T ss_pred             ccccccccc
Confidence            544444434

Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=85.07  E-value=1  Score=37.32  Aligned_cols=48  Identities=15%  Similarity=0.164  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+++....|-..
T Consensus       136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  183 (187)
T TIGR02948       136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ  183 (187)
T ss_pred             hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            477777777777666 689999999999999999999999998887764

This sigma factor is restricted to certain lineages of the order Bacillales.

>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=85.06  E-value=1.1  Score=34.26  Aligned_cols=48  Identities=19%  Similarity=0.196  Sum_probs=42.9

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccc-cHHHHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGV-SQPTMCRLVKEVSKAL   83 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgi-s~stv~~~~~~v~~~l   83 (314)
                      +..+|.+.++-++-.++..|.+...+|..||| +.+++++|+.+....-
T Consensus         5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~   53 (116)
T COG2963           5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGG   53 (116)
T ss_pred             cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcc
Confidence            45689999999999999999999999999996 9999999998877643

>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=85.02  E-value=0.58  Score=32.52  Aligned_cols=45  Identities=13%  Similarity=0.085  Sum_probs=33.9

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCcccccCCccc-ccHHHHHHHHHHH
Q psy672           35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG-VSQPTMCRLVKEV   79 (314)
Q Consensus        35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fg-is~stv~~~~~~v   79 (314)
                      +...+.-.-++++.|..-.++.++.++|..|| .+.|||...++++
T Consensus        25 R~~~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki   70 (70)
T PF08299_consen   25 RKRKIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI   70 (70)
T ss_dssp             --HHHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred             CChhhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence            33445667788888888888999999999999 9999999887764

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=84.85  E-value=1.2  Score=37.09  Aligned_cols=48  Identities=23%  Similarity=0.130  Sum_probs=41.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+++....|-+.
T Consensus       131 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  178 (184)
T PRK12539        131 RLPEKMRLAIQAVKL-EGLSVAEAATRSGMSESAVKVSVHRGLKALAAL  178 (184)
T ss_pred             hCCHHHHHHHHHHHH-cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            477788877877777 499999999999999999999999999888763

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=84.84  E-value=0.45  Score=36.85  Aligned_cols=30  Identities=23%  Similarity=0.341  Sum_probs=26.4

Q ss_pred             HHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672           49 IQFYATGNFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        49 L~~L~~g~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      |-++..|.+..+++..|+||.+||.+|+.+
T Consensus        12 l~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~   41 (119)
T PF01710_consen   12 LAYIEKGKSIREAAKRFGVSRNTVYRWLKR   41 (119)
T ss_pred             HHHHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence            357778889999999999999999999884

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=84.78  E-value=1.2  Score=38.00  Aligned_cols=48  Identities=8%  Similarity=-0.022  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|-+.
T Consensus       148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~  195 (206)
T PRK12544        148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLREC  195 (206)
T ss_pred             hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4777777777777655 88999999999999999999999999988874

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=84.76  E-value=1.4  Score=36.83  Aligned_cols=48  Identities=10%  Similarity=0.059  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-+.
T Consensus       131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~  178 (191)
T PRK12520        131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLREC  178 (191)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            477778877777665 468899999999999999999999999888763

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=84.69  E-value=1.1  Score=35.81  Aligned_cols=46  Identities=4%  Similarity=0.029  Sum_probs=37.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .+|+.++-++.|.|+ .|.++.++|..+|+|.+||.....+....|-
T Consensus       106 ~L~~~~r~ii~l~~~-~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr  151 (154)
T PRK06759        106 VLDEKEKYIIFERFF-VGKTMGEIALETEMTYYQVRWIYRQALEKMR  151 (154)
T ss_pred             hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            467777777766665 5788999999999999999999998777664

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=84.64  E-value=1.3  Score=38.20  Aligned_cols=47  Identities=23%  Similarity=0.390  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.|+|+ .|.++.++|+.+|+|.+||....++....|-.
T Consensus       178 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~  224 (227)
T TIGR02980       178 ALPERERRILLLRFF-EDKTQSEIAERLGISQMHVSRLLRRALKKLRE  224 (227)
T ss_pred             cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            478888888878765 68899999999999999999999998887764

This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=84.46  E-value=0.24  Score=31.45  Aligned_cols=21  Identities=24%  Similarity=0.273  Sum_probs=18.0

Q ss_pred             ccccCCcccccHHHHHHHHHH
Q psy672           58 QIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        58 ~~~l~~~fgis~stv~~~~~~   78 (314)
                      ..++|+..|+|.+||+++++.
T Consensus         2 i~dIA~~agvS~~TVSr~ln~   22 (46)
T PF00356_consen    2 IKDIAREAGVSKSTVSRVLNG   22 (46)
T ss_dssp             HHHHHHHHTSSHHHHHHHHTT
T ss_pred             HHHHHHHHCcCHHHHHHHHhC
Confidence            467899999999999998864

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=84.40  E-value=1  Score=40.50  Aligned_cols=48  Identities=15%  Similarity=0.071  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHHHhh-cCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYA-TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~-~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .++..++..+.++|+. .+.++.++|..+|||+++|+++-++.+.-|-.
T Consensus       230 ~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~  278 (284)
T PRK06596        230 GLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKA  278 (284)
T ss_pred             cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            4788899999999975 57899999999999999999999988877765

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=84.12  E-value=1.4  Score=36.16  Aligned_cols=47  Identities=13%  Similarity=0.022  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+...-+..
T Consensus       119 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~  165 (172)
T PRK12523        119 KLSSKARAAFLYNRL-DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI  165 (172)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            467777777777665 58999999999999999999999888777664

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=84.03  E-value=1.4  Score=38.92  Aligned_cols=47  Identities=23%  Similarity=0.237  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.|.|+ .|.++.++|..+|||.+||....++....|-.
T Consensus       205 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~  251 (257)
T PRK08583        205 VLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLRE  251 (257)
T ss_pred             hCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            477777777777664 78899999999999999999999999888765

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=83.98  E-value=1.3  Score=38.41  Aligned_cols=48  Identities=15%  Similarity=0.086  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.|.|+   ..|.++.++|+.+|+|.+||.+..++....|-.
T Consensus       174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~  224 (227)
T TIGR02846       174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK  224 (227)
T ss_pred             hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            578888888888886   488999999999999999999999988887765

The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=83.69  E-value=1.1  Score=39.03  Aligned_cols=48  Identities=8%  Similarity=0.101  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++..+.|+|.   ..+.++..+|..+|||.++|.++..+...-|-.
T Consensus       176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~  226 (238)
T TIGR02393       176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRH  226 (238)
T ss_pred             hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence            478889999999884   467899999999999999999999988877764

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=83.43  E-value=1.2  Score=39.91  Aligned_cols=50  Identities=12%  Similarity=0.048  Sum_probs=43.7

Q ss_pred             CCCHHHHHHHHHHH-h--hcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQF-Y--ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~-L--~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|..++..+.|+| |  -.|.++.++|..+|+|.+||....++....|-...
T Consensus       222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l  274 (285)
T TIGR02394       222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL  274 (285)
T ss_pred             cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            58888999999988 4  57889999999999999999999999988887643

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=83.07  E-value=1.3  Score=39.84  Aligned_cols=49  Identities=12%  Similarity=0.076  Sum_probs=43.2

Q ss_pred             CCCHHHHHHHHHHHh-hcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFY-ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L-~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++.++.|+|+ ..+.++.++|..+|||+++|..+.++...-|-..
T Consensus       227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~  276 (289)
T PRK07500        227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRA  276 (289)
T ss_pred             cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            488899999999886 3688999999999999999999999998888763

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=82.87  E-value=1.8  Score=35.32  Aligned_cols=47  Identities=19%  Similarity=0.139  Sum_probs=39.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+..+.++.|. +-.|.++.++|+.+|+|.+||...+.+....+..
T Consensus       118 ~L~~~~r~v~~L~-~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~  164 (168)
T PRK12525        118 GLSGKARAAFLMS-QLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ  164 (168)
T ss_pred             hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            3777777766666 4678899999999999999999999988887765

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=82.83  E-value=1.7  Score=37.59  Aligned_cols=47  Identities=23%  Similarity=0.357  Sum_probs=39.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|..++.++.|+|+ .|.+..++|..+|+|.++|+++.++...-|-.
T Consensus       183 ~L~~~e~~i~~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~  229 (231)
T TIGR02885       183 KLDERERQIIMLRYF-KDKTQTEVANMLGISQVQVSRLEKKVLKKMKE  229 (231)
T ss_pred             cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            577888888777664 67899999999999999999999998877654

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=82.67  E-value=1.6  Score=36.44  Aligned_cols=48  Identities=13%  Similarity=0.004  Sum_probs=38.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++|+.++-++.|.|+ .|.++.++|+.+|+|.+||...+.+....|-+.
T Consensus       131 ~L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~  178 (188)
T TIGR02943       131 HLPEQTARVFMMREV-LGFESDEICQELEISTSNCHVLLYRARLSLRAC  178 (188)
T ss_pred             hCCHHHHHHHHHHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            356666665555554 489999999999999999999999998888764

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=82.61  E-value=1.7  Score=38.39  Aligned_cols=47  Identities=26%  Similarity=0.420  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+++.++.++.+.|+ .|.++.++|..+|+|.++|+++.++...-|-.
T Consensus       209 ~L~~~er~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~  255 (258)
T PRK08215        209 KLNDREKLILNLRFF-QGKTQMEVAEEIGISQAQVSRLEKAALKHMRK  255 (258)
T ss_pred             cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            477888888888775 67899999999999999999999998877654

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=82.35  E-value=1.5  Score=38.17  Aligned_cols=52  Identities=6%  Similarity=-0.137  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcccc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNY   90 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~   90 (314)
                      .+|+.++.++.|.++- |.++.++|+.+|+|.+||...+.+....|-+...+-
T Consensus       116 ~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~~  167 (228)
T PRK06704        116 SLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEG  167 (228)
T ss_pred             hCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence            4677777776666544 799999999999999999999999999988765443

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=82.21  E-value=1.5  Score=32.77  Aligned_cols=44  Identities=14%  Similarity=0.154  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      +.|--+.-.|+-...|.+.+|+.+|||+..|+..+++....|..
T Consensus        20 ~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~   63 (101)
T PF04297_consen   20 EKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE   63 (101)
T ss_dssp             HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            44444555778889999999999999999999999999988874

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=82.17  E-value=1.6  Score=37.86  Aligned_cols=48  Identities=17%  Similarity=0.186  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|.| -.|.++.++|..+|+|.+||....++....|-..
T Consensus       184 ~L~~~~r~vl~l~~-~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~  231 (236)
T PRK06986        184 SLPEREQLVLSLYY-QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR  231 (236)
T ss_pred             hCCHHHHHHHHhHh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            46777777777766 4788999999999999999999999998888764

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=82.11  E-value=2.1  Score=33.88  Aligned_cols=48  Identities=17%  Similarity=0.122  Sum_probs=40.8

Q ss_pred             CCHHHHHHHHHHHhhc-CCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYAT-GNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~-g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++.+++-++-+.|+.. ..++..+|..+|+|++|+++.-++++..+...
T Consensus        83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~  131 (134)
T TIGR01636        83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE  131 (134)
T ss_pred             CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            6788898999988753 34899999999999999999999988887753

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=81.62  E-value=2  Score=35.54  Aligned_cols=47  Identities=13%  Similarity=0.130  Sum_probs=38.7

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|..++-++.|.+ -.|.++.++|+.+|+|.+||....++....|-+.
T Consensus       136 L~~~~r~vl~l~~-~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~  182 (186)
T PRK13919        136 LSPEERRVIEVLY-YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEV  182 (186)
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            6666676666665 5688899999999999999999999988888753

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=81.61  E-value=3  Score=33.22  Aligned_cols=45  Identities=7%  Similarity=-0.068  Sum_probs=32.7

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ..+++.+-.++...+-..+.+..++++.++++++|+++.+++...
T Consensus        36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~   80 (144)
T PRK11512         36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC   80 (144)
T ss_pred             cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            456665554433334455678999999999999999998887654

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=81.51  E-value=2.1  Score=35.69  Aligned_cols=47  Identities=13%  Similarity=0.107  Sum_probs=38.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      ++|+.++-++.|.|+. |.++.++|..+|+|.+||...+++....|-.
T Consensus       139 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~  185 (189)
T PRK09648        139 TLPEKQREILILRVVV-GLSAEETAEAVGSTPGAVRVAQHRALARLRA  185 (189)
T ss_pred             hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            4667777666666655 8889999999999999999999988877765

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=81.39  E-value=1.6  Score=35.82  Aligned_cols=52  Identities=8%  Similarity=0.028  Sum_probs=40.8

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccccc
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYV   91 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i   91 (314)
                      +|+..+ -+++.++-.|.++.++|..+|+|.+||...+.+....|-+....+|
T Consensus       120 L~~~~r-~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~  171 (173)
T PRK12522        120 LNEKYK-TVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV  171 (173)
T ss_pred             CCHHHH-HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            444444 3444556688999999999999999999999999999988666554

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=81.27  E-value=1.8  Score=36.51  Aligned_cols=47  Identities=6%  Similarity=0.089  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.| ++ .|.++.++|..+|+|.+||...+++....|-+.
T Consensus       155 ~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~  201 (208)
T PRK08295        155 LLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKY  201 (208)
T ss_pred             hCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            466777777777 55 789999999999999999999999988887763

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=81.23  E-value=1.7  Score=38.27  Aligned_cols=47  Identities=21%  Similarity=0.407  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+++.++.++.++|+ .|.++.++|..+|+|.++|+++.++.+.-|-.
T Consensus       206 ~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~  252 (254)
T TIGR02850       206 RLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK  252 (254)
T ss_pred             cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence            578888888888775 67899999999999999999999988876653

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family

Probab=81.23  E-value=1.4  Score=39.89  Aligned_cols=45  Identities=11%  Similarity=0.102  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      .+|+.++..+.|+|.   ..+.++.++|..+|||+++|..+.++...-
T Consensus       249 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~k  296 (298)
T TIGR02997       249 ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRK  296 (298)
T ss_pred             cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            488999999999885   578899999999999999999998887654

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=81.03  E-value=2.1  Score=37.59  Aligned_cols=48  Identities=23%  Similarity=0.319  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .++-.+|+.+.|+| -.+.++..+|+..|||++.|+++..+.+..|-+.
T Consensus       196 ~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr~~  243 (247)
T COG1191         196 PLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKE  243 (247)
T ss_pred             ccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence            47778899999988 5678889999999999999999999998887753

>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=80.84  E-value=1.4  Score=29.72  Aligned_cols=26  Identities=23%  Similarity=0.279  Sum_probs=22.3

Q ss_pred             CcccccCCcccccHHHHHHHHHHHHH
Q psy672           56 NFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        56 ~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      .+..++++.+|+|++|++++++....
T Consensus        26 ~s~~ela~~~g~s~~tv~r~l~~L~~   51 (67)
T cd00092          26 LTRQEIADYLGLTRETVSRTLKELEE   51 (67)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            46678999999999999999888765

>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=80.79  E-value=2  Score=28.66  Aligned_cols=40  Identities=23%  Similarity=0.312  Sum_probs=30.7

Q ss_pred             HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           45 LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        45 l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      +-+++....+| ++...|+.+++|++++++.+++.-..+..
T Consensus         4 l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~   43 (60)
T PF00126_consen    4 LRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELGV   43 (60)
T ss_dssp             HHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence            33344444444 78899999999999999999998887764

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=80.62  E-value=2.2  Score=37.46  Aligned_cols=47  Identities=9%  Similarity=0.066  Sum_probs=40.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-.
T Consensus       201 ~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~  247 (251)
T PRK07670        201 QLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKK  247 (251)
T ss_pred             cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            477888888887774 88899999999999999999999998887765

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=80.55  E-value=1.9  Score=31.14  Aligned_cols=40  Identities=28%  Similarity=0.330  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHhhc---CCcccccCCcccccHHHHHHHHHHHHH
Q psy672           42 MTRLLAVIQFYAT---GNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        42 ~~~l~~~L~~L~~---g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ..+.+..|.+++.   +.+..++++.+|++++|+++++.....
T Consensus         4 ~~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~   46 (91)
T smart00346        4 LERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE   46 (91)
T ss_pred             HHHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3455556666654   367789999999999999999988765

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=80.54  E-value=2.3  Score=34.24  Aligned_cols=48  Identities=15%  Similarity=0.103  Sum_probs=38.6

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      +|++++-++.| .+-.|.++.++|..+|+|.+||...+.+....|-...
T Consensus       106 L~~~~r~v~~l-~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l  153 (159)
T PRK12527        106 LPPACRDSFLL-RKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM  153 (159)
T ss_pred             CCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            66666655555 4568889999999999999999999999988887643

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=80.14  E-value=2.4  Score=34.15  Aligned_cols=47  Identities=11%  Similarity=-0.005  Sum_probs=37.2

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|+.++-++.|. +-.|.++.++|+.+|+|.+||...+.+....|-+.
T Consensus       107 Lp~~~r~v~~l~-~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~  153 (160)
T PRK09642        107 LPENYRDVVLAH-YLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKH  153 (160)
T ss_pred             CCHHHHHHHHHH-HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            555555555444 45788999999999999999999999988888764

>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons

Probab=80.11  E-value=1.8  Score=29.43  Aligned_cols=43  Identities=21%  Similarity=0.157  Sum_probs=38.0

Q ss_pred             HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      ++-.+..+|+...+..++|+..|+...++.+++..+-..+.++
T Consensus         2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L   44 (65)
T PF05344_consen    2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL   44 (65)
T ss_pred             cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence            3445678899999999999999999999999999999999875

>PRK06930 positive control sigma-like factor; Validated

Probab=80.11  E-value=2.1  Score=35.41  Aligned_cols=48  Identities=10%  Similarity=0.104  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|. +..|.++.++|..+|+|.+||...+.+....|-..
T Consensus       114 ~L~~rer~V~~L~-~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~  161 (170)
T PRK06930        114 VLTEREKEVYLMH-RGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQ  161 (170)
T ss_pred             hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4666666555544 58899999999999999999999999998888763

---

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	314
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-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 = 42.5 bits (99), Expect = 1e-04
 Identities = 41/313 (13%), Positives = 87/313 (27%), Gaps = 73/313 (23%)

Query: 12  FSKDVVLNIIFPLARNVLETNTMQG-VKQPP----MTRLLAVIQFYATGNFQIFTGDSHG 66
           F  +     +  + +++L    +   +          RL   +        Q F  +   
Sbjct: 29  FVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVL- 87

Query: 67  VSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQL 126
             +     L+  +     Q  +    + EQ       +     F               +
Sbjct: 88  --RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL---YNDNQVFA-----------KYNV 131

Query: 127 PSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGS-----------------VHD 169
             ++       R+    L        N+    ++ G  GS                   D
Sbjct: 132 SRLQPYLKL--RQALLELRP----AKNV----LIDGVLGSGKTWVALDVCLSYKVQCKMD 181

Query: 170 SRIF-TNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNS 228
            +IF  N + C+  E   V  +L       Q    +T   + ++  + R +      +  
Sbjct: 182 FKIFWLNLKNCNSPE--TVLEMLQ--KLLYQIDPNWTSRSDHSSNIKLRIHSI----QAE 233

Query: 229 VERLFGIWKRRFACL-------RRKLANS-PVTCTHIVTA--CAVLHNIAVQTRQELPAE 278
           + RL    K    CL         K  N+  ++C  ++T     V   ++  T   +  +
Sbjct: 234 LRRLL-KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292

Query: 279 DEV----EEEVEE 287
                   +EV+ 
Sbjct: 293 HHSMTLTPDEVKS 305

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	314
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.57
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	96.25
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	95.89
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	95.35
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	95.26
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	94.91
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	94.41
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	94.33
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	94.17
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	94.11
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	94.03
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	93.87
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	93.48
1u78_A	141	TC3 transposase, transposable element TC3 transpos	93.09
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	93.03
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	92.8
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	92.65
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	91.98
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	91.91
3c57_A	95	Two component transcriptional regulatory protein;	91.9
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	91.87
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	91.81
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	91.75
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	91.71
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	91.62
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	90.83
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	90.64
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	90.45
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	90.31
3pvv_A	101	Chromosomal replication initiator protein DNAA; he	90.25
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	89.85
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	89.67
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	89.59
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	89.4
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	87.76
1u78_A	141	TC3 transposase, transposable element TC3 transpos	87.74
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	87.24
2nnn_A	140	Probable transcriptional regulator; structural gen	87.22
2k27_A	159	Paired box protein PAX-8; paired domain, solution	87.22
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	83.69
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	82.51
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	82.28
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	82.1
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	81.71
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	81.69
3frw_A	107	Putative Trp repressor protein; structural genomic	81.46
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	81.21
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	81.08
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	80.98
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	80.97
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	80.9
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	80.58

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=96.57  E-value=0.0017  Score=40.48  Aligned_cols=43  Identities=9%  Similarity=-0.067  Sum_probs=34.5

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672           35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      |+..++.+++..+.+. +..|.+..++|..+|||.+||.+++++
T Consensus         2 R~~~l~~~~~~~i~~~-~~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            2 RGSALSDTERAQLDVM-KLLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CSCCCCHHHHHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            4556788777655554 468899999999999999999998864

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=96.25  E-value=0.0039  Score=40.86  Aligned_cols=47  Identities=15%  Similarity=0.112  Sum_probs=39.4

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCc----ccccCCcccccHHHHHHHHHHHHHH
Q psy672           35 QGVKQPPMTRLLAVIQFYATGNF----QIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        35 ~~~~~s~~~~l~~~L~~L~~g~~----~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      ++...|++.++.+ +.++..|.+    ...+|..||||.+|+.+|+...-..
T Consensus         2 ~r~~ys~efK~~~-~~~~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~~~~   52 (59)
T 2glo_A            2 SRRIFTPHFKLQV-LESYRNDNDCKGNQRATARKYNIHRRQIQKWLQCESNL   52 (59)
T ss_dssp             CCCCCCHHHHHHH-HHHHHHCTTTTTCHHHHHHHTTSCHHHHHHHHTTHHHH
T ss_pred             CCCcCCHHHHHHH-HHHHHcCCCcchHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            4567889999988 778888888    8999999999999999998765443

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=95.89  E-value=0.0074  Score=44.23  Aligned_cols=61  Identities=13%  Similarity=0.065  Sum_probs=49.7

Q ss_pred             cccCHHHHHHhhHHhhhhhhcccCCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           10 LRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        10 frmsr~~f~~~L~~~l~~~~~~~~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      =|||.+.|. .+...++            ++ +..+-++=.||-.|.++.++|..+|+|+++|++.+.+.-+...
T Consensus         3 ~rmT~~eFe-~~~~~l~------------~~-~~~~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~   63 (101)
T 2w7n_A            3 KRLTESQFQ-EAIQGLE------------VG-QQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFE   63 (101)
T ss_dssp             CCCCHHHHH-HHHTTCC------------CC-HHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHH-HHHccCC------------hH-HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            379999999 7775551            21 3446677788999999999999999999999999999887764

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=95.35  E-value=0.005  Score=38.60  Aligned_cols=42  Identities=10%  Similarity=0.059  Sum_probs=30.4

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      ...++.++. ..++..+..|.+..++|..+|||.+|+++++.+
T Consensus         3 p~~~~~~~~-~~i~~l~~~g~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C            3 PRAINKHEQ-EQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             CCSSCTTHH-HHHHHHHHTTCCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             CCCCCHHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            344555443 333444678899999999999999999998653

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=95.26  E-value=0.0065  Score=44.48  Aligned_cols=45  Identities=20%  Similarity=0.060  Sum_probs=35.4

Q ss_pred             CCHHHHHHHHHHH-----hhcC-CcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQF-----YATG-NFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        39 ~s~~~~l~~~L~~-----L~~g-~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      +++.++-.+.++|     |..| .+++++|+..|||.+||+|+ ++.+.-+.
T Consensus        36 LT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~   86 (101)
T 1jhg_A           36 LTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAP   86 (101)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSC
T ss_pred             CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHcc
Confidence            6788887666665     3466 99999999999999999999 66555444

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=94.91  E-value=0.017  Score=41.84  Aligned_cols=44  Identities=11%  Similarity=0.062  Sum_probs=37.9

Q ss_pred             CCCCHHHHHHHHHHHhhc-CCcccccCCcccccHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYAT-GNFQIFTGDSHGVSQPTMCRLVKEVS   80 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~-g~~~~~l~~~fgis~stv~~~~~~v~   80 (314)
                      ...|++.++.+.-.++.. |.+...+|..||||.+|+++|+.+.-
T Consensus         4 ~~ys~e~k~~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~~~~   48 (97)
T 2jn6_A            4 KTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYG   48 (97)
T ss_dssp             CCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHHHHh
Confidence            457888888888778777 89999999999999999999987653

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=94.41  E-value=0.033  Score=39.47  Aligned_cols=48  Identities=8%  Similarity=0.120  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHHh-h--cCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFY-A--TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L-~--~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-.+.|+|+ .  .|.++.++|..+|+|.+||..+..+....|-.
T Consensus        18 ~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~   68 (87)
T 1tty_A           18 TLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRH   68 (87)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBT
T ss_pred             hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            478899988888884 4  78999999999999999999999988877754

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=94.33  E-value=0.039  Score=37.56  Aligned_cols=48  Identities=10%  Similarity=0.077  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHHHHHh-h--cCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFY-A--TGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L-~--~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      ..+|+.++-.+.|.|+ .  .|.++.++|..+|+|.+||..+..+....|-
T Consensus         9 ~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A            9 SKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK   59 (73)
T ss_dssp             TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            3588999988888884 3  7899999999999999999999999988887

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=94.17  E-value=0.024  Score=38.03  Aligned_cols=48  Identities=10%  Similarity=0.099  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHHHH-h--hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQF-Y--ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~-L--~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-.+.|+| +  ..|.++.++|..+|+|.+||..+..+....|-.
T Consensus         5 ~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~   55 (68)
T 2p7v_B            5 GLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH   55 (68)
T ss_dssp             CCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGS
T ss_pred             cCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            57889998888887 3  578999999999999999999999988776654

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=94.11  E-value=0.042  Score=36.70  Aligned_cols=47  Identities=15%  Similarity=0.006  Sum_probs=39.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-++.|.| ..|.++.++|..+|+|.+||.+..++....|-.
T Consensus        15 ~L~~~~r~il~l~~-~~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~   61 (70)
T 2o8x_A           15 DLTTDQREALLLTQ-LLGLSYADAAAVCGCPVGTIRSRVARARDALLA   61 (70)
T ss_dssp             SSCHHHHHHHHHHH-TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC
T ss_pred             hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            47788887766655 568999999999999999999999999888775

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=94.03  E-value=0.046  Score=39.05  Aligned_cols=49  Identities=12%  Similarity=0.079  Sum_probs=40.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|..++-++.|+| -.|.++.++|..+|||.+||...+.+....|-..+
T Consensus        37 ~L~~~~r~vl~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l   85 (92)
T 3hug_A           37 QLSAEHRAVIQRSY-YRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTL   85 (92)
T ss_dssp             TSCHHHHHHHHHHH-TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            37778887777665 47889999999999999999999999988887643

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=93.87  E-value=0.041  Score=38.99  Aligned_cols=45  Identities=18%  Similarity=0.232  Sum_probs=35.6

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      ...+.+.+..+.-.+ ..|.+...+|..||||.+|+++|+.+.-..
T Consensus        21 ~~ys~e~k~~~v~~~-~~g~s~~~iA~~~gIs~sTl~rW~k~~~~~   65 (87)
T 2elh_A           21 RSLTPRDKIHAIQRI-HDGESKASVARDIGVPESTLRGWCKNEDKL   65 (87)
T ss_dssp             SSCCHHHHHHHHHHH-HHTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHHHHHhc
Confidence            467888776555444 678899999999999999999998876543

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=93.48  E-value=0.061  Score=39.20  Aligned_cols=48  Identities=10%  Similarity=0.077  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      .+|+.++-.+.|+|+   ..+.++.++|..+|+|.+||.....+....|-.
T Consensus        19 ~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~   69 (99)
T 3t72_q           19 GLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH   69 (99)
T ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            488999999999886   368999999999999999999999998888775

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=93.09  E-value=0.044  Score=42.07  Aligned_cols=44  Identities=9%  Similarity=-0.088  Sum_probs=35.9

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672           35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV   79 (314)
Q Consensus        35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v   79 (314)
                      +...++.+++..+...+ ..|.+...+|..+|+|.+||.+++.+.
T Consensus         3 r~~~~s~~~r~~i~~~~-~~G~s~~~ia~~lgis~~Tv~r~~~~~   46 (141)
T 1u78_A            3 RGSALSDTERAQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLKDP   46 (141)
T ss_dssp             CSCCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHSG
T ss_pred             CcccCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHcc
Confidence            44667888877665544 789999999999999999999998764

>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides}

Probab=93.03  E-value=0.078  Score=38.32  Aligned_cols=45  Identities=9%  Similarity=-0.111  Sum_probs=40.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVS   80 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~   80 (314)
                      ...++.+.++.+++..+..+.+..+++.+|+||.+++.+|...+.
T Consensus        30 ~rrWs~~~Kl~VV~~~~~g~~s~~e~arry~Is~s~i~~W~r~~~   74 (95)
T 2jrt_A           30 TRRWVASRKAAVVKAVIHGLITEREALDRYSLSEEEFALWRSAVA   74 (95)
T ss_dssp             CCCCCHHHHHHHHHHHHTTSSCHHHHHHHTTCCHHHHHHHHHHTT
T ss_pred             hhccCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            445899999999999999999999999999999999998887663

>1j1v_A Chromosomal replication initiator protein DNAA, 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'; protein-DNA complex; 2.10A {Escherichia coli} SCOP: a.4.12.2

Probab=92.80  E-value=0.076  Score=38.30  Aligned_cols=53  Identities=9%  Similarity=0.077  Sum_probs=46.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcc-cccHHHHHHHHHHHHHHHHH
Q psy672           33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSH-GVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~f-gis~stv~~~~~~v~~~l~~   85 (314)
                      ..|...+...-|++|.|.+--++.++..+|+.| |.+.|||...++++-..+.+
T Consensus        24 ~~R~~~i~~aRqiamyL~r~~t~~Sl~~IG~~fggrdHsTV~ha~~ki~~~~~~   77 (94)
T 1j1v_A           24 KRRSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREE   77 (94)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCchhHHHHHHHHHHHHHHHCcCHHHHHHHhCCCCHHHHHHHHHHHHHHHHh
Confidence            345567888899999999999999999999999 89999999999999887753

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=92.65  E-value=0.11  Score=35.09  Aligned_cols=46  Identities=9%  Similarity=-0.027  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      ..+++.++-++.+  +..|.+..++|+.+|+|.+||..++.+....|.
T Consensus        10 ~~L~~~e~~il~~--~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~   55 (74)
T 1fse_A           10 PLLTKREREVFEL--LVQDKTTKEIASELFISEKTVRNHISNAMQKLG   55 (74)
T ss_dssp             CCCCHHHHHHHHH--HTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            4578888876666  378899999999999999999999998887665

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=91.98  E-value=0.2  Score=36.44  Aligned_cols=59  Identities=12%  Similarity=0.045  Sum_probs=44.9

Q ss_pred             hhHHhhhhhhcccCCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           20 IIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        20 ~L~~~l~~~~~~~~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .+++.|.+.    ......+++.++-++.|  +..|.+..++|+.+|||.+||..++.++...|.
T Consensus        20 ~~l~~l~~~----~~~~~~Lt~re~~Vl~l--~~~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLg   78 (99)
T 1p4w_A           20 KLLEKISAG----GYGDKRLSPKESEVLRL--FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG   78 (99)
T ss_dssp             HHHHHHHCC----CCSSSSCCHHHHHHHHH--HHHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHccC----CcccCCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            455555432    22345688888866655  468999999999999999999999998887765

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=91.91  E-value=0.073  Score=33.80  Aligned_cols=36  Identities=17%  Similarity=0.074  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672           41 PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK   77 (314)
Q Consensus        41 ~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~   77 (314)
                      ++..-.+.. ++..|.+..++|..+|||++||++++.
T Consensus        18 ~~~~~~i~~-l~~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           18 DDLVSVAHE-LAKMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             HHHHHHHHH-HHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHH-HHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            444333333 357889999999999999999999875

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=91.90  E-value=0.13  Score=36.91  Aligned_cols=47  Identities=15%  Similarity=0.051  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      ..++..++-++.|+  ..|.++.++|..+|+|.+||..++.+....|-.
T Consensus        26 ~~Lt~~e~~vl~l~--~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   72 (95)
T 3c57_A           26 SGLTDQERTLLGLL--SEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGM   72 (95)
T ss_dssp             -CCCHHHHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             hcCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            35888888777774  899999999999999999999999998887764

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=91.87  E-value=0.1  Score=33.83  Aligned_cols=33  Identities=12%  Similarity=0.004  Sum_probs=30.0

Q ss_pred             hhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           52 YATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        52 L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      +..|.+..++|+.+|+|.+||..++.+...-|.
T Consensus        10 ~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~   42 (61)
T 2jpc_A           10 IDEGYTNHGISEKLHISIKTVETHRMNMMRKLQ   42 (61)
T ss_dssp             HHTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHC
Confidence            688999999999999999999999998877665

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=91.81  E-value=0.13  Score=40.00  Aligned_cols=44  Identities=14%  Similarity=0.031  Sum_probs=37.4

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ..++.+.+..+...+ ..|.+...+|..||||.+||++|+++...
T Consensus        31 ~~~s~e~r~~iv~~~-~~G~s~~~iA~~lgis~~TV~rw~~~~~~   74 (149)
T 1k78_A           31 RPLPDVVRQRIVELA-HQGVRPCDISRQLRVSHGCVSKILGRYYE   74 (149)
T ss_dssp             SCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            468888888777666 57899999999999999999999988754

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=91.75  E-value=0.13  Score=38.36  Aligned_cols=44  Identities=18%  Similarity=0.129  Sum_probs=36.3

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ..++.+.+..+...+ ..|.+...+|..||||.+||++|+.+...
T Consensus        16 ~~~s~~~r~~i~~~~-~~g~s~~~ia~~lgis~~Tv~~w~~~~~~   59 (128)
T 1pdn_C           16 RPLPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILNRYQE   59 (128)
T ss_dssp             SCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            357888887766554 58899999999999999999999987653

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=91.71  E-value=0.069  Score=39.27  Aligned_cols=44  Identities=16%  Similarity=0.099  Sum_probs=37.1

Q ss_pred             CCCCCHHHHHHHHHHHhhcC-------CcccccCCcccccHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATG-------NFQIFTGDSHGVSQPTMCRLVKEV   79 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g-------~~~~~l~~~fgis~stv~~~~~~v   79 (314)
                      +...|++.++.++..++..+       .+...+|..||||.+|+++|+.+.
T Consensus         4 ~~~ys~e~K~~~v~~~~~~~~~~~s~g~s~~~va~~~gIs~~tl~~W~~~~   54 (108)
T 2rn7_A            4 NTRFSPEVRQRAVRMVLESQGEYDSQWATICSIAPKIGCTPETLRVWVRQH   54 (108)
T ss_dssp             SCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcccccccccccHHHHHHHHCcCHHHHHHHHHHH
Confidence            34688999988888787765       788999999999999999998864

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=91.62  E-value=0.099  Score=36.46  Aligned_cols=46  Identities=17%  Similarity=0.162  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      ..++..++-++.|  +..|.++.++|+.+|+|.+||..++.+....|.
T Consensus        20 ~~Lt~~e~~vl~l--~~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~   65 (82)
T 1je8_A           20 NQLTPRERDILKL--IAQGLPNKMIARRLDITESTVKVHVKHMLKKMK   65 (82)
T ss_dssp             GGSCHHHHHHHHH--HTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTT
T ss_pred             ccCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHc
Confidence            3578888877777  378999999999999999999999998877665

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=90.83  E-value=0.17  Score=38.40  Aligned_cols=49  Identities=8%  Similarity=0.060  Sum_probs=39.6

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCccc-ccCCcccccHHHHHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQI-FTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~-~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      +..++.+.++-+.-.+..+|.+.. ++|..||||.+|++++++.-.....
T Consensus         5 r~~~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~~~~~~   54 (131)
T 1hlv_A            5 RRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILA   54 (131)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHHHHHH
T ss_pred             ceeCCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhchhhhcc
Confidence            456899999888777767776665 8999999999999999987665443

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=90.64  E-value=0.14  Score=36.30  Aligned_cols=45  Identities=11%  Similarity=0.046  Sum_probs=38.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .+++.++-++.|  +..|.++.++|..+|+|.+||..++.+....|-
T Consensus        29 ~Lt~~e~~vl~l--~~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~   73 (91)
T 2rnj_A           29 MLTEREMEILLL--IAKGYSNQEIASASHITIKTVKTHVSNILSKLE   73 (91)
T ss_dssp             GCCSHHHHHHHH--HHTTCCTTHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             cCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            477788777766  378999999999999999999999998876664

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=90.31  E-value=0.23  Score=40.04  Aligned_cols=51  Identities=10%  Similarity=-0.029  Sum_probs=41.5

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcccc
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNY   90 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~   90 (314)
                      +|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+.+..+
T Consensus       141 L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~  191 (194)
T 1or7_A          141 LPEDLRMAITLREL-DGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQPL  191 (194)
T ss_dssp             SCHHHHHHHHHHHT-TCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHCC-
T ss_pred             CCHHHHHHhHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            66777777767665 6789999999999999999999999999888755443

>3pvv_A Chromosomal replication initiator protein DNAA; helix-turn-helix motif, interacting with DNAA-BOX, DNAA-box; HET: DNA; 2.00A {Mycobacterium tuberculosis} PDB: 3pvp_A*

Probab=90.25  E-value=0.21  Score=36.50  Aligned_cols=53  Identities=9%  Similarity=0.004  Sum_probs=46.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      ..|...+...-|++|.|.+=-++.++..+|..||...|||...++++-+.+.+
T Consensus        28 ~~R~~~i~~aRqiAmYL~r~~t~~Sl~~IG~~fgRDHsTV~ha~~ki~~~~~~   80 (101)
T 3pvv_A           28 PGKTRALAQSRQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEMAE   80 (101)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCchhhHHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            34555677888999999988899999999999999999999999999987764

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=89.85  E-value=0.16  Score=34.69  Aligned_cols=44  Identities=11%  Similarity=-0.042  Sum_probs=36.0

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      +++.++-++.| + ..|.++.++|..+|+|.+||..++.+...-|-
T Consensus        17 L~~~e~~vl~l-~-~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~   60 (79)
T 1x3u_A           17 LSERERQVLSA-V-VAGLPNKSIAYDLDISPRTVEVHRANVMAKMK   60 (79)
T ss_dssp             HCHHHHHHHHH-H-TTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHH-H-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHc
Confidence            45666666666 3 78999999999999999999999988877665

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=89.67  E-value=0.24  Score=35.21  Aligned_cols=47  Identities=13%  Similarity=0.029  Sum_probs=37.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      ...++..++-.+.|  +..|.+..++|+.+|||.+||..++.++..-|.
T Consensus        27 ~~~Lt~rE~~Vl~l--~~~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klg   73 (90)
T 3ulq_B           27 QDVLTPRECLILQE--VEKGFTNQEIADALHLSKRSIEYSLTSIFNKLN   73 (90)
T ss_dssp             --CCCHHHHHHHHH--HHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             ccCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            45688887766555  449999999999999999999999999876654

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=89.59  E-value=0.29  Score=40.75  Aligned_cols=50  Identities=16%  Similarity=0.127  Sum_probs=43.1

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      ..+|+.++-++.|+|+ .|.++.++|..+|||.+||....++....|-..+
T Consensus       186 ~~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l  235 (239)
T 1rp3_A          186 SKLPEREKLVIQLIFY-EELPAKEVAKILETSVSRVSQLKAKALERLREML  235 (239)
T ss_dssp             TTSCHHHHHHHHHHHT-SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            3588899988888775 6889999999999999999999999988887643

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=89.40  E-value=0.26  Score=36.74  Aligned_cols=47  Identities=17%  Similarity=0.108  Sum_probs=38.5

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|+.++-++.|+| ..|.++.++|..+|+|.+||...+++....|-..
T Consensus        23 L~~~~r~vl~l~y-~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~   69 (113)
T 1s7o_A           23 LTDKQMNYIELYY-ADDYSLAEIADEFGVSRQAVYDNIKRTEKILETY   69 (113)
T ss_dssp             SCHHHHHHHHHHH-HTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            6677776555544 5788999999999999999999999999888764

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=87.76  E-value=0.38  Score=35.72  Aligned_cols=48  Identities=10%  Similarity=0.062  Sum_probs=39.3

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      +|+.++-++.|+ +..|.++.++|..+|+|.+||...+++....|-...
T Consensus        26 L~~~~r~vl~l~-~~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l   73 (113)
T 1xsv_A           26 LTNKQRNYLELF-YLEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYE   73 (113)
T ss_dssp             SCHHHHHHHHHH-HTSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            667777665554 467889999999999999999999999998887643

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=87.74  E-value=0.84  Score=34.60  Aligned_cols=70  Identities=6%  Similarity=-0.059  Sum_probs=45.4

Q ss_pred             cccccCHHHHHHhhHHhhhhhh-cccCCCCCCCCHHHHHHHHHHHhhcCCcccccCCccc--ccHHHHHHHHHH
Q psy672            8 EALRFSKDVVLNIIFPLARNVL-ETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG--VSQPTMCRLVKE   78 (314)
Q Consensus         8 ~~frmsr~~f~~~L~~~l~~~~-~~~~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fg--is~stv~~~~~~   78 (314)
                      +.|.+++.++. ..+......- ....++...++.++...+.-.......+...++..+|  +|.+||++++++
T Consensus        30 ~~lgis~~Tv~-r~~~~~~~~g~~~~~gr~~~l~~~~~~~i~~~~~~~~~s~~~i~~~lg~~~s~~tV~r~l~~  102 (141)
T 1u78_A           30 RKISRSRHCIR-VYLKDPVSYGTSKRAPRRKALSVRDERNVIRAASNSCKTARDIRNELQLSASKRTILNVIKR  102 (141)
T ss_dssp             HHHTCCHHHHH-HHHHSGGGTTCCCCCCCCCSSCHHHHHHHHHHHHHCCCCHHHHHHHTTCCSCHHHHHHHHHH
T ss_pred             HHHCcCHHHHH-HHHHcccccCCcCCCCCCCcCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCccHHHHHHHHHH
Confidence            56788999998 7666554321 1123444567766654333222233467788888888  899999999876

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=87.24  E-value=0.41  Score=37.17  Aligned_cols=48  Identities=4%  Similarity=-0.022  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH   87 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~   87 (314)
                      .+|+.++-++.  ++-.|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       109 ~L~~~~r~v~~--~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l  156 (164)
T 3mzy_A          109 NFSKFEKEVLT--YLIRGYSYREIATILSKNLKSIDNTIQRIRKKSEEWI  156 (164)
T ss_dssp             HSCHHHHHHHH--HHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHH--HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            36677776665  3558999999999999999999999999988887644

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=87.22  E-value=0.84  Score=34.37  Aligned_cols=45  Identities=16%  Similarity=-0.008  Sum_probs=32.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      .+++.+..++...+-..+.+..++++.+|++++|+++.+++....
T Consensus        35 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~~   79 (140)
T 2nnn_A           35 GLTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKR   79 (140)
T ss_dssp             CCCHHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            576655443333333447889999999999999999988776543

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=87.22  E-value=0.27  Score=38.73  Aligned_cols=42  Identities=17%  Similarity=0.092  Sum_probs=34.3

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      ...++.+.+..+...+ ..|.+...+|..||||.+||++|+++
T Consensus        23 ~~~~s~e~r~~ii~l~-~~G~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           23 GRPLPEVVRQRIVDLA-HQGVRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             SCSSCHHHHHHHHHHH-HHTCCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCCCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3467888887766555 68899999999999999999998764

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=83.69  E-value=1.1  Score=34.16  Aligned_cols=45  Identities=13%  Similarity=0.053  Sum_probs=32.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      .+++.+-.++...+-..+.+..++++.+|++++|+++.+++....
T Consensus        37 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~   81 (148)
T 3nrv_A           37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEK   81 (148)
T ss_dssp             TCCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            576665544333333346788899999999999999988876654

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

Probab=82.51  E-value=0.7  Score=30.70  Aligned_cols=40  Identities=13%  Similarity=0.057  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      .++++-.|.--....+..++|+.+|+|++||++.+.....
T Consensus        12 ~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~   51 (67)
T 2heo_A           12 EQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKK   51 (67)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4455555533123467789999999999999998877654

>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=82.28  E-value=0.83  Score=32.74  Aligned_cols=29  Identities=14%  Similarity=0.006  Sum_probs=24.7

Q ss_pred             hcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           53 ATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        53 ~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ..+.+..++++.+|+|++|++++++....
T Consensus        34 ~~~~t~~ela~~l~is~~tv~~~l~~L~~   62 (109)
T 2d1h_A           34 EKPITSEELADIFKLSKTTVENSLKKLIE   62 (109)
T ss_dssp             CSCEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45678899999999999999998887654

>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=82.10  E-value=0.83  Score=31.33  Aligned_cols=40  Identities=13%  Similarity=0.173  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHhhc--CCcccccCCcccccHHHHHHHHHHHHH
Q psy672           42 MTRLLAVIQFYAT--GNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        42 ~~~l~~~L~~L~~--g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +.+++.+|.-.+.  +.+..++|..+|+|++||.+.+.+...
T Consensus        16 ~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~   57 (77)
T 1qgp_A           16 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAK   57 (77)
T ss_dssp             HHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4556655655553  467889999999999999988877654

>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=81.71  E-value=0.78  Score=32.58  Aligned_cols=37  Identities=11%  Similarity=0.268  Sum_probs=28.2

Q ss_pred             HHHHHHHhhcC---CcccccCCcccccHHHHHHHHHHHHH
Q psy672           45 LLAVIQFYATG---NFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        45 l~~~L~~L~~g---~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ++..|..-..+   .+..++++.+|++++|+++++++...
T Consensus        17 iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~   56 (95)
T 2qvo_A           17 ILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKFEE   56 (95)
T ss_dssp             HHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            44444444445   78899999999999999999887765

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=81.69  E-value=0.44  Score=33.21  Aligned_cols=40  Identities=5%  Similarity=0.077  Sum_probs=31.1

Q ss_pred             CHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           40 PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        40 s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +..++++..|.  .+|.+..+||..+|+|+++|.+.+.....
T Consensus        17 ~~~~~IL~lL~--~~g~sa~eLAk~LgiSk~aVr~~L~~Le~   56 (82)
T 1oyi_A           17 EIVCEAIKTIG--IEGATAAQLTRQLNMEKREVNKALYDLQR   56 (82)
T ss_dssp             HHHHHHHHHHS--SSTEEHHHHHHHSSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45666665555  56688899999999999999988776644

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=81.46  E-value=0.58  Score=34.25  Aligned_cols=31  Identities=13%  Similarity=0.239  Sum_probs=26.1

Q ss_pred             HHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672           49 IQFYATGNFQIFTGDSHGVSQPTMCRLVKEV   79 (314)
Q Consensus        49 L~~L~~g~~~~~l~~~fgis~stv~~~~~~v   79 (314)
                      ...|..|.+|+++++..|+|.+|++|+-+..
T Consensus        52 a~lL~~G~SyreIa~~tG~StaTIsRv~r~L   82 (107)
T 3frw_A           52 AKMLTDKRTYLDISEKTGASTATISRVNRSL   82 (107)
T ss_dssp             HHHHHTTCCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHCccHHHHHHHHHHH
Confidence            3348899999999999999999999865543

>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=81.21  E-value=1  Score=34.24  Aligned_cols=46  Identities=11%  Similarity=0.017  Sum_probs=30.5

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      ..+++.+-.++...+-..+.+..++++.+|++++|+++.+++....
T Consensus        33 ~~lt~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~   78 (142)
T 3ech_A           33 LDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGR   78 (142)
T ss_dssp             CCCCHHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            4566666544433333457889999999999999999988877653

>2oa4_A SIR5; structure, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Silicibacter pomeroyi} SCOP: a.4.12.3

Probab=81.08  E-value=0.99  Score=32.75  Aligned_cols=43  Identities=9%  Similarity=-0.028  Sum_probs=37.6

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +....++.++.....++.+..+.+..|+||.+++.+|...+..
T Consensus        34 Wva~rK~~VV~~v~~g~lS~~EAa~ry~Is~~ei~~W~r~y~~   76 (101)
T 2oa4_A           34 WVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAE   76 (101)
T ss_dssp             CCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4456799999999999999999999999999999988877643

>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7

Probab=80.98  E-value=0.35  Score=37.57  Aligned_cols=47  Identities=11%  Similarity=0.028  Sum_probs=38.2

Q ss_pred             CCCCCCHHHHHHHHHHH--hhcCCcccccCC----cc--cccHHHHHHHHHHHHH
Q psy672           35 QGVKQPPMTRLLAVIQF--YATGNFQIFTGD----SH--GVSQPTMCRLVKEVSK   81 (314)
Q Consensus        35 ~~~~~s~~~~l~~~L~~--L~~g~~~~~l~~----~f--gis~stv~~~~~~v~~   81 (314)
                      .+..++.++++.+..++  -..+.+..++|.    .|  |||+|||+++++.=-.
T Consensus         8 ~R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk~k~~   62 (144)
T 1iuf_A            8 KRRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILSSKYS   62 (144)
T ss_dssp             SSSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHHHHH
T ss_pred             cCccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhhHHH
Confidence            45679999999999888  334567788999    89  9999999999987443

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=80.97  E-value=1  Score=36.85  Aligned_cols=41  Identities=17%  Similarity=0.151  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV   79 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v   79 (314)
                      .|..+.=.-+.+++..|.++.++|..+|||+++|++++...
T Consensus         8 ~sl~eiG~ria~~y~~g~tQ~eIA~~lGiSr~~VSR~L~~A   48 (192)
T 1zx4_A            8 HSIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQAA   48 (192)
T ss_dssp             SCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHh
Confidence            34444444444457899999999999999999999987653

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=80.90  E-value=0.32  Score=40.55  Aligned_cols=45  Identities=24%  Similarity=0.385  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL   83 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l   83 (314)
                      .+|+.++-++.|+++ .|.++.++|..+|||.+||....++....|
T Consensus       198 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~L  242 (243)
T 1l0o_C          198 ELDERERLIVYLRYY-KDQTQSEVASRLGISQVQMSRLEKKILQHI  242 (243)
T ss_dssp             ----------------------------------------------
T ss_pred             hCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence            578888888887765 678999999999999999999888766543

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=80.58  E-value=2.1  Score=31.55  Aligned_cols=62  Identities=6%  Similarity=0.084  Sum_probs=41.6

Q ss_pred             cccccCHHHHHHhhHHhhhhhhcccCCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672            8 EALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus         8 ~~frmsr~~f~~~L~~~l~~~~~~~~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ....|+...+. .+...++.-..         +...+++..|.  ..+.+..++++.+|+|++|+++.++....
T Consensus        10 ~~~~~~~~~~~-~~~~~~~~l~~---------~~~~~il~~L~--~~~~s~~ela~~l~is~stvsr~l~~Le~   71 (119)
T 2lkp_A           10 PSAPLDSQAAA-QVASTLQALAT---------PSRLMILTQLR--NGPLPVTDLAEAIGMEQSAVSHQLRVLRN   71 (119)
T ss_dssp             CCSCCHHHHHH-HHHHHHHHHCC---------HHHHHHHHHHH--HCCCCHHHHHHHHSSCHHHHHHHHHHHHH
T ss_pred             cccccCHHHHH-HHHHHHHHhCC---------HHHHHHHHHHH--HCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34556666666 66666653321         12333333333  24788999999999999999999998877

---

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	314
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	97.46
d1hlva1	66	DNA-binding domain of centromere binding protein B	96.03
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.31
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	94.12
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	93.28
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	93.28
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	91.18
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	90.96
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	90.54
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	90.08
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	89.86
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	89.81
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	89.55
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	89.49
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	88.57
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	88.47
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	87.42
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	87.34
d1l8qa1	110	Chromosomal replication initiation factor DnaA C-t	85.68
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	85.39
d1zyba1	73	Probable transcription regulator BT4300, C-termina	85.38
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	84.2
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	83.92
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	82.45
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	82.11
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	81.95
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	81.78
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	81.76
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	81.73
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	81.58
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	81.07
d1j1va_	94	Chromosomal replication initiation factor DnaA C-t	80.95
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	80.66
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	80.27

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=97.46  E-value=2.6e-05  Score=47.37  Aligned_cols=41  Identities=10%  Similarity=0.064  Sum_probs=35.7

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHH
Q psy672           35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLV   76 (314)
Q Consensus        35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~   76 (314)
                      |++.++. +|+..+...++.|.+..++|..||||++|+++|+
T Consensus         2 R~~~lt~-~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           2 RPRAINK-HEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCCSSCH-HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CCCcCCH-HHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            4556654 7888888999999999999999999999999986

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.03  E-value=0.0021  Score=41.48  Aligned_cols=51  Identities=8%  Similarity=-0.031  Sum_probs=40.0

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcC-CcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           34 MQGVKQPPMTRLLAVIQFYATG-NFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        34 ~~~~~~s~~~~l~~~L~~L~~g-~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      +.+..++.++++-+.-++=.+. .+..++|..|||++|||+.|+++=-..+.
T Consensus         3 ~kRk~LT~~eK~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKnK~kil~   54 (66)
T d1hlva1           3 PKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILA   54 (66)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHHHHHH
T ss_pred             cccccCCHHHHHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence            3456799999998876665554 46788999999999999999987555444

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.31  E-value=0.0087  Score=39.00  Aligned_cols=48  Identities=17%  Similarity=0.152  Sum_probs=41.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      .+|+.++-++.|+|+ .|.++.++|..+|+|.+||...+++....|-..
T Consensus        21 ~L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~   68 (71)
T d1rp3a2          21 KLPEREKLVIQLIFY-EELPAKEVAKILETSVSRVSQLKAKALERLREM   68 (71)
T ss_dssp             TSCHHHHHHHHHHHT-SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh-HhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            488888888888776 678999999999999999999999998887764

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.12  E-value=0.026  Score=35.82  Aligned_cols=46  Identities=9%  Similarity=0.040  Sum_probs=34.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +++..++...++++-+   ...|.+-+++|.+|+||.+||++|.++.-+
T Consensus        11 ~GrPls~DLR~Riv~~---~~~G~s~r~aA~rf~VS~s~v~k~l~r~re   56 (63)
T d1k78a1          11 NGRPLPDVVRQRIVEL---AHQGVRPCDISRQLRVSHGCVSKILGRYYE   56 (63)
T ss_dssp             TTSCCCHHHHHHHHHH---HHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHH---HHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3444444555555532   458999999999999999999999988654

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=93.28  E-value=0.035  Score=40.40  Aligned_cols=46  Identities=20%  Similarity=0.176  Sum_probs=37.6

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      +.++|.+.+.-+.-. +..|.+.+++|..|+||.+||++|+.+.-+.
T Consensus        14 GrpLs~dlR~rIv~~-~~~G~s~r~iA~~~~VS~~tV~k~l~r~~~~   59 (123)
T d1pdnc_          14 GRPLPNNIRLKIVEM-AADGIRPCVISRQLRVSHGCVSKILNRYQET   59 (123)
T ss_dssp             TSCCCHHHHHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CcCCCHHHHHHHHHH-HHhcCCHHHHHHHHCcCHHHHHHHHHHHHcc
Confidence            456777777666554 4689999999999999999999999988764

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=93.28  E-value=0.027  Score=38.45  Aligned_cols=43  Identities=12%  Similarity=0.061  Sum_probs=36.7

Q ss_pred             CCCCHHHHHHHHHHHhhc-CCcccccCCcccccHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYAT-GNFQIFTGDSHGVSQPTMCRLVKEV   79 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~-g~~~~~l~~~fgis~stv~~~~~~v   79 (314)
                      ...|++-+.-++=.++.+ |.+..++|..+|||.+|+++|+++.
T Consensus         4 k~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1           4 KTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             CCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            357889888887666754 8999999999999999999998875

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=91.18  E-value=0.11  Score=33.22  Aligned_cols=47  Identities=11%  Similarity=-0.003  Sum_probs=39.5

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA   86 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~   86 (314)
                      +|+.++-++.|+|+. |.++.++|..+|+|.+||...+.+....|-+.
T Consensus        19 Lp~~~r~v~~l~~~~-~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~   65 (68)
T d1or7a1          19 LPEDLRMAITLRELD-GLSYEEIAAIMDCPVGTVRSRIFRAREAIDNK   65 (68)
T ss_dssp             SCHHHHHHHHHHHTT-CCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            778888888777765 56689999999999999999999988877653

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=90.96  E-value=0.056  Score=34.63  Aligned_cols=45  Identities=18%  Similarity=0.259  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .+++.+.  -+|.+++.|.+..++|...|+|..||..++.++..-+.
T Consensus         6 ~LT~rE~--~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   50 (67)
T d1a04a1           6 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK   50 (67)
T ss_dssp             GSCHHHH--HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             cCCHHHH--HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence            3555554  34667899999999999999999999999999887665

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=90.54  E-value=0.063  Score=34.15  Aligned_cols=45  Identities=18%  Similarity=0.179  Sum_probs=36.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .+++.++=  .|.+++.|.+..++|..+++|.+||..++.++..-+.
T Consensus         4 ~Lt~rE~~--vl~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   48 (65)
T d1l3la1           4 WLDPKEAT--YLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD   48 (65)
T ss_dssp             CCCHHHHH--HHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             ccCHHHHH--HHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            35555543  4577999999999999999999999999998877664

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=90.08  E-value=0.095  Score=36.88  Aligned_cols=46  Identities=17%  Similarity=0.126  Sum_probs=39.6

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      +|+.++-++.|+| -.|.++..+|+.+|||.+||+..+++....|-+
T Consensus        17 Lp~~qR~v~~L~y-~~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~   62 (106)
T d1s7oa_          17 LTDKQMNYIELYY-ADDYSLAEIADEFGVSRQAVYDNIKRTEKILET   62 (106)
T ss_dssp             SCHHHHHHHHHHH-HTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            6777777777765 468889999999999999999999999998875

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=89.86  E-value=0.082  Score=30.40  Aligned_cols=40  Identities=13%  Similarity=0.227  Sum_probs=29.3

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672           35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~   78 (314)
                      |++.+..++    .......|.....+|...|||++||++++++
T Consensus         2 Rk~~Id~~~----V~~L~~~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1           2 RKRKIDRDA----VLNMWQQGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             SCCCSCHHH----HHHHHHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             CCCccCHHH----HHHHHHcCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            444555543    2233468888899999999999999998763

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.81  E-value=0.12  Score=33.06  Aligned_cols=41  Identities=20%  Similarity=0.172  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHhhcC-------------CcccccCCcccccHHHHHHHHHHHHH
Q psy672           41 PMTRLLAVIQFYATG-------------NFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        41 ~~~~l~~~L~~L~~g-------------~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      +..+|+-+|..|+..             .+..++|...|+|+.||++.++++.+
T Consensus         2 v~~Rla~~Ll~l~~~~g~~~~~~~i~l~lt~~~lA~~~G~sRetvsr~L~~l~~   55 (69)
T d1i5za1           2 VTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLED   55 (69)
T ss_dssp             HHHHHHHHHHHGGGSTTCCCCSSSCEEECCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCCCCeeecCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            455666666666521             45567889999999999999998765

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=89.55  E-value=0.084  Score=33.72  Aligned_cols=46  Identities=9%  Similarity=0.017  Sum_probs=38.0

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      +.+++.++=.  |.+++.|.+..++|..+|+|.+||..++.++..-+.
T Consensus         3 p~LT~rE~~v--l~l~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~   48 (67)
T d1fsea_           3 PLLTKREREV--FELLVQDKTTKEIASELFISEKTVRNHISNAMQKLG   48 (67)
T ss_dssp             CCCCHHHHHH--HHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHH--HHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            4566666543  466899999999999999999999999998877665

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=89.49  E-value=0.25  Score=33.22  Aligned_cols=46  Identities=17%  Similarity=0.186  Sum_probs=38.2

Q ss_pred             CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      ..+++.+.  -+|.+|+.|.+..++|..+++|.+||..+..++..-+.
T Consensus        21 ~~LT~rE~--~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~   66 (87)
T d1p4wa_          21 KRLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG   66 (87)
T ss_dssp             SSCCHHHH--HHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            46777764  34567899999999999999999999999998877654

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=88.57  E-value=0.085  Score=34.06  Aligned_cols=44  Identities=11%  Similarity=0.116  Sum_probs=35.6

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      +++.+.-.  |.+++.|.+..++|..+|+|.+||..++.++..-|.
T Consensus        13 LT~rE~~v--l~~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   56 (70)
T d1yioa1          13 LTGREQQV--LQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQKLN   56 (70)
T ss_dssp             SCHHHHHH--HHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHH--HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            55555543  455889999999999999999999999998876654

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=88.47  E-value=0.15  Score=35.72  Aligned_cols=46  Identities=9%  Similarity=0.058  Sum_probs=38.5

Q ss_pred             CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~   85 (314)
                      +|+.++-++.|+| -.|.++..+|...|||++||...+++....|-+
T Consensus        19 Lpe~QR~vl~L~~-~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~   64 (106)
T d1xsva_          19 LTNKQRNYLELFY-LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVED   64 (106)
T ss_dssp             SCHHHHHHHHHHH-TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HhCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            5667776666554 568889999999999999999999999998875

>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=87.42  E-value=0.17  Score=33.32  Aligned_cols=42  Identities=14%  Similarity=-0.010  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHhhc--------------CCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           41 PMTRLLAVIQFYAT--------------GNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        41 ~~~~l~~~L~~L~~--------------g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      ++++|+-+|.+|+.              ..+..++|...|+|+.||++.++++.+.
T Consensus         2 v~~Rla~~Ll~l~~~~g~~~~~~~~i~~~~t~~eiA~~lG~sretvsr~l~~l~~~   57 (80)
T d1ft9a1           2 IKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIKE   57 (80)
T ss_dssp             HHHHHHHHHHHTCBCCCSCC--CCCCEECCCHHHHHHHHCSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCeEEecCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            45667766766643              2345688899999999999999988764

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=87.34  E-value=0.28  Score=30.56  Aligned_cols=47  Identities=11%  Similarity=0.123  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHHHH-h--hcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQF-Y--ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        38 ~~s~~~~l~~~L~~-L--~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .++..++-.+.++| |  ....++.++|..+|||++.|..+-.+.+.-|-
T Consensus         8 ~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR   57 (61)
T d1ku3a_           8 KLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK   57 (61)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            47889999999998 3  34467789999999999999999888876653

>d1l8qa1 a.4.12.2 (A:290-399) Chromosomal replication initiation factor DnaA C-terminal domain IV {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Chromosomal replication initiation factor DnaA C-terminal domain IV
domain: Chromosomal replication initiation factor DnaA C-terminal domain IV
species: Aquifex aeolicus [TaxId: 63363]

Probab=85.68  E-value=0.35  Score=34.02  Aligned_cols=70  Identities=9%  Similarity=0.102  Sum_probs=53.1

Q ss_pred             HHHHHHhhHHhhhhhhcc------cCCCCCCCCHHHHHHHHHHHhhcCCcccccCCccc-ccHHHHHHHHHHHHHHHH
Q psy672           14 KDVVLNIIFPLARNVLET------NTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG-VSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        14 r~~f~~~L~~~l~~~~~~------~~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fg-is~stv~~~~~~v~~~l~   84 (314)
                      +.+.. .|++.+...+.-      ...|...+...-++++.|.+--++.++.++|..|| -+.|||...++.+-..+.
T Consensus        13 ~~~l~-~Ii~~Va~~f~i~~~di~sk~R~~~vv~aR~ia~yL~r~~t~~sl~~IG~~fg~rdHsTV~~a~kki~~~~~   89 (110)
T d1l8qa1          13 RDKLM-QIVEFVANYYAVKVEDILSDKRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKK   89 (110)
T ss_dssp             HHHHH-HHHHHHHHHHSCCHHHHSSCCCCSSSHHHHHHHHHHHHHHHCCCHHHHHHHSSCCCSTHHHHHHHHHHHTTC
T ss_pred             CCCHH-HHHHHHHHHhCCCHHHHhCCCCcHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCCccHHHHHHHHHHHHHH
Confidence            34555 666666655331      23455677778889999998889999999999996 899999999888776554

>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=85.39  E-value=0.29  Score=32.14  Aligned_cols=42  Identities=7%  Similarity=-0.060  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHhhc-------------CCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           41 PMTRLLAVIQFYAT-------------GNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        41 ~~~~l~~~L~~L~~-------------g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      +.++|+-+|.+|+.             ..+..++|...|+|+.||++.++++.+.
T Consensus         2 v~~Rla~~Ll~l~~~~g~~~~~~~i~~~lt~~eLA~~~G~sretvsr~L~~l~~~   56 (81)
T d2gaua1           2 VRGRLAETLLILKENFGFENDGATLSIYLSREELATLSNMTVSNAIRTLSTFVSE   56 (81)
T ss_dssp             HHHHHHHHHHHHHHHHCBCTTSSBBSCCCCHHHHHHHTTSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCEEeecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            34556666655542             2355678999999999999999988764

>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=85.38  E-value=0.26  Score=31.92  Aligned_cols=44  Identities=2%  Similarity=-0.072  Sum_probs=32.8

Q ss_pred             CCHHHHHHHHHHHhhcC--------CcccccCCcccccHHHHHHHHHHHHHH
Q psy672           39 QPPMTRLLAVIQFYATG--------NFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        39 ~s~~~~l~~~L~~L~~g--------~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      .+++++|+-+|..+...        .+..++|...|+|+.|+++.++++.+.
T Consensus         3 ~dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~lg~sr~tvsr~l~~l~~~   54 (73)
T d1zyba1           3 LDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDN   54 (73)
T ss_dssp             CSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            45677777766554431        356789999999999999999988764

>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=84.20  E-value=0.22  Score=36.34  Aligned_cols=44  Identities=16%  Similarity=0.077  Sum_probs=32.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      .+++.+-.++...+-..+.+..++|+..|++++|+++++++...
T Consensus        27 glt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~   70 (139)
T d2a61a1          27 GITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEA   70 (139)
T ss_dssp             TCCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHh
Confidence            46666554444444556788999999999999999988877654

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=83.92  E-value=0.48  Score=31.75  Aligned_cols=47  Identities=9%  Similarity=0.142  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHHHH-hh--cCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQF-YA--TGNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        38 ~~s~~~~l~~~L~~-L~--~g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .+++.++..+.++| |.  ...+...+|..||||+..|..+-.+.+.-|-
T Consensus        18 ~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~kLr   67 (87)
T d1ttya_          18 TLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLR   67 (87)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHB
T ss_pred             cCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence            47889999999998 43  3367789999999999999998888777664

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=82.45  E-value=0.13  Score=31.73  Aligned_cols=22  Identities=14%  Similarity=0.110  Sum_probs=19.0

Q ss_pred             cccccCCcccccHHHHHHHHHH
Q psy672           57 FQIFTGDSHGVSQPTMCRLVKE   78 (314)
Q Consensus        57 ~~~~l~~~fgis~stv~~~~~~   78 (314)
                      +..++|+..|||.+||+++++.
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~   23 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINK   23 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHCC
Confidence            4578899999999999999864

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=82.11  E-value=0.37  Score=30.71  Aligned_cols=47  Identities=9%  Similarity=0.071  Sum_probs=37.4

Q ss_pred             CCCHHHHHHHHHHH-hhc--CCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672           38 KQPPMTRLLAVIQF-YAT--GNFQIFTGDSHGVSQPTMCRLVKEVSKALA   84 (314)
Q Consensus        38 ~~s~~~~l~~~L~~-L~~--g~~~~~l~~~fgis~stv~~~~~~v~~~l~   84 (314)
                      .+++.++..+.++| |..  ..++..+|..+|||+..|..+-.+.+.-|-
T Consensus         5 ~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr   54 (68)
T d2p7vb1           5 GLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR   54 (68)
T ss_dssp             CCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGG
T ss_pred             cCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            47889999999888 332  357889999999999999988887665553

>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=81.95  E-value=0.37  Score=30.16  Aligned_cols=33  Identities=18%  Similarity=0.364  Sum_probs=24.8

Q ss_pred             HHHhhcC--CcccccCCcccccHHHHHHHHHHHHH
Q psy672           49 IQFYATG--NFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        49 L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      |..|..+  .+..++|+.||||++||.+.+.....
T Consensus        11 L~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~   45 (63)
T d1biaa1          11 IALLANGEFHSGEQLGETLGMSRAAINKHIQTLRD   45 (63)
T ss_dssp             HHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3444544  45678999999999999999877543

>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=81.78  E-value=0.35  Score=33.70  Aligned_cols=41  Identities=12%  Similarity=-0.040  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      +-+++..|+.-....+..++|+.+|++++||++.+++....
T Consensus        23 ~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~   63 (109)
T d2d1ha1          23 DVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIEL   63 (109)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHHC
Confidence            34455555443334688999999999999999999887753

>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=81.76  E-value=0.57  Score=30.30  Aligned_cols=41  Identities=5%  Similarity=0.123  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHhh---cCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           42 MTRLLAVIQFYA---TGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        42 ~~~l~~~L~~L~---~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      -++.+-.|..++   .+.+..++++..|++++|+++++...++.
T Consensus         4 l~r~l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~   47 (75)
T d1mkma1           4 LKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEK   47 (75)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            445555666665   34678899999999999999998876653

>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=81.73  E-value=0.44  Score=30.42  Aligned_cols=32  Identities=9%  Similarity=0.066  Sum_probs=26.6

Q ss_pred             HhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672           51 FYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        51 ~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      +-....+-.++|+..|+|.+||++++.+.++.
T Consensus        16 ~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~   47 (71)
T d1z05a1          16 DQKGPISRIDLSKESELAPASITKITRELIDA   47 (71)
T ss_dssp             HHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            34456788899999999999999999887764

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=81.07  E-value=0.19  Score=31.45  Aligned_cols=28  Identities=11%  Similarity=-0.234  Sum_probs=24.2

Q ss_pred             HHhhcCCcccccCCcccccHHHHHHHHH
Q psy672           50 QFYATGNFQIFTGDSHGVSQPTMCRLVK   77 (314)
Q Consensus        50 ~~L~~g~~~~~l~~~fgis~stv~~~~~   77 (314)
                      .+-..|.++.++|+.+|||.+|+++|=+
T Consensus         7 ~R~~~gltQ~elA~~lGvs~~tvs~~E~   34 (62)
T d2ppxa1           7 IRRALKLTQEEFSARYHIPLGTLRDWEQ   34 (62)
T ss_dssp             HHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            3456789999999999999999998865

>d1j1va_ a.4.12.2 (A:) Chromosomal replication initiation factor DnaA C-terminal domain IV {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Chromosomal replication initiation factor DnaA C-terminal domain IV
domain: Chromosomal replication initiation factor DnaA C-terminal domain IV
species: Escherichia coli [TaxId: 562]

Probab=80.95  E-value=0.55  Score=31.88  Aligned_cols=53  Identities=9%  Similarity=0.077  Sum_probs=45.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCcccccCCccc-ccHHHHHHHHHHHHHHHHH
Q psy672           33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG-VSQPTMCRLVKEVSKALAQ   85 (314)
Q Consensus        33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fg-is~stv~~~~~~v~~~l~~   85 (314)
                      ..|...+...-++++.|.+=-++.++.++|..|| -+.|||..-++.+-..+..
T Consensus        24 ~~R~~~iv~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHsTV~~a~kki~~~~~~   77 (94)
T d1j1va_          24 KRRSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREE   77 (94)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCchhHHHHHHHHHHHHHHHhCCCHHHHHHHhCCCCchHHHHHHHHHHHHHHh
Confidence            3455567778899999999999999999999995 7999999999988887653

>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=80.66  E-value=1.1  Score=32.57  Aligned_cols=46  Identities=11%  Similarity=0.014  Sum_probs=34.6

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672           36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK   81 (314)
Q Consensus        36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~   81 (314)
                      ...+++.+--++....-..|.+..+++..+++++++|++++++...
T Consensus        31 ~~~lt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~~L~~   76 (141)
T d1lnwa_          31 RLDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEG   76 (141)
T ss_dssp             TCCCCHHHHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHHHHHH
Confidence            3457766665544444455689999999999999999999887654

>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=80.27  E-value=0.66  Score=30.23  Aligned_cols=42  Identities=21%  Similarity=0.332  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHhhcC--------------CcccccCCcccccHHHHHHHHHHHHHH
Q psy672           41 PMTRLLAVIQFYATG--------------NFQIFTGDSHGVSQPTMCRLVKEVSKA   82 (314)
Q Consensus        41 ~~~~l~~~L~~L~~g--------------~~~~~l~~~fgis~stv~~~~~~v~~~   82 (314)
                      +..+|+-+|..|+..              .+..++|...|+|+.||++.++++...
T Consensus         2 ~~~Rla~~L~~L~~~~g~~~~~~~~i~~~lt~~elA~~~g~sretvsr~l~~l~~~   57 (80)
T d3e5ua1           2 PTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRE   57 (80)
T ss_dssp             HHHHHHHHHHHHHHHHCEEETTEEECCSCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCeEEeeCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            456677777666421              244678889999999999999988775