Psyllid ID: psy13113

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280------
Protein Sequence
PVLDSNDARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARREAPPPENNELPVNVHIRDADDNRLGAAVREAFINEHF
Secondary Structure (PSIPRED)
cEEEccccccccccHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccccEEEEEEccEEEccccccccccccccccccEEEEEEEEEcccccEEEEEEcccccccHHHHHHccHHcHHHHccccccEEEccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHHHHHHHHHHHHccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccccEEEEEEccEEEEEccccHHHHHHcccccccEEEEEEEEccccEEEEEEEcccccccHHHHHHHcHHHHHccccccccEEEEcccccccccEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
pvldsndargvihSPVVKLLAVLRFYAtgnfqidsedyhdisQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNqfsgiagfprvvvgcidgthvpielpsiengehyrnrkhfYSINvqviggpnleiydvvaswpgsthdsrifqnsrvysrfdrREIRGLLLGDIgyaqneftftpvrnpitptpsqvayNAAQIRTRNSVERLFGVLKRRFACLRKklanqpttcSHIITACAVLHNIAIarreapppennelpvnvhirdaddnrLGAAVREAFINEHF
Flexible Loop (DISEMBL)
pvldsndargvihsPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASwpgsthdsrifqnsrvysrfdRREIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKlanqpttcsHIITACAVLHNIAIARREAPPPENNELPVNVHIRDADDNRLGAAVREAFINEHF
Low Complexity Region (SEG)
PVLDSNDARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIarreapppenneLPVNVHIRDADDNRLGAAVREAFINEHF
Disordered region (IsUnstruct)
*********GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIAR**************************************
Disordered Region (DISOPRED)
PVLDS*****V**SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARREAPPPENNELP***************AVREAFINEHF
Disordered Region (DISEMBL)
PVLDSNDARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARREAPPPENNELPVNVHIRDADDNRLGAAVREAFINEHF
Disordered Region (DISPRO)
**********VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARREA***********************AA*REAFINE*F
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
PVLDSNDARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARREAPPPENNELPVNVHIRDADDNRLGAAVREAFINEHF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	286	2.2.26 [Sep-21-2011]
Q17QR8	349	Putative nuclease HARBI1	yes	N/A	0.916	0.750	0.345	5e-36
Q8BR93	349	Putative nuclease HARBI1	yes	N/A	0.800	0.656	0.387	5e-36
B0BN95	349	Putative nuclease HARBI1	yes	N/A	0.916	0.750	0.345	1e-35
Q96MB7	349	Putative nuclease HARBI1	yes	N/A	0.916	0.750	0.339	1e-34
Q6AZB8	349	Putative nuclease HARBI1	no	N/A	0.923	0.756	0.344	1e-34
Q5U538	347	Putative nuclease HARBI1	N/A	N/A	0.800	0.659	0.329	3e-26

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

 Score =  151 bits (382), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 101/292 (34%), Positives = 147/292 (50%), Gaps = 30/292 (10%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
           SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+IHFP D   
Sbjct: 68  SPETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPADEAS 127

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
           +Q  K++F G+AG P  V+G +D  HV I+ P+ E+   Y NRK  +S+N  ++      
Sbjct: 128 VQALKDEFYGLAGIPG-VIGVVDCMHVAIKAPNAEDLS-YVNRKGLHSLNCLMVCDIRGA 185

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFDR-REIRGLLLGDIGYAQNEFTFTPVRNPITPT 189
           +  V  SWPGS  D  + Q S + S+F+        LLGD  +    +  TP+  P   T
Sbjct: 186 LMTVETSWPGSLQDCVVLQQSSLSSQFEAGMHKESWLLGDSSFFLRTWLMTPLHIP--ET 243

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
           P++  YN A   T + +E+ F  L  RF CL   +  L   P   SHII AC VLHNI++
Sbjct: 244 PAEYRYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKSSHIILACCVLHNISL 303

Query: 247 ARR------------EAPPPENNELPVNVHIRDADDNRLGAAVREAFINEHF 286
                          E PP E  E   ++   D + +R    +R+  +  HF
Sbjct: 304 EHGMDVWSSPVTGPVEQPPEEEYE---HMESLDLEADR----IRQELMLTHF 348

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

 Score =  151 bits (381), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 131/240 (54%), Gaps = 11/240 (4%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
           SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+IHFP D   
Sbjct: 68  SPETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPVDEAA 127

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
           +Q+ K++F G+AG P  V+G  D  HV I+ P+ E+   Y NRK  +S+N  V+      
Sbjct: 128 VQSLKDEFYGLAGMPG-VIGVADCIHVAIKAPNAED-LSYVNRKGLHSLNCLVVCDIRGA 185

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIR-GLLLGDIGYAQNEFTFTPVRNPITPT 189
           +  V  SWPGS  D  + Q S + S+F+    +   LLGD  +    +  TP+  PI  T
Sbjct: 186 LMTVETSWPGSLQDCAVLQRSSLTSQFETGMPKDSWLLGDSSFFLRSWLLTPL--PIPET 243

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
            ++  YN A   T + +ER    L  RF CL   +  L   P  CSHII AC VLHNI++
Sbjct: 244 AAEYRYNRAHSATHSVIERTLQTLCCRFRCLDGSKGALQYSPEKCSHIILACCVLHNISL 303

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

 Score =  150 bits (379), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 101/292 (34%), Positives = 148/292 (50%), Gaps = 30/292 (10%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
           SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+IHFP D   
Sbjct: 68  SPETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPADEAA 127

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
           +Q+ K++F G+AG P  V+G +D  HV I+ P+ E+   Y NRK  +S+N  V+      
Sbjct: 128 IQSLKDEFYGLAGMPG-VIGAVDCIHVAIKAPNAED-LSYVNRKGLHSLNCLVVCDIRGA 185

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIR-GLLLGDIGYAQNEFTFTPVRNPITPT 189
           +  V  SWPGS  D  + Q S + S+F+    +   LLGD  +  + +  TP+  P   T
Sbjct: 186 LMTVETSWPGSLQDCAVLQQSSLSSQFETGMPKDSWLLGDSSFFLHTWLLTPLHIP--ET 243

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
           P++  YN A   T + +E+    L  RF CL   +  L   P   SHII AC VLHNI++
Sbjct: 244 PAEYRYNRAHSATHSVIEKTLRTLCCRFRCLDGSKGALQYSPEKSSHIILACCVLHNISL 303

Query: 247 ARR------------EAPPPENNELPVNVHIRDADDNRLGAAVREAFINEHF 286
                          E PP   +E    +   D + +R    +R+  I  HF
Sbjct: 304 EHGMDVWSSPVTGPIEQPPEGEDE---QMESLDLEADR----IRQELILTHF 348

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

 Score =  147 bits (370), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 99/292 (33%), Positives = 147/292 (50%), Gaps = 30/292 (10%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
           SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+I FP D   
Sbjct: 68  SPETQVLAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIRFPADEAS 127

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
           +Q  K++F G+AG P  V+G +D  HV I+ P+ E+   Y NRK  +S+N  ++      
Sbjct: 128 IQALKDEFYGLAGMPG-VMGVVDCIHVAIKAPNAEDLS-YVNRKGLHSLNCLMVCDIRGT 185

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIR-GLLLGDIGYAQNEFTFTPVRNPITPT 189
           +  V  +WPGS  D  + Q S + S+F+    +   LLGD  +    +  TP+  P   T
Sbjct: 186 LMTVETNWPGSLQDCAVLQQSSLSSQFEAGMHKDSWLLGDSSFFLRTWLMTPLHIP--ET 243

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
           P++  YN A   T + +E+ F  L  RF CL   +  L   P   SHII AC VLHNI++
Sbjct: 244 PAEYRYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKSSHIILACCVLHNISL 303

Query: 247 AR------------REAPPPENNELPVNVHIRDADDNRLGAAVREAFINEHF 286
                          E PP E  E   ++   D + +R    +R+  +  HF
Sbjct: 304 EHGMDVWSSPMTGPMEQPPEEEYE---HMESLDLEADR----IRQELMLTHF 348

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

 Score =  146 bits (369), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 100/290 (34%), Positives = 146/290 (50%), Gaps = 26/290 (8%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQT 73
           SP V++LA L FY +G+FQ    D   ISQ+++ R V+ V++ L +   ++I F  D  T
Sbjct: 68  SPDVQILAALGFYTSGSFQSKMGDAIGISQASMSRCVSNVTKALIEKAPEFIGFTRDEAT 127

Query: 74  A---KNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
               K++F  IAG P  V G +D  H+ I+ P+ ++   Y N+K F+SIN Q++      
Sbjct: 128 KQQFKDEFYRIAGIPN-VTGVVDCAHIAIKAPNADDSS-YVNKKGFHSINCQLVCDARGL 185

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRRE--IRGLLLGDIGYAQNEFTFTPVRNPITP 188
           +      WPGS  D  +F+ S V   F+ +E    G LLGD  Y   ++  TPV++P   
Sbjct: 186 LLSAETHWPGSLTDRAVFKQSNVAKLFEEQENDDEGWLLGDNRYPLKKWLMTPVQSP--E 243

Query: 189 TPSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIA 245
           +P+   YN A   T   V+R F  ++ RF CL   +  L   P  CSHII AC VLHNI+
Sbjct: 244 SPADYRYNLAHTTTHEIVDRTFRAIQTRFRCLDGAKGYLQYSPEKCSHIIQACCVLHNIS 303

Query: 246 I---------ARREAPPPENNELPVNVHIRDADDNRLGAAVREAFINEHF 286
           +          R EA      ++  +    D DD      VR+  I  HF
Sbjct: 304 LQSGLDAWTFERTEATDQSGEDIDPS----DTDDPE-ALRVRQELIQNHF 348

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 =  119 bits (297), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 79/240 (32%), Positives = 122/240 (50%), Gaps = 11/240 (4%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
           SP  +++A L FY +G+FQ    D   ISQ+++ R V  V+E L +   Q+I FP D   
Sbjct: 68  SPETQIMAALGFYTSGSFQTRMGDTIGISQASMSRCVTNVTEALVERASQFISFPRDERS 127

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
           +Q  K++F  +AG P  V+G +D T V I+ P+ E+   Y N +  +S+N  ++      
Sbjct: 128 VQGLKDEFYNLAGVPG-VLGVVDCTQVNIKAPNSEDLS-YVNSRGLHSLNCLLVCDARGS 185

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFD-RREIRGLLLGDIGYAQNEFTFTPVRNPITPT 189
           +     S  GS  D+ +   S +   F+ +   +G LL D  +    +  TPV+ P   +
Sbjct: 186 LLWAETSRLGSMQDNAVLHQSELSGLFETKMHKQGWLLADNAFILRPWLMTPVQIP--ES 243

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
           PS   YN A   T + +ER    L+ RF CL   R  L   P   + I+ AC +LHNIA+
Sbjct: 244 PSDYRYNMAHTATHSVMERTQRSLRLRFRCLDGSRATLQYSPEKSAQIVLACCILHNIAL 303

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	286
328704555	370	PREDICTED: putative nuclease HARBI1-like	0.944	0.729	0.433	6e-52
328705831	326	PREDICTED: putative nuclease HARBI1-like	0.944	0.828	0.433	6e-52
328711563	335	PREDICTED: putative nuclease HARBI1-like	0.937	0.8	0.419	2e-50
332374146	353	unknown [Dendroctonus ponderosae]	0.863	0.699	0.416	2e-50
328697485	681	PREDICTED: hypothetical protein LOC10057	0.856	0.359	0.429	2e-49
328696997	356	PREDICTED: putative nuclease HARBI1-like	0.898	0.721	0.430	3e-49
270015185	561	hypothetical protein TcasGA2_TC000011 [T	0.923	0.470	0.419	1e-47
270012680	358	hypothetical protein TcasGA2_TC015989 [T	0.944	0.754	0.419	3e-47
350536511	353	uncharacterized protein LOC100569528 [Ac	0.944	0.764	0.417	8e-47
193666845	342	PREDICTED: putative nuclease HARBI1-like	0.800	0.669	0.453	1e-46

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

 Score =  210 bits (535), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 124/286 (43%), Positives = 169/286 (59%), Gaps = 16/286 (5%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE---D 70
           +P+ +LL  LRFYATGNF I   D+  IS ++  ++V +VS  LA    ++I  PE   +
Sbjct: 85  APMTQLLITLRFYATGNFLITVGDFGGISVASAGKIVKRVSYALAFLSSRYIRLPETPEE 144

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
               K QF G+A FP+V+ G ID TH+ ++ PS E GE YRNRK ++S+NVQ +   NLE
Sbjct: 145 KMELKVQFYGLARFPKVI-GAIDCTHIKLQCPSKEYGELYRNRKGYFSLNVQALVNANLE 203

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRG-LLLGDIGYAQNEFTFTPVRNPITPT 189
             DVV  WPGS HDS IF NSR+ +R +  E    ++LGD GYA + +  TP+ +  T T
Sbjct: 204 FMDVVVRWPGSAHDSNIFANSRLKARIELPEFSDCIILGDSGYALSHYLLTPLAH--TTT 261

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARR 249
            ++  YN +QIRTRN VER FGV KRRF  L   L  +  T   +I ACAVLHN+A  + 
Sbjct: 262 NAERLYNESQIRTRNVVERSFGVWKRRFPVLFFGLRLKMETTMAVIQACAVLHNMARLQN 321

Query: 250 EAPPP---ENNELPVNVHIRDADD------NRLGAAVREAFINEHF 286
           +  PP   EN +  ++  I + +       N    A+R A I EHF
Sbjct: 322 DPQPPDDIENIKQLLSAEISEIEAATQPQINSPAQALRTALIMEHF 367

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 =  210 bits (534), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 124/286 (43%), Positives = 167/286 (58%), Gaps = 16/286 (5%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE---D 70
           +P+ +LL  LRFYATGNF I   D+  IS ++  ++V +VS  LA    ++I  PE   +
Sbjct: 41  APMTQLLITLRFYATGNFLITVGDFGGISVASAGKIVKRVSYALAFLSSRYIRLPETPEE 100

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
               K QF G+A FP+V+ G ID TH+ ++ PS E GE YRNRK ++S+NVQ +   NLE
Sbjct: 101 KMELKVQFYGLARFPKVI-GAIDCTHIKLQCPSKEYGELYRNRKGYFSLNVQALVNANLE 159

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRG-LLLGDIGYAQNEFTFTPVRNPITPT 189
             DVV  WPGS HDS IF NSR+ +R +  E    ++LGD GYA + +  TP+    T T
Sbjct: 160 FMDVVVRWPGSAHDSNIFANSRLKARIELPEFSDCIILGDSGYALSHYLLTPLAR--TTT 217

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARR 249
            ++  YN +QIRTRN VER FGV KRRF  L   L  +  T   +I ACAVLHN+A  + 
Sbjct: 218 NAERLYNESQIRTRNVVERSFGVWKRRFPVLFFGLRLKMETTMAVIQACAVLHNMARLQN 277

Query: 250 EAPPPENNE-----LPVNVHIRDADD----NRLGAAVREAFINEHF 286
           +  PP++ E     L   +   +A      N    A+R A I EHF
Sbjct: 278 DPQPPDDKENIKQLLSAEISEIEAATQPQINSPAQALRTALIMEHF 323

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 =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 120/286 (41%), Positives = 168/286 (58%), Gaps = 18/286 (6%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE---D 70
           SP+ +LL  LRF+ATGNF I + D+  +S +   ++V +VS  LA    ++I  P+   +
Sbjct: 52  SPMTQLLLTLRFFATGNFLITAGDFSGVSVAAAGQIVKRVSYVLATKSDKYIKMPKTTAE 111

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
           +   K +F G+A F +V+ G ID TH+ ++ PS E GE YRNR  ++S+N+Q +   NLE
Sbjct: 112 IMELKVKFYGLARFLKVI-GAIDCTHIKLQSPSREYGEQYRNRNGYFSLNLQALVNANLE 170

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRG-LLLGDIGYAQNEFTFTPVRNPITPT 189
             DVVA WPGS HDS +F NSR+ +R +  E +  ++LGD GYA + +  TP+ NP   T
Sbjct: 171 FLDVVARWPGSAHDSNVFANSRLRARMELHEFKDCVILGDPGYALSHYLLTPIANP--TT 228

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIA-IAR 248
            ++  YN +QIRTRN VER FGV KRRF  L   L  +  T   +I +CA+LHNIA +A 
Sbjct: 229 KAERLYNESQIRTRNVVERTFGVWKRRFPVLFFGLRLKMETSMAVIQSCAILHNIARLAN 288

Query: 249 REAPPPE--------NNELPVNVHIRDADDNRLGAAVREAFINEHF 286
              PP E         NEL     +   + N  G  +R A I EHF
Sbjct: 289 DPQPPDEVENITDLLTNELMDIEDVIQPEHNNCG--LRNALIAEHF 332

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 104/250 (41%), Positives = 153/250 (61%), Gaps = 3/250 (1%)

Query: 9   RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFP 68
           RG+    ++ LL  L+FY +G+ +I   +     QST+ R++ KV+  + +  + +I FP
Sbjct: 73  RGLPVPLIIGLLLTLQFYGSGSLRIICGELKGFHQSTVSRVITKVTRSIYEQSRNYIKFP 132

Query: 69  EDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPN 128
           E+L T + QF  I  FP V+ GCI    +PI  P   N E +RN K  +S+NVQ++ GP+
Sbjct: 133 ENLNTVQTQFQTIRNFPNVI-GCIGCAQIPIMSPGGPNAELFRNGKRSFSLNVQIVAGPD 191

Query: 129 LEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPITP 188
           LEIYD+VA+ PGS  +  +F  S V +RF+++++ G LLGD GY    +  TP R+P T 
Sbjct: 192 LEIYDIVATNPGSYRNDHVFNKSAVKTRFEKKQLPGYLLGDSGYPSLTYLLTPFRDPCTN 251

Query: 189 TPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIAR 248
              +  YN A  + RN V+R FGVL+ RF+CLR+ L ++  T   II ACAVLHNI+IA 
Sbjct: 252 EEKR--YNEAHAQIRNIVDRTFGVLRHRFSCLRRLLRHKHETICCIIVACAVLHNISIAH 309

Query: 249 REAPPPENNE 258
           RE   P+  +
Sbjct: 310 REVVEPDGED 319

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  201 bits (512), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 109/254 (42%), Positives = 156/254 (61%), Gaps = 9/254 (3%)

Query: 5   SNDARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQW 64
           +N  R ++  P+ KLL  LRFYA G   + + D+  +S+++ C +V  V+E +A     +
Sbjct: 69  TNRNRAIL--PITKLLLTLRFYALGTILLANGDFVGVSKTSACNIVRTVTEAIASLRPLY 126

Query: 65  IHFPE---DLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINV 121
           I  PE   ++Q  + +F  IA FPR++ G ID THV ++ P     E YRNRK ++S+NV
Sbjct: 127 IKMPEHHCNIQETRLKFYNIARFPRII-GAIDCTHVKLQSPGGNIAEVYRNRKGYFSLNV 185

Query: 122 QVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREI-RGLLLGDIGYAQNEFTFT 180
           QV+GG +LEI D+VA WPGSTHD  IF NS ++ +F+  E+   +LLGD GY    +   
Sbjct: 186 QVVGGRSLEILDIVARWPGSTHDQVIFNNSTIHFKFETNEMGDNILLGDGGYECRPYILV 245

Query: 181 PVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAV 240
           P+ +P   T +++ YN +QIRTRN++ERLFGV KRRF  L   +   P     II A AV
Sbjct: 246 PLISP--NTNAELLYNESQIRTRNTIERLFGVWKRRFPILSLGIRTTPDRAQAIIVATAV 303

Query: 241 LHNIAIARREAPPP 254
           LHN+A    E+ PP
Sbjct: 304 LHNLASVLGESIPP 317

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 =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 114/265 (43%), Positives = 158/265 (59%), Gaps = 8/265 (3%)

Query: 1   PVLDSNDARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC 60
           P + SN  R    +   KLL  LRFYATG+F I + D   +S+ST C +V  VS  LA+ 
Sbjct: 64  PSISSNTDRNNAVTTTQKLLLALRFYATGSFLISAGDVVGVSKSTACVIVRDVSVALAQL 123

Query: 61  HQQWIHFPE---DLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFY 117
             Q+I  PE   +++  + QF GIA FP +V+G ID TH+ I+ P   N E++RNRK ++
Sbjct: 124 RPQFIKMPETNDEIKELQKQFYGIAKFP-LVIGAIDCTHIKIQSPGGPNAEYFRNRKGWF 182

Query: 118 SINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRG--LLLGDIGYAQN 175
           S+NVQ +    L+I D+V  WPGSTHDS IF  S++ +     +  G  L++ D GYA  
Sbjct: 183 SLNVQTVVSAKLKIMDIVVRWPGSTHDSTIFSRSKINNDLHVEQKWGNSLIVADSGYANT 242

Query: 176 EFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHII 235
           +   TP  NP    P  + YN +QIRTRN VER +GVLKRRF  L   +  Q +   ++I
Sbjct: 243 KHIVTPFLNP-QAGPENL-YNESQIRTRNPVERCYGVLKRRFPVLSLGMRLQISNIQNVI 300

Query: 236 TACAVLHNIAIARREAPPPENNELP 260
            AC+VLHNIAI   +  P ++ +LP
Sbjct: 301 IACSVLHNIAIDCNDVMPMDDVQLP 325

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 =  196 bits (497), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 119/284 (41%), Positives = 160/284 (56%), Gaps = 20/284 (7%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFP---ED 70
           S   ++L  LRFYATG F     D+  + +S ICR++ +V+ E+A+    +I  P   E+
Sbjct: 285 SAQTQMLIALRFYATGGFLELLGDWIHVHKSNICRVIQRVTHEIARLSPHYIKMPRTAEE 344

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
           L   K +F  I GFPRVV G ID THV I+ P   N E YRNRK ++SINVQ I   +L+
Sbjct: 345 LMATKRKFFRICGFPRVV-GAIDCTHVGIQSPGGANAELYRNRKGYFSINVQTICDADLK 403

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPITPTP 190
           +  +++ WPGS HDS IF NS +   F  R  RG LLGD GY   ++   PVRNP     
Sbjct: 404 LLHIISRWPGSVHDSTIFNNSPLPVDF--RLGRGYLLGDGGYPCQQYLLIPVRNP--NNA 459

Query: 191 SQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARRE 250
           SQ AYN A I+TRN++ER FG+LKRRF  L+  L  +  T   +I AC VL+NI   R +
Sbjct: 460 SQEAYNRAYIKTRNTIERFFGILKRRFPLLKSGLRLKIDTIVQVIVACGVLYNICKERND 519

Query: 251 APPPENNELPVNVHIRDADD--------NRLGAAVREAFINEHF 286
                 +E+  N    D +D        N +  AVR + I+  F
Sbjct: 520 HIEEYFDEVMEN----DEEDFIYQENNINNVNFAVRNSLIDTIF 559

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  194 bits (494), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 118/281 (41%), Positives = 159/281 (56%), Gaps = 11/281 (3%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFP--EDL 71
           S + K+L  +R+ ATG+FQ    D   + +ST+C ++  V +++A+   Q+I  P  E+L
Sbjct: 80  SAINKILITMRYLATGSFQQLVGDTVAVHKSTVCVVIKSVIQKIAQLKPQFIKMPNREEL 139

Query: 72  QTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEI 131
              + +F      PRV+ G ID +HV IE P   N E +RNRK F+SINVQ +   +L+I
Sbjct: 140 HNVQLKFYRKRRMPRVI-GAIDCSHVRIESPGGPNAEIFRNRKGFFSINVQAVCDADLQI 198

Query: 132 YDVVASWPGSTHDSRIFQNSRVYSRFDRREIR-GLLLGDIGYAQNEFTFTPVRNPITPTP 190
            ++VA WPGS HDS IF +S + +  +R E   G LLGD GYA   F  TPV NP   T 
Sbjct: 199 RNIVARWPGSVHDSTIFNDSSLCAHLERGEYENGFLLGDSGYACRPFLLTPVLNP--RTA 256

Query: 191 SQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARRE 250
           ++ AYN +   TRN++ER FGVLKRRF CL   L  +  T    I ACAVLHNIAI   +
Sbjct: 257 AEEAYNLSHRTTRNAIERCFGVLKRRFPCLSLGLRTKMNTTLATIVACAVLHNIAIFTND 316

Query: 251 APPPENN--ELPVNVHIRDADDN---RLGAAVREAFINEHF 286
             PP +   E+P  + I     N       A R A I  HF
Sbjct: 317 NEPPRDPDVEVPQELEIEPVHRNNNINENTAARTALIRTHF 357

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350536511|ref|NP_001233059.1| uncharacterized protein LOC100569528 [Acyrthosiphon pisum] gi|239789800|dbj|BAH71500.1| hypothetical protein [Acyrthosiphon pisum]

 Score =  193 bits (490), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 116/278 (41%), Positives = 156/278 (56%), Gaps = 8/278 (2%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFP---ED 70
           + + KLL  LRFYATGNF I S D+  +S++T   +V  VS  +AK   ++I  P    +
Sbjct: 76  TSINKLLLALRFYATGNFLITSGDFLGVSKTTASLIVRDVSIAIAKLRPRFIQMPTTERE 135

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
           +   +  F  IA FPR + G ID THV I+ P   N E++RNRK ++SINVQ I  PNL+
Sbjct: 136 ISKLQRSFYQIARFPRTI-GAIDCTHVKIQNPGGPNAEYFRNRKGYFSINVQTIACPNLK 194

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRF-DRREIRGLLLGDIGYAQNEFTFTPVRNPITPT 189
           I DVVA WPGS HD  IF+ S++Y    + +    L++ D GYA +    TP  NP    
Sbjct: 195 IMDVVARWPGSCHDQTIFKKSQIYYNLINGKWGNSLIVADSGYANSRHLVTPFLNPRNDI 254

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAIARR 249
             +  YN + IRTRN VER +GVLKRRF  L   L  +  T   +I AC VLHNIA    
Sbjct: 255 --EELYNESIIRTRNPVERSYGVLKRRFPVLSLGLRLKLETTQAVIVACCVLHNIACDNN 312

Query: 250 EAPPPENN-ELPVNVHIRDADDNRLGAAVREAFINEHF 286
           +  PP  +  LP N +I   +    G   R+  + E+F
Sbjct: 313 DMDPPALDIVLPENENINIEEQQPEGENARQQLMQEYF 350

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193666845|ref|XP_001944531.1| PREDICTED: putative nuclease HARBI1-like [Acyrthosiphon pisum]

 Score =  192 bits (489), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 107/236 (45%), Positives = 143/236 (60%), Gaps = 7/236 (2%)

Query: 14  SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFP---ED 70
           SP  ++L  LRFYA G       D+  +S +T  R++ +V+ E+AK  +  I  P   E+
Sbjct: 78  SPENQVLLTLRFYALGTIYQAVGDFVGVSTATAGRIIPRVTHEIAKMRKDIIRMPSTQEE 137

Query: 71  LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
           +  AK  F  IA FPRV+ G ID THV I  P  +N E +RNRK ++SINVQ++ G +L+
Sbjct: 138 INQAKLNFFSIAKFPRVI-GVIDCTHVKILSPGGDNAEIFRNRKGYFSINVQIVAGADLK 196

Query: 131 IYDVVASWPGSTHDSRIFQNSRVYSRF-DRREIRGLLLGDIGYAQNEFTFTPVRNPITPT 189
           I ++VA WPGS HDS IF NSR+ ++F D      LLLGD GY  + +  T +  P   T
Sbjct: 197 IKNIVARWPGSAHDSNIFSNSRIRAQFEDNMFGDALLLGDSGYGVSNYMMTILNEP--RT 254

Query: 190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIA 245
             +  YN + IRTRN+VERLFGVLKRRF  +   + +       II ACAVLHNIA
Sbjct: 255 EGEQLYNESLIRTRNTVERLFGVLKRRFPIISLGIKSSLELTQGIIVACAVLHNIA 310

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

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	286
UNIPROTKB|E1BQ99	348	HARBI1 "Uncharacterized protei	0.800	0.658	0.379	1.2e-35
MGI|MGI:2443194	349	Harbi1 "harbinger transposase	0.800	0.656	0.387	1.1e-34
ZFIN|ZDB-GENE-040608-1	349	harbi1 "harbinger transposase	0.940	0.770	0.340	2.2e-34
UNIPROTKB|Q17QR8	349	HARBI1 "Putative nuclease HARB	0.800	0.656	0.379	2.8e-34
RGD|1584007	349	Harbi1 "harbinger transposase	0.800	0.656	0.379	2.8e-34
UNIPROTKB|F1SIA2	349	HARBI1 "Uncharacterized protei	0.800	0.656	0.370	7.4e-34
UNIPROTKB|E2RCW9	349	HARBI1 "Uncharacterized protei	0.800	0.656	0.370	5.2e-33
UNIPROTKB|Q96MB7	349	HARBI1 "Putative nuclease HARB	0.800	0.656	0.370	5.2e-33
TAIR|locus:2143104	502	AT5G12010 [Arabidopsis thalian	0.793	0.452	0.292	3.1e-19
ZFIN|ZDB-GENE-060810-147	395	si:dkey-197c15.6 "si:dkey-197c	0.786	0.569	0.297	3.6e-19

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

 Score = 385 (140.6 bits), Expect = 1.2e-35, P = 1.2e-35
 Identities = 91/240 (37%), Positives = 132/240 (55%)

Query:    14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
             SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+IHFPED   
Sbjct:    68 SPETQVLAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERAPQFIHFPEDEAA 127

Query:    71 LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
             +Q+ K+ F  +AG P V+ G +D THV I+ P+ E+   Y NRK  +S+N  ++      
Sbjct:   128 VQSLKDDFYALAGMPGVL-GVVDCTHVAIKAPNAEDLS-YVNRKGLHSLNCLMVCDARGA 185

Query:   131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIR-GLLLGDIGYAQNEFTFTPVRNPITPT 189
             +      WPGS  D  + Q + + S+F+    + G LLGD  +    +  TP+  P   T
Sbjct:   186 LLSAETHWPGSMPDCNVLQQAALTSQFENELYKDGWLLGDSSFFLRTWLMTPLHIP--ET 243

Query:   190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
             P++  YN A   T N +ER F  ++ RF CL   +  L   P   SHII AC VLHNI++
Sbjct:   244 PAEYRYNMAHSATHNVIERTFRTIRSRFRCLDGSKGTLQYSPEKSSHIILACCVLHNISL 303

GO:0005737 "cytoplasm" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

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

 Score = 376 (137.4 bits), Expect = 1.1e-34, P = 1.1e-34
 Identities = 93/240 (38%), Positives = 131/240 (54%)

Query:    14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
             SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+IHFP D   
Sbjct:    68 SPETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPVDEAA 127

Query:    71 LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
             +Q+ K++F G+AG P V+ G  D  HV I+ P+ E+   Y NRK  +S+N  V+      
Sbjct:   128 VQSLKDEFYGLAGMPGVI-GVADCIHVAIKAPNAEDLS-YVNRKGLHSLNCLVVCDIRGA 185

Query:   131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIR-GLLLGDIGYAQNEFTFTPVRNPITPT 189
             +  V  SWPGS  D  + Q S + S+F+    +   LLGD  +    +  TP+  PI  T
Sbjct:   186 LMTVETSWPGSLQDCAVLQRSSLTSQFETGMPKDSWLLGDSSFFLRSWLLTPL--PIPET 243

Query:   190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
              ++  YN A   T + +ER    L  RF CL   +  L   P  CSHII AC VLHNI++
Sbjct:   244 AAEYRYNRAHSATHSVIERTLQTLCCRFRCLDGSKGALQYSPEKCSHIILACCVLHNISL 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 = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 97/285 (34%), Positives = 142/285 (49%)

Query:    14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQT 73
             SP V++LA L FY +G+FQ    D   ISQ+++ R V+ V++ L +   ++I F  D  T
Sbjct:    68 SPDVQILAALGFYTSGSFQSKMGDAIGISQASMSRCVSNVTKALIEKAPEFIGFTRDEAT 127

Query:    74 A---KNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
                 K++F  IAG P V  G +D  H+ I+ P+ ++   Y N+K F+SIN Q++      
Sbjct:   128 KQQFKDEFYRIAGIPNVT-GVVDCAHIAIKAPNADDSS-YVNKKGFHSINCQLVCDARGL 185

Query:   131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREI--RGLLLGDIGYAQNEFTFTPVRNPITP 188
             +      WPGS  D  +F+ S V   F+ +E    G LLGD  Y   ++  TPV++P   
Sbjct:   186 LLSAETHWPGSLTDRAVFKQSNVAKLFEEQENDDEGWLLGDNRYPLKKWLMTPVQSP--E 243

Query:   189 TPSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIA 245
             +P+   YN A   T   V+R F  ++ RF CL   +  L   P  CSHII AC VLHNI+
Sbjct:   244 SPADYRYNLAHTTTHEIVDRTFRAIQTRFRCLDGAKGYLQYSPEKCSHIIQACCVLHNIS 303

Query:   246 IXXXXXXXXXXXXLPVNVHIRDAD----DNRLGAAVREAFINEHF 286
             +               +    D D    D+     VR+  I  HF
Sbjct:   304 LQSGLDAWTFERTEATDQSGEDIDPSDTDDPEALRVRQELIQNHF 348

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

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

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 91/240 (37%), Positives = 130/240 (54%)

Query:    14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
             SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+IHFP D   
Sbjct:    68 SPETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPADEAS 127

Query:    71 LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
             +Q  K++F G+AG P V+ G +D  HV I+ P+ E+   Y NRK  +S+N  ++      
Sbjct:   128 VQALKDEFYGLAGIPGVI-GVVDCMHVAIKAPNAEDLS-YVNRKGLHSLNCLMVCDIRGA 185

Query:   131 IYDVVASWPGSTHDSRIFQNSRVYSRFDR-REIRGLLLGDIGYAQNEFTFTPVRNPITPT 189
             +  V  SWPGS  D  + Q S + S+F+        LLGD  +    +  TP+  P   T
Sbjct:   186 LMTVETSWPGSLQDCVVLQQSSLSSQFEAGMHKESWLLGDSSFFLRTWLMTPLHIP--ET 243

Query:   190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
             P++  YN A   T + +E+ F  L  RF CL   +  L   P   SHII AC VLHNI++
Sbjct:   244 PAEYRYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKSSHIILACCVLHNISL 303

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

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

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 91/240 (37%), Positives = 132/240 (55%)

Query:    14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
             SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+IHFP D   
Sbjct:    68 SPETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIHFPADEAA 127

Query:    71 LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
             +Q+ K++F G+AG P V+ G +D  HV I+ P+ E+   Y NRK  +S+N  V+      
Sbjct:   128 IQSLKDEFYGLAGMPGVI-GAVDCIHVAIKAPNAEDLS-YVNRKGLHSLNCLVVCDIRGA 185

Query:   131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIR-GLLLGDIGYAQNEFTFTPVRNPITPT 189
             +  V  SWPGS  D  + Q S + S+F+    +   LLGD  +  + +  TP+  P   T
Sbjct:   186 LMTVETSWPGSLQDCAVLQQSSLSSQFETGMPKDSWLLGDSSFFLHTWLLTPLHIP--ET 243

Query:   190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
             P++  YN A   T + +E+    L  RF CL   +  L   P   SHII AC VLHNI++
Sbjct:   244 PAEYRYNRAHSATHSVIEKTLRTLCCRFRCLDGSKGALQYSPEKSSHIILACCVLHNISL 303

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

 Score = 368 (134.6 bits), Expect = 7.4e-34, P = 7.4e-34
 Identities = 89/240 (37%), Positives = 129/240 (53%)

Query:    14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
             SP  ++LA L FY +G+FQ    D   ISQ+++ R V  V+E L +   Q+I FP D   
Sbjct:    68 SPETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVTNVTEALVERASQFIRFPADEAS 127

Query:    71 LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
             +Q  K++F G+AG P V+ G +D  HV I+ P+ E+   Y NRK  +S+N  ++      
Sbjct:   128 VQALKDEFYGLAGMPGVI-GVVDCIHVAIKAPNAEDLS-YVNRKGLHSLNCLMVCDIRGT 185

Query:   131 IYDVVASWPGSTHDSRIFQNSRVYSRFDR-REIRGLLLGDIGYAQNEFTFTPVRNPITPT 189
             +  V  +WPGS  D  + Q S + S+F+        LLGD  +    +  TP+  P   T
Sbjct:   186 LMTVETNWPGSLQDCVVLQQSSLSSQFEAGMHKESWLLGDSSFFLRSWLMTPLHIP--ET 243

Query:   190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
             P++  YN A   T + +E+ F  L  RF CL   +  L   P  CSHII AC VLHNI++
Sbjct:   244 PAEYRYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKCSHIILACCVLHNISL 303

GO:0005813 "centrosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 89/240 (37%), Positives = 129/240 (53%)

Query:    14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
             SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+I FP D   
Sbjct:    68 SPETQILAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERATQFIRFPADEAS 127

Query:    71 LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
             +Q  K++F G+AG P V+ G +D  HV I+ P+ E+   Y NRK  +S+N  ++      
Sbjct:   128 MQALKDEFYGLAGMPGVI-GVVDCIHVAIKAPNAEDLS-YVNRKGLHSLNCLMVCDIRGA 185

Query:   131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIR-GLLLGDIGYAQNEFTFTPVRNPITPT 189
             +  V  +WPGS  D  + Q S + S F+    +   LLGD  +    +  TP+  P   T
Sbjct:   186 LMTVETNWPGSLQDYAVLQQSSLNSHFEAGMHKDSWLLGDSSFFLRTWLMTPLHIP--ET 243

Query:   190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
             P++  YN A   T + +E+ F  L  RF CL   +  L   P   SHII AC VLHNI++
Sbjct:   244 PAEYRYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKSSHIILACCVLHNISL 303

GO:0005813 "centrosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 89/240 (37%), Positives = 130/240 (54%)

Query:    14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPED--- 70
             SP  ++LA L FY +G+FQ    D   ISQ+++ R VA V+E L +   Q+I FP D   
Sbjct:    68 SPETQVLAALGFYTSGSFQTRMGDAIGISQASMSRCVANVTEALVERASQFIRFPADEAS 127

Query:    71 LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLE 130
             +Q  K++F G+AG P V+ G +D  HV I+ P+ E+   Y NRK  +S+N  ++      
Sbjct:   128 IQALKDEFYGLAGMPGVM-GVVDCIHVAIKAPNAEDLS-YVNRKGLHSLNCLMVCDIRGT 185

Query:   131 IYDVVASWPGSTHDSRIFQNSRVYSRFDRREIR-GLLLGDIGYAQNEFTFTPVRNPITPT 189
             +  V  +WPGS  D  + Q S + S+F+    +   LLGD  +    +  TP+  P   T
Sbjct:   186 LMTVETNWPGSLQDCAVLQQSSLSSQFEAGMHKDSWLLGDSSFFLRTWLMTPLHIP--ET 243

Query:   190 PSQVAYNAAQIRTRNSVERLFGVLKRRFACL---RKKLANQPTTCSHIITACAVLHNIAI 246
             P++  YN A   T + +E+ F  L  RF CL   +  L   P   SHII AC VLHNI++
Sbjct:   244 PAEYRYNMAHSATHSVIEKTFRTLCSRFRCLDGSKGALQYSPEKSSHIILACCVLHNISL 303

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

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

 Score = 237 (88.5 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 71/243 (29%), Positives = 121/243 (49%)

Query:    15 PVVKLLAVLRF-YATGN-FQIDSEDYHDISQSTICRLVAKVSEELAKCHQ-QWIHFPED- 70
             PV + +AV  +  ATG   ++ S+ +  +  ST  +LV +V + +      +++ +P+D 
Sbjct:   209 PVRQRVAVCIWRLATGEPLRLVSKKF-GLGISTCHKLVLEVCKAIKDVLMPKYLQWPDDE 267

Query:    71 -LQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIE-----NGEHY-RNRKHFYSINVQV 123
              L+  + +F  ++G P VV G +  TH+PI  P I      N  H  RN+K  YSI +Q 
Sbjct:   268 SLRNIRERFESVSGIPNVV-GSMYTTHIPIIAPKISVASYFNKRHTERNQKTSYSITIQA 326

Query:   124 IGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREI-RGL-LLGDIGYAQNEFTFTP 181
             +  P     D+   WPGS  D ++ + S +Y R +   + +G+ + G  G+   ++   P
Sbjct:   327 VVNPKGVFTDLCIGWPGSMPDDKVLEKSLLYQRANNGGLLKGMWVAGGPGHPLLDWVLVP 386

Query:   182 VRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVL 241
                    T +Q A+N      +   +  FG LK R+ACL+K+   +      ++ AC VL
Sbjct:   387 YTQQ-NLTWTQHAFNEKMSEVQGVAKEAFGRLKGRWACLQKRTEVKLQDLPTVLGACCVL 445

Query:   242 HNI 244
             HNI
Sbjct:   446 HNI 448

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

ZFIN|ZDB-GENE-060810-147 si:dkey-197c15.6 "si:dkey-197c15.6" [Danio rerio (taxid:7955)]

 Score = 233 (87.1 bits), Expect = 3.6e-19, P = 3.6e-19
 Identities = 69/232 (29%), Positives = 108/232 (46%)

Query:    19 LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE---DLQTAK 75
             +LA L +YA G+      D   I Q T C  V   ++ L+    ++I FP    D   A 
Sbjct:   101 ILAALAYYAQGSLPNKVTDRLRIDQKTACEAVKATTKLLSDLTPEFITFPNSYNDRMGAA 160

Query:    76 NQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVV 135
               F  ++G P VV G +   H+ +  P +E    Y N   ++SI VQVI   +  ++ V 
Sbjct:   161 QAFKNLSGIPHVV-GVLGYLHIRVRPPVLEE-RMYVNTLGYHSIMVQVIFDADGNLFSVE 218

Query:   136 ASWPGSTHDSRIFQNSRVYSRFDR-REIRGLLLGDIGYAQNEFTFTPVRNPITPTPSQVA 194
                PG T +  +++NS +  +F   +     ++G           TPV      + + V 
Sbjct:   219 QCCPGGTPEHSVWENSDIGRQFSIFQHGHTWIIGSPSLLGCGHVLTPVETIRIKSNAAVQ 278

Query:   195 YNAAQIRTRNSVERLFGVLKRRFACLRKKLANQ-PTTCSHIITACAVLHNIA 245
             +N A     NS + +FG LK RF CL+   + Q P + + +I AC VLHNI+
Sbjct:   279 FNKAHALLYNSSQHVFGSLKSRFQCLQDFGSIQSPESVACMIRACCVLHNIS 330

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

---

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, ., -, ., -	0.3458	0.9160	0.7507	yes	N/A
Q96MB7	HARB1_HUMAN	3, ., 1, ., -, ., -	0.3390	0.9160	0.7507	yes	N/A
B0BN95	HARB1_RAT	3, ., 1, ., -, ., -	0.3458	0.9160	0.7507	yes	N/A
Q8BR93	HARB1_MOUSE	3, ., 1, ., -, ., -	0.3875	0.8006	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	286
pfam13359	155	pfam13359, DDE_4, DDE superfamily endonuclease	5e-39
pfam04827	205	pfam04827, Plant_tran, Plant transposon protein	3e-05

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

 Score =  133 bits (338), Expect = 5e-39
 Identities = 50/160 (31%), Positives = 71/160 (44%), Gaps = 13/160 (8%)

Query: 92  IDGTHVPIELPSI--ENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQ 149
           IDGT +PIE P    E  + Y   K   ++ V ++  P+  I  V   WPGS  D RI +
Sbjct: 1   IDGTEIPIERPKSLEEQAQTYSGYKKHNTLKVLIVVDPDGRIIFVSVGWPGSVSDKRILE 60

Query: 150 NSRVYSRFDRREIRGLLLGDIGYAQNEFT-----FTPVRNPITPTPSQVAYNAAQIRTRN 204
           NS +  +    +    +L D G+  ++         P       T  +V +N      R 
Sbjct: 61  NSGLLEKLPPGDY---VLADRGFPLSDSLLAPPAKKPGGAQ--LTEEEVEFNRRIASARI 115

Query: 205 SVERLFGVLKRRFACLRKKLAN-QPTTCSHIITACAVLHN 243
            VER+ G LK RF  LR +L   + TT   I+  C  LHN
Sbjct: 116 HVERVIGRLKGRFRILRGRLRISKLTTLDKIVLVCCALHN 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 = 43.4 bits (102), Expect = 3e-05
 Identities = 47/186 (25%), Positives = 77/186 (41%), Gaps = 20/186 (10%)

Query: 77  QFSGIAGFPRVVVGCIDGTHVPIE-LPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVV 135
                 GFP ++ G +D  H   +  P+   G++ R      +I ++ +   +L I+   
Sbjct: 17  HIGESRGFPGML-GSLDCMHWKWKNCPTAWKGQYTRGDSKSPTIILEAVASYDLWIWHAF 75

Query: 136 ASWPGSTHDSRIFQNSRVYS----------RFDRREIR---GLLLGDIGYAQNEFTFTPV 182
              PGS +D  +   S ++           R+     +   G  L D  Y +       +
Sbjct: 76  FGCPGSNNDINVLNQSPIFDDILQGTAPRVRYTVNGRQYNMGYYLADGIYPEWATFVKSI 135

Query: 183 RNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRK--KLANQPTTCSHIITACAV 240
           R P        A    Q   R  VER FGVL+ RF  +    +L NQ +  S+I+TAC +
Sbjct: 136 RLPQLEKHKLFAQQ--QEACRKDVERAFGVLQARFKIVATPARLWNQ-SDLSNIMTACII 192

Query: 241 LHNIAI 246
           LHN+ +
Sbjct: 193 LHNMIV 198

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	286
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
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	99.3
PF13612	155	DDE_Tnp_1_3: Transposase DDE domain	99.28
PF01609	213	DDE_Tnp_1: Transposase DDE domain; InterPro: IPR00	98.19
PF13586	88	DDE_Tnp_1_2: Transposase DDE domain	98.15
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	97.31
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	97.08
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.95
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	96.84
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	96.69
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	96.37
PF13518	52	HTH_28: Helix-turn-helix domain	96.3
smart00351	125	PAX Paired Box domain.	96.14
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	96.09
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	95.91
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	95.81
PRK09413	121	IS2 repressor TnpA; Reviewed	95.67
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	95.65
cd00131	128	PAX Paired Box domain	95.63
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	95.47
PF13340	75	DUF4096: Putative transposase of IS4/5 family (DUF	95.4
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	95.15
COG3415	138	Transposase and inactivated derivatives [DNA repli	95.14
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	95.12
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	95.08
PRK00118	104	putative DNA-binding protein; Validated	94.75
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	94.57
PRK04217	110	hypothetical protein; Provisional	94.45
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	94.3
PRK12529	178	RNA polymerase sigma factor; Provisional	94.1
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	94.05
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	93.85
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	93.51
PRK06030	124	hypothetical protein; Provisional	93.35
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	93.14
TIGR02844	80	spore_III_D sporulation transcriptional regulator	93.12
PHA00675	78	hypothetical protein	92.98
PRK08301	234	sporulation sigma factor SigE; Reviewed	92.82
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	92.71
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	92.7
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	92.69
PRK03975	141	tfx putative transcriptional regulator; Provisiona	92.61
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	92.59
PHA00542	82	putative Cro-like protein	92.47
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	92.45
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	92.34
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	92.27
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	92.22
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	92.2
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	92.16
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	92.16
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	92.12
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	92.1
PRK12547	164	RNA polymerase sigma factor; Provisional	92.03
PRK15320	251	transcriptional activator SprB; Provisional	92.03
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	91.96
PRK12514	179	RNA polymerase sigma factor; Provisional	91.96
PRK12511	182	RNA polymerase sigma factor; Provisional	91.93
PRK12519	194	RNA polymerase sigma factor; Provisional	91.93
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	91.92
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	91.72
PRK12524	196	RNA polymerase sigma factor; Provisional	91.71
PRK12530	189	RNA polymerase sigma factor; Provisional	91.7
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	91.66
PF13730	55	HTH_36: Helix-turn-helix domain	91.64
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	91.61
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	91.61
PRK12515	189	RNA polymerase sigma factor; Provisional	91.6
PRK05803	233	sporulation sigma factor SigK; Reviewed	91.56
PRK09415	179	RNA polymerase factor sigma C; Reviewed	91.56
PRK12533	216	RNA polymerase sigma factor; Provisional	91.56
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	91.52
PF13551	112	HTH_29: Winged helix-turn helix	91.44
COG2963	116	Transposase and inactivated derivatives [DNA repli	91.41
PRK12537	182	RNA polymerase sigma factor; Provisional	91.4
PRK12531	194	RNA polymerase sigma factor; Provisional	91.31
PRK15418	318	transcriptional regulator LsrR; Provisional	91.3
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	91.3
PRK12512	184	RNA polymerase sigma factor; Provisional	91.23
PRK12516	187	RNA polymerase sigma factor; Provisional	91.18
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	91.13
PRK09047	161	RNA polymerase factor sigma-70; Validated	91.07
PRK11924	179	RNA polymerase sigma factor; Provisional	91.0
PRK05602	186	RNA polymerase sigma factor; Reviewed	90.9
PRK12534	187	RNA polymerase sigma factor; Provisional	90.85
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	90.85
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	90.82
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	90.75
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	90.69
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	90.59
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	90.57
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	90.53
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	90.39
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	90.35
PRK12546	188	RNA polymerase sigma factor; Provisional	90.07
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	90.06
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	90.03
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	90.03
PRK05572	252	sporulation sigma factor SigF; Validated	90.03
PF08299	70	Bac_DnaA_C: Bacterial dnaA protein helix-turn-heli	89.98
PRK06811	189	RNA polymerase factor sigma-70; Validated	89.96
PRK12540	182	RNA polymerase sigma factor; Provisional	89.93
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	89.91
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	89.8
PRK12532	195	RNA polymerase sigma factor; Provisional	89.79
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	89.73
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	89.72
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	89.71
PRK06759	154	RNA polymerase factor sigma-70; Validated	89.63
PRK06704	228	RNA polymerase factor sigma-70; Validated	89.6
PRK12544	206	RNA polymerase sigma factor; Provisional	89.56
PRK08583	257	RNA polymerase sigma factor SigB; Validated	89.51
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	89.4
PRK08215	258	sporulation sigma factor SigG; Reviewed	89.31
PRK12523	172	RNA polymerase sigma factor; Reviewed	89.29
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	89.27
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	89.07
PRK12539	184	RNA polymerase sigma factor; Provisional	89.04
PRK12528	161	RNA polymerase sigma factor; Provisional	89.03
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	89.0
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	88.97
PRK12520	191	RNA polymerase sigma factor; Provisional	88.91
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	88.8
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	88.73
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	88.66
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	88.64
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	88.61
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	88.53
PRK06930	170	positive control sigma-like factor; Validated	88.37
PRK12522	173	RNA polymerase sigma factor; Provisional	88.32
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	88.17
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	88.15
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	88.02
PF05344	65	DUF746: Domain of Unknown Function (DUF746); Inter	88.0
PRK12525	168	RNA polymerase sigma factor; Provisional	87.84
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	87.8
PRK07405	317	RNA polymerase sigma factor SigD; Validated	87.78
COG3293	124	Transposase and inactivated derivatives [DNA repli	87.71
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	87.47
PRK07670	251	RNA polymerase sigma factor SigD; Validated	87.47
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	87.33
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	87.05
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	87.01
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	87.0
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	86.96
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	86.86
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	86.85
PRK13919	186	putative RNA polymerase sigma E protein; Provision	86.83
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	86.78
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	86.75
PRK12527	159	RNA polymerase sigma factor; Reviewed	86.69
PRK08295	208	RNA polymerase factor sigma-70; Validated	86.68
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	86.67
PRK12542	185	RNA polymerase sigma factor; Provisional	86.56
PRK12536	181	RNA polymerase sigma factor; Provisional	86.48
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	86.47
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	86.38
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	86.33
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	86.23
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	86.22
PRK12541	161	RNA polymerase sigma factor; Provisional	86.06
PRK12543	179	RNA polymerase sigma factor; Provisional	85.88
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	85.72
PF13751	125	DDE_Tnp_1_6: Transposase DDE domain	85.67
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	85.45
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	85.38
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	85.32
PRK12535	196	RNA polymerase sigma factor; Provisional	85.32
PRK12526	206	RNA polymerase sigma factor; Provisional	85.27
PRK14088	440	dnaA chromosomal replication initiation protein; P	85.09
PF13610	140	DDE_Tnp_IS240: DDE domain	84.92
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	84.86
PRK12545	201	RNA polymerase sigma factor; Provisional	84.84
PRK11922	231	RNA polymerase sigma factor; Provisional	84.84
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	84.82
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	84.66
PRK12517	188	RNA polymerase sigma factor; Provisional	84.57
PRK15201	198	fimbriae regulatory protein FimW; Provisional	84.3
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	84.25
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	84.09
PRK03573	144	transcriptional regulator SlyA; Provisional	83.93
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	83.87
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	83.79
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	83.73
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	83.73
PRK00149	450	dnaA chromosomal replication initiation protein; R	83.62
PRK07598	415	RNA polymerase sigma factor SigC; Validated	83.61
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	83.52
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	83.49
PRK12538	233	RNA polymerase sigma factor; Provisional	83.36
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	83.2
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	83.2
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	83.11
PF07638	185	Sigma70_ECF: ECF sigma factor	83.1
PRK13870	234	transcriptional regulator TraR; Provisional	83.06
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	83.01
PF00872	381	Transposase_mut: Transposase, Mutator family; Inte	82.81
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	82.78
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	82.57
PRK14086	617	dnaA chromosomal replication initiation protein; P	82.52
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	82.49
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	82.27
PRK08241	339	RNA polymerase factor sigma-70; Validated	82.26
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	82.24
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	82.14
PRK05949	327	RNA polymerase sigma factor; Validated	81.85
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	81.58
PF10668	60	Phage_terminase: Phage terminase small subunit; In	81.53
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	81.53
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	81.43
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	81.24
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	81.24
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	81.16
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	81.11
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	81.01
PHA02591	83	hypothetical protein; Provisional	80.96
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	80.84
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	80.28
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	80.23

>PF13359 DDE_Tnp_4: DDE superfamily endonuclease

Probab=100.00  E-value=1e-38  Score=256.56  Aligned_cols=152  Identities=43%  Similarity=0.690  Sum_probs=139.6

Q ss_pred             eeeeEEEecCCCC--CCccccccCCCccccceeeecCCCccEEEeccCCCCccccccccccchhhhhcc-ccccceEEEc
Q psy13113         92 IDGTHVPIELPSI--ENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFD-RREIRGLLLG  168 (286)
Q Consensus        92 iDgt~i~i~~P~~--~~~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~-~~~~~~~llg  168 (286)
                      ||||+|++++|..  .+...|+++|+.|++|+|++||++|+|++++.++||++||..+|++|++...++ ..+.++++||
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  378899999999999999999999999999999999999999999999988876 2222789999


Q ss_pred             cccCCCCCcccccccCC--CCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhhccccCC-ccchHHHHHHHHHHHh
Q psy13113        169 DIGYAQNEFTFTPVRNP--ITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQ-PTTCSHIITACAVLHN  243 (286)
Q Consensus       169 D~gY~~~~~l~~p~~~~--~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~~~-~~~~~~ii~a~~~LhN  243 (286)
                      |+||++.+++++|++++  ..++++|+.||+.+++.|++||++||+||+||++|..+++.+ +..+.++|.+||+|||
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            99999999999999843  348899999999999999999999999999999999899998 9999999999999999

>KOG4585|consensus

Probab=100.00  E-value=3.5e-34  Score=251.99  Aligned_cols=256  Identities=27%  Similarity=0.432  Sum_probs=202.3

Q ss_pred             HHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCch--hHHHHHHHhhhhcCCCCceEeee
Q psy13113         15 PVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE--DLQTAKNQFSGIAGFPRVVVGCI   92 (286)
Q Consensus        15 ~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~--~~~~~~~~f~~~~~~p~~~~g~i   92 (286)
                      +.+++++.++.++++.+++.++..||...+|.     .+...+...++.++.||.  ....+...+++   +|+| +|++
T Consensus        41 ~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~~~~~~~~~p~~~~~~~i~~~~~~---~~~~-~g~~  111 (326)
T KOG4585|consen   41 ADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKEDLAPHFLKWPSRRILYEIRERFES---LPNC-VGAI  111 (326)
T ss_pred             HHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhcccchhhcCchhhhhhhhcccccc---ccch-hccc
Confidence            88999999999999999999999999999998     555666678999999998  56666666665   9999 9999


Q ss_pred             eeeEEEecCCCCCCccccccCCCccccceeeecCCCccEEEeccCCCCccccccccccchhhhhccccccceEEEcccc-
Q psy13113         93 DGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIG-  171 (286)
Q Consensus        93 Dgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~~~~~~~llgD~g-  171 (286)
                      |+||+++..| ......|.++  .++.++|++||.+++|+++.+++||+.||..++..+.+......+....|.|.|.| 
T Consensus       112 d~~hi~~~~~-~~~~~~~~n~--~~~~Nvlav~n~d~~f~~v~vg~~Gs~~D~kvl~~~~~~~~~~~~~~~k~yl~d~~~  188 (326)
T KOG4585|consen  112 DTTHIPIRVP-PKSGSVYFNK--EQSKNLLAVCNFDMRFIYVDVGWPGSAHDTKVLQDSLLYKRNFPHPPLKYYLVDSGY  188 (326)
T ss_pred             cccccceecC-cccccccccc--ccchhhhheecCCceEEEEEccCCCCccHHHHHHhhcccccccccCCccccccccCc
Confidence            9999999988 5555556665  78889999999999999999999999999999999887766554432244444555 


Q ss_pred             -----------CCCCCcccccccCCCCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhhccccCCccchHHHHHHHHH
Q psy13113        172 -----------YAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAV  240 (286)
Q Consensus       172 -----------Y~~~~~l~~p~~~~~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~~~~~~~~~ii~a~~~  240 (286)
                                 |+..+++++|+..+. .+..+..||+.|+..|.++|++||.||.||++|.+....+.++..++|.+||+
T Consensus       189 ~~~~~~~g~~~~~~~~~~~~~~~~~~-~~~~~elFN~rh~~~r~v~e~~fg~lk~rw~il~~~~~~~~~~~~~iV~a~ca  267 (326)
T KOG4585|consen  189 PLRPGLLGPIGFPLYSLLMFPYGGPQ-PTNSQELFNKRHSSLRSVAERAFGVLKAKWRILQRREKYDLKKLPKIVTACCA  267 (326)
T ss_pred             ccccccccccccccchhhhcccCCCC-CCchHHHHhhhhhhHHHHHHHHHHHhhhhhHHHhhcccccccchHHHHHHHHH
Confidence                       445555566665554 35788899999999999999999999999999998767789999999999999


Q ss_pred             HHhhhhhcCCCCCCCC--CCCCCc-cc---CC-CCcccHHHHHHHHHHHH
Q psy13113        241 LHNIAIARREAPPPEN--NELPVN-VH---IR-DADDNRLGAAVREAFIN  283 (286)
Q Consensus       241 LhN~~~~~~~~~~~~~--~~~~~~-~~---~~-~~~~~~~~~~~r~~~~~  283 (286)
                      |||++.+..+.++++.  +..+.. ++   .. .......+...|+.+..
T Consensus       268 LHN~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~~~~~~~~~r~~l~~  317 (326)
T KOG4585|consen  268 LHNIIRDSDEEDPDDPKWEKFDDYGENVAHLRYAPQQRDYMEKIRDNLLS  317 (326)
T ss_pred             HHHHHHhhcccccccccccccccccccchhcccchhHHHHHHHHHHHHHH
Confidence            9999999888654433  222221 11   11 22334566677777654

>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-35  Score=231.93  Aligned_cols=185  Identities=25%  Similarity=0.422  Sum_probs=166.7

Q ss_pred             cccCCch--hHHHHHHHhhhhcCCCCceEeeeeeeEEEec-CCCCCCccccccCCCccccceeeecCCCccEEEeccCCC
Q psy13113         63 QWIHFPE--DLQTAKNQFSGIAGFPRVVVGCIDGTHVPIE-LPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWP  139 (286)
Q Consensus        63 ~~i~~P~--~~~~~~~~f~~~~~~p~~~~g~iDgt~i~i~-~P~~~~~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~  139 (286)
                      .|++-|+  +.+++. ...+..||||+ +|.|||+|+.+. +|..-.+.+.+|++|..|+.+++|++.+.+|+++..|.|
T Consensus         2 ~YLr~P~~~d~~rll-~~~e~rGFpGm-lGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~   79 (205)
T PF04827_consen    2 EYLRRPTNEDLERLL-QIGEARGFPGM-LGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMP   79 (205)
T ss_pred             cccCCCChhHHHHHH-HhhhhcCCCcc-ccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccC
Confidence            4778888  778887 44566799999 999999999999 674444566669999999999999999999999999999


Q ss_pred             Cccccccccccchhhhhcccccc-------------ceEEEccccCCCCCcccccccCCCCCChhhHHhHHHHHHHHHHH
Q psy13113        140 GSTHDSRIFQNSRVYSRFDRREI-------------RGLLLGDIGYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSV  206 (286)
Q Consensus       140 Gs~~D~~~~~~s~l~~~l~~~~~-------------~~~llgD~gY~~~~~l~~p~~~~~~l~~~~~~~N~~~~~~R~~v  206 (286)
                      ||.||..++..|+++..+.++..             -.|.|+|..||....++.+++.|..  .+++.|.+...++|.-|
T Consensus        80 GS~NDiNVL~~Splf~~~~~G~ap~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p~~--~k~k~fa~~QE~~RKDV  157 (205)
T PF04827_consen   80 GSNNDINVLDRSPLFDDLLQGQAPRVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLPQG--EKRKLFAKHQESARKDV  157 (205)
T ss_pred             CcccccccccccHHHHHHhcCcCCceEEEecCeecccceeeccCcCcchHhHhhhcchhhc--hhhHHHHHhCHHHHHHH
Confidence            99999999999999999887743             4589999999999999999999976  89999999999999999


Q ss_pred             HHHHHHHHhhhhhhhccccC-CccchHHHHHHHHHHHhhhhhcCCC
Q psy13113        207 ERLFGVLKRRFACLRKKLAN-QPTTCSHIITACAVLHNIAIARREA  251 (286)
Q Consensus       207 E~~~~~lK~rf~~L~~~~~~-~~~~~~~ii~a~~~LhN~~~~~~~~  251 (286)
                      |++||.|++||+|++.+.+. +.+.+..|+.||++||||+++++..
T Consensus       158 ErAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr~  203 (205)
T PF04827_consen  158 ERAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDERD  203 (205)
T ss_pred             HHHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEecccc
Confidence            99999999999999998887 8899999999999999999987653

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

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

Probab=99.30  E-value=6.7e-12  Score=81.25  Aligned_cols=51  Identities=24%  Similarity=0.068  Sum_probs=48.1

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      +++++++|++++|.||++|.+++++|..||||+|||+++++++++.|+...
T Consensus         1 ~kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l   51 (53)
T PF13613_consen    1 RKLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL   51 (53)
T ss_pred             CCCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence            468999999999999999999999999999999999999999999998754

>PF13612 DDE_Tnp_1_3: Transposase DDE domain

Probab=99.28  E-value=2.2e-12  Score=102.14  Aligned_cols=124  Identities=23%  Similarity=0.395  Sum_probs=94.3

Q ss_pred             EeeeeeeEEEecCCCCCC---------ccccccCCCccccceeeecCCCccEEEeccCCCCccccccccccchhhhhccc
Q psy13113         89 VGCIDGTHVPIELPSIEN---------GEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDR  159 (286)
Q Consensus        89 ~g~iDgt~i~i~~P~~~~---------~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~  159 (286)
                      +.+||++.+|++.+....         .-.|+..+-+|++|++++|+..|.++.+... ||+.||..++..  +...+  
T Consensus         7 i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~lT-~an~~D~~~~~~--l~~~~--   81 (155)
T PF13612_consen    7 IYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTLT-PANVHDRKVLEE--LSENL--   81 (155)
T ss_pred             EEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEEc-cccccccccccc--ccccc--
Confidence            889999999999763221         1234555556999999999999999998776 999999998854  22222  


Q ss_pred             cccceEEEccccCCCCC----------cccccccCCCCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhh
Q psy13113        160 REIRGLLLGDIGYAQNE----------FTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLR  221 (286)
Q Consensus       160 ~~~~~~llgD~gY~~~~----------~l~~p~~~~~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~  221 (286)
                         ...++||+||-...          .++||.+++.. ......+++.+.+.|..||.+|+.||+.|.+=.
T Consensus        82 ---~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk-~~~~~~~~~~l~~~R~~IETvfs~Lk~~~~ie~  149 (155)
T PF13612_consen   82 ---KGKLFGDKGYISKELKDELKEQGIKLITPRRKNMK-NKLMPLFDKLLLRKRRIIETVFSQLKNQFNIEH  149 (155)
T ss_pred             ---ccceecchhhhcchHHhhhhhceEEEecccccccc-ccccchhhhhhhheeeEeehHHHHHHHhhceEe
Confidence               34899999996432          36899887653 123356788999999999999999999887654

>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=98.19  E-value=3.3e-08  Score=81.99  Aligned_cols=149  Identities=20%  Similarity=0.252  Sum_probs=85.6

Q ss_pred             EeeeeeeEEEecCCCCCCccccccCCCccccceeeecC-CCccEEEeccCCCCccccccccccchhhhhccccccceEEE
Q psy13113         89 VGCIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGG-PNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLL  167 (286)
Q Consensus        89 ~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~vvd-~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~~~~~~~ll  167 (286)
                      +.+||+|.++.. +.......+.+++...+++.++++| ..|.++.+... +|+.+|...+..  +.+. .....+..++
T Consensus         6 ~~~iD~T~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~-~~~~~~~~vv   80 (213)
T PF01609_consen    6 VVAIDGTTIRTP-HDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER-KPGRKPDLVV   80 (213)
T ss_dssp             EEEEETTT--EE-EEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT------EEEEE
T ss_pred             EEEEECcEEEee-cchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc-ccccccccee
Confidence            779999999998 2112223445556667889999994 67777777777 999999988876  3333 1122277999


Q ss_pred             ccccCCCCCc----------ccccccCCCCC---------------------------------ChhhHHhHHH------
Q psy13113        168 GDIGYAQNEF----------TFTPVRNPITP---------------------------------TPSQVAYNAA------  198 (286)
Q Consensus       168 gD~gY~~~~~----------l~~p~~~~~~l---------------------------------~~~~~~~N~~------  198 (286)
                      +|+||...+.          .+.|.+.....                                 ....+.....      
T Consensus        81 ~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (213)
T PF01609_consen   81 ADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKKGYFLVTNIT  160 (213)
T ss_dssp             E-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--TTS---EEE
T ss_pred             ecccccceeccccccccccccccccccccccccccchhhccccccccccccccccccccccccccccccccccccccccc
Confidence            9999976542          13343322210                                 0011111122      


Q ss_pred             --------HHHHHHHHHHHHHHHHhhhhhhhccccC-CccchHHHHHHHHHHHhh
Q psy13113        199 --------QIRTRNSVERLFGVLKRRFACLRKKLAN-QPTTCSHIITACAVLHNI  244 (286)
Q Consensus       199 --------~~~~R~~vE~~~~~lK~rf~~L~~~~~~-~~~~~~~ii~a~~~LhN~  244 (286)
                              +.+.|..||+.|..+|+.|. +. .++. +...+...+.++++-.|+
T Consensus       161 ~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~-~~~~~~~~~~~~~~~~~~la~nl  213 (213)
T PF01609_consen  161 TLPRDTAALYRRRWQIERFFRELKQFLG-LE-RLRVRSPERIEAHLFLTLLAYNL  213 (213)
T ss_dssp             EEESS--SHHHCGGHHHHHHHHHTTTTT-GG-GS--SSHHHHHHHHHHHHHH---
T ss_pred             ccccccceeecccchhhHHHHHHHhcCC-Cc-hhcccCHHHHHHHHHHHHhhCcC
Confidence                    89999999999999999544 33 2444 667777777777777764

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.

>PF13586 DDE_Tnp_1_2: Transposase DDE domain

Probab=98.15  E-value=8.6e-07  Score=63.68  Aligned_cols=76  Identities=21%  Similarity=0.316  Sum_probs=54.6

Q ss_pred             EEccccCCCCCc--------c--cccccCCCCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhhccccCCccchHHHH
Q psy13113        166 LLGDIGYAQNEF--------T--FTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHII  235 (286)
Q Consensus       166 llgD~gY~~~~~--------l--~~p~~~~~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~~~~~~~~~ii  235 (286)
                      ++||+||.....        +  ..|.+..... .....+...+.+.|.+||++|++||. |+.|...+.........++
T Consensus         1 v~aDkgYd~~~~r~~l~~~gi~~~i~~~~~~~~-~~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek~~~s~~~~v   78 (88)
T PF13586_consen    1 VLADKGYDSRALREYLRERGIRPVIPKRGRRKK-RRPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEKLASSFLAFV   78 (88)
T ss_pred             CcccCCcCCHHHHHHHHHCCCEEecCCCCCccc-cccCccchhhhccceehhhhhHHHHH-cCccccccccCHHHHHHHH
Confidence            579999976321        1  2222222111 33667889999999999999999999 9999988888777777777


Q ss_pred             HHHHHHHh
Q psy13113        236 TACAVLHN  243 (286)
Q Consensus       236 ~a~~~LhN  243 (286)
                      ..+|++-+
T Consensus        79 ~la~~~i~   86 (88)
T PF13586_consen   79 HLACIVIW   86 (88)
T ss_pred             HHHHHHHH
Confidence            76666654

>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=97.31  E-value=0.00033  Score=43.38  Aligned_cols=43  Identities=21%  Similarity=0.245  Sum_probs=32.9

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      ||+..++.+ ++.-++..+..|.+..++|..||||++||+++++
T Consensus         1 GRp~~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen    1 GRPPKLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             SSSSSSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             CcCCCCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            455666665 5667777889999999999999999999999875

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=97.08  E-value=0.0024  Score=40.34  Aligned_cols=46  Identities=22%  Similarity=0.249  Sum_probs=39.0

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEEL   57 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l   57 (286)
                      ..+|++++-.+.++| -.+.++.++|..+|+|.+||+++.++.+.-|
T Consensus         3 ~~L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL   48 (50)
T PF04545_consen    3 DQLPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL   48 (50)
T ss_dssp             CTS-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence            368999999999999 6678999999999999999999999887655

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=96.95  E-value=0.0011  Score=40.80  Aligned_cols=41  Identities=15%  Similarity=0.017  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      ..|+.+++..+.-+ +..|.+.+.+|..+|+|++||++.+++
T Consensus         3 ~~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHH-HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            46778888777644 689999999999999999999998875

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=96.84  E-value=0.0044  Score=43.60  Aligned_cols=49  Identities=16%  Similarity=0.148  Sum_probs=44.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113          7 DARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         7 ~~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +.++..|++..++.++-..+..|.+...+|..||||..|+++|+.++-.
T Consensus         3 ~H~nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra   51 (85)
T PF13011_consen    3 SHKNARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA   51 (85)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4577889999999999999999999999999999999999999987653

>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=96.69  E-value=0.003  Score=40.54  Aligned_cols=43  Identities=19%  Similarity=0.189  Sum_probs=32.2

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      .+..+++++++-+.-. +-.|.+..++|..|||+.||++.|++.
T Consensus         3 kR~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    3 KRKSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             SSSS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             CCccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            4678999999887655 677789999999999999999998864

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.

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

Probab=96.37  E-value=0.0037  Score=39.42  Aligned_cols=38  Identities=13%  Similarity=0.089  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        16 ~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      +.++.+...+. .|.+..++|..+|||++||++|++++.
T Consensus         5 ~~R~~ii~l~~-~G~s~~~ia~~lgvs~~Tv~~w~kr~~   42 (50)
T PF13384_consen    5 ERRAQIIRLLR-EGWSIREIAKRLGVSRSTVYRWIKRYR   42 (50)
T ss_dssp             -----HHHHHH-HT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred             hHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence            34444444444 499999999999999999999998764

>PF13518 HTH_28: Helix-turn-helix domain

Probab=96.30  E-value=0.0083  Score=37.98  Aligned_cols=37  Identities=24%  Similarity=0.300  Sum_probs=31.2

Q ss_pred             HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ++.+...++ .|.+...+|..||||.+||++|++....
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            456667777 5679999999999999999999988765

>smart00351 PAX Paired Box domain

Probab=96.14  E-value=0.017  Score=44.25  Aligned_cols=46  Identities=13%  Similarity=0.045  Sum_probs=39.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ....+|.+.+.-+.+.+. .|.+..++|..||||.+||++|++++.+
T Consensus        14 ~~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~   59 (125)
T smart00351       14 NGRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE   59 (125)
T ss_pred             CCCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            345689998888887775 7899999999999999999999998754

>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=96.09  E-value=0.014  Score=36.04  Aligned_cols=37  Identities=14%  Similarity=0.064  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHHH
Q psy13113         16 VVKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        16 ~~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      ++++..+|..+..| .+++..|..|||+++|+++.++.
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            67888888889998 89999999999999999987653

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.

>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=95.91  E-value=0.021  Score=32.70  Aligned_cols=41  Identities=22%  Similarity=0.116  Sum_probs=31.1

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLV   50 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~   50 (286)
                      ++..++.+++..+... +..+.+..+++..||+|.+|+++++
T Consensus         2 r~~~~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           2 RPPKLTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCCcCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence            4556777666555444 4577799999999999999999863

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

>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=95.81  E-value=0.032  Score=35.66  Aligned_cols=44  Identities=18%  Similarity=0.271  Sum_probs=33.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      .+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....
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            578888888888777 56899999999999999999998876654

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.

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=95.67  E-value=0.035  Score=42.20  Aligned_cols=48  Identities=13%  Similarity=0.078  Sum_probs=43.7

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .++...+.+.++-++...+..|.+..++|..||||.+|+++|++.+..
T Consensus         8 ~~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~   55 (121)
T PRK09413          8 EKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE   55 (121)
T ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence            346779999999999999999999999999999999999999998753

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

Probab=95.65  E-value=0.017  Score=39.80  Aligned_cols=46  Identities=24%  Similarity=0.203  Sum_probs=38.8

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ++...|++.++-++-.++..|.+..+++..+||+.+|+++|++...
T Consensus         3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    3 KRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence            5678899999999999999999999999999999999999999887

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.

>cd00131 PAX Paired Box domain

Probab=95.63  E-value=0.035  Score=42.67  Aligned_cols=46  Identities=13%  Similarity=0.117  Sum_probs=39.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ...++|.+.+.-+.+.+ ..|.+.+.+|..||||.+||++|++++.+
T Consensus        14 m~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e   59 (128)
T cd00131          14 NGRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYE   59 (128)
T ss_pred             CCCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45778888888887765 68999999999999999999999987765

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=95.47  E-value=0.066  Score=38.35  Aligned_cols=52  Identities=19%  Similarity=0.064  Sum_probs=46.7

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhcc-ccHhHHHHHHHHHHHHHHh
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHD-ISQSTICRLVAKVSEELAK   59 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fg-vs~stv~~~~~~v~~~l~~   59 (286)
                      ++...+....++++.|..--+|.++.++|..|| .+.|||+..++++...+..
T Consensus        23 ~R~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~   75 (90)
T cd06571          23 SRKKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE   75 (90)
T ss_pred             CCCcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence            455578889999999999999999999999999 9999999999999988864

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.

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

Probab=95.40  E-value=0.014  Score=40.37  Aligned_cols=47  Identities=21%  Similarity=0.024  Sum_probs=41.5

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +++...+..+-+-..|+.|++|+++++|...|| +.+||++.+++...
T Consensus        20 ~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~   66 (75)
T PF13340_consen   20 GGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR   66 (75)
T ss_pred             CCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence            345678999999999999999999999999999 88899999887754

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=95.15  E-value=0.088  Score=33.45  Aligned_cols=45  Identities=18%  Similarity=0.198  Sum_probs=35.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .++..++-++.+  +..|.+..++|..+|+|.+||.+++.+....|.
T Consensus         3 ~l~~~e~~i~~~--~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~   47 (58)
T smart00421        3 SLTPREREVLRL--LAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG   47 (58)
T ss_pred             CCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            466666654433  578899999999999999999999998876664

lux regulon (activates the bioluminescence operon

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

Probab=95.14  E-value=0.042  Score=42.55  Aligned_cols=44  Identities=20%  Similarity=0.112  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ..+.+.+-+++..++..|.+.+.+|..||||.+|+.+++++.-+
T Consensus         4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e   47 (138)
T COG3415           4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE   47 (138)
T ss_pred             hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence            45667888889999999999999999999999999999998764

>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=95.12  E-value=0.069  Score=33.35  Aligned_cols=44  Identities=18%  Similarity=0.157  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      .++++++-++.+.++ .+.++.++|..+|+|.+|+.+++.+....
T Consensus        10 ~l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            467777777777665 77899999999999999999999876543

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

>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=95.08  E-value=0.038  Score=38.02  Aligned_cols=41  Identities=12%  Similarity=0.050  Sum_probs=28.4

Q ss_pred             HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .+-++=+.+.+..+-+..|..||||+|||++=+.+=+..+.
T Consensus         8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in   48 (82)
T PF12116_consen    8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKIN   48 (82)
T ss_dssp             HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-
T ss_pred             HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcC
Confidence            35566777889999999999999999999987665444444

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.

>PRK00118 putative DNA-binding protein; Validated

Probab=94.75  E-value=0.1  Score=38.44  Aligned_cols=49  Identities=8%  Similarity=0.117  Sum_probs=40.2

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+.++..++-++.|++. .+.++..+|..+|+|.+||++.+++....|.+
T Consensus        15 ~~~L~ekqRevl~L~y~-eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~   63 (104)
T PRK00118         15 GSLLTEKQRNYMELYYL-DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED   63 (104)
T ss_pred             hccCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            35677777777766544 58999999999999999999999988877775

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

Probab=94.57  E-value=0.056  Score=34.20  Aligned_cols=31  Identities=19%  Similarity=0.187  Sum_probs=25.5

Q ss_pred             HHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         23 LRFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        23 L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      +..|....++.++|..+|||.+||.+++++.
T Consensus        21 ~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   21 LKLLRESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            3444455699999999999999999999864

>PRK04217 hypothetical protein; Provisional

Probab=94.45  E-value=0.15  Score=37.89  Aligned_cols=49  Identities=14%  Similarity=0.070  Sum_probs=38.5

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ...++.+++-++.|+ .-.+.++.++|..+|||.+||++.+++....|.+
T Consensus        40 ~~~Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre   88 (110)
T PRK04217         40 PIFMTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ   88 (110)
T ss_pred             cccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            455777776444443 3377899999999999999999999988877765

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=94.30  E-value=0.12  Score=41.21  Aligned_cols=49  Identities=16%  Similarity=0.219  Sum_probs=43.3

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      ..+|++++-++.|.+  .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       111 ~~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l  159 (166)
T PRK09639        111 AKMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY  159 (166)
T ss_pred             HcCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            358889999999988  9999999999999999999999999888887643

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=94.10  E-value=0.16  Score=41.13  Aligned_cols=49  Identities=18%  Similarity=0.102  Sum_probs=42.3

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      ..||++++.++.|.++ .|.++.++|..+|+|.+||...+++.+..+.+.
T Consensus       126 ~~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~  174 (178)
T PRK12529        126 DTLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL  174 (178)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence            3578888889999888 789999999999999999999988877777653

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

Probab=94.05  E-value=0.2  Score=31.72  Aligned_cols=43  Identities=21%  Similarity=0.276  Sum_probs=33.7

Q ss_pred             CHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        14 ~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      +..++-++.+  +..|.+..++|..+++|.+|+...++++...+.
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            4445554433  458899999999999999999999998876654

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

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=93.85  E-value=0.16  Score=34.78  Aligned_cols=42  Identities=10%  Similarity=0.033  Sum_probs=37.4

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      ..+|...+.+..|.+.-.+.++.++|...|+|.+||..+++.
T Consensus        14 ~~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879        14 TWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             hcCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            457888888888888889999999999999999999988764

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.

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=93.51  E-value=0.14  Score=36.47  Aligned_cols=32  Identities=28%  Similarity=0.295  Sum_probs=27.5

Q ss_pred             HHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      ...+.++..|.+..++|..+|+|.+|++++.+
T Consensus        41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        41 LQVAKMLKQGKTYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45566788999999999999999999999553

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.

>PRK06030 hypothetical protein; Provisional

Probab=93.35  E-value=0.31  Score=37.11  Aligned_cols=48  Identities=8%  Similarity=-0.057  Sum_probs=43.4

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEEL   57 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l   57 (286)
                      +..+...-|++|.|.+--++.++.+++..||.+.|||.-.++.+-+.+
T Consensus        50 rk~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~   97 (124)
T PRK06030         50 RREVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR   97 (124)
T ss_pred             CcccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence            367889999999999999999999999999999999999999777655

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=93.14  E-value=0.23  Score=39.91  Aligned_cols=48  Identities=13%  Similarity=0.027  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++.++.|.++ .|.+++++|..+|+|.+||...+.+...-|-..
T Consensus       128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  175 (182)
T PRK09652        128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK  175 (182)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            577888888888776 678999999999999999999988887777653

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=93.12  E-value=0.18  Score=35.27  Aligned_cols=37  Identities=14%  Similarity=0.182  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHH
Q psy13113         15 PVVKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        15 ~~~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      .++++...+-+|..+ .+..++|..||||.+||++.++
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            356677777777764 3888999999999999999775

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.

>PHA00675 hypothetical protein

Probab=92.98  E-value=0.2  Score=34.26  Aligned_cols=41  Identities=7%  Similarity=-0.100  Sum_probs=29.6

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      ..|...+--.+-..+-+.|.++..||..||||++||+.|.+
T Consensus        21 AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         21 AKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             cccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence            34444444444433337888999999999999999998765

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=92.82  E-value=0.27  Score=41.69  Aligned_cols=50  Identities=32%  Similarity=0.250  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      .+|+.++-++.|+|.   -.|.++.++|..+|+|.+||....++....|-...
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            477778888888774   57899999999999999999999998888876543

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=92.71  E-value=0.3  Score=42.18  Aligned_cols=49  Identities=12%  Similarity=0.116  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      .+|+.++..+.|+|+ .+.++.++|..+|+|.++|+...++....|-..+
T Consensus       205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l  253 (257)
T PRK05911        205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATL  253 (257)
T ss_pred             cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            588888888888886 6789999999999999999999999888877643

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

Probab=92.70  E-value=0.42  Score=30.53  Aligned_cols=42  Identities=14%  Similarity=0.040  Sum_probs=31.5

Q ss_pred             HHHHHHHHHhhcC-----CChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         17 VKLLAVLRFYATG-----NFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        17 ~~l~~~L~~L~~~-----~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ..++.+-+.++..     .+..+||..+|||++|+++.+++...-|.
T Consensus         6 ~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kli   52 (53)
T PF04967_consen    6 REILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKLI   52 (53)
T ss_pred             HHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence            4445555555543     47788999999999999999998876553

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

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

Probab=92.69  E-value=0.38  Score=37.67  Aligned_cols=47  Identities=19%  Similarity=0.176  Sum_probs=39.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|+++ .|.++.++|..+|+|.+||...+++....|-+
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            467788888888776 68899999999999999999999887776643

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.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=92.61  E-value=0.79  Score=35.71  Aligned_cols=49  Identities=14%  Similarity=0.107  Sum_probs=40.7

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ....+++.++-.+.|  ...|.++.++|..+|+|++||+.+.++....|..
T Consensus         3 ~~~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~   51 (141)
T PRK03975          3 MESFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIEK   51 (141)
T ss_pred             cccCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            346688888888877  3699999999999999999999999887766553

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=92.59  E-value=0.45  Score=36.86  Aligned_cols=47  Identities=11%  Similarity=0.097  Sum_probs=39.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ...++..++-.+.|+  ..|.++.++|..+|+|++||+.+.++...-|.
T Consensus         4 ~~~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr   50 (137)
T TIGR00721         4 KTFLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIE   50 (137)
T ss_pred             cCCCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence            356788888777773  69999999999999999999999888777765

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

>PHA00542 putative Cro-like protein

Probab=92.47  E-value=0.21  Score=35.09  Aligned_cols=32  Identities=34%  Similarity=0.404  Sum_probs=27.1

Q ss_pred             HHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      -+...+...|.++.++|...|||++|++++.+
T Consensus        22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~   53 (82)
T PHA00542         22 ELVCALIRAGWSQEQIADATDVSQPTICRIYS   53 (82)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHc
Confidence            33445678899999999999999999999875

>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=92.45  E-value=0.41  Score=29.62  Aligned_cols=28  Identities=29%  Similarity=0.272  Sum_probs=22.6

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+.+..++|..+|+|.+|+++++++..+
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            3479999999999999999999987754

...

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

Probab=92.34  E-value=0.41  Score=38.04  Aligned_cols=47  Identities=17%  Similarity=0.164  Sum_probs=40.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++.++.|+|+ .|.++.++|..+|+|.+||...+.+....|-.
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            688888888888777 47999999999999999999999888877653

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.

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

Probab=92.27  E-value=0.39  Score=35.08  Aligned_cols=43  Identities=23%  Similarity=0.262  Sum_probs=36.9

Q ss_pred             CHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113         14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEEL   57 (286)
Q Consensus        14 ~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l   57 (286)
                      .++++.++.++|+ .+.++.+++...++|++|++++-+..+..|
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            4678889999999 578899999999999999999988776544

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.

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=92.22  E-value=0.42  Score=37.83  Aligned_cols=47  Identities=11%  Similarity=-0.003  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|++++-++.|.++. |.++.++|..+|+|.+||...+.+....|-.
T Consensus       109 ~L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~  155 (163)
T PRK07037        109 ELPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRK  155 (163)
T ss_pred             hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            4677777777777665 8899999999999999999998888777765

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

Probab=92.20  E-value=0.62  Score=41.47  Aligned_cols=52  Identities=12%  Similarity=0.128  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQW   64 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~   64 (286)
                      .||+.++.++.|.++ .|.+++++|..+|+|.+||...+.+....|.+.+...
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            456666666666665 7789999999999999999999999999998755543

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.

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=92.16  E-value=0.38  Score=38.98  Aligned_cols=48  Identities=15%  Similarity=0.130  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|.+++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-..
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            467777777878777 689999999999999999999999888877653

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=92.16  E-value=0.53  Score=30.90  Aligned_cols=41  Identities=12%  Similarity=0.126  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         15 PVVKLLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        15 ~~~~l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ..+.-+-+++.|.   ...+-.++|..+|||.+||++.+++..+
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            4567777888888   4458889999999999999999887654

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 ....

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

Probab=92.12  E-value=0.42  Score=36.78  Aligned_cols=47  Identities=19%  Similarity=0.208  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.+.++ .|.++.++|..+|+|.+||++...++...|-.
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            577777777776665 68999999999999999999999988776643

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.

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=92.10  E-value=0.2  Score=40.33  Aligned_cols=48  Identities=19%  Similarity=0.202  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
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            478888888888877 689999999999999999999998888877653

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=92.03  E-value=0.47  Score=37.74  Aligned_cols=47  Identities=17%  Similarity=0.068  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus       112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~  158 (164)
T PRK12547        112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQE  158 (164)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            577788888888877 88999999999999999999999988887765

>PRK15320 transcriptional activator SprB; Provisional

Probab=92.03  E-value=0.41  Score=39.26  Aligned_cols=46  Identities=17%  Similarity=0.136  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .++..+.  -.|.+|+.|.+.+++|..+++|.+||+.+..++.+-|..
T Consensus       164 ~LSdREI--EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA  209 (251)
T PRK15320        164 GVTQAKY--ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM  209 (251)
T ss_pred             CCCHHHH--HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence            3444443  678889999999999999999999999999998888764

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

Probab=91.96  E-value=0.46  Score=37.35  Aligned_cols=47  Identities=11%  Similarity=0.105  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
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            588888888888776 78999999999999999999999888777754

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).

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=91.96  E-value=0.47  Score=38.27  Aligned_cols=48  Identities=13%  Similarity=0.119  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|++++-.+.|.++ .|.++.++|..+|+|..||...+.+....|-..
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            477888888888876 779999999999999999999999888877653

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=91.93  E-value=0.44  Score=38.79  Aligned_cols=49  Identities=10%  Similarity=-0.009  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-...
T Consensus       111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~  159 (182)
T PRK12511        111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE  159 (182)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence            578888888888887 5899999999999999999999988888876543

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=91.93  E-value=0.3  Score=40.01  Aligned_cols=48  Identities=15%  Similarity=0.068  Sum_probs=39.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|++++-++.|+++. |.+++++|..+|+|.+||...+.+....|-..
T Consensus       141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  188 (194)
T PRK12519        141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLREL  188 (194)
T ss_pred             hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            3677777777777665 79999999999999999999999888877653

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=91.92  E-value=0.34  Score=34.83  Aligned_cols=40  Identities=15%  Similarity=-0.072  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHH------hhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRF------YATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        13 ~~~~~~l~~~L~~------L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      ++++++-++.++|      +..+.+++.++...|||.+||+|+-+.
T Consensus        33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~   78 (94)
T TIGR01321        33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNN   78 (94)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhh
Confidence            5666666666553      356789999999999999999987653

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.

>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=91.72  E-value=0.52  Score=30.66  Aligned_cols=26  Identities=27%  Similarity=0.353  Sum_probs=22.1

Q ss_pred             CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         30 NFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        30 ~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+..+++..++++++|+++++++...
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            58999999999999999999887654

...

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=91.71  E-value=0.48  Score=38.91  Aligned_cols=47  Identities=19%  Similarity=0.169  Sum_probs=41.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus       136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~  182 (196)
T PRK12524        136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAA  182 (196)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            578888888888877 78999999999999999999999998888765

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=91.70  E-value=0.46  Score=38.86  Aligned_cols=47  Identities=17%  Similarity=0.058  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|+++- |.++.++|..+|+|.+||...+.+....|-.
T Consensus       134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~  180 (189)
T PRK12530        134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQA  180 (189)
T ss_pred             hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            4677788888888776 8999999999999999999999888887765

>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=91.66  E-value=0.37  Score=29.78  Aligned_cols=39  Identities=18%  Similarity=0.113  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .++-+.........+..+++..+|+|++|+++.++...+
T Consensus         3 ~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~   41 (47)
T PF01022_consen    3 TRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE   41 (47)
T ss_dssp             HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence            344554444445568999999999999999998876543

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 ....

>PF13730 HTH_36: Helix-turn-helix domain

Probab=91.64  E-value=0.51  Score=30.05  Aligned_cols=43  Identities=23%  Similarity=0.210  Sum_probs=32.0

Q ss_pred             CCH-HHHHHHHHHHhhcC-----CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         13 HSP-VVKLLAVLRFYATG-----NFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        13 ~~~-~~~l~~~L~~L~~~-----~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +++ +..|.+.|..+..+     .++..++...|+|+.||.+++++..+
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            455 45566667666632     27789999999999999999987653

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

Probab=91.61  E-value=0.14  Score=31.68  Aligned_cols=21  Identities=24%  Similarity=0.251  Sum_probs=18.8

Q ss_pred             ChHhhhhhccccHhHHHHHHH
Q psy13113         31 FQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        31 ~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      +.+++|...|||.+||+++++
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln   21 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLN   21 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHh
Confidence            357899999999999999886

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 ....

>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=91.61  E-value=0.52  Score=30.40  Aligned_cols=41  Identities=20%  Similarity=0.276  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         15 PVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        15 ~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ..+-.++...+=..+.+..+++..++++++|+++++++...
T Consensus         3 ~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~   43 (59)
T PF01047_consen    3 PSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEK   43 (59)
T ss_dssp             HHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence            33333333333344579999999999999999999886653

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 ....

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=91.60  E-value=0.5  Score=38.54  Aligned_cols=47  Identities=19%  Similarity=0.195  Sum_probs=41.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|++++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus       131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~  177 (189)
T PRK12515        131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAE  177 (189)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            578888888888877 88999999999999999999999988887765

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=91.56  E-value=0.45  Score=40.38  Aligned_cols=48  Identities=21%  Similarity=0.188  Sum_probs=41.3

Q ss_pred             CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++.++.|.|+   -.|.+++++|..+|+|.+||.+..++....|..
T Consensus       175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~  225 (233)
T PRK05803        175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK  225 (233)
T ss_pred             hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            578889999999886   467899999999999999999988887777765

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=91.56  E-value=0.48  Score=38.33  Aligned_cols=48  Identities=15%  Similarity=0.099  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|...
T Consensus       127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~  174 (179)
T PRK09415        127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKG  174 (179)
T ss_pred             hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            5778888888888776 79999999999999999999999888887763

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=91.56  E-value=0.48  Score=39.82  Aligned_cols=48  Identities=17%  Similarity=0.084  Sum_probs=41.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|+|+ .+.++.++|..+|+|.+||...+++....|...
T Consensus       134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~  181 (216)
T PRK12533        134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAAL  181 (216)
T ss_pred             cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            467778888888877 689999999999999999999999888877763

>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=91.52  E-value=0.5  Score=30.08  Aligned_cols=29  Identities=17%  Similarity=0.024  Sum_probs=23.6

Q ss_pred             CCChHhhhhhccccHhHHHHHHHHHHHHH
Q psy13113         29 GNFQIDSEDYHDISQSTICRLVAKVSEEL   57 (286)
Q Consensus        29 ~~~~~~l~~~Fgvs~stv~~~~~~v~~~l   57 (286)
                      +.+..++|..+|||+.||.+.++..-+.+
T Consensus        15 ~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   15 PITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            36889999999999999999998765544

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 ....

>PF13551 HTH_29: Winged helix-turn helix

Probab=91.44  E-value=0.34  Score=35.65  Aligned_cols=35  Identities=23%  Similarity=0.267  Sum_probs=30.2

Q ss_pred             HHHHHhhcCCC-hHhhhhhccccHhHHHHHHHHHHH
Q psy13113         21 AVLRFYATGNF-QIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        21 ~~L~~L~~~~~-~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+|..+..|.+ ...+|..+|+|.+||+++++++..
T Consensus         3 ~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~   38 (112)
T PF13551_consen    3 QILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYRE   38 (112)
T ss_pred             HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHc
Confidence            35667888995 999999999999999999998753

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

Probab=91.41  E-value=0.6  Score=34.94  Aligned_cols=48  Identities=19%  Similarity=0.153  Sum_probs=43.8

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccc-cHhHHHHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDI-SQSTICRLVAKVSEEL   57 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgv-s~stv~~~~~~v~~~l   57 (286)
                      +...|.|.++-++-.++..|.+...+|..||| +.+++++|+.+..+.-
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            67899999999999999999999999999996 9999999998877643

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=91.40  E-value=0.58  Score=37.93  Aligned_cols=47  Identities=11%  Similarity=0.111  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++.++.|. .-.|.++.++|..+|+|.+||...+++....|-.
T Consensus       133 ~L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~  179 (182)
T PRK12537        133 QLEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE  179 (182)
T ss_pred             hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence            4666677666666 4578999999999999999999999998887765

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=91.31  E-value=0.59  Score=38.35  Aligned_cols=47  Identities=11%  Similarity=0.024  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|++++-++.|+++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus       141 ~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~  187 (194)
T PRK12531        141 RLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRH  187 (194)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence            466677777777766 78999999999999999999988888877765

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=91.30  E-value=0.51  Score=42.18  Aligned_cols=69  Identities=12%  Similarity=0.093  Sum_probs=50.7

Q ss_pred             HHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH-HHhhcccccCCch-hHHHHHHHhhhhcCCCCceEee
Q psy13113         19 LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE-LAKCHQQWIHFPE-DLQTAKNQFSGIAGFPRVVVGC   91 (286)
Q Consensus        19 l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~-l~~~~~~~i~~P~-~~~~~~~~f~~~~~~p~~~~g~   91 (286)
                      +-++-+|+-.|.++.++|..+|+|+++|+|++.+.-+. |.+   --|.-|. ....+...+++++++..| +.+
T Consensus        19 ~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~---I~I~~~~~~~~~Le~~L~~~fgLk~~-iVv   89 (318)
T PRK15418         19 ARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIR---VQINSRFEGCLELENALRQHFSLQHI-RVL   89 (318)
T ss_pred             HHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEE---EEEeCCCccHHHHHHHHHHHhCCCEE-EEE
Confidence            33677888899999999999999999999999876544 332   2233343 445566677888899988 554

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=91.30  E-value=0.51  Score=41.06  Aligned_cols=48  Identities=8%  Similarity=0.011  Sum_probs=41.8

Q ss_pred             CCCHHHHHHHHHHHhh-cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYA-TGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~-~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .||..++..+.|+|+. .+.++.++|..+|||..+|+++.++.+.-|-.
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            5888899999999974 47899999999999999999999888877754

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.

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=91.23  E-value=0.6  Score=37.83  Aligned_cols=48  Identities=10%  Similarity=-0.003  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|++++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..
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            5677777788887776 89999999999999999999999988888753

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=91.18  E-value=0.59  Score=38.20  Aligned_cols=48  Identities=13%  Similarity=0.016  Sum_probs=41.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .||+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~  163 (187)
T PRK12516        116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEI  163 (187)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            467788888888777 789999999999999999999999888887763

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=91.13  E-value=0.51  Score=38.31  Aligned_cols=50  Identities=16%  Similarity=0.060  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQ   62 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~   62 (286)
                      .+|++++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-+.+.
T Consensus       138 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~  187 (190)
T TIGR02939       138 ALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR  187 (190)
T ss_pred             cCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            456666666666665 78999999999999999999999999888876443

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.

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=91.07  E-value=0.67  Score=36.50  Aligned_cols=48  Identities=13%  Similarity=0.138  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++ .|.+++++|..+|+|.+||...+.+....|...
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            467777777777765 579999999999999999999999988888753

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=91.00  E-value=0.56  Score=37.45  Aligned_cols=47  Identities=11%  Similarity=0.104  Sum_probs=40.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus       125 ~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~  171 (179)
T PRK11924        125 ALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLRE  171 (179)
T ss_pred             hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            477787877777777 68999999999999999999999988877765

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=90.90  E-value=0.59  Score=37.97  Aligned_cols=48  Identities=23%  Similarity=0.268  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++. |.++.++|..+|+|..||...+++....|...
T Consensus       128 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~  175 (186)
T PRK05602        128 ALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQ  175 (186)
T ss_pred             hCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence            4688888888888775 89999999999999999999999888887763

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=90.85  E-value=0.7  Score=37.52  Aligned_cols=48  Identities=17%  Similarity=0.169  Sum_probs=38.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-..
T Consensus       137 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  184 (187)
T PRK12534        137 ELEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC  184 (187)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence            455666666666654 789999999999999999999999888877653

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=90.85  E-value=0.55  Score=38.02  Aligned_cols=49  Identities=16%  Similarity=0.208  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|....
T Consensus       136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l  184 (187)
T TIGR02948       136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL  184 (187)
T ss_pred             hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            567777777777666 5799999999999999999999999888876543

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

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=90.82  E-value=0.63  Score=38.13  Aligned_cols=48  Identities=15%  Similarity=0.030  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++.++.|+++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~  181 (192)
T PRK09643        134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAEL  181 (192)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            478888888877777 779999999999999999998888877777653

>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=90.75  E-value=0.53  Score=30.45  Aligned_cols=44  Identities=20%  Similarity=0.180  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ++..+.-  +|.+++.|.+..++|...|+|.+||......+..-|.
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  6777999999999999999999999999988877664

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 ....

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=90.69  E-value=0.25  Score=38.69  Aligned_cols=47  Identities=13%  Similarity=0.117  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+
T Consensus       105 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~  151 (154)
T TIGR02950       105 RLPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKK  151 (154)
T ss_pred             hCCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            356666666666666 68999999999999999999999988877765

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.

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=90.59  E-value=0.6  Score=38.13  Aligned_cols=51  Identities=16%  Similarity=0.102  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhccc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQ   63 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~   63 (286)
                      .+|++++-++.|.++ .|.++.++|..+|+|..||...+.+....|-.....
T Consensus       138 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~  188 (193)
T PRK11923        138 QLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQP  188 (193)
T ss_pred             hCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            457777777777776 779999999999999999999999988888764433

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=90.57  E-value=0.58  Score=41.06  Aligned_cols=48  Identities=6%  Similarity=-0.005  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHHHhh-cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYA-TGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~-~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .++..++..+.++|+. .+.++.++|..+|||+++|+++.++.+.-|-.
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            5888899999999975 57899999999999999999999988877754

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=90.53  E-value=0.72  Score=39.78  Aligned_cols=48  Identities=21%  Similarity=0.150  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+++.++.++.|+|+ .+.++.++|..+|+|.+||++..++....|-..
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            478888888888886 588999999999999999999999988877653

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

Probab=90.39  E-value=0.78  Score=36.22  Aligned_cols=48  Identities=15%  Similarity=0.124  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|++++.++.|.+ -.|.++.++|..+|+|.+||...+.+....|-..
T Consensus       110 ~L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  157 (162)
T TIGR02983       110 RLPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLREL  157 (162)
T ss_pred             hCCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            45778888877777 4589999999999999999999999988887653

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.

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

Probab=90.35  E-value=0.7  Score=39.60  Aligned_cols=47  Identities=26%  Similarity=0.215  Sum_probs=40.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|..++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
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            467777777777776 78999999999999999999999998888775

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.

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=90.07  E-value=0.83  Score=37.39  Aligned_cols=49  Identities=10%  Similarity=0.010  Sum_probs=43.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      .+|+.++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-..+
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            578888888888888 8899999999999999999999999988887643

>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=90.06  E-value=0.66  Score=30.61  Aligned_cols=40  Identities=18%  Similarity=0.246  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHhhc----------CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYAT----------GNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        16 ~~~l~~~L~~L~~----------~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +++++-.|..|..          ..+..+++..+|+|++|++++++....
T Consensus         2 ~~ria~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~   51 (67)
T cd00092           2 KERLASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEE   51 (67)
T ss_pred             chHHHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3566666665542          248889999999999999998887654

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

Probab=90.03  E-value=0.98  Score=36.55  Aligned_cols=47  Identities=15%  Similarity=0.106  Sum_probs=39.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.++ .|.++.++|...|+|.+||...+++....|-.
T Consensus       140 ~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~  186 (189)
T TIGR02984       140 KLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ  186 (189)
T ss_pred             cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            567777777777776 78999999999999999999999988877754

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).

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

Probab=90.03  E-value=0.92  Score=38.20  Aligned_cols=47  Identities=21%  Similarity=0.324  Sum_probs=40.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|+|+ .|.++.++|..+|+|.+||+...++....|-.
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            578888888888776 57899999999999999999999998887754

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.

>PRK05572 sporulation sigma factor SigF; Validated

Probab=90.03  E-value=0.88  Score=39.10  Aligned_cols=47  Identities=21%  Similarity=0.323  Sum_probs=41.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|..++.++.|+|+ .+.++.++|..+|+|.+||+++.++.+..|-.
T Consensus       202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~  248 (252)
T PRK05572        202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKE  248 (252)
T ss_pred             cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            688888888888876 57899999999999999999999999888765

>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=89.98  E-value=0.32  Score=33.04  Aligned_cols=42  Identities=17%  Similarity=0.086  Sum_probs=33.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhcc-ccHhHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHD-ISQSTICRLVAKV   53 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fg-vs~stv~~~~~~v   53 (286)
                      .+.-..++++.|.+-.++.++.+++..|| .+.|||...++++
T Consensus        28 ~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki   70 (70)
T PF08299_consen   28 KIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI   70 (70)
T ss_dssp             HHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred             hhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence            45567888888888888999999999999 9999999888764

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.

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=89.96  E-value=0.85  Score=37.21  Aligned_cols=48  Identities=13%  Similarity=0.117  Sum_probs=41.9

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..+|++++-++.|+|+ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus       130 ~~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~  177 (189)
T PRK06811        130 NDLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK  177 (189)
T ss_pred             HhCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            3588888888888886 67999999999999999999999988877764

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=89.93  E-value=0.88  Score=36.98  Aligned_cols=48  Identities=15%  Similarity=-0.005  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       111 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~  158 (182)
T PRK12540        111 KLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSAL  158 (182)
T ss_pred             hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            567788888888776 889999999999999999999999888888763

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

Probab=89.91  E-value=0.93  Score=36.11  Aligned_cols=48  Identities=13%  Similarity=0.162  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|..++-++.|.++. |.++.++|..+|+|.+||...+.+....|...
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            5777777777777765 79999999999999999999999888887653

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.

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

Probab=89.80  E-value=0.75  Score=39.17  Aligned_cols=48  Identities=8%  Similarity=0.105  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++..+.|+|.   ..+.+++.+|..+|||.++|+++..+.+.-|-.
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            578889999999984   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.

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=89.79  E-value=0.87  Score=37.29  Aligned_cols=48  Identities=17%  Similarity=0.162  Sum_probs=40.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
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            466777777777776 688999999999999999999999988888763

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=89.73  E-value=1.2  Score=34.39  Aligned_cols=48  Identities=17%  Similarity=0.096  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .++.+++-++-+.|+.. ..++..+|..+|+|++|+++.-+.++..+..
T Consensus        82 ~Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~  130 (134)
T TIGR01636        82 EADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAE  130 (134)
T ss_pred             hCCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            37788888999988754 3499999999999999999998888887765

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.

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=89.72  E-value=0.91  Score=38.51  Aligned_cols=49  Identities=33%  Similarity=0.273  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++.++.|+++   -.|.++.++|...|+|.+||.....+....|-..
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            578888899999885   3688999999999999999999988888777653

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.

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

Probab=89.71  E-value=0.35  Score=36.53  Aligned_cols=30  Identities=13%  Similarity=0.289  Sum_probs=26.5

Q ss_pred             HHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         24 RFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        24 ~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      .+...|.+...+|..|+||.+||.+|+.+.
T Consensus        13 ~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~~   42 (119)
T PF01710_consen   13 AYIEKGKSIREAAKRFGVSRNTVYRWLKRK   42 (119)
T ss_pred             HHHHccchHHHHHHHhCcHHHHHHHHHHhc
Confidence            577788899999999999999999998743

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 [].

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=89.63  E-value=0.96  Score=35.30  Aligned_cols=46  Identities=11%  Similarity=0.151  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-
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            578888888888776 4689999999999999999999988777663

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=89.60  E-value=1.5  Score=37.23  Aligned_cols=68  Identities=10%  Similarity=0.068  Sum_probs=50.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCch---hHHHHHHHhhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE---DLQTAKNQFSG   80 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~---~~~~~~~~f~~   80 (286)
                      .+|+.++.++.|.++- |.+++++|...|+|.+||...+.+....|-.....-..-+.   +.+.+...|.+
T Consensus       116 ~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~~~~~~~~~~~~~~~~~~~~~  186 (228)
T PRK06704        116 SLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIVEFTDDMEVVVTSIRE  186 (228)
T ss_pred             hCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCccccHHHHHHHHHh
Confidence            5778888877777654 79999999999999999999999999888875544333222   45555555554

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=89.56  E-value=1  Score=37.46  Aligned_cols=48  Identities=15%  Similarity=0.081  Sum_probs=39.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++- |.++.++|..+|+|.+||...+++....|-+.
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            4666777777776654 89999999999999999999999998888763

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=89.51  E-value=1  Score=38.81  Aligned_cols=47  Identities=21%  Similarity=0.189  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|+|+ .|.++.++|..+|||.+||....++....|-.
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            467777777777775 68899999999999999999999998888764

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=89.40  E-value=1.1  Score=37.82  Aligned_cols=47  Identities=21%  Similarity=0.331  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|..++.++.|+|+ .+.++.++|..+|+|.++|+++.++...-|-.
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            577888888888765 57899999999999999999999988877754

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.

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=89.31  E-value=1.1  Score=38.69  Aligned_cols=47  Identities=28%  Similarity=0.383  Sum_probs=40.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+++.++.++.++|+ .|.++.++|..+|+|.++|+++.++...-|-.
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            678888888888775 57899999999999999999999988877754

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=89.29  E-value=1.1  Score=35.77  Aligned_cols=47  Identities=11%  Similarity=-0.010  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....+..
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            467778888888776 57999999999999999999998887776654

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=89.27  E-value=0.86  Score=40.10  Aligned_cols=48  Identities=15%  Similarity=0.055  Sum_probs=42.8

Q ss_pred             CCCHHHHHHHHHHHhh-cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYA-TGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~-~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++..+.|+|+. .+.++.++|..+|||.++|..+.++.+.-|-.
T Consensus       227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~  275 (289)
T PRK07500        227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRR  275 (289)
T ss_pred             cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            5889999999999863 67899999999999999999999998888875

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=89.07  E-value=2.1  Score=37.40  Aligned_cols=67  Identities=16%  Similarity=0.117  Sum_probs=48.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCchhHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFS   79 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~   79 (286)
                      .+|+.++-++.|+++ .+.+++++|..+|+|.+||...+++....|-+..+..-.-|.+.+.+...|.
T Consensus       108 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~f~  174 (281)
T TIGR02957       108 RLSPLERAVFVLREV-FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPRFEVSREESRQLLERFV  174 (281)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHHHH
Confidence            466666666666544 5789999999999999999999999999998755543222224445555554

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=89.04  E-value=1.1  Score=36.27  Aligned_cols=49  Identities=14%  Similarity=0.028  Sum_probs=42.4

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      ..+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|-..
T Consensus       130 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  178 (184)
T PRK12539        130 ARLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAAL  178 (184)
T ss_pred             HhCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            35788888888888874 89999999999999999999999998888763

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=89.03  E-value=1.1  Score=35.39  Aligned_cols=46  Identities=22%  Similarity=0.062  Sum_probs=37.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .+|++++-++.|.++ .|.++.++|..+|+|.+||...+.+....|.
T Consensus       113 ~L~~~~r~v~~L~~~-~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~  158 (161)
T PRK12528        113 GLPPLVKRAFLLAQV-DGLGYGEIATELGISLATVKRYLNKAAMRCY  158 (161)
T ss_pred             HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            467777777777665 5799999999999999999999988876654

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=89.00  E-value=1.2  Score=35.49  Aligned_cols=47  Identities=17%  Similarity=0.123  Sum_probs=39.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus       118 ~L~~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~  164 (173)
T PRK09645        118 QLSPEHRAVLVRSYY-RGWSTAQIAADLGIPEGTVKSRLHYALRALRL  164 (173)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            467777777777665 47999999999999999999988888877765

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=88.97  E-value=0.97  Score=32.10  Aligned_cols=37  Identities=14%  Similarity=0.118  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         16 VVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        16 ~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      .+++.++=-.|..|.+|++++...|+|-.|++|.-+.
T Consensus        36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~   72 (87)
T PF01371_consen   36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRC   72 (87)
T ss_dssp             HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            3455555557889999999999999999999986543

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=88.91  E-value=1.1  Score=36.49  Aligned_cols=47  Identities=11%  Similarity=0.026  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.++ .|.+++++|..+|+|.+||...+.+....|..
T Consensus       131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~  177 (191)
T PRK12520        131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLRE  177 (191)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            467777777777765 46899999999999999999999988888765

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=88.80  E-value=1.4  Score=35.60  Aligned_cols=46  Identities=22%  Similarity=0.167  Sum_probs=39.3

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      +|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus       135 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~  180 (183)
T TIGR02999       135 VDPRQAEVVELRFF-AGLTVEEIAELLGVSVRTVERDWRFARAWLAD  180 (183)
T ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            77787877777766 56899999999999999999999988887764

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.73  E-value=1.6  Score=31.64  Aligned_cols=41  Identities=15%  Similarity=0.190  Sum_probs=33.5

Q ss_pred             HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      +--+-| |+....|...+|..|+||++.|+..|+++...|..
T Consensus        23 ~~Y~~l-yy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~   63 (105)
T COG2739          23 KNYLEL-YYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED   63 (105)
T ss_pred             HHHHHH-HHHhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence            333444 44466899999999999999999999999998874

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

Probab=88.66  E-value=1.2  Score=36.35  Aligned_cols=48  Identities=17%  Similarity=0.068  Sum_probs=38.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.|+ .|.+++++|..+|+|.+||...+.+....|-..
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            345555666666655 479999999999999999999999888888764

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.

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=88.64  E-value=1.2  Score=38.23  Aligned_cols=48  Identities=23%  Similarity=0.346  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..+++.++.++.++|+ .+.++.++|..+|+|.++|+++.++.+.-|..
T Consensus       205 ~~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~  252 (254)
T TIGR02850       205 KRLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK  252 (254)
T ss_pred             HcCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence            3688888888888875 57899999999999999999999988877653

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.

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=88.61  E-value=1.2  Score=37.61  Aligned_cols=49  Identities=16%  Similarity=0.146  Sum_probs=41.5

Q ss_pred             CCCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..+|+.++-++.|+|+   ..+.++.++|...|+|.+||....++....|-.
T Consensus       173 ~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~  224 (227)
T TIGR02846       173 SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK  224 (227)
T ss_pred             HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            4577888888888876   378899999999999999999998888877754

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.

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=88.53  E-value=1.2  Score=36.18  Aligned_cols=48  Identities=15%  Similarity=-0.058  Sum_probs=39.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|++++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-+.
T Consensus       106 ~L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~  153 (181)
T PRK09637        106 ALPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL  153 (181)
T ss_pred             hCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            567777777777664 678999999999999999999998888777653

>PRK06930 positive control sigma-like factor; Validated

Probab=88.37  E-value=1.4  Score=35.50  Aligned_cols=47  Identities=17%  Similarity=0.294  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|. +..|.++.++|..+|+|.+||...+.+....|-.
T Consensus       114 ~L~~rer~V~~L~-~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~  160 (170)
T PRK06930        114 VLTEREKEVYLMH-RGYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR  160 (170)
T ss_pred             hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            5667666666665 4688999999999999999999999988887765

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=88.32  E-value=1.2  Score=35.65  Aligned_cols=52  Identities=12%  Similarity=0.148  Sum_probs=39.1

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhccccc
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWI   65 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i   65 (286)
                      +|+..+-++.| +.-.|.+++++|...|+|.+||...+.+....|...+..+|
T Consensus       120 L~~~~r~i~~l-~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~  171 (173)
T PRK12522        120 LNEKYKTVLVL-YYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV  171 (173)
T ss_pred             CCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44444433333 34467999999999999999999999999988887655554

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=88.17  E-value=1.1  Score=39.23  Aligned_cols=49  Identities=6%  Similarity=0.034  Sum_probs=42.6

Q ss_pred             CCCHHHHHHHHHHH-h--hcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRF-Y--ATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~-L--~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .||..++..+.|+| |  -.+.+++++|..+|+|.+||....++....|-..
T Consensus       222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~  273 (285)
T TIGR02394       222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRI  273 (285)
T ss_pred             cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            57888888999988 4  4678999999999999999999999988888764

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).

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=88.15  E-value=1.3  Score=37.57  Aligned_cols=48  Identities=10%  Similarity=0.051  Sum_probs=40.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-..
T Consensus       184 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~  231 (236)
T PRK06986        184 SLPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR  231 (236)
T ss_pred             hCCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            467777777777764 678999999999999999999999888887653

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=88.02  E-value=2.7  Score=36.96  Aligned_cols=67  Identities=12%  Similarity=0.028  Sum_probs=47.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCchhHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFS   79 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~   79 (286)
                      .+|+.++-++.|+++ .+.++.++|..+|+|.+||...+.+....|-+..+..-.-|.+-.++...|.
T Consensus       115 ~L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~v~~f~  181 (293)
T PRK09636        115 RLSPLERAAFLLHDV-FGVPFDEIASTLGRSPAACRQLASRARKHVRAARPRFPVSDEEGAELVEAFF  181 (293)
T ss_pred             hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCCCCchHHHHHHHHHH
Confidence            466776766666655 4699999999999999999999999999998765543222223334444443

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

Probab=88.00  E-value=1.3  Score=29.37  Aligned_cols=43  Identities=19%  Similarity=0.127  Sum_probs=38.5

Q ss_pred             HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      ++-.+..+|....+..+.|...|++..++.+++..+-..+.++
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            3446788999999999999999999999999999999998875

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=87.84  E-value=1.8  Score=34.48  Aligned_cols=47  Identities=11%  Similarity=-0.003  Sum_probs=39.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++.++.|.+ -.|.++.++|..+|+|.+||...+.+....+..
T Consensus       118 ~L~~~~r~v~~L~~-~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~  164 (168)
T PRK12525        118 GLSGKARAAFLMSQ-LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ  164 (168)
T ss_pred             hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            47888888777775 567999999999999999999998888777654

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

Probab=87.80  E-value=1.2  Score=28.05  Aligned_cols=38  Identities=21%  Similarity=0.237  Sum_probs=27.6

Q ss_pred             HHHHHHHHhhcC---CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         18 KLLAVLRFYATG---NFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        18 ~l~~~L~~L~~~---~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +.+-.|..++..   .+..+++...|++++|+++++.....
T Consensus         4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~   44 (52)
T PF09339_consen    4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE   44 (52)
T ss_dssp             HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            445555566543   36899999999999999999876553

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

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=87.78  E-value=1.3  Score=39.57  Aligned_cols=48  Identities=19%  Similarity=0.152  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++..+.|+|.   ..+.++.++|..+|||+.+|..+..+...-|-.
T Consensus       256 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~  306 (317)
T PRK07405        256 DLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK  306 (317)
T ss_pred             cCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            588999999999986   466899999999999999999999988887765

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

Probab=87.71  E-value=0.33  Score=36.80  Aligned_cols=97  Identities=15%  Similarity=0.146  Sum_probs=63.0

Q ss_pred             ceeeecCCCccEEEeccCCCCccccccccccchhhhhccccccceEEEccccCCCCCcccccccCCCC---CC--hhhHH
Q psy13113        120 NVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRNPIT---PT--PSQVA  194 (286)
Q Consensus       120 ~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~~~~~~~llgD~gY~~~~~l~~p~~~~~~---l~--~~~~~  194 (286)
                      +.+.++|..|+++....+ +|..+ ..... ..+-+  .+   -.-+|+|.+|....+...|-..+..   ..  ..+.-
T Consensus         2 ~~~~l~D~~~~~i~~~lp-~~~~~-~~~~~-~~~~~--~~---v~~~i~~~~~~g~~wr~~p~~~~~~~~~~~~~~~~~~   73 (124)
T COG3293           2 KLHALVDAEWRPVEPLLP-PAKYG-GPPGV-TLLRD--RE---VLNGIADLLYTGCAWRALPADFPPATTVIPYRRFRRW   73 (124)
T ss_pred             CcccccccccceeeccCC-CcccC-CCCCC-ccccc--HH---HHHHHHHHhccchHHHHhHHHhCCCceEeCCCcchhh
Confidence            467899999999998886 44433 21111 00100  01   1256789999887776544433211   11  23677


Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhhhhhhcccc
Q psy13113        195 YNAAQIRTRNSVERLFGVLKRRFACLRKKLA  225 (286)
Q Consensus       195 ~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~  225 (286)
                      ++..+...|..+|+.|+.+|. |+.+...++
T Consensus        74 ~~~g~~~~~~~~~~~f~~~~~-~r~~~~~~~  103 (124)
T COG3293          74 FKRGLWKRRNLVERTFGRLKQ-FRRTATRYD  103 (124)
T ss_pred             HHHHHHHHHHHHHHHHHHHhc-ccceecchh
Confidence            899999999999999999998 888876533

>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]

Probab=87.47  E-value=1.5  Score=35.56  Aligned_cols=48  Identities=17%  Similarity=0.164  Sum_probs=40.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|++++-++.|.++ .|.++.++|...|||.+||...+++....|...
T Consensus       127 ~Lp~~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~  174 (182)
T COG1595         127 RLPPRQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLHRARKKLREQ  174 (182)
T ss_pred             hCCHHHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            467777777777776 568999999999999999999999988888764

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=87.47  E-value=1.7  Score=37.33  Aligned_cols=47  Identities=19%  Similarity=0.111  Sum_probs=40.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.|+ .+.+++++|..+|+|.+||...+++....|-.
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            467778888888775 78899999999999999999999888877754

>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=87.33  E-value=2.1  Score=27.83  Aligned_cols=39  Identities=26%  Similarity=0.229  Sum_probs=30.3

Q ss_pred             HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      -+++....+ .++...|...++|++++++.++++...+..
T Consensus         5 ~~f~~v~~~-gs~~~AA~~l~is~~~vs~~i~~LE~~lg~   43 (60)
T PF00126_consen    5 RYFLAVAET-GSISAAAEELGISQSAVSRQIKQLEEELGV   43 (60)
T ss_dssp             HHHHHHHHH-SSHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHh-CCHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence            333333444 489999999999999999999988877764

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 ....

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

Probab=87.05  E-value=1.6  Score=37.43  Aligned_cols=47  Identities=30%  Similarity=0.294  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .++-.+|+.+.|+| -.+.++..+|...|||++.||++.++.+..|-.
T Consensus       196 ~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr~  242 (247)
T COG1191         196 PLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLRK  242 (247)
T ss_pred             ccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence            67888999999998 456899999999999999999999998888765

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=87.01  E-value=2  Score=33.83  Aligned_cols=48  Identities=6%  Similarity=-0.042  Sum_probs=38.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~  153 (160)
T PRK09642        106 ELPENYRDVVLAHYL-EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKH  153 (160)
T ss_pred             hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            356666666666554 679999999999999999999888888777653

>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=87.00  E-value=2  Score=31.39  Aligned_cols=40  Identities=10%  Similarity=0.152  Sum_probs=30.7

Q ss_pred             HHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      -+.-.|+-.+.|...+|..+|||+.+|+..+++....|..
T Consensus        24 ~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~   63 (101)
T PF04297_consen   24 EILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE   63 (101)
T ss_dssp             HHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            3444566778999999999999999999999999988875

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.

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=86.96  E-value=1.8  Score=35.21  Aligned_cols=47  Identities=9%  Similarity=0.054  Sum_probs=39.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|.|+. |.++.++|..+|+|.+||...+++....|-.
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            5677777777777665 7899999999999999999999888777754

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=86.86  E-value=1.8  Score=37.18  Aligned_cols=47  Identities=23%  Similarity=0.174  Sum_probs=40.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-.+.|+|+ .|.++.++|..+|+|.+||....++....|-.
T Consensus       205 ~L~~~~r~ii~l~~~-~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~  251 (255)
T TIGR02941       205 ILSEREKSIIHCTFE-ENLSQKETGERLGISQMHVSRLQRQAISKLKE  251 (255)
T ss_pred             cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            567888888888775 67899999999999999999999888877754

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=86.85  E-value=1.8  Score=30.43  Aligned_cols=40  Identities=33%  Similarity=0.338  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHhhc---CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYAT---GNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        16 ~~~l~~~L~~L~~---~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      -++.+-.|.+|..   +.+..+++..+|++++|+++++.....
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            3455556666664   368999999999999999999987754

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=86.83  E-value=2.1  Score=34.66  Aligned_cols=47  Identities=13%  Similarity=0.199  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|..++-++.|+++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus       135 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~  181 (186)
T PRK13919        135 ALSPEERRVIEVLYY-QGYTHREAAQLLGLPLGTLKTRARRALSRLKE  181 (186)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            467777777777764 57899999999999999999999988887765

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=86.78  E-value=1.6  Score=35.47  Aligned_cols=47  Identities=17%  Similarity=0.044  Sum_probs=39.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ++|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+
T Consensus       130 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~  176 (185)
T PRK09649        130 DLTTDQREALLLTQL-LGLSYADAAAVCGCPVGTIRSRVARARDALLA  176 (185)
T ss_pred             hCCHHHhHHhhhHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            467777777777766 56889999999999999999999988887764

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=86.75  E-value=1.5  Score=29.71  Aligned_cols=26  Identities=19%  Similarity=0.351  Sum_probs=22.4

Q ss_pred             CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         30 NFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        30 ~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+..++|...|+|..|++++++++.+
T Consensus        29 lt~~~iA~~~g~sr~tv~r~l~~l~~   54 (76)
T PF13545_consen   29 LTQEEIADMLGVSRETVSRILKRLKD   54 (76)
T ss_dssp             SSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            36889999999999999999887654

...

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=86.69  E-value=2.1  Score=33.71  Aligned_cols=48  Identities=15%  Similarity=0.068  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|++++-++.|.+ -.|.++.++|..+|+|.+||...+.+....|-..
T Consensus       105 ~L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~  152 (159)
T PRK12527        105 ELPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVR  152 (159)
T ss_pred             hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            46677666666654 5779999999999999999999999888887653

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=86.68  E-value=1.7  Score=35.76  Aligned_cols=47  Identities=17%  Similarity=0.189  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.| ++ .|.+++++|..+|+|.+||...+.+....|-..
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            567777777777 55 789999999999999999999998888777653

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=86.67  E-value=1.8  Score=37.50  Aligned_cols=47  Identities=28%  Similarity=0.316  Sum_probs=40.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|+|+ .+.++.++|..+|+|.+||.++.++....|-.
T Consensus       215 ~L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~  261 (264)
T PRK07122        215 ALPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRD  261 (264)
T ss_pred             cCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            567777888888875 58899999999999999999999988877754

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=86.56  E-value=2.1  Score=34.67  Aligned_cols=50  Identities=2%  Similarity=0.014  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQ   62 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~   62 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-....
T Consensus       122 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~  171 (185)
T PRK12542        122 ELNESNRQVFKYKVF-YNLTYQEISSVMGITEANVRKQFERARKRVQNMIG  171 (185)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence            356666666555544 66999999999999999999999998888876443

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=86.48  E-value=2  Score=34.65  Aligned_cols=47  Identities=15%  Similarity=0.043  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++.++.|.++ .|.+++++|..+|+|.+||...+++....|..
T Consensus       129 ~L~~~~r~v~~l~~~-~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~  175 (181)
T PRK12536        129 QLPDRQRLPIVHVKL-EGLSVAETAQLTGLSESAVKVGIHRGLKALAA  175 (181)
T ss_pred             HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            466666766666554 67999999999999999999999988887765

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

Probab=86.47  E-value=1.1  Score=25.36  Aligned_cols=25  Identities=24%  Similarity=0.462  Sum_probs=19.6

Q ss_pred             CChHhhhhhccccHhHHHHHHHHHH
Q psy13113         30 NFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        30 ~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .+.+++|...|++..||+|++..+.
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~   27 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLE   27 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence            4678999999999999999988654

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

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family

Probab=86.38  E-value=2.2  Score=35.82  Aligned_cols=47  Identities=13%  Similarity=0.165  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|+|+ .+.++.++|..+|+|.+||....++....|-.
T Consensus       175 ~L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~  221 (224)
T TIGR02479       175 SLSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRA  221 (224)
T ss_pred             hCCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            467777777888775 67899999999999999999999888777654

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

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

Probab=86.33  E-value=2.1  Score=31.95  Aligned_cols=48  Identities=21%  Similarity=0.095  Sum_probs=38.2

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..++.+++- ....++.+.++.++++..+|||=+||..-+.+++.+|.-
T Consensus        32 ~~L~~E~~~-Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   32 ARLSPEQLE-FIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hcCCHHHHH-HHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            445655554 455566677899999999999999999999999988864

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=86.23  E-value=3.6  Score=36.20  Aligned_cols=67  Identities=13%  Similarity=0.068  Sum_probs=46.7

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCchhHHHHHHHhhh
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSG   80 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~   80 (286)
                      +|+.++-++.|+++ .|.++.++|...|+|.+||...+.+....|-...+.+-.-|.+.+.+...|..
T Consensus       119 L~p~~R~vf~L~~~-~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~f~~  185 (290)
T PRK09635        119 LGPAERVVFVLHEI-FGLPYQQIATTIGSQASTCRQLAHRARRKINESRIAASVEPAQHRVVTRAFIE  185 (290)
T ss_pred             CCHHHHHHhhHHHH-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHHHHH
Confidence            44555555544443 58999999999999999999999999999887554432222244556666643

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

Probab=86.22  E-value=2  Score=28.89  Aligned_cols=41  Identities=12%  Similarity=0.137  Sum_probs=31.3

Q ss_pred             CHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         14 SPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        14 ~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      +.+++++.+|..-+. +.+..+||...|++.++|++.+....
T Consensus         6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~   47 (68)
T smart00550        6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE   47 (68)
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            456777777765544 47899999999999999998776443

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

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=86.06  E-value=2  Score=33.88  Aligned_cols=47  Identities=13%  Similarity=0.044  Sum_probs=39.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-+
T Consensus       112 ~L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~  158 (161)
T PRK12541        112 SLPLERRNVLLLRDY-YGFSYKEIAEMTGLSLAKVKIELHRGRKETKS  158 (161)
T ss_pred             HCCHHHHHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            577888887777766 56899999999999999999999988877754

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=85.88  E-value=2.1  Score=34.45  Aligned_cols=48  Identities=13%  Similarity=0.117  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++ .|.+++++|..+|+|.+||...+++....|-..
T Consensus       117 ~Lp~~~r~i~~l~~~-e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~  164 (179)
T PRK12543        117 KLPYKLRQVIILRYL-HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQK  164 (179)
T ss_pred             hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            477878877777655 568999999999999999999888888777653

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=85.72  E-value=2.2  Score=33.76  Aligned_cols=48  Identities=8%  Similarity=-0.083  Sum_probs=39.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       108 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~  155 (165)
T PRK09644        108 TLPVIEAQAILLCDV-HELTYEEAASVLDLKLNTYKSHLFRGRKRLKAL  155 (165)
T ss_pred             hCCHHHHHHHHhHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            467777776666655 568999999999999999999999988887653

>PF13751 DDE_Tnp_1_6: Transposase DDE domain

Probab=85.67  E-value=0.37  Score=36.54  Aligned_cols=48  Identities=23%  Similarity=0.297  Sum_probs=36.4

Q ss_pred             HHHHHHHHH-HHHHHHHHHHhhhhhhhccccC-CccchHHHHHHHHHHHhhh
Q psy13113        196 NAAQIRTRN-SVERLFGVLKRRFACLRKKLAN-QPTTCSHIITACAVLHNIA  245 (286)
Q Consensus       196 N~~~~~~R~-~vE~~~~~lK~rf~~L~~~~~~-~~~~~~~ii~a~~~LhN~~  245 (286)
                      .+.+.+.|. .||.+||.||. +--+. .+++ ...++..-+...++.|||-
T Consensus        73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~-r~~~rG~~kv~~~~~l~a~a~Nl~  122 (125)
T PF13751_consen   73 GKELYKQRSIKVEGVFGTIKR-NHGLR-RFRYRGLEKVRIEFLLAAIAYNLK  122 (125)
T ss_pred             hhhhhheeecccccccccchh-ccCCc-cccccchhhhHHHHHHHHHHHHHH
Confidence            456778888 99999999999 44444 2343 6677778888888889985

>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A

Probab=85.45  E-value=1.3  Score=29.21  Aligned_cols=33  Identities=33%  Similarity=0.264  Sum_probs=23.5

Q ss_pred             HHHHHHHh--hcCCChHhhhhhccccHhHHHHHHH
Q psy13113         19 LLAVLRFY--ATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        19 l~~~L~~L--~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      |+..|..+  +.|.++.++|...|+|.+|++++-+
T Consensus         2 lg~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~   36 (64)
T PF13560_consen    2 LGRRLRRLRERAGLSQAQLADRLGVSQSTVSRIER   36 (64)
T ss_dssp             HHHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            33344444  4678999999999999999998754

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=85.38  E-value=3.2  Score=37.07  Aligned_cols=69  Identities=25%  Similarity=0.269  Sum_probs=47.1

Q ss_pred             HHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccccCCch-hHHHHHHHhhhhcCCCCceEeee
Q psy13113         21 AVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQWIHFPE-DLQTAKNQFSGIAGFPRVVVGCI   92 (286)
Q Consensus        21 ~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~i~~P~-~~~~~~~~f~~~~~~p~~~~g~i   92 (286)
                      ++-.|+-.|.++.++|..+|+|+.||+|.+....+.  -+..-.|..|. ..-.+....+++++++.| +.+-
T Consensus        18 ~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~--GiV~I~i~~~~~~~~~Le~~L~~~fgL~~a-~VVp   87 (321)
T COG2390          18 AAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREE--GIVKISINSPVEGCLELEQQLKERFGLKEA-IVVP   87 (321)
T ss_pred             HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CeEEEEeCCCCcchHHHHHHHHHhcCCCeE-EEEc
Confidence            455677788999999999999999999988765432  02333344333 333455566777888888 5543

>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx

Probab=85.32  E-value=2.5  Score=27.44  Aligned_cols=44  Identities=14%  Similarity=0.009  Sum_probs=29.7

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCC---ChHhhhhhccccHhHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGN---FQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~---~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      |.+...+++-+|-+.-++..++.   .++..|..|||++..|.+|..
T Consensus         1 g~rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~k   47 (58)
T PF09607_consen    1 GSRRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRK   47 (58)
T ss_dssp             -------HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred             CCccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHH
Confidence            45677889999988888888875   579999999999999988765

100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=85.32  E-value=2.5  Score=34.73  Aligned_cols=52  Identities=17%  Similarity=0.133  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcccc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQW   64 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~~   64 (286)
                      .+|+.++-++.|.++ .|.+++++|..+|+|.+||...+.+....|-..+.++
T Consensus       133 ~Lp~~~r~v~~l~~~-~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~  184 (196)
T PRK12535        133 ALPPERREALILTQV-LGYTYEEAAKIADVRVGTIRSRVARARADLIAATATG  184 (196)
T ss_pred             cCCHHHHHHhhhHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence            466777777777665 4688999999999999999999999999888765554

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=85.27  E-value=2.4  Score=35.07  Aligned_cols=47  Identities=6%  Similarity=-0.045  Sum_probs=38.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|++++.++.|.|+ .|.+++++|..+|+|.+||...+++....|..
T Consensus       153 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~  199 (206)
T PRK12526        153 KLPEAQQTVVKGVYF-QELSQEQLAQQLNVPLGTVKSRLRLALAKLKV  199 (206)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            466666767666554 57899999999999999999999888877765

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=85.09  E-value=2.5  Score=39.62  Aligned_cols=51  Identities=16%  Similarity=0.079  Sum_probs=46.2

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      +|...+....|++|.|.+=-++.++.+++..||.+.|||...++++-..+.
T Consensus       366 ~R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~~  416 (440)
T PRK14088        366 SRNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSLL  416 (440)
T ss_pred             CCCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence            466788899999999999889999999999999999999999999998763

>PF13610 DDE_Tnp_IS240: DDE domain

Probab=84.92  E-value=1.5  Score=33.99  Aligned_cols=130  Identities=15%  Similarity=0.081  Sum_probs=73.9

Q ss_pred             eeeeeEEEecCCCCCCccccccCCCccccceeeecCCCccEEEeccCCCCccccccccccchhhhhcccc-ccceEEEcc
Q psy13113         91 CIDGTHVPIELPSIENGEHYRNRKHFYSINVQVIGGPNLEIYDVVASWPGSTHDSRIFQNSRVYSRFDRR-EIRGLLLGD  169 (286)
Q Consensus        91 ~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~vvd~~g~i~~~~~~~~Gs~~D~~~~~~s~l~~~l~~~-~~~~~llgD  169 (286)
                      .+|-|.|.|.--   .            .=+-..+|.+|+++++.+.-.-...++..|    +.+.+... ..+..++.|
T Consensus         5 ~~DEt~iki~G~---~------------~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~F----l~~~l~~~~~~p~~ivtD   65 (140)
T PF13610_consen    5 HVDETYIKIKGK---W------------HYLWRAIDAEGNILDFYLSKRRDTAAAKRF----LKRALKRHRGEPRVIVTD   65 (140)
T ss_pred             EEeeEEEEECCE---E------------EEEEEeecccccchhhhhhhhcccccceee----ccccceeeccccceeecc
Confidence            689999887721   0            112478999999988888633233333222    22223322 125677878


Q ss_pred             cc--CCCC-CcccccccCCCCCChhhHHhHHHHHHHHHHHHHHHHHHHhhhhhhhccccCCccchHHHHHHHHHHHhhhh
Q psy13113        170 IG--YAQN-EFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFACLRKKLANQPTTCSHIITACAVLHNIAI  246 (286)
Q Consensus       170 ~g--Y~~~-~~l~~p~~~~~~l~~~~~~~N~~~~~~R~~vE~~~~~lK~rf~~L~~~~~~~~~~~~~ii~a~~~LhN~~~  246 (286)
                      +.  |+.- ..+......+.....      ....-.++.||+-+..+|.|.+... ++ .+...+..++..-.+.||+..
T Consensus        66 k~~aY~~A~~~l~~~~~~~~~v~~------~~~k~~nN~iE~~h~~~K~r~r~~~-gF-ks~~~A~~~l~~~~~~~n~~r  137 (140)
T PF13610_consen   66 KLPAYPAAIKELNPEGRLHDKVEH------RQRKYLNNRIERDHRTIKRRTRPMN-GF-KSFRSAQRTLSGFEAYHNFRR  137 (140)
T ss_pred             cCCccchhhhhcccccccccccce------eechhhhChhhHhhhhhhhhccccc-Cc-CCHHHHHHHHHHHHHHHHHhC
Confidence            75  3221 111111100000000      1111346679999999999886554 34 367888899999999999975


Q ss_pred             h
Q psy13113        247 A  247 (286)
Q Consensus       247 ~  247 (286)
                      .
T Consensus       138 ~  138 (140)
T PF13610_consen  138 P  138 (140)
T ss_pred             C
Confidence            4

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=84.86  E-value=2.3  Score=38.11  Aligned_cols=48  Identities=8%  Similarity=0.056  Sum_probs=41.8

Q ss_pred             CCCHHHHHHHHHHH-hh--cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRF-YA--TGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~-L~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .||+.++.++.++| |.  .+.++..+|...|||.+||..+.++....|-.
T Consensus       262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~  312 (325)
T PRK05657        262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE  312 (325)
T ss_pred             cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            68888888888887 54  56899999999999999999999998888865

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=84.84  E-value=2.6  Score=34.76  Aligned_cols=48  Identities=10%  Similarity=0.061  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       139 ~Lp~~~r~v~~L~~~-eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~  186 (201)
T PRK12545        139 HLPEQIGRVFMMREF-LDFEIDDICTELTLTANHCSVLLYRARTRLRTC  186 (201)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            456666666666654 678999999999999999999988888877653

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=84.84  E-value=1.2  Score=37.70  Aligned_cols=49  Identities=10%  Similarity=0.064  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      .+|+.++-++.|+++ .|.+++++|..+|+|.+||...+.+....|-...
T Consensus       149 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l  197 (231)
T PRK11922        149 ALPDAFRAVFVLRVV-EELSVEETAQALGLPEETVKTRLHRARRLLRESL  197 (231)
T ss_pred             hCCHHHhhhheeehh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            356666666666654 4899999999999999999999988887777643

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=84.82  E-value=2.9  Score=33.36  Aligned_cols=48  Identities=15%  Similarity=-0.027  Sum_probs=40.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       100 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~  147 (170)
T TIGR02959       100 ELPDEYREAIRLTEL-EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL  147 (170)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            577888777777765 568999999999999999999998888777653

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=84.66  E-value=2  Score=34.74  Aligned_cols=45  Identities=13%  Similarity=0.117  Sum_probs=37.1

Q ss_pred             CCCHHHHHHHHHHHhhc--------------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYAT--------------GNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~--------------~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ..+++++|+-+|..|+.              ..+..++|...|+++.||+|+++++...
T Consensus       112 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~  170 (193)
T TIGR03697       112 HRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK  170 (193)
T ss_pred             hCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence            35788999999887742              2478899999999999999999887654

Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=84.57  E-value=2.6  Score=34.33  Aligned_cols=49  Identities=12%  Similarity=0.154  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      .+|...+-++.|.++ .|.++.++|...|+|.+||...+.+....|...+
T Consensus       128 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  176 (188)
T PRK12517        128 KLDPEYREPLLLQVI-GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL  176 (188)
T ss_pred             hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            456666665555544 5799999999999999999999999888887643

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=84.30  E-value=2  Score=34.73  Aligned_cols=46  Identities=15%  Similarity=0.187  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.|+  =+|.+++.|.+.+++|...++|.+||..++.++..-|..
T Consensus       133 ~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLgV  178 (198)
T PRK15201        133 HFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHV  178 (198)
T ss_pred             CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            3677655  456668999999999999999999999999988877753

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=84.25  E-value=2.4  Score=38.72  Aligned_cols=48  Identities=17%  Similarity=0.153  Sum_probs=41.6

Q ss_pred             CCCHHHHHHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+++.++..+.|+|.-   .+.++..+|..+|||+.+|+.+-.+.+.-|-.
T Consensus       311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~  361 (373)
T PRK07406        311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH  361 (373)
T ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            5899999999998862   45799999999999999999999988877754

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

Probab=84.09  E-value=2.2  Score=30.73  Aligned_cols=27  Identities=4%  Similarity=0.085  Sum_probs=22.8

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ...+..++|...|+|+.||++.+++..
T Consensus        46 ~~is~~eLa~~~g~sr~tVsr~L~~Le   72 (95)
T TIGR01610        46 DRVTATVIAELTGLSRTHVSDAIKSLA   72 (95)
T ss_pred             CccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            346889999999999999999887654

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

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=83.93  E-value=2.7  Score=32.59  Aligned_cols=43  Identities=14%  Similarity=0.101  Sum_probs=30.1

Q ss_pred             CCCHHH-HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         12 IHSPVV-KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        12 ~~~~~~-~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .+++.+ .++..|.....+.+..+|+..++++++|+++.+++..
T Consensus        28 glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le   71 (144)
T PRK03573         28 ELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE   71 (144)
T ss_pred             CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH
Confidence            455554 3344443333456899999999999999999887554

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

Probab=83.87  E-value=3.1  Score=27.49  Aligned_cols=29  Identities=21%  Similarity=0.157  Sum_probs=23.8

Q ss_pred             hhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         26 YATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        26 L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..++.+..+++..+|++.+|+++.++.+.
T Consensus        17 ~~~~~~~~ei~~~~~i~~~~i~~~l~~L~   45 (78)
T cd00090          17 LEGPLTVSELAERLGLSQSTVSRHLKKLE   45 (78)
T ss_pred             HHCCcCHHHHHHHHCcCHhHHHHHHHHHH
Confidence            33448899999999999999999887653

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

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=83.79  E-value=1.1  Score=28.25  Aligned_cols=28  Identities=29%  Similarity=0.196  Sum_probs=22.5

Q ss_pred             HhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         25 FYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      +...|.++.++|...|+|++|++++.+.
T Consensus         5 r~~~gls~~~la~~~gis~~~i~~~~~g   32 (55)
T PF01381_consen    5 RKEKGLSQKELAEKLGISRSTISRIENG   32 (55)
T ss_dssp             HHHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred             HHHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence            3467899999999999999999998864

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=83.73  E-value=3  Score=35.34  Aligned_cols=46  Identities=15%  Similarity=0.218  Sum_probs=38.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .++..++-.+.|+|. .+.++.++|..+|+|+++|+++.+....-|-
T Consensus       183 ~L~~~er~vi~l~~~-~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr  228 (231)
T PRK12427        183 QLDEREQLILHLYYQ-HEMSLKEIALVLDLTEARICQLNKKIAQKIK  228 (231)
T ss_pred             cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            567777888888874 6789999999999999999999888777663

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

Probab=83.73  E-value=2  Score=28.32  Aligned_cols=35  Identities=37%  Similarity=0.415  Sum_probs=25.1

Q ss_pred             HHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         22 VLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        22 ~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      +|+++.   ...+..+++..++++++++++.+++.++.
T Consensus         8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~   45 (68)
T PF13463_consen    8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK   45 (68)
T ss_dssp             HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred             HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            455565   34588999999999999999988876543

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=83.62  E-value=3.3  Score=38.82  Aligned_cols=52  Identities=13%  Similarity=-0.004  Sum_probs=46.9

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhc-cccHhHHHHHHHHHHHHHHh
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYH-DISQSTICRLVAKVSEELAK   59 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~F-gvs~stv~~~~~~v~~~l~~   59 (286)
                      +|...+....|++|.|.+--++.++.++|..| |.+.|||...++++-..+..
T Consensus       381 ~R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~  433 (450)
T PRK00149        381 SRTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLEE  433 (450)
T ss_pred             CCCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHHh
Confidence            45677888999999999999999999999999 59999999999999987753

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=83.61  E-value=2.6  Score=39.01  Aligned_cols=48  Identities=13%  Similarity=0.095  Sum_probs=41.2

Q ss_pred             CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+++.++-.+.|+|.   ..+.++.++|..+|+|.++|..+.++....|-.
T Consensus       350 ~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~  400 (415)
T PRK07598        350 DLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ  400 (415)
T ss_pred             hCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            588889989999885   355799999999999999999999988877763

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=83.52  E-value=3.4  Score=33.80  Aligned_cols=47  Identities=11%  Similarity=0.058  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .||..++-++.|.|+ .|.++.++|...|+|.+||...+++....|-.
T Consensus       142 ~L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~  188 (194)
T PRK09646        142 ALTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRDGLIRLRD  188 (194)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence            577777777777664 56999999999999999999999988887765

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=83.49  E-value=3  Score=34.03  Aligned_cols=38  Identities=13%  Similarity=0.137  Sum_probs=30.9

Q ss_pred             HHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         21 AVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        21 ~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      +.+.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus       158 i~~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~  195 (198)
T TIGR02859       158 VLQSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK  195 (198)
T ss_pred             HHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            334454 78999999999999999999888887776654

Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=83.36  E-value=2.4  Score=35.95  Aligned_cols=48  Identities=8%  Similarity=0.110  Sum_probs=39.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|..++-++.|+|+ .|.+++++|..+|+|.+||...+.+....|-..
T Consensus       171 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~  218 (233)
T PRK12538        171 RLPEQQRIAVILSYH-ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDL  218 (233)
T ss_pred             hCCHHHHHHhhhHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            456677776666664 679999999999999999999999988888764

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=83.20  E-value=2.9  Score=27.21  Aligned_cols=32  Identities=13%  Similarity=0.077  Sum_probs=26.2

Q ss_pred             HHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         19 LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        19 l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      .+..|++  .|-+..++|...|++.+||+.+..+
T Consensus         5 ~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r   36 (58)
T PF06056_consen    5 QARSLYL--QGWSIKEIAEELGVPRSTVYSWKDR   36 (58)
T ss_pred             HHHHHHH--cCCCHHHHHHHHCCChHHHHHHHHh
Confidence            4455553  5899999999999999999998864

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=83.20  E-value=3.7  Score=31.85  Aligned_cols=46  Identities=4%  Similarity=-0.033  Sum_probs=33.2

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ...+++.+-.++...+-..+.+..+|+..++++++|+++.+++...
T Consensus        35 ~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~   80 (144)
T PRK11512         35 PLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC   80 (144)
T ss_pred             ccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3456666554444334445679999999999999999998876543

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=83.11  E-value=1.6  Score=27.84  Aligned_cols=25  Identities=8%  Similarity=0.159  Sum_probs=21.6

Q ss_pred             ChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         31 FQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        31 ~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +..+++..||+|++|+.+.+.....
T Consensus        22 s~~~la~~~~vs~~tv~~~l~~L~~   46 (60)
T smart00345       22 SERELAAQLGVSRTTVREALSRLEA   46 (60)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6888999999999999998876554

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=83.10  E-value=4  Score=33.25  Aligned_cols=46  Identities=22%  Similarity=0.289  Sum_probs=35.5

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      +++++.=.+.|+++ .|.++.++|...|||.+||.+.....-..|..
T Consensus       136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~  181 (185)
T PF07638_consen  136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRR  181 (185)
T ss_pred             cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            45555555556555 77899999999999999999988877766654

>PRK13870 transcriptional regulator TraR; Provisional

Probab=83.06  E-value=1.9  Score=36.73  Aligned_cols=47  Identities=13%  Similarity=0.171  Sum_probs=39.8

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..+++.|+  =+|.|.+.|.+..++|...|||++||.-.++++..-|..
T Consensus       172 ~~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga  218 (234)
T PRK13870        172 AWLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV  218 (234)
T ss_pred             CCCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            34666554  467889999999999999999999999999998887764

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=83.01  E-value=2.7  Score=34.60  Aligned_cols=45  Identities=9%  Similarity=0.030  Sum_probs=35.4

Q ss_pred             CCCCHHHHHHHHHHHhhc-------------CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYAT-------------GNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~-------------~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ...++.++++-+|..|+.             ..+..++|...|+++.|++|+++++.+
T Consensus       137 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~  194 (211)
T PRK11753        137 AFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLED  194 (211)
T ss_pred             HhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            346788999998887763             235688999999999999998876543

>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=82.81  E-value=2.4  Score=38.89  Aligned_cols=120  Identities=18%  Similarity=0.149  Sum_probs=66.5

Q ss_pred             hhcCCChHhhhh----hcc---ccHhHHHHHHHHHHHHHHhhcccccCCchhHHHHHHHhhhhcCCCCceEeeeeeeEEE
Q psy13113         26 YATGNFQIDSED----YHD---ISQSTICRLVAKVSEELAKCHQQWIHFPEDLQTAKNQFSGIAGFPRVVVGCIDGTHVP   98 (286)
Q Consensus        26 L~~~~~~~~l~~----~Fg---vs~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~~~~~p~~~~g~iDgt~i~   98 (286)
                      +..|.+.+++..    ..|   +|.+||++++..+.+.+.....+-                ..+.|-. +..|||+++.
T Consensus       111 y~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R~----------------L~~~~y~-~l~iD~~~~k  173 (381)
T PF00872_consen  111 YLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNRP----------------LESEPYP-YLWIDGTYFK  173 (381)
T ss_pred             hccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhhc----------------ccccccc-ceeeeeeecc
Confidence            556676666444    446   999999999988877665532111                1122223 5699999998


Q ss_pred             ecCCCCCCccccccCCCccccceeeecCCCcc--EEEeccCCCCccccccccccchhhhhcc-cccc-ceEEEccccCCC
Q psy13113         99 IELPSIENGEHYRNRKHFYSINVQVIGGPNLE--IYDVVASWPGSTHDSRIFQNSRVYSRFD-RREI-RGLLLGDIGYAQ  174 (286)
Q Consensus        99 i~~P~~~~~~~y~~~k~~~s~~~q~vvd~~g~--i~~~~~~~~Gs~~D~~~~~~s~l~~~l~-~~~~-~~~llgD~gY~~  174 (286)
                      +..-         +.-..-++-+-+.+|.+|+  ++.+..+..   -....|.+  +...|. +|.. ...+++|..=.+
T Consensus       174 vr~~---------~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~---Es~~~W~~--~l~~L~~RGl~~~~lvv~Dg~~gl  239 (381)
T PF00872_consen  174 VRED---------GRVVKKAVYVAIGIDEDGRREVLGFWVGDR---ESAASWRE--FLQDLKERGLKDILLVVSDGHKGL  239 (381)
T ss_pred             cccc---------cccccchhhhhhhhhcccccceeeeecccC---CccCEeee--cchhhhhccccccceeeccccccc
Confidence            8732         1111224455566677774  677666522   22333332  333332 2222 557778865444


Q ss_pred             CC
Q psy13113        175 NE  176 (286)
Q Consensus       175 ~~  176 (286)
                      ..
T Consensus       240 ~~  241 (381)
T PF00872_consen  240 KE  241 (381)
T ss_pred             cc
Confidence            33

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

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=82.78  E-value=2.2  Score=35.49  Aligned_cols=46  Identities=17%  Similarity=0.267  Sum_probs=39.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+++.|+  =.|.+++.|.+.+++|...++|.+||..++.++..-|..
T Consensus       137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v  182 (207)
T PRK15411        137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT  182 (207)
T ss_pred             cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            4777665  456679999999999999999999999999988877763

>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family

Probab=82.57  E-value=1.5  Score=35.80  Aligned_cols=48  Identities=10%  Similarity=-0.030  Sum_probs=37.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+..+-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       131 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~  178 (193)
T TIGR02947       131 GLPEEFRQAVYLADV-EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ  178 (193)
T ss_pred             hCCHHHhhheeehhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            355555666666543 568999999999999999999999888888653

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=82.52  E-value=3.6  Score=40.02  Aligned_cols=52  Identities=12%  Similarity=-0.001  Sum_probs=47.0

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .|...+....|++|.|.+=-++.++..++..||.+.+||...++++-..|.+
T Consensus       548 ~R~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~  599 (617)
T PRK14086        548 SRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE  599 (617)
T ss_pred             CCCcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence            3555788899999999999999999999999999999999999999988764

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

Probab=82.49  E-value=2.3  Score=28.38  Aligned_cols=38  Identities=24%  Similarity=0.264  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        16 ~~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      |.++..+|.  .++ .+..+++...|++++||++++++..+
T Consensus        10 E~~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~   48 (68)
T PF01978_consen   10 EAKVYLALL--KNGPATAEEIAEELGISRSTVYRALKSLEE   48 (68)
T ss_dssp             HHHHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            445555553  444 68999999999999999998876543

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

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=82.27  E-value=2.9  Score=38.15  Aligned_cols=48  Identities=15%  Similarity=0.099  Sum_probs=40.5

Q ss_pred             CCCHHHHHHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .|+..++..+.|+|.-   .+.++..+|..||||+..|+++-.+.+.-|-.
T Consensus       305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~  355 (367)
T PRK09210        305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH  355 (367)
T ss_pred             hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhC
Confidence            6889999999998853   45799999999999999999998877776653

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=82.26  E-value=5.1  Score=35.90  Aligned_cols=49  Identities=16%  Similarity=0.176  Sum_probs=38.7

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhcc
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQ   62 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~   62 (286)
                      ||+.++-++.|+++ .|.+++++|..+|+|.+||...+.+....|-...+
T Consensus       154 Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~  202 (339)
T PRK08241        154 LPPRQRAVLILRDV-LGWSAAEVAELLDTSVAAVNSALQRARATLAERGP  202 (339)
T ss_pred             CCHHHhhhhhhHHh-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCC
Confidence            45555555555443 67899999999999999999999999999987444

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=82.24  E-value=3.3  Score=35.92  Aligned_cols=47  Identities=17%  Similarity=0.164  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|+|+ .+.++.++|..+|+|.+||....++....|-.
T Consensus       212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~  258 (268)
T PRK06288        212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRA  258 (268)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            578888888888775 57899999999999999999888877776654

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=82.14  E-value=1.3  Score=36.13  Aligned_cols=46  Identities=17%  Similarity=0.164  Sum_probs=34.5

Q ss_pred             CHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         14 SPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        14 ~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      |+.++=++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       136 ~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  181 (188)
T PRK09640        136 NPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREK  181 (188)
T ss_pred             ChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3443333344443 678999999999999999999999888887654

>PRK05949 RNA polymerase sigma factor; Validated

Probab=81.85  E-value=3.3  Score=37.18  Aligned_cols=48  Identities=15%  Similarity=0.147  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHHHHHh-h--cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFY-A--TGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L-~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+++.++-.+.|+|. .  .+.++.++|..+|+|..+|..+..+....|-.
T Consensus       266 ~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~  316 (327)
T PRK05949        266 ELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR  316 (327)
T ss_pred             hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            588888999999884 3  45799999999999999999999988887765

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=81.58  E-value=2.1  Score=25.91  Aligned_cols=28  Identities=7%  Similarity=0.189  Sum_probs=23.3

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      -..+..++|..+|+|.+|+++.++....
T Consensus         7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~   34 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTLKRLEK   34 (48)
T ss_pred             eccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3467889999999999999998876654

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=81.53  E-value=2.3  Score=27.89  Aligned_cols=29  Identities=17%  Similarity=0.077  Sum_probs=22.8

Q ss_pred             HHHhhcC--CChHhhhhhccccHhHHHHHHH
Q psy13113         23 LRFYATG--NFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        23 L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      -.|+.++  ....++|..+|||.+||..|-.
T Consensus        14 e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~   44 (60)
T PF10668_consen   14 EIYKESNGKIKLKDIAEKLGVSESTIRKWKS   44 (60)
T ss_pred             HHHHHhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence            3456554  5899999999999999997643

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=81.53  E-value=2.5  Score=27.03  Aligned_cols=29  Identities=21%  Similarity=0.193  Sum_probs=24.2

Q ss_pred             hcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         27 ATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ....+..+++..+|+|.+|+++.++....
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~   36 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLRE   36 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            44568899999999999999998876554

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=81.43  E-value=3.3  Score=33.15  Aligned_cols=47  Identities=17%  Similarity=0.046  Sum_probs=36.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|++++-++.|.++ .|.++.++|..+|+|.+||...+++....+-.
T Consensus       119 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~  165 (172)
T PRK09651        119 GLNGKTREAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL  165 (172)
T ss_pred             hCCHHHhHHhhhhhc-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            466666655555444 56899999999999999999998888777654

>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A

Probab=81.24  E-value=1.8  Score=25.85  Aligned_cols=29  Identities=21%  Similarity=0.094  Sum_probs=21.7

Q ss_pred             hhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         26 YATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        26 L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      |.++.+..++|..+|+|.+++++.|++..
T Consensus         5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~~   33 (42)
T PF00165_consen    5 LQQKLTLEDIAEQAGFSPSYFSRLFKKET   33 (42)
T ss_dssp             T-SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred             ccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45677889999999999999999998753

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=81.24  E-value=4.2  Score=33.63  Aligned_cols=48  Identities=13%  Similarity=0.054  Sum_probs=37.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-.+.|.+ -.|.++.++|..+|+|.+||...+.+....|-..
T Consensus       138 ~L~~~~r~v~~L~~-~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~  185 (203)
T PRK09647        138 SLPPEFRAAVVLCD-IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAA  185 (203)
T ss_pred             hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            35555555555554 4679999999999999999999999988887763

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=81.16  E-value=3.7  Score=31.50  Aligned_cols=46  Identities=15%  Similarity=0.070  Sum_probs=38.1

Q ss_pred             CCHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      +..+++-.+-|+|.+. +.+|-.+|..+++|++|+.++..+|-+.++
T Consensus        82 l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i~  128 (130)
T PF05263_consen   82 LIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDIY  128 (130)
T ss_pred             hCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence            4556777778888877 689999999999999999999988876553

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=81.11  E-value=3  Score=35.03  Aligned_cols=57  Identities=12%  Similarity=0.146  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHhhcC----CChHhhhhhccccHhHHHHHHHHHHHH-HHhhcccccCCc
Q psy13113         12 IHSPVVKLLAVLRFYATG----NFQIDSEDYHDISQSTICRLVAKVSEE-LAKCHQQWIHFP   68 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~----~~~~~l~~~Fgvs~stv~~~~~~v~~~-l~~~~~~~i~~P   68 (286)
                      ..+++++|+.+|..+..+    .+..++|...|+++.|++|.++++.+. +.+.....|..+
T Consensus       148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I~  209 (226)
T PRK10402        148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIK  209 (226)
T ss_pred             cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEEe
Confidence            358899999999876532    367899999999999999999988764 444433334333

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

Probab=81.01  E-value=2.6  Score=27.87  Aligned_cols=37  Identities=14%  Similarity=0.002  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      ++++-+|.....+.+-+++|..+|+|..++..++...
T Consensus         3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~L   39 (62)
T PF04703_consen    3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKL   39 (62)
T ss_dssp             HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            4566667777788899999999999999999887643

>PHA02591 hypothetical protein; Provisional

Probab=80.96  E-value=3.5  Score=28.36  Aligned_cols=38  Identities=8%  Similarity=-0.033  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         15 PVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        15 ~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      -++-+-++=...+.|.+...+|...|+++.+|+++++.
T Consensus        45 ~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~   82 (83)
T PHA02591         45 EDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES   82 (83)
T ss_pred             cchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence            34455556666778999999999999999999999864

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

Probab=80.84  E-value=2.6  Score=27.44  Aligned_cols=30  Identities=23%  Similarity=0.108  Sum_probs=24.5

Q ss_pred             hhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         26 YATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        26 L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      -..+.+..+++..+|++.+|+++.++...+
T Consensus        21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~   50 (61)
T PF12840_consen   21 SNGPMTVSELAEELGISQSTVSYHLKKLEE   50 (61)
T ss_dssp             HCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            456679999999999999999998876654

...

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

Probab=80.28  E-value=6.8  Score=23.56  Aligned_cols=26  Identities=15%  Similarity=0.175  Sum_probs=19.9

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      .-.++..+|...|+|.+||.+-+++.
T Consensus        16 ~r~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen   16 GRRSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence            33599999999999999999877653

...

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=80.23  E-value=5.8  Score=28.04  Aligned_cols=46  Identities=13%  Similarity=0.136  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ..++..+..++.+.....+.+..+++..+++|++|+++.++...+.
T Consensus         6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~   51 (101)
T smart00347        6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK   51 (101)
T ss_pred             cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence            3455544444444444445799999999999999999999877664

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	286
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	97.18
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	97.07
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	96.3
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	96.27
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	95.85
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	95.85
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	95.85
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	95.75
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	95.73
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	95.62
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	95.24
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	95.06
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	94.97
1u78_A	141	TC3 transposase, transposable element TC3 transpos	94.94
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	94.74
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	94.7
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	94.69
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	94.63
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	94.48
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	94.39
3c57_A	95	Two component transcriptional regulatory protein;	94.23
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	94.1
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	94.06
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	94.04
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	93.9
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	93.43
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	93.4
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	93.1
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	93.0
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	92.85
2k27_A	159	Paired box protein PAX-8; paired domain, solution	92.71
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	92.71
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	92.64
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	92.6
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	92.27
3pvv_A	101	Chromosomal replication initiator protein DNAA; he	91.97
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	90.7
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	90.57
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	90.52
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	90.07
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	89.87
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	89.69
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	89.22
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	89.19
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	88.96
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	88.69
3frw_A	107	Putative Trp repressor protein; structural genomic	88.59
3mky_B	189	Protein SOPB; partition, F plasmid, centromere, DN	88.4
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	88.31
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	88.21
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	87.95
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	87.88
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	87.8
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	87.57
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	87.08
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	87.06
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	87.02
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	86.46
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	86.44
1y0u_A	96	Arsenical resistance operon repressor, putative; s	86.42
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	86.25
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	86.01
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	85.86
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	85.81
3r0a_A	123	Putative transcriptional regulator; structural gen	85.78
1sfx_A	109	Conserved hypothetical protein AF2008; structural	85.77
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	85.54
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	85.43
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	85.41
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	85.38
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	85.17
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	85.17
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	84.97
2pg4_A	95	Uncharacterized protein; structural genomics, join	84.65
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	84.63
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	84.42
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	84.17
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	84.16
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	84.16
2gxg_A	146	146AA long hypothetical transcriptional regulator;	84.11
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	83.92
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	83.79
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	83.69
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	83.67
2nnn_A	140	Probable transcriptional regulator; structural gen	83.65
3b02_A	195	Transcriptional regulator, CRP family; structural	83.65
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	83.53
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	83.51
1ku9_A	152	Hypothetical protein MJ223; putative transcription	83.4
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	83.39
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	83.38
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	83.31
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	83.29
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	83.24
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	83.22
2pex_A	153	Transcriptional regulator OHRR; transcription regu	82.96
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	82.85
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	82.8
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	82.49
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	82.42
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	82.4
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	82.39
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	82.32
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	82.29
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	82.26
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	82.23
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	82.21
1z91_A	147	Organic hydroperoxide resistance transcriptional;	82.13
2q0o_A	236	Probable transcriptional activator protein TRAR; h	82.11
1u78_A	141	TC3 transposase, transposable element TC3 transpos	81.87
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	81.66
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	81.59
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	81.53
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	81.49
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	81.31
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	81.21
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	81.17
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	81.01
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	81.0
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	80.68
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	80.67
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	80.62
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	80.55
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	80.4
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	80.39
1ft9_A	222	Carbon monoxide oxidation system transcription reg	80.37
2eth_A	154	Transcriptional regulator, putative, MAR family; M	80.37
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	80.19
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	80.15
2hin_A	71	GP39, repressor protein; transcription factor, dim	80.14
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	80.12
2w25_A	150	Probable transcriptional regulatory protein; trans	80.09
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	80.05

>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=97.18  E-value=0.0009  Score=40.76  Aligned_cols=44  Identities=11%  Similarity=-0.072  Sum_probs=35.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      +|+..++.+++..+... +..|.+..++|..+|||.+||++++++
T Consensus         1 GR~~~l~~~~~~~i~~~-~~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            1 PRGSALSDTERAQLDVM-KLLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCSCCCCHHHHHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            45667888887666554 467899999999999999999998864

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

Probab=97.07  E-value=0.0011  Score=42.64  Aligned_cols=47  Identities=23%  Similarity=0.219  Sum_probs=40.3

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCC----hHhhhhhccccHhHHHHHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNF----QIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~----~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +++...|++.++-+ +.++..+.+    ...+|..|||+.+|+++|++..-.
T Consensus         1 g~r~~ys~efK~~~-~~~~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~~~   51 (59)
T 2glo_A            1 GSRRIFTPHFKLQV-LESYRNDNDCKGNQRATARKYNIHRRQIQKWLQCESN   51 (59)
T ss_dssp             CCCCCCCHHHHHHH-HHHHHHCTTTTTCHHHHHHHTTSCHHHHHHHHTTHHH
T ss_pred             CCCCcCCHHHHHHH-HHHHHcCCCcchHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45678999999988 778888888    999999999999999999875443

>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=96.30  E-value=0.005  Score=37.67  Aligned_cols=43  Identities=16%  Similarity=0.105  Sum_probs=31.8

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      ++..++.++.- .++.++..|.+..++|..+|||.+|+++++++
T Consensus         2 Rp~~~~~~~~~-~i~~l~~~g~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C            2 RPRAINKHEQE-QISRLLEKGHPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             CCCSSCTTHHH-HHHHHHHTTCCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             CCCCCCHHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            44556665433 33344667899999999999999999998753

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

Probab=96.27  E-value=0.0073  Score=42.73  Aligned_cols=45  Identities=18%  Similarity=0.049  Sum_probs=39.3

Q ss_pred             CCCCCHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      +...|++.++.+.-.++.. |.+...+|..||||.+|+++|+++.-
T Consensus         3 r~~ys~e~k~~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~~~~   48 (97)
T 2jn6_A            3 TKTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYG   48 (97)
T ss_dssp             CCCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHHHHh
Confidence            4678999999888888877 89999999999999999999987653

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

Probab=95.85  E-value=0.022  Score=39.41  Aligned_cols=49  Identities=14%  Similarity=0.245  Sum_probs=42.7

Q ss_pred             CCCCHHHHHHHHHHH-hh--cCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRF-YA--TGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~-L~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..+|+.++-.+.|+| |.  .+.++.++|..+|+|.+||...+.+....|-.
T Consensus        17 ~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~   68 (87)
T 1tty_A           17 KTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRH   68 (87)
T ss_dssp             TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBT
T ss_pred             HhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            358999999999988 44  78899999999999999999999988887754

>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=95.85  E-value=0.024  Score=37.70  Aligned_cols=48  Identities=13%  Similarity=0.086  Sum_probs=42.7

Q ss_pred             CCCCHHHHHHHHHHHh-h--cCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFY-A--TGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L-~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ..+|+.++-.+.|+|. .  .|.++.++|..+|+|.+||.....+....|-
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            4689999999999884 3  6799999999999999999999999988887

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

Probab=95.85  E-value=0.019  Score=40.57  Aligned_cols=47  Identities=11%  Similarity=-0.093  Sum_probs=42.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113          7 DARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus         7 ~~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      .......+.+.++.+++.++..+.+..++|..|+||.+++.+|.+.+
T Consensus        27 ~~~~rrWs~~~Kl~VV~~~~~g~~s~~e~arry~Is~s~i~~W~r~~   73 (95)
T 2jrt_A           27 PLDTRRWVASRKAAVVKAVIHGLITEREALDRYSLSEEEFALWRSAV   73 (95)
T ss_dssp             CSSCCCCCHHHHHHHHHHHHTTSSCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             hHhhhccCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            34566799999999999999999999999999999999999988765

>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=95.75  E-value=0.016  Score=38.05  Aligned_cols=49  Identities=16%  Similarity=0.136  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHHHHH-h--hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRF-Y--ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~-L--~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..+|+.++-.+.|+| +  ..|.++.++|..+|+|.+||.....+....|-.
T Consensus         4 ~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~   55 (68)
T 2p7v_B            4 AGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH   55 (68)
T ss_dssp             CCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGS
T ss_pred             HcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            358999999988888 3  478999999999999999999999888777654

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

Probab=95.73  E-value=0.021  Score=39.53  Aligned_cols=45  Identities=16%  Similarity=0.119  Sum_probs=36.1

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +...+.+.+..+.-.+ ..|.+...+|..||||.+|+++|+++.-.
T Consensus        20 ~~~ys~e~k~~~v~~~-~~g~s~~~iA~~~gIs~sTl~rW~k~~~~   64 (87)
T 2elh_A           20 LRSLTPRDKIHAIQRI-HDGESKASVARDIGVPESTLRGWCKNEDK   64 (87)
T ss_dssp             CSSCCHHHHHHHHHHH-HHTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            4578888876655544 57899999999999999999999876544

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

Probab=95.62  E-value=0.034  Score=36.29  Aligned_cols=48  Identities=17%  Similarity=0.043  Sum_probs=41.1

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+.+++....|..
T Consensus        14 ~~L~~~~r~il~l~~~-~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~   61 (70)
T 2o8x_A           14 ADLTTDQREALLLTQL-LGLSYADAAAVCGCPVGTIRSRVARARDALLA   61 (70)
T ss_dssp             TSSCHHHHHHHHHHHT-SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            4588888888777664 67999999999999999999999998888765

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

Probab=95.24  E-value=0.049  Score=37.98  Aligned_cols=48  Identities=13%  Similarity=0.050  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .++..++-++.|+|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus        37 ~L~~~~r~vl~l~~~-~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~   84 (92)
T 3hug_A           37 QLSAEHRAVIQRSYY-RGWSTAQIATDLGIAEGTVKSRLHYAVRALRLT   84 (92)
T ss_dssp             TSCHHHHHHHHHHHT-SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            477888888877765 678999999999999999999999888877653

>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=95.06  E-value=0.048  Score=38.81  Aligned_cols=48  Identities=17%  Similarity=0.115  Sum_probs=42.7

Q ss_pred             CCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-.+.|+|.   ..+.++.++|..+|+|.+||.....+....|-.
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            589999999999886   367899999999999999999999988888765

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

Probab=94.97  E-value=0.016  Score=36.17  Aligned_cols=42  Identities=10%  Similarity=-0.053  Sum_probs=30.5

Q ss_pred             CCCCCC--HHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113          9 RGVIHS--PVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus         9 ~~~~~~--~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      ++..++  ++..-.+... +..|.++.++|..+|+|.+||+++++
T Consensus        10 ~~~~l~~~~~~~~~i~~l-~~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           10 VRYYVESEDDLVSVAHEL-AKMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             EEEEECSHHHHHHHHHHH-HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHhcCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            333455  5444333333 56889999999999999999999875

>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=94.94  E-value=0.044  Score=41.09  Aligned_cols=45  Identities=11%  Similarity=-0.093  Sum_probs=37.1

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      ++...++.+++..+...+ ..|.+...+|..+|+|.+||++++++.
T Consensus         2 gr~~~~s~~~r~~i~~~~-~~G~s~~~ia~~lgis~~Tv~r~~~~~   46 (141)
T 1u78_A            2 PRGSALSDTERAQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLKDP   46 (141)
T ss_dssp             CCSCCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHSG
T ss_pred             CCcccCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHcc
Confidence            356778888887766554 688999999999999999999998753

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

Probab=94.74  E-value=0.099  Score=34.39  Aligned_cols=49  Identities=10%  Similarity=0.033  Sum_probs=40.9

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ....+++.++-.+.+  +..|.++.++|..+|+|.+||...+.+....|..
T Consensus         8 ~~~~L~~~e~~il~~--~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   56 (74)
T 1fse_A            8 SKPLLTKREREVFEL--LVQDKTTKEIASELFISEKTVRNHISNAMQKLGV   56 (74)
T ss_dssp             CCCCCCHHHHHHHHH--HTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            456688888877766  3788999999999999999999999988877753

>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=94.70  E-value=0.097  Score=39.81  Aligned_cols=45  Identities=18%  Similarity=0.146  Sum_probs=38.2

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ...++.+.+..+...+ ..|.+...+|..||||.+||++|+++...
T Consensus        30 ~~~~s~e~r~~iv~~~-~~G~s~~~iA~~lgis~~TV~rw~~~~~~   74 (149)
T 1k78_A           30 GRPLPDVVRQRIVELA-HQGVRPCDISRQLRVSHGCVSKILGRYYE   74 (149)
T ss_dssp             TSCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4578999888877666 57899999999999999999999987643

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

Probab=94.69  E-value=0.029  Score=40.37  Aligned_cols=44  Identities=16%  Similarity=0.053  Sum_probs=37.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcC-------CChHhhhhhccccHhHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATG-------NFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~-------~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      ++...|++.++.++-.++..+       .+...+|..||||.+|+++|++.
T Consensus         3 ~~~~ys~e~K~~~v~~~~~~~~~~~s~g~s~~~va~~~gIs~~tl~~W~~~   53 (108)
T 2rn7_A            3 KNTRFSPEVRQRAVRMVLESQGEYDSQWATICSIAPKIGCTPETLRVWVRQ   53 (108)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhcccccccccccHHHHHHHHCcCHHHHHHHHHH
Confidence            356789999998888887765       78999999999999999998875

>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=94.63  E-value=0.071  Score=39.60  Aligned_cols=50  Identities=12%  Similarity=0.062  Sum_probs=41.1

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChH-hhhhhccccHhHHHHHHHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQI-DSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~-~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .+..++.+.++-+.-.+..+|.+.. ++|..||||.+|++++++.-...+.
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~~~~~~   54 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILA   54 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHHHHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhchhhhcc
Confidence            4678999999988877767776655 9999999999999999997665544

>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=94.48  E-value=0.039  Score=39.36  Aligned_cols=45  Identities=16%  Similarity=0.034  Sum_probs=32.8

Q ss_pred             CCHHHHHHHHHHH-----hhcC-CChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRF-----YATG-NFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        13 ~~~~~~l~~~L~~-----L~~~-~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      +++.++-++.++|     |..| .+|+++|...|+|.+||+|+ ++.+.-+.
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            5666665554443     3356 89999999999999999999 65554443

>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=94.39  E-value=0.087  Score=38.47  Aligned_cols=44  Identities=14%  Similarity=0.095  Sum_probs=36.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ...++.+.+..+...+ ..|.+...+|..||+|.+||++|+++..
T Consensus        15 ~~~~s~~~r~~i~~~~-~~g~s~~~ia~~lgis~~Tv~~w~~~~~   58 (128)
T 1pdn_C           15 GRPLPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILNRYQ   58 (128)
T ss_dssp             TSCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4568888887776655 5789999999999999999999998654

>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=94.23  E-value=0.11  Score=36.42  Aligned_cols=47  Identities=15%  Similarity=0.072  Sum_probs=40.5

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..++..++-++.|+  ..|.+++++|..+|+|.+||...+.+....|..
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            46888888887774  889999999999999999999999988887764

>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=94.10  E-value=0.087  Score=35.88  Aligned_cols=48  Identities=19%  Similarity=0.062  Sum_probs=40.1

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      -..++..++-++.|  +..|.++.++|..+|+|.+||...+.+....|..
T Consensus        19 ~~~Lt~~e~~vl~l--~~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   66 (82)
T 1je8_A           19 VNQLTPRERDILKL--IAQGLPNKMIARRLDITESTVKVHVKHMLKKMKL   66 (82)
T ss_dssp             GGGSCHHHHHHHHH--HTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             HccCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            34688888877777  3789999999999999999999999888777653

>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=94.06  E-value=0.07  Score=37.55  Aligned_cols=52  Identities=12%  Similarity=0.013  Sum_probs=45.7

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhc-cccHhHHHHHHHHHHHHHHh
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYH-DISQSTICRLVAKVSEELAK   59 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~F-gvs~stv~~~~~~v~~~l~~   59 (286)
                      .|...+...-|+++.|.+--++.++..++..| |.+.+||...++.+...+..
T Consensus        25 ~R~~~i~~aRqiamyL~r~~t~~Sl~~IG~~fggrdHsTV~ha~~ki~~~~~~   77 (94)
T 1j1v_A           25 RRSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREE   77 (94)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCchhHHHHHHHHHHHHHHHCcCHHHHHHHhCCCCHHHHHHHHHHHHHHHHh
Confidence            34556777889999999999999999999999 89999999999999887753

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

Probab=94.04  E-value=0.11  Score=36.84  Aligned_cols=50  Identities=18%  Similarity=0.062  Sum_probs=41.6

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .....+++.++-.+.|  +..|.+++++|...|+|.+||...+.++...|..
T Consensus        30 ~~~~~Lt~re~~Vl~l--~~~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv   79 (99)
T 1p4w_A           30 YGDKRLSPKESEVLRL--FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV   79 (99)
T ss_dssp             CSSSSCCHHHHHHHHH--HHHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             cccCCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            3467789988876655  4589999999999999999999999988877753

>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=93.90  E-value=0.12  Score=37.55  Aligned_cols=48  Identities=8%  Similarity=0.054  Sum_probs=40.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|+|+ .|.++.++|..+|+|.+||...+++....|...
T Consensus        22 ~L~~~~r~vl~l~y~-~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~   69 (113)
T 1s7o_A           22 LLTDKQMNYIELYYA-DDYSLAEIADEFGVSRQAVYDNIKRTEKILETY   69 (113)
T ss_dssp             GSCHHHHHHHHHHHH-TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            578888877766654 678999999999999999999999998888764

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

Probab=93.43  E-value=0.12  Score=32.72  Aligned_cols=34  Identities=15%  Similarity=0.051  Sum_probs=30.4

Q ss_pred             hhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         26 YATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        26 L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      +..|.+++++|..+|+|.+||...+.++...|..
T Consensus        10 ~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   43 (61)
T 2jpc_A           10 IDEGYTNHGISEKLHISIKTVETHRMNMMRKLQV   43 (61)
T ss_dssp             HHTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTC
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCC
Confidence            6889999999999999999999999988877653

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

Probab=93.40  E-value=0.17  Score=35.96  Aligned_cols=42  Identities=10%  Similarity=0.094  Sum_probs=36.1

Q ss_pred             HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ..+-++-.|+-.|.++.++|..+|+|+++|++.+.+.-+...
T Consensus        22 ~~~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~   63 (101)
T 2w7n_A           22 QTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFE   63 (101)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            445567778889999999999999999999999998877754

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

Probab=93.10  E-value=0.14  Score=34.21  Aligned_cols=44  Identities=18%  Similarity=0.016  Sum_probs=36.5

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      +++.++-++.| + ..|.++.++|..+|+|.+||...+.+....|-
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            56666666666 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=93.00  E-value=0.21  Score=34.67  Aligned_cols=49  Identities=14%  Similarity=0.108  Sum_probs=37.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .....++..++-.+.|  +..|.++.++|...|+|.+||...+.++..-|.
T Consensus        25 ~~~~~Lt~rE~~Vl~l--~~~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klg   73 (90)
T 3ulq_B           25 KEQDVLTPRECLILQE--VEKGFTNQEIADALHLSKRSIEYSLTSIFNKLN   73 (90)
T ss_dssp             ----CCCHHHHHHHHH--HHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             ccccCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            3456688877766555  449999999999999999999999998877664

>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=92.85  E-value=0.22  Score=39.25  Aligned_cols=51  Identities=14%  Similarity=0.070  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhccc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCHQQ   63 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~~~   63 (286)
                      .+|+.++-++.|+++ .|.++.++|...|+|.+||...+.+....|-..+..
T Consensus       140 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~  190 (194)
T 1or7_A          140 SLPEDLRMAITLREL-DGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQP  190 (194)
T ss_dssp             HSCHHHHHHHHHHHT-TCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hCCHHHHHHhHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            367777777777766 578999999999999999999999998888765443

>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=92.71  E-value=0.18  Score=38.76  Aligned_cols=43  Identities=16%  Similarity=0.143  Sum_probs=35.8

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      +...++.+.+..+...+ ..|.+...+|..||||.+||++|+++
T Consensus        22 ~~~~~s~e~r~~ii~l~-~~G~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           22 NGRPLPEVVRQRIVDLA-HQGVRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             SSCSSCHHHHHHHHHHH-HHTCCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34578888887776655 57899999999999999999998863

>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=92.71  E-value=0.074  Score=40.53  Aligned_cols=52  Identities=17%  Similarity=0.087  Sum_probs=42.8

Q ss_pred             CCCCCCCCHHHHHHHHHHH--hhcCCChHhhhh----hc--cccHhHHHHHHHHHHHHHH
Q psy13113          7 DARGVIHSPVVKLLAVLRF--YATGNFQIDSED----YH--DISQSTICRLVAKVSEELA   58 (286)
Q Consensus         7 ~~~~~~~~~~~~l~~~L~~--L~~~~~~~~l~~----~F--gvs~stv~~~~~~v~~~l~   58 (286)
                      ...+..++.++++.+..++  -..+.++.+||.    .|  |||++||+++++.=-..+.
T Consensus         6 ~~~R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk~k~~~l~   65 (144)
T 1iuf_A            6 KIKRRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILSSKYSYLD   65 (144)
T ss_dssp             CCSSSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHHHHHHTT
T ss_pred             CCcCccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhhHHHHhh
Confidence            4568899999999999998  335568889999    99  9999999999987555443

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

Probab=92.64  E-value=0.14  Score=35.52  Aligned_cols=47  Identities=15%  Similarity=0.114  Sum_probs=39.2

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..+++.++-++.|  +..|.++.++|..+|+|.+||...+.+....|..
T Consensus        28 ~~Lt~~e~~vl~l--~~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   74 (91)
T 2rnj_A           28 EMLTEREMEILLL--IAKGYSNQEIASASHITIKTVKTHVSNILSKLEV   74 (91)
T ss_dssp             GGCCSHHHHHHHH--HHTTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             hcCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            4578877777777  3789999999999999999999999888776653

>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=92.60  E-value=0.24  Score=40.32  Aligned_cols=49  Identities=24%  Similarity=0.184  Sum_probs=42.5

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      ..+|+.++-++.|+|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       186 ~~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~  234 (239)
T 1rp3_A          186 SKLPEREKLVIQLIFY-EELPAKEVAKILETSVSRVSQLKAKALERLREM  234 (239)
T ss_dssp             TTSCHHHHHHHHHHHT-SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            3588888888888886 579999999999999999999999988887653

>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=92.27  E-value=0.34  Score=35.17  Aligned_cols=49  Identities=6%  Similarity=0.087  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhhc
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKCH   61 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~~   61 (286)
                      .+|+.++-++.|+| ..|.++.++|..+|+|.+||...+++....|-...
T Consensus        25 ~L~~~~r~vl~l~~-~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l   73 (113)
T 1xsv_A           25 LLTNKQRNYLELFY-LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYE   73 (113)
T ss_dssp             GSCHHHHHHHHHHH-TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            47777777776655 46799999999999999999999999988887643

>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=91.97  E-value=0.21  Score=35.57  Aligned_cols=51  Identities=12%  Similarity=-0.031  Sum_probs=44.9

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      |...+...-|++|.|.+=-++.++..++..||-+.+||...++.+.+.+.+
T Consensus        30 R~~~i~~aRqiAmYL~r~~t~~Sl~~IG~~fgRDHsTV~ha~~ki~~~~~~   80 (101)
T 3pvv_A           30 KTRALAQSRQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEMAE   80 (101)
T ss_dssp             CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCchhhHHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            444677788999999888899999999999999999999999999888774

>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=90.70  E-value=0.46  Score=33.68  Aligned_cols=42  Identities=10%  Similarity=-0.012  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .....++.++........+..+.+..|+||.+++.+|.+.+.
T Consensus        34 Wva~rK~~VV~~v~~g~lS~~EAa~ry~Is~~ei~~W~r~y~   75 (101)
T 2oa4_A           34 WVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALA   75 (101)
T ss_dssp             CCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            334479999999999999999999999999999999887654

>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=90.57  E-value=0.43  Score=36.13  Aligned_cols=47  Identities=9%  Similarity=0.001  Sum_probs=38.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++. + .-.|.++.++|..+|+|.+||...+.+....|-..
T Consensus       109 ~L~~~~r~v~~-~-~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~  155 (164)
T 3mzy_A          109 NFSKFEKEVLT-Y-LIRGYSYREIATILSKNLKSIDNTIQRIRKKSEEW  155 (164)
T ss_dssp             HSCHHHHHHHH-H-HTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHH-H-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            46777776666 4 45789999999999999999999999888877653

>4dyq_A Gene 1 protein; GP1, octamer, DNA-binding, viral protein; 1.50A {Shigella phage SF6} PDB: 4dyc_A 4dyr_A 3hef_A 4dzj_A 4dzp_A

Probab=90.52  E-value=0.36  Score=36.47  Aligned_cols=48  Identities=19%  Similarity=0.187  Sum_probs=35.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccc-cHhHHHHHHHHH
Q psy13113          5 SNDARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDI-SQSTICRLVAKV   53 (286)
Q Consensus         5 ~~~~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgv-s~stv~~~~~~v   53 (286)
                      ...||.+.++.+. .--.+.+++.|.+...++..+|| |.+|+++|+++-
T Consensus         5 ~k~GRPtk~t~e~-~e~I~~~i~~G~sl~~i~~~~~~ps~~T~~~W~~~~   53 (140)
T 4dyq_A            5 PKAGRPSDYMPEV-ADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKH   53 (140)
T ss_dssp             -----CCSCCTTH-HHHHHHHHHTTCCHHHHHTSTTCCCHHHHHHHHHHC
T ss_pred             CCCCCCCCCCHHH-HHHHHHHHHCCCcHHHHHhcCCCCCHHHHHHHHHcC
Confidence            4456777777653 34466778899999999999999 999999999863

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=89.87  E-value=0.67  Score=32.21  Aligned_cols=48  Identities=13%  Similarity=0.077  Sum_probs=37.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhc--CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113          7 DARGVIHSPVVKLLAVLRFYAT--GNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus         7 ~~~~~~~~~~~~l~~~L~~L~~--~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..+-..++.++.+.+.+.+-+.  |..+++|+...+++++|+.+++++..
T Consensus        12 ~~k~~~Lt~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE   61 (91)
T 2dk5_A           12 AGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLE   61 (91)
T ss_dssp             CCCCCCSCSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HhhhcCCCHHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3456678887776666665533  78999999999999999999887653

>2cob_A LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.15

Probab=89.69  E-value=0.65  Score=30.41  Aligned_cols=39  Identities=15%  Similarity=0.050  Sum_probs=34.2

Q ss_pred             CHHHHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHHH
Q psy13113         14 SPVVKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        14 ~~~~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      =.+++|..++.-++.| .+....|..|||..+|+..-++.
T Consensus        14 Yte~~L~~Ai~aVr~g~mS~~~Aak~yGVP~sTL~~RVk~   53 (70)
T 2cob_A           14 YNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKE   53 (70)
T ss_dssp             CCHHHHHHHHHHHHTTSSCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCccHHHHHHHhCCChHHHHHHHHh
Confidence            4578999999999999 79999999999999999876653

>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=89.22  E-value=0.6  Score=32.71  Aligned_cols=28  Identities=14%  Similarity=0.114  Sum_probs=23.7

Q ss_pred             hcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         27 ATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..+.+..+++..+|+|++|++++++...
T Consensus        34 ~~~~t~~ela~~l~is~~tv~~~l~~L~   61 (109)
T 2d1h_A           34 EKPITSEELADIFKLSKTTVENSLKKLI   61 (109)
T ss_dssp             CSCEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4457999999999999999999887554

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

Probab=89.19  E-value=0.64  Score=37.12  Aligned_cols=43  Identities=23%  Similarity=0.207  Sum_probs=33.6

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      ..+|..+.=.-+.+++..|.++.++|..+|||+++|++++...
T Consensus         6 ke~sl~eiG~ria~~y~~g~tQ~eIA~~lGiSr~~VSR~L~~A   48 (192)
T 1zx4_A            6 LQHSIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQAA   48 (192)
T ss_dssp             CSSCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHh
Confidence            3456655555555557889999999999999999999988653

>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=88.96  E-value=0.63  Score=31.19  Aligned_cols=39  Identities=13%  Similarity=0.128  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHhhc--CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYAT--GNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        16 ~~~l~~~L~~L~~--~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      +++++-+|.-.+.  +.+..++|..+|+|++||.+.+.+..
T Consensus        16 ~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~   56 (77)
T 1qgp_A           16 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLA   56 (77)
T ss_dssp             HHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3555555555552  45889999999999999998876553

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

Probab=88.69  E-value=0.66  Score=30.08  Aligned_cols=39  Identities=13%  Similarity=0.085  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        16 ~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      +++++-.|.--....+..+||..+|+|++||++.+....
T Consensus        12 ~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~   50 (67)
T 2heo_A           12 EQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLK   50 (67)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            455555554322346899999999999999999887544

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

Probab=88.59  E-value=0.5  Score=33.77  Aligned_cols=30  Identities=17%  Similarity=0.204  Sum_probs=25.8

Q ss_pred             HHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         23 LRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        23 L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      ..+|..|.+|++++...|+|.+|++|+-+.
T Consensus        52 a~lL~~G~SyreIa~~tG~StaTIsRv~r~   81 (107)
T 3frw_A           52 AKMLTDKRTYLDISEKTGASTATISRVNRS   81 (107)
T ss_dssp             HHHHHTTCCHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHCccHHHHHHHHHH
Confidence            445889999999999999999999986553

>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A*

Probab=88.40  E-value=0.73  Score=36.52  Aligned_cols=44  Identities=14%  Similarity=-0.045  Sum_probs=38.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcC--CChHhhhhhccccHhHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATG--NFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      ...+|..++=.-.+..|..|  .++..+|..+|||++.|+|+++-.
T Consensus        21 ~rplS~yErg~~y~r~L~~g~~~~Q~~lA~~~giS~a~VSR~L~~A   66 (189)
T 3mky_B           21 YRPTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTA   66 (189)
T ss_dssp             --CCCHHHHHHHHHHHHHTTTTTCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcCcccCHHHHHHHHCCCHHHHHHHHHHh
Confidence            46799999999999999887  799999999999999999999744

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=88.31  E-value=0.7  Score=33.72  Aligned_cols=32  Identities=25%  Similarity=0.240  Sum_probs=27.9

Q ss_pred             HHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         20 LAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        20 ~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      .-.+..|+.|.+|++++...|+|..||+|+-+
T Consensus        66 ~eV~klL~~G~syreIA~~~g~S~aTIsRv~r   97 (119)
T 3kor_A           66 LQVAKMIKQGYTYATIEQESGASTATISRVKR   97 (119)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            44667789999999999999999999998654

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=88.21  E-value=0.95  Score=30.67  Aligned_cols=38  Identities=13%  Similarity=0.121  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHhhc--CCChHhhhhhccccHhHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYAT--GNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        16 ~~~l~~~L~~L~~--~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      +++++-.|.-.+-  ..+..+||..+|||++||.+.+.+.
T Consensus        12 ~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~L   51 (81)
T 1qbj_A           12 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSL   51 (81)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4556655554442  3588999999999999999877644

>2l1p_A DNA-binding protein SATB1; PSI-biology, NESG, structural genomics, protein structure in northeast structural genomics consortium; NMR {Homo sapiens} PDB: 3nzl_A*

Probab=87.95  E-value=0.67  Score=31.29  Aligned_cols=34  Identities=21%  Similarity=0.096  Sum_probs=27.8

Q ss_pred             HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      -|-..|..+..|..+.+||...|||++|++.+++
T Consensus        21 ~~~~kLK~il~GikQ~eLAK~iGIsqsTLSaIen   54 (83)
T 2l1p_A           21 TVRNALKDLLKDMNQSSLAKECPLSQSMISSIVN   54 (83)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHSSSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHhcCHHHHHHHcCCCHHHHHHHHc
Confidence            3445556666699999999999999999998775

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=87.88  E-value=0.78  Score=35.25  Aligned_cols=42  Identities=12%  Similarity=-0.056  Sum_probs=33.3

Q ss_pred             CCCCCHHHHHHHHHHHhhc--------CCChHhhhhhccccHhHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYAT--------GNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~--------~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      +..++.+.+.++.+.-...        +.+..++|...|||++|+++|.+
T Consensus        21 ~r~yt~EfK~aAv~l~~~~~~~p~~~~~lTv~eIA~~LGIS~~TLyrW~k   70 (155)
T 2ao9_A           21 KQKLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRT   70 (155)
T ss_dssp             HTTSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             hhhcCHHHHHHHHHHHHccccccccccCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4557888777776543222        57999999999999999999998

>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=87.80  E-value=0.67  Score=32.12  Aligned_cols=37  Identities=14%  Similarity=0.196  Sum_probs=28.0

Q ss_pred             HHHHHHHhhcC---CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         19 LLAVLRFYATG---NFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        19 l~~~L~~L~~~---~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ++.+|..-..+   .+..+++..++++++|+++++++...
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            34444444445   78999999999999999999886654

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=87.57  E-value=0.34  Score=31.41  Aligned_cols=21  Identities=10%  Similarity=0.067  Sum_probs=19.1

Q ss_pred             ChHhhhhhccccHhHHHHHHH
Q psy13113         31 FQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        31 ~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      +..++|...|||.+||+++++
T Consensus         2 T~~diA~~aGVS~sTVSrvLn   22 (65)
T 1uxc_A            2 KLDEIARLAGVSRTTASYVIN   22 (65)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHc
Confidence            578999999999999999886

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=87.08  E-value=0.66  Score=32.41  Aligned_cols=26  Identities=15%  Similarity=0.064  Sum_probs=23.0

Q ss_pred             hcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         27 ATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        27 ~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      ..+.+..++|..+|||.+||+++++.
T Consensus        18 ~~~~ti~dlA~~~gVS~~TVsR~L~~   43 (93)
T 2l0k_A           18 ETKKTVRVIAKEFGVSKSTVHKDLTE   43 (93)
T ss_dssp             HHCCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence            34579999999999999999999875

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=87.06  E-value=0.64  Score=30.10  Aligned_cols=29  Identities=17%  Similarity=0.133  Sum_probs=23.0

Q ss_pred             HHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         23 LRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        23 L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      |..+....++..+|..+|||+++|+++++
T Consensus         7 Lk~l~~~~sq~~~A~~Lgvsq~aVS~~~~   35 (65)
T 2cw1_A            7 LKKFVEDKNQEYAARALGLSQKLIEEVLK   35 (65)
T ss_dssp             HHHHHTTSCHHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHHHcCHHHHHHHhCCCHHHHHHHHH
Confidence            33334445999999999999999999873

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=87.02  E-value=1.2  Score=27.97  Aligned_cols=36  Identities=14%  Similarity=0.136  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHhhc--CCChHhhhhhc-----cccHhHHHHHHH
Q psy13113         16 VVKLLAVLRFYAT--GNFQIDSEDYH-----DISQSTICRLVA   51 (286)
Q Consensus        16 ~~~l~~~L~~L~~--~~~~~~l~~~F-----gvs~stv~~~~~   51 (286)
                      .++..+.+..+..  ..+..+++..+     +||.+||++.++
T Consensus         4 ~~R~~~i~~ll~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~   46 (64)
T 2p5k_A            4 GQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIK   46 (64)
T ss_dssp             HHHHHHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence            3455544445543  35788999999     999999999887

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

Probab=86.46  E-value=0.57  Score=31.87  Aligned_cols=38  Identities=5%  Similarity=0.116  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         15 PVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        15 ~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..++++..|.  ..+.+..+||..+|+|+++|.+.+....
T Consensus        18 ~~~~IL~lL~--~~g~sa~eLAk~LgiSk~aVr~~L~~Le   55 (82)
T 1oyi_A           18 IVCEAIKTIG--IEGATAAQLTRQLNMEKREVNKALYDLQ   55 (82)
T ss_dssp             HHHHHHHHHS--SSTEEHHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4455555444  4557999999999999999998876553

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=86.44  E-value=1  Score=35.81  Aligned_cols=44  Identities=11%  Similarity=-0.010  Sum_probs=37.8

Q ss_pred             CCHHHHHHHHHHHhhc-------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYAT-------GNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~-------~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      .+++++++..|..+..       ..+..++|...|+|+.|++|+++++.+.
T Consensus       146 ~~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~  196 (220)
T 3dv8_A          146 KSLDKRVASFLLEETSIEGTNELKITHETIANHLGSHREVITRMLRYFQVE  196 (220)
T ss_dssp             SCHHHHHHHHHHHHHHHHTSSEECCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHhhhhcCCceecCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            5788999999988875       5689999999999999999999877543

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=86.42  E-value=0.94  Score=31.39  Aligned_cols=28  Identities=7%  Similarity=0.045  Sum_probs=23.7

Q ss_pred             hcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         27 ATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ....+..+++..+|+|++|+++.++...
T Consensus        41 ~~~~~~~eLa~~l~is~~tv~~~L~~L~   68 (96)
T 1y0u_A           41 DKGRSEEEIMQTLSLSKKQLDYHLKVLE   68 (96)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            5567999999999999999999876543

>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=86.25  E-value=1.4  Score=32.62  Aligned_cols=45  Identities=13%  Similarity=-0.053  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ..+++.+-..+...+-..+.+..+++..+|++++|+++.+++...
T Consensus        33 ~~lt~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~   77 (142)
T 3ech_A           33 LDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEG   77 (142)
T ss_dssp             CCCCHHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            456766544444433345679999999999999999998886654

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=86.01  E-value=0.56  Score=35.81  Aligned_cols=49  Identities=18%  Similarity=0.201  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      ..+|+.++-++.|.++ .|.++.++|...|+|.+||...+.+....|-..
T Consensus        92 ~~Lp~~~r~vl~L~~~-~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~  140 (157)
T 2lfw_A           92 ARMTPLSRQALLLTAM-EGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQ  140 (157)
T ss_dssp             TTSCTTHHHHHTTTSS-SCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTT
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4688888888777655 468999999999999999999999888888764

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=85.86  E-value=1.5  Score=34.15  Aligned_cols=49  Identities=12%  Similarity=-0.012  Sum_probs=31.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113          7 DARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         7 ~~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ++....++..++-++.+..-....++.++|..+|+|++|+.+.+++..+
T Consensus         9 ~~~~~~ld~~d~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L~~   57 (171)
T 2ia0_A            9 GSSEIHLDDLDRNILRLLKKDARLTISELSEQLKKPESTIHFRIKKLQE   57 (171)
T ss_dssp             -----CCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCcCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3445556665543333322233469999999999999999998876643

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=85.81  E-value=1  Score=33.36  Aligned_cols=40  Identities=18%  Similarity=0.189  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        16 ~~~l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ..+++..|+.+.   .+.+..++|..+|++++||++.+++...
T Consensus        15 ~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~Le~   57 (139)
T 2x4h_A           15 EFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHLEE   57 (139)
T ss_dssp             HHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHHHH
Confidence            455666777663   3459999999999999999998875543

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=85.78  E-value=0.75  Score=33.71  Aligned_cols=44  Identities=14%  Similarity=0.037  Sum_probs=30.3

Q ss_pred             CCHH-HHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         13 HSPV-VKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        13 ~~~~-~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ++.. .+++..|..-... .+..+++...|+|++||++.+......
T Consensus        24 Lt~~e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~   69 (123)
T 3r0a_A           24 LTKADLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEK   69 (123)
T ss_dssp             CCHHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4443 3344444332222 589999999999999999999877654

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=85.77  E-value=1.7  Score=30.16  Aligned_cols=30  Identities=10%  Similarity=-0.012  Sum_probs=25.4

Q ss_pred             hcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         27 ATGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ..+.+..+++..+|++++||++.++.....
T Consensus        32 ~~~~s~~ela~~l~is~~tv~~~l~~L~~~   61 (109)
T 1sfx_A           32 RGGMRVSEIARELDLSARFVRDRLKVLLKR   61 (109)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            356799999999999999999998876544

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=85.54  E-value=1.3  Score=29.71  Aligned_cols=31  Identities=13%  Similarity=0.049  Sum_probs=23.7

Q ss_pred             HHHHhhc--CCChHhhhhhccccHhHHHHHHHH
Q psy13113         22 VLRFYAT--GNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        22 ~L~~L~~--~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      .|.+|+.  ..+..+|+..|+||..|+.+-+..
T Consensus         7 Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~   39 (78)
T 1xn7_A            7 VRDLLALRGRMEAAQISQTLNTPQPMINAMLQQ   39 (78)
T ss_dssp             HHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHH
Confidence            3445543  358899999999999999986653

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=85.43  E-value=1.5  Score=29.35  Aligned_cols=38  Identities=13%  Similarity=0.136  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHh-----hcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         16 VVKLLAVLRFY-----ATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        16 ~~~l~~~L~~L-----~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      .++++-+|.--     +...+.+++|..||+|.+||.+.+...
T Consensus         6 ~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~L   48 (77)
T 2jt1_A            6 VTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQL   48 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34555555544     345689999999999999988877543

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=85.41  E-value=0.91  Score=28.93  Aligned_cols=26  Identities=23%  Similarity=0.236  Sum_probs=22.3

Q ss_pred             HhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         25 FYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      ....| ++..+|...|+|+++++++++
T Consensus        10 ~~~~g-s~~~~A~~lgis~~~vs~~~~   35 (67)
T 2pij_A           10 LEEHG-TQSALAAALGVNQSAISQMVR   35 (67)
T ss_dssp             HHHTC-CHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHcC-CHHHHHHHHCcCHHHHHHHHc
Confidence            34456 999999999999999999873

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=85.38  E-value=1.5  Score=33.26  Aligned_cols=42  Identities=14%  Similarity=0.083  Sum_probs=29.5

Q ss_pred             CCCHHH-HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         12 IHSPVV-KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        12 ~~~~~~-~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      .+++.+ .++..|.....+.+..+||..++++++|+++++++.
T Consensus        28 gLt~~q~~vL~~L~~~~~~~~~~eLa~~l~~~~~tvs~~v~~L   70 (151)
T 4aik_A           28 ELTQTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQL   70 (151)
T ss_dssp             CCCHHHHHHHHHHHHSCTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            466654 344444444455677899999999999999987643

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=85.17  E-value=1.4  Score=32.68  Aligned_cols=44  Identities=5%  Similarity=0.013  Sum_probs=34.8

Q ss_pred             CCCCCCCHHHHHHHHHHH------hhcCC---ChHhhhhhccccHhHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRF------YATGN---FQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~------L~~~~---~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      ++.+.+|..+|+.-.|..      |.-|.   +-+.||..||||+.||.+.+.
T Consensus         8 d~~s~~PlY~QI~~~i~~~I~~G~l~pG~~LPser~La~~~gVSr~tVReAl~   60 (134)
T 4ham_A            8 NTKSQLPIYEQIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQ   60 (134)
T ss_dssp             CTTSSSCHHHHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHcCCCCCCCCCccHHHHHHHHCCCHHHHHHHHH
Confidence            466778999999888766      34454   567899999999999998665

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=85.17  E-value=1.3  Score=40.12  Aligned_cols=47  Identities=15%  Similarity=0.131  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHHHHH-hh--cCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRF-YA--TGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        12 ~~~~~~~l~~~L~~-L~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .|+..++-.+.|+| |.  .+.++..+|..+|||..||..+..+....|-
T Consensus       375 ~L~ereR~VI~LRygL~~~e~~TleEIAe~LgIS~erVRqi~~RAlkKLR  424 (438)
T 1l9z_H          375 KLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK  424 (438)
T ss_pred             hCCHHHHHHHHHHHhccCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            57888888888888 44  5689999999999999999999998888776

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=84.65  E-value=0.62  Score=32.24  Aligned_cols=41  Identities=12%  Similarity=0.180  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHhhc---CCChHhhhhhccccHhH-HHHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYAT---GNFQIDSEDYHDISQST-ICRLVAKVSEE   56 (286)
Q Consensus        16 ~~~l~~~L~~L~~---~~~~~~l~~~Fgvs~st-v~~~~~~v~~~   56 (286)
                      ..+.+.+|..+..   +.+..+++..+|++++| +++.+++....
T Consensus        14 ~~~~l~~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~l~~Le~~   58 (95)
T 2pg4_A           14 LIRILPTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLIRA   58 (95)
T ss_dssp             HHHHHHHHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCchHHHHHHHHHHHHC
Confidence            3344555555543   46999999999999999 99998876554

>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1

Probab=84.63  E-value=1.4  Score=34.67  Aligned_cols=42  Identities=19%  Similarity=-0.034  Sum_probs=37.1

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      |..+++-++......++..|.+...+|..+|+|+++|+++++
T Consensus        33 RedL~piE~A~a~~~L~~~G~t~eeiA~~lG~s~s~V~~~Lr   74 (178)
T 1r71_A           33 RNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVT   74 (178)
T ss_dssp             TTCCCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             cCCCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            567888888888888888899999999999999999998875

>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...

Probab=84.42  E-value=1.4  Score=34.67  Aligned_cols=43  Identities=12%  Similarity=0.075  Sum_probs=35.6

Q ss_pred             CCHHHHHHHHHHHhhcC-------------CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYATG-------------NFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~-------------~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+++++|+.+|..++..             .+..++|...|+|+.|++|+++++.+
T Consensus       138 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~iA~~lg~sr~tvsR~l~~L~~  193 (210)
T 3ryp_A          138 LDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLED  193 (210)
T ss_dssp             SCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhcCcCCCCCceEeccCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            57889999999988642             36789999999999999999876543

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

Probab=84.17  E-value=2.1  Score=28.51  Aligned_cols=27  Identities=4%  Similarity=0.026  Sum_probs=22.5

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ...+..++|..+|+|++||++.+....
T Consensus        13 ~~~s~~eLa~~lgvs~~tv~r~L~~L~   39 (81)
T 2htj_A           13 NGGKTAEIAEALAVTDYQARYYLLLLE   39 (81)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            346899999999999999998876443

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=84.16  E-value=1.5  Score=32.62  Aligned_cols=38  Identities=11%  Similarity=0.114  Sum_probs=28.2

Q ss_pred             HHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         17 VKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        17 ~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      +..+..|+.+   ..+.+..++|..+|+|++||++.++...
T Consensus         7 ~~~L~~i~~l~~~~~~~~~~ela~~l~vs~~tvs~~l~~Le   47 (142)
T 1on2_A            7 EMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLD   47 (142)
T ss_dssp             HHHHHHHHHHHHHHSSCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            4444444444   3567999999999999999999887543

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=84.16  E-value=1.4  Score=30.49  Aligned_cols=28  Identities=14%  Similarity=0.050  Sum_probs=24.3

Q ss_pred             cCCChHhh----hhhccccHhHHHHHHHHHHH
Q psy13113         28 TGNFQIDS----EDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        28 ~~~~~~~l----~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+.+..++    +..++++++|+++.+++...
T Consensus        21 ~~~~~~el~~~la~~l~is~~tvs~~l~~Le~   52 (99)
T 1tbx_A           21 EGIATYDLYKKVNAEFPMSTATFYDAKKFLIQ   52 (99)
T ss_dssp             TTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            35688899    99999999999999988776

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=84.11  E-value=1.8  Score=31.99  Aligned_cols=43  Identities=16%  Similarity=-0.059  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..+++.+..++...+ ..+.+..+++..+|++++|+++.+++..
T Consensus        33 ~~l~~~~~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~l~~Le   75 (146)
T 2gxg_A           33 LNLSYLDFLVLRATS-DGPKTMAYLANRYFVTQSAITASVDKLE   75 (146)
T ss_dssp             TTCCHHHHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHh-cCCcCHHHHHHHhCCCchhHHHHHHHHH
Confidence            346665443333333 6667999999999999999999876443

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=83.92  E-value=2.2  Score=31.63  Aligned_cols=44  Identities=11%  Similarity=-0.059  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..+++.+..++...+-..+.+..+++..+|++++|+++.+++..
T Consensus        38 ~~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le   81 (150)
T 2rdp_A           38 YPITPPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRME   81 (150)
T ss_dssp             SSSCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHH
Confidence            45666543333322224467999999999999999999886544

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=83.79  E-value=2.3  Score=31.45  Aligned_cols=43  Identities=5%  Similarity=-0.102  Sum_probs=31.1

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      ..+++.+-.++...+-..+.+..+++..+|++++|+++.+++.
T Consensus        27 ~~lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L   69 (145)
T 3g3z_A           27 QDLNYNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCKTL   69 (145)
T ss_dssp             TTCCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3566655444444344456899999999999999999987644

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=83.69  E-value=2.2  Score=31.06  Aligned_cols=43  Identities=12%  Similarity=0.093  Sum_probs=29.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .+++.+..++...+-..+.+..+++..+|++++|+++.+++..
T Consensus        26 ~l~~~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~   68 (138)
T 3bpv_A           26 NLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLE   68 (138)
T ss_dssp             TCCHHHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4565544333333334567999999999999999999876543

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=83.67  E-value=1.2  Score=35.53  Aligned_cols=43  Identities=14%  Similarity=0.097  Sum_probs=36.1

Q ss_pred             CCHHHHHHHHHHHhhc--------------CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYAT--------------GNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~--------------~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+++++|+.+|..+..              ..+..++|...|+|+.|++++++++.+
T Consensus       137 ~~~~~Rl~~~L~~l~~~~g~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~  193 (220)
T 2fmy_A          137 KDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKK  193 (220)
T ss_dssp             HHHHHHHHHHHHHHHHHHCEEETTEEEEECSSCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            3678899999988763              458899999999999999999987754

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

Probab=83.65  E-value=2.3  Score=31.07  Aligned_cols=45  Identities=13%  Similarity=-0.050  Sum_probs=31.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      .++..+..++...+-..+.+..+++..+|++++|+++.+++....
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            566654433333333346799999999999999999988765543

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=83.65  E-value=2.2  Score=33.28  Aligned_cols=45  Identities=13%  Similarity=0.155  Sum_probs=37.7

Q ss_pred             CCCHHHHHHHHHHHhhc-------------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYAT-------------GNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~-------------~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ..+++++|+.+|..|+.             ..+..++|...|+|+.|++++++++.+.
T Consensus       109 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~  166 (195)
T 3b02_A          109 TGELRARIARYLLFLADTPLSARDRQGIYVTVSHEEIADATASIRESVSKVLADLRRE  166 (195)
T ss_dssp             SSCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHcCCCCCCCeeeccCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            46789999999998763             2478899999999999999999987654

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=83.53  E-value=2.5  Score=30.83  Aligned_cols=46  Identities=4%  Similarity=-0.013  Sum_probs=32.1

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ..++..+...+...+-..+.+..+++..+|++++|+++++++....
T Consensus        30 ~~lt~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~   75 (138)
T 1jgs_A           30 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK   75 (138)
T ss_dssp             TTSCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHHHHHHHC
Confidence            3466655433333333456799999999999999999988765543

>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2

Probab=83.51  E-value=1.7  Score=34.14  Aligned_cols=42  Identities=7%  Similarity=-0.013  Sum_probs=35.0

Q ss_pred             CCHHHHHHHHHHHhhc-------------CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYAT-------------GNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~-------------~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .+++++++-+|..|+.             ..+..++|...|+|+.|++|+++++.
T Consensus       135 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~  189 (207)
T 2oz6_A          135 LDVTGRVARTLLDLCQQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKSLE  189 (207)
T ss_dssp             CCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCCCceecccCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            5788999999888764             14778999999999999999988654

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=83.40  E-value=1  Score=33.51  Aligned_cols=40  Identities=15%  Similarity=0.061  Sum_probs=29.0

Q ss_pred             CCCHH-HHHHHHHHHh-hcCCChHhhhhhccccHhHHHHHHHH
Q psy13113         12 IHSPV-VKLLAVLRFY-ATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        12 ~~~~~-~~l~~~L~~L-~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      .+++. .+++..| ++ ..+.+..+++..+|++++|+++.++.
T Consensus        23 gl~~~~~~il~~L-~~~~~~~t~~ela~~l~~~~stvs~~l~~   64 (152)
T 1ku9_A           23 GLNKSVGAVYAIL-YLSDKPLTISDIMEELKISKGNVSMSLKK   64 (152)
T ss_dssp             TCCHHHHHHHHHH-HHCSSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCChhHHHHHHHH-HHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34554 4455555 54 35569999999999999999987753

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=83.39  E-value=1.8  Score=36.00  Aligned_cols=47  Identities=21%  Similarity=0.046  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ..+|+.++-++.|.  ..|.++.++|...|+|.+||...+++....|-.
T Consensus       196 ~~L~~~erevl~L~--~~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL~~  242 (258)
T 3clo_A          196 NILSEREKEILRCI--RKGLSSKEIAATLYISVNTVNRHRQNILEKLSV  242 (258)
T ss_dssp             TSSCHHHHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             ccCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            57899999888885  499999999999999999999999988877653

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=83.38  E-value=1.7  Score=30.66  Aligned_cols=29  Identities=10%  Similarity=0.043  Sum_probs=24.7

Q ss_pred             hcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         27 ATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ..+.+..+++..+|+|++|+++.++...+
T Consensus        37 ~~~~~~~ela~~l~is~stvs~~L~~L~~   65 (106)
T 1r1u_A           37 VSEASVGHISHQLNLSQSNVSHQLKLLKS   65 (106)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34469999999999999999999887664

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=83.31  E-value=2.7  Score=30.70  Aligned_cols=44  Identities=18%  Similarity=0.090  Sum_probs=30.2

Q ss_pred             CCCHHHH-HHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         12 IHSPVVK-LLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        12 ~~~~~~~-l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+++.+. ++..|+.-.. +.+..+++..+|++++|+++.+++...
T Consensus        31 ~lt~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~   76 (141)
T 3bro_A           31 DLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEI   76 (141)
T ss_dssp             TCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHH
Confidence            4666543 3334433322 579999999999999999998865543

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=83.29  E-value=2  Score=31.68  Aligned_cols=46  Identities=11%  Similarity=-0.104  Sum_probs=32.8

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ...+++.+-.++...+-..+.+..+++..+|++++|+++.+++...
T Consensus        32 ~~~lt~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~   77 (143)
T 3oop_A           32 SYDVTPEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLR   77 (143)
T ss_dssp             TSSSCHHHHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHHHHHHH
Confidence            3456766544443333346679999999999999999998875543

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

Probab=83.24  E-value=2.4  Score=30.45  Aligned_cols=28  Identities=11%  Similarity=0.024  Sum_probs=25.3

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ...+..+++..+|+|++|+++.++....
T Consensus        44 ~~~s~~ela~~l~is~stvsr~l~~Le~   71 (119)
T 2lkp_A           44 GPLPVTDLAEAIGMEQSAVSHQLRVLRN   71 (119)
T ss_dssp             CCCCHHHHHHHHSSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3689999999999999999999988776

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=83.22  E-value=2.1  Score=33.59  Aligned_cols=44  Identities=9%  Similarity=0.083  Sum_probs=36.9

Q ss_pred             CCHHHHHHHHHHHhhc-------------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYAT-------------GNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~-------------~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      .+++++|+-+|..|+.             ..+..++|...|+|+.|++++++++.+.
T Consensus       117 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~  173 (202)
T 2zcw_A          117 QRLKNRMAAALLELSETPLAHEEEGKVVLKATHDELAAAVGSVRETVTKVIGELARE  173 (202)
T ss_dssp             CCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCCcEEccCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            5789999999998863             2478899999999999999999877543

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=82.96  E-value=2  Score=32.06  Aligned_cols=44  Identities=7%  Similarity=0.046  Sum_probs=30.1

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      ...+++.+..++...+-..+.+..+++..++++++|+++++++.
T Consensus        42 ~~~l~~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~L   85 (153)
T 2pex_A           42 ALDLTYPQYLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRL   85 (153)
T ss_dssp             TTTCCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HCCCCHHHHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHHHH
Confidence            34566654433333333345689999999999999999987644

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=82.85  E-value=2  Score=31.46  Aligned_cols=44  Identities=5%  Similarity=-0.114  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+++.+..++...+-..+.+..+++..+|++++|+++.+++...
T Consensus        33 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l~~Le~   76 (142)
T 2fbi_A           33 GLTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLER   76 (142)
T ss_dssp             TCCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHHHHHHH
Confidence            35554443333333334579999999999999999998875544

>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum SENS binding, transcription; 2.30A {Xanthomonas campestris PV}

Probab=82.80  E-value=2.1  Score=34.14  Aligned_cols=42  Identities=10%  Similarity=0.055  Sum_probs=35.4

Q ss_pred             CCHHHHHHHHHHHhhcC-------------CChHhhhhhccccHhHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYATG-------------NFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~-------------~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .+++++|+-+|..++..             .+..++|...|+|+.|++|+++++.
T Consensus       158 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~lt~~~lA~~lg~sr~tvsR~l~~L~  212 (230)
T 3iwz_A          158 LDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQ  212 (230)
T ss_dssp             CCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhCCCCCCCceecCCCHHHHHHHhCCcHHHHHHHHHHHH
Confidence            57889999999988642             3688999999999999999887654

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=82.49  E-value=1.9  Score=35.15  Aligned_cols=43  Identities=14%  Similarity=0.141  Sum_probs=35.9

Q ss_pred             CCHHHHHHHHHHHhhc--------------CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYAT--------------GNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~--------------~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+++++|+-+|..++.              ..+..++|...|+|+.|++|+++++.+
T Consensus       163 ~~~~~Rla~~L~~l~~~~g~~~~~~~~i~~~lt~~~lA~~lG~sr~tvsR~l~~L~~  219 (243)
T 3la7_A          163 RDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRE  219 (243)
T ss_dssp             SSHHHHHHHHHHHHHHHHEEECSSSEEECSCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCCCCeEEeccCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence            5789999999988752              347899999999999999999876543

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

Probab=82.42  E-value=1.2  Score=30.59  Aligned_cols=27  Identities=15%  Similarity=0.207  Sum_probs=23.1

Q ss_pred             CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         29 GNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        29 ~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +.+..+++..+|+|++|+++.++...+
T Consensus        38 ~~s~~ela~~l~is~~tvs~~l~~L~~   64 (99)
T 3cuo_A           38 GTSAGELTRITGLSASATSQHLARMRD   64 (99)
T ss_dssp             SEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            358899999999999999998876643

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=82.40  E-value=2.6  Score=31.01  Aligned_cols=43  Identities=12%  Similarity=0.076  Sum_probs=29.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .+++.+..++...+-..+.+..+++..+|++++|+++.+++..
T Consensus        30 ~l~~~~~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l~~L~   72 (145)
T 2a61_A           30 GITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLE   72 (145)
T ss_dssp             TCCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHH
Confidence            3555443333322234567999999999999999999886543

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

Probab=82.39  E-value=2.4  Score=31.42  Aligned_cols=46  Identities=13%  Similarity=0.024  Sum_probs=32.7

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ..+++.+-.++...+-..+.+..+++..+|++++|+++.+++....
T Consensus        36 ~~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~   81 (148)
T 3nrv_A           36 FGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEK   81 (148)
T ss_dssp             GTCCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            3577765444433333346799999999999999999988765543

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=82.32  E-value=0.42  Score=31.18  Aligned_cols=22  Identities=18%  Similarity=0.129  Sum_probs=19.8

Q ss_pred             CChHhhhhhccccHhHHHHHHH
Q psy13113         30 NFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        30 ~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      .+..++|...|||.+||+++++
T Consensus        10 ~t~~diA~~aGVS~sTVSr~ln   31 (67)
T 2l8n_A           10 ATMKDVALKAKVSTATVSRALM   31 (67)
T ss_dssp             CCHHHHHHHTTCCHHHHHHTTT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHc
Confidence            4789999999999999999774

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=82.29  E-value=1.9  Score=31.83  Aligned_cols=43  Identities=16%  Similarity=0.053  Sum_probs=29.6

Q ss_pred             CCCHHH-HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         12 IHSPVV-KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        12 ~~~~~~-~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .+++.+ .++..|..-..+.+..+++..+|++++|+++.+++..
T Consensus        34 ~l~~~~~~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l~~L~   77 (146)
T 2fbh_A           34 GLSQARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLE   77 (146)
T ss_dssp             CCTTTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH
Confidence            355543 3333442334567999999999999999999876443

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H

Probab=82.26  E-value=1.6  Score=39.41  Aligned_cols=47  Identities=13%  Similarity=0.112  Sum_probs=36.6

Q ss_pred             CCCHHHHHHHHHHH-hh--cCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRF-YA--TGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        12 ~~~~~~~l~~~L~~-L~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .||+.++-.+.|+| |.  .+.++.++|..+|||..||..+..+....|-
T Consensus       360 ~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS~erVrqi~~rAl~kLR  409 (423)
T 2a6h_F          360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK  409 (423)
T ss_dssp             SSCHHHHHHHHHHHHTTCC-----CHHHHSSSSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            47788888888888 44  5679999999999999999999998888776

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=82.23  E-value=2.6  Score=31.89  Aligned_cols=43  Identities=5%  Similarity=-0.138  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      ..+++.+-.++...+-..+.+..+|+..+|++++|+++++++.
T Consensus        42 ~glt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L   84 (162)
T 3k0l_A           42 LEISLPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKILQDL   84 (162)
T ss_dssp             TTCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3566655444333333346799999999999999999988644

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=82.21  E-value=2.9  Score=34.03  Aligned_cols=48  Identities=8%  Similarity=0.054  Sum_probs=40.4

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ...+++.++-.+.|  +..|.+..++|...|+|.+||...+.++...|..
T Consensus       171 ~~~Lt~~e~~vl~~--~~~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  218 (234)
T 1l3l_A          171 AAWLDPKEATYLRW--IAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV  218 (234)
T ss_dssp             CCCCCHHHHHHHHH--HTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            44688888866555  5799999999999999999999999988877753

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=82.13  E-value=2.2  Score=31.60  Aligned_cols=44  Identities=7%  Similarity=-0.026  Sum_probs=29.8

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..+++.+..++...+-..+.+..+++..++++++|+++.+++..
T Consensus        36 ~~l~~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~   79 (147)
T 1z91_A           36 LNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRME   79 (147)
T ss_dssp             TCCCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCcCcHHHHHHHHH
Confidence            34666544333322223456999999999999999999886543

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=82.11  E-value=2.5  Score=34.51  Aligned_cols=48  Identities=19%  Similarity=0.187  Sum_probs=40.3

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      ...+++.++-.+.|  +..|.+..++|...|+|.+||...+.++..-|..
T Consensus       173 ~~~Lt~~e~~vl~~--~~~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (236)
T 2q0o_A          173 KQMLSPREMLCLVW--ASKGKTASVTANLTGINARTVQHYLDKARAKLDA  220 (236)
T ss_dssp             GGSCCHHHHHHHHH--HHTTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             cCCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            45688888776655  5799999999999999999999999988877753

>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=81.87  E-value=3.5  Score=30.24  Aligned_cols=47  Identities=13%  Similarity=-0.010  Sum_probs=32.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCChHhhhhhcc--ccHhHHHHHHHHH
Q psy13113          7 DARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHD--ISQSTICRLVAKV   53 (286)
Q Consensus         7 ~~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fg--vs~stv~~~~~~v   53 (286)
                      .++...++.++...+.-.......+...++..+|  +|.+||++++++.
T Consensus        55 ~gr~~~l~~~~~~~i~~~~~~~~~s~~~i~~~lg~~~s~~tV~r~l~~~  103 (141)
T 1u78_A           55 APRRKALSVRDERNVIRAASNSCKTARDIRNELQLSASKRTILNVIKRS  103 (141)
T ss_dssp             CCCCCSSCHHHHHHHHHHHHHCCCCHHHHHHHTTCCSCHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCccHHHHHHHHHHC
Confidence            3455668877654433223334478999999998  8999999999763

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=81.66  E-value=1.9  Score=31.40  Aligned_cols=45  Identities=16%  Similarity=0.063  Sum_probs=31.5

Q ss_pred             CCCCHHHH-HHHHHHHhh--cCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         11 VIHSPVVK-LLAVLRFYA--TGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        11 ~~~~~~~~-l~~~L~~L~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ..+++.+- ++..|+. .  .+.+..+|+..++++++|+++.+++....
T Consensus        33 ~~lt~~q~~vL~~l~~-~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~   80 (127)
T 2frh_A           33 FSISFEEFAVLTYISE-NKEKEYYLKDIINHLNYKQPQVVKAVKILSQE   80 (127)
T ss_dssp             TCCCHHHHHHHHHHHH-TCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHh-ccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            35666543 3333332 3  45689999999999999999988876543

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=81.59  E-value=1.7  Score=34.43  Aligned_cols=43  Identities=14%  Similarity=0.098  Sum_probs=35.4

Q ss_pred             CHHHHHHHHHHHhhcC-------CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         14 SPVVKLLAVLRFYATG-------NFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        14 ~~~~~l~~~L~~L~~~-------~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      +++++|+.+|..++..       .+..++|...|+++.|++|+++++.+.
T Consensus       141 ~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~  190 (216)
T 4ev0_A          141 EARNRVAYALLKLLRQGLGPLFQIRHHELAALAGTSRETVSRVLHALAEE  190 (216)
T ss_dssp             HHHHHHHHHHHHHHHTTCCSEEECCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHhhcCCccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            5688999999877532       378999999999999999999877644

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=81.53  E-value=3.6  Score=30.93  Aligned_cols=44  Identities=14%  Similarity=0.068  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ++..++-++.+..-....++.++|..+|+|++|+++.+++..+.
T Consensus         5 ld~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   48 (151)
T 2cyy_A            5 LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES   48 (151)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            45444333322222345799999999999999999988876544

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=81.49  E-value=2.8  Score=30.64  Aligned_cols=27  Identities=11%  Similarity=0.181  Sum_probs=22.7

Q ss_pred             hcCCChHhhhhhccccHhHHHHHHHHH
Q psy13113         27 ATGNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      ..+.+..+++..+|+|++|+++.+++.
T Consensus        43 ~~~~~~~ela~~l~is~~~vs~~l~~L   69 (142)
T 3bdd_A           43 DAPLHQLALQERLQIDRAAVTRHLKLL   69 (142)
T ss_dssp             HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            345799999999999999999977643

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=81.31  E-value=2.1  Score=34.53  Aligned_cols=45  Identities=9%  Similarity=-0.035  Sum_probs=37.3

Q ss_pred             CCCCCHHHHHHHHHHHhhcC--------CChHhhhhhccccHhHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATG--------NFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~--------~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      -...+++++|+.+|..++..        .+..++|...|+++.|++|+++++.
T Consensus       159 l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~t~~~lA~~lG~sr~tvsR~l~~l~  211 (232)
T 1zyb_A          159 EPTLDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQ  211 (232)
T ss_dssp             CCCCSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HhhcCHHHHHHHHHHHHHhhcCCeEEecCCHHHHHHHhCCChhHHHHHHHHHH
Confidence            34578999999999887532        4889999999999999999988664

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=81.21  E-value=2.2  Score=36.65  Aligned_cols=37  Identities=22%  Similarity=0.223  Sum_probs=29.6

Q ss_pred             HHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         19 LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        19 l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .-++..|...+.+..++|..||||++||+|.+....+
T Consensus        11 ~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~~l~~   47 (315)
T 2w48_A           11 VKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGRE   47 (315)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3345556667789999999999999999998876543

>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=81.17  E-value=0.49  Score=30.05  Aligned_cols=24  Identities=13%  Similarity=-0.011  Sum_probs=20.7

Q ss_pred             hcCCChHhhhhhccccHhHHHHHH
Q psy13113         27 ATGNFQIDSEDYHDISQSTICRLV   50 (286)
Q Consensus        27 ~~~~~~~~l~~~Fgvs~stv~~~~   50 (286)
                      ..+.++.+||...|||++||++|.
T Consensus         8 ~~~~tq~~lA~~lGvs~~~Vs~we   31 (61)
T 1rzs_A            8 DHFGTQRAVAKALGISDAAVSQWK   31 (61)
T ss_dssp             HHHSSHHHHHHHHTCCHHHHHHCC
T ss_pred             HHcCCHHHHHHHhCCCHHHHHHHH
Confidence            344589999999999999999975

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=81.01  E-value=3.1  Score=31.29  Aligned_cols=42  Identities=14%  Similarity=0.184  Sum_probs=28.8

Q ss_pred             CCCHHHH-HHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         12 IHSPVVK-LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        12 ~~~~~~~-l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .++..+. ++..|.. ..+.+..+++..+|++++|+++.+++..
T Consensus        46 ~lt~~~~~iL~~l~~-~~~~t~~ela~~l~is~~tvs~~l~~Le   88 (162)
T 2fa5_A           46 GMAIPEWRVITILAL-YPGSSASEVSDRTAMDKVAVSRAVARLL   88 (162)
T ss_dssp             CCCHHHHHHHHHHHH-STTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh-CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3555443 3333332 4567899999999999999999886544

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=81.00  E-value=1.4  Score=30.31  Aligned_cols=30  Identities=13%  Similarity=-0.036  Sum_probs=23.0

Q ss_pred             HHHHhhc--CCChHhhhhhccccHhHHHHHHH
Q psy13113         22 VLRFYAT--GNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        22 ~L~~L~~--~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      .|.+|+.  ..+..+|+..|+||..||.+.+.
T Consensus         7 Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~   38 (87)
T 2k02_A            7 VRDMLALQGRMEAKQLSARLQTPQPLIDAMLE   38 (87)
T ss_dssp             HHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence            3444543  35888999999999999998665

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

Probab=80.68  E-value=2.1  Score=30.29  Aligned_cols=29  Identities=7%  Similarity=0.071  Sum_probs=24.4

Q ss_pred             hcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         27 ATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        27 ~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ..+.+..+++..+|+|++|+++.++....
T Consensus        32 ~~~~~~~ela~~l~is~~tv~~~l~~L~~   60 (114)
T 2oqg_A           32 RADQSASSLATRLPVSRQAIAKHLNALQA   60 (114)
T ss_dssp             HSCBCHHHHHHHSSSCHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            44579999999999999999998876644

>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3

Probab=80.67  E-value=3.2  Score=27.66  Aligned_cols=34  Identities=18%  Similarity=0.066  Sum_probs=29.2

Q ss_pred             HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         18 KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        18 ~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      .+.-.|..++...++.++|...|||++|++++-+
T Consensus        16 ~~g~~l~~~R~~~sq~~lA~~~gis~~~is~~E~   49 (86)
T 2ofy_A           16 RLGELLRSARGDMSMVTVAFDAGISVETLRKIET   49 (86)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHCCHHHHHHHhCCCHHHHHHHHc
Confidence            3666788888777999999999999999998765

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=80.62  E-value=3.5  Score=30.32  Aligned_cols=44  Identities=9%  Similarity=0.090  Sum_probs=31.0

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ...+++.+...+... ..++.+..++|..+|++++|+++.+++..
T Consensus        33 ~~~lt~~~~~iL~~l-~~~~~t~~eLa~~l~~s~~tvs~~l~~L~   76 (146)
T 3tgn_A           33 EVALTNTQEHILMLL-SEESLTNSELARRLNVSQAAVTKAIKSLV   76 (146)
T ss_dssp             SSCCCHHHHHHHHHH-TTCCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHHH-HhCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            345676554433332 23448999999999999999999887554

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=80.55  E-value=3.5  Score=30.78  Aligned_cols=27  Identities=7%  Similarity=0.012  Sum_probs=23.1

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ...++.++|..+|+|++|+++.+++..
T Consensus        18 ~~~s~~ela~~lg~s~~tv~~~l~~L~   44 (144)
T 2cfx_A           18 SRLSMRELGRKIKLSPPSVTERVRQLE   44 (144)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            346999999999999999999887554

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=80.40  E-value=2.4  Score=31.99  Aligned_cols=43  Identities=14%  Similarity=-0.065  Sum_probs=28.6

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .++..+..++...+-..+.+..+++..+|++++|+++.+++..
T Consensus        49 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le   91 (162)
T 3cjn_A           49 GLSTAKMRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQ   91 (162)
T ss_dssp             TCCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence            3555443333222223456999999999999999999886543

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=80.39  E-value=2.5  Score=31.52  Aligned_cols=44  Identities=9%  Similarity=0.015  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..+++.+-.++...+-..+.+..+++..++++++|+++.+++..
T Consensus        37 ~~lt~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l~~L~   80 (149)
T 4hbl_A           37 FGITYSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPMLKRLE   80 (149)
T ss_dssp             TTCCHHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            34666553333333334566999999999999999999886543

>1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1

Probab=80.37  E-value=1.8  Score=34.51  Aligned_cols=44  Identities=11%  Similarity=0.018  Sum_probs=36.5

Q ss_pred             CCHHHHHHHHHHHhhc--------------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYAT--------------GNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~--------------~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      .+++++|+-+|..+..              ..+..++|...|+|+.|++++++++...
T Consensus       133 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~~t~~~lA~~lG~sr~tvsR~l~~L~~~  190 (222)
T 1ft9_A          133 HDIKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIKE  190 (222)
T ss_dssp             HHHHHHHHHHHHHTCBCCCSCC--CCCCEECCCHHHHHHHHCSCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence            4678899999988862              2478899999999999999999987644

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=80.37  E-value=2.9  Score=31.31  Aligned_cols=28  Identities=7%  Similarity=0.183  Sum_probs=23.3

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+.+..+++..++++++|+++.+++...
T Consensus        57 ~~~t~~ela~~l~is~~tvs~~l~~Le~   84 (154)
T 2eth_A           57 GPKKMKEIAEFLSTTKSNVTNVVDSLEK   84 (154)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4679999999999999999998765443

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=80.19  E-value=3.1  Score=27.61  Aligned_cols=40  Identities=13%  Similarity=0.032  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHHHHhhcCC--ChHhhhhhccccHhHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYATGN--FQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~--~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      +...+++.-++..|..+.  +...+|..+|+++++|.+.+..
T Consensus        11 ~~~~~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~   52 (75)
T 1sfu_A           11 AEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYK   52 (75)
T ss_dssp             HHHHHHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHH
Confidence            456788888899999876  8889999999999998876653

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=80.15  E-value=2.8  Score=34.29  Aligned_cols=48  Identities=15%  Similarity=0.002  Sum_probs=39.9

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ....+++.++-.+.|  ++.|.+.+++|...|+|.+||...+.++..-|.
T Consensus       172 ~~~~Lt~re~~vl~~--~~~G~s~~eIa~~l~is~~tV~~~~~~~~~kl~  219 (237)
T 3szt_A          172 SNVRLTARETEMLKW--TAVGKTYGEIGLILSIDQRTVKFHIVNAMRKLN  219 (237)
T ss_dssp             GGCCCCHHHHHHHHH--HHTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence            356788877765555  689999999999999999999999998876664

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=80.14  E-value=1.1  Score=29.44  Aligned_cols=21  Identities=0%  Similarity=-0.084  Sum_probs=19.4

Q ss_pred             ChHhhhhhccccHhHHHHHHH
Q psy13113         31 FQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        31 ~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      +...||..+|||++||++|++
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~   32 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQ   32 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHh
Confidence            488999999999999999986

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=80.12  E-value=2.7  Score=30.75  Aligned_cols=44  Identities=16%  Similarity=0.033  Sum_probs=29.8

Q ss_pred             CCCHHHH-HHHHHHHhh-cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         12 IHSPVVK-LLAVLRFYA-TGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        12 ~~~~~~~-l~~~L~~L~-~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .+++.+- ++..|..-. .+.+..+++..+|++++|+++.+++...
T Consensus        28 ~lt~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~   73 (139)
T 3eco_A           28 DITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLER   73 (139)
T ss_dssp             TCCHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHH
Confidence            4555433 333333322 2679999999999999999998876543

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=80.09  E-value=3.6  Score=30.90  Aligned_cols=27  Identities=11%  Similarity=0.030  Sum_probs=22.7

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ...++.++|..+|+|++|+++.+++..
T Consensus        20 ~~~s~~ela~~lg~s~~tv~~~l~~L~   46 (150)
T 2w25_A           20 GRATLSELATRAGLSVSAVQSRVRRLE   46 (150)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            346999999999999999998876543

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=80.05  E-value=3.1  Score=30.77  Aligned_cols=27  Identities=15%  Similarity=0.121  Sum_probs=23.5

Q ss_pred             CCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         29 GNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        29 ~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ..++.++|..+|+|++|+++.+++...
T Consensus        18 ~~~~~ela~~lg~s~~tv~~~l~~L~~   44 (141)
T 1i1g_A           18 RTPFTEIAKKLGISETAVRKRVKALEE   44 (141)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            469999999999999999998876654

---

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	286
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	97.87
d1hlva1	66	DNA-binding domain of centromere binding protein B	97.17
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.17
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	95.57
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	95.2
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	95.19
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	94.72
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	94.5
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	94.36
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	93.88
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	93.22
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	93.14
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	93.01
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	92.96
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	92.85
d1zyba1	73	Probable transcription regulator BT4300, C-termina	92.38
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	92.28
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	92.01
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	91.77
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	91.77
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	91.68
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	90.98
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	90.9
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	90.69
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	90.59
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	90.38
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	90.37
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	90.12
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	89.68
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	88.84
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	88.66
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	88.53
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	88.41
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	88.07
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	87.5
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	87.41
d1l8qa1	110	Chromosomal replication initiation factor DnaA C-t	87.25
d1j1va_	94	Chromosomal replication initiation factor DnaA C-t	87.03
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	85.86
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	84.32
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	84.1
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	83.56
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	83.42
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	83.37
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	82.79
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	82.51
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	81.92
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	81.91
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	81.87
d2oa4a1	93	Uncharacterized protein SPO1678 {Silicibacter pome	81.65
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	81.62
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	80.97
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	80.88
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	80.86
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	80.85
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	80.85
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	80.17

>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=97.87  E-value=9.8e-06  Score=48.15  Aligned_cols=42  Identities=17%  Similarity=0.112  Sum_probs=36.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLV   50 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~   50 (286)
                      ||++.++. +|+..+..+++.|.+..++|..||||++|+++++
T Consensus         1 GR~~~lt~-~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           1 GRPRAINK-HEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCCCSSCH-HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CCCCcCCH-HHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            46667776 6788888889999999999999999999999986

>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=97.17  E-value=0.0004  Score=43.95  Aligned_cols=52  Identities=12%  Similarity=-0.020  Sum_probs=42.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcC-CChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113          7 DARGVIHSPVVKLLAVLRFYATG-NFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus         7 ~~~~~~~~~~~~l~~~L~~L~~~-~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ++++..|+.++++-+.-++=.+. .++.++|..|||++|||+.|+++=-..+.
T Consensus         2 ~~kRk~LT~~eK~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKnK~kil~   54 (66)
T d1hlva1           2 GPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILA   54 (66)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHHHHHH
T ss_pred             CcccccCCHHHHHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence            35678899999999988777765 47899999999999999999986544443

>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=96.17  E-value=0.0074  Score=38.43  Aligned_cols=48  Identities=25%  Similarity=0.195  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      .+|+.++-++.|+|+ .|.++.++|..+|+|.+||...+.+....|-..
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            588999999988886 578999999999999999999999988877653

>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=95.57  E-value=0.022  Score=35.31  Aligned_cols=44  Identities=11%  Similarity=0.169  Sum_probs=32.7

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      +.-+++..+++.-+   ...|.+.+++|..|+||.+|+++|+++.-+
T Consensus        13 rPls~DLR~Riv~~---~~~G~s~r~aA~rf~VS~s~v~k~l~r~re   56 (63)
T d1k78a1          13 RPLPDVVRQRIVEL---AHQGVRPCDISRQLRVSHGCVSKILGRYYE   56 (63)
T ss_dssp             SCCCHHHHHHHHHH---HHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHH---HHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            33344445555533   348899999999999999999999987643

>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=95.20  E-value=0.021  Score=40.64  Aligned_cols=46  Identities=15%  Similarity=0.120  Sum_probs=37.7

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ++..+|.+.+.-+.-.+ ..|.+.+++|..|+||.+||++|+.+.-+
T Consensus        13 ~GrpLs~dlR~rIv~~~-~~G~s~r~iA~~~~VS~~tV~k~l~r~~~   58 (123)
T d1pdnc_          13 NGRPLPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILNRYQE   58 (123)
T ss_dssp             TTSCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCcCCCHHHHHHHHHHH-HhcCCHHHHHHHHCcCHHHHHHHHHHHHc
Confidence            46678887776666654 57899999999999999999999987655

>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=95.19  E-value=0.018  Score=38.46  Aligned_cols=44  Identities=18%  Similarity=0.047  Sum_probs=37.4

Q ss_pred             CCCCCHHHHHHHHHHHhhc-CCChHhhhhhccccHhHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYAT-GNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~-~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      +...|++-+.-++=.++.+ |.+..++|..||||.+|+++|+++.
T Consensus         3 rk~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1           3 TKTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             CCCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            4568999888877666754 7999999999999999999999865

>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=94.72  E-value=0.045  Score=34.29  Aligned_cols=47  Identities=13%  Similarity=0.089  Sum_probs=40.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      .+|+.++-++.|+|+. |.++.++|..+|+|.+||...+.+....|-.
T Consensus        18 ~Lp~~~r~v~~l~~~~-~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~   64 (68)
T d1or7a1          18 SLPEDLRMAITLRELD-GLSYEEIAAIMDCPVGTVRSRIFRAREAIDN   64 (68)
T ss_dssp             HSCHHHHHHHHHHHTT-CCCHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            4788888888888875 5789999999999999999999988877765

>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=94.50  E-value=0.041  Score=37.93  Aligned_cols=47  Identities=9%  Similarity=0.036  Sum_probs=41.8

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHhh
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAKC   60 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~~   60 (286)
                      +|+.++-++.|+|+ .+.++..+|..+|||.+||+..+++....|-..
T Consensus        17 Lp~~qR~v~~L~y~-~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~   63 (106)
T d1s7oa_          17 LTDKQMNYIELYYA-DDYSLAEIADEFGVSRQAVYDNIKRTEKILETY   63 (106)
T ss_dssp             SCHHHHHHHHHHHH-TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            78888888888876 569999999999999999999999999988753

>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=94.36  E-value=0.048  Score=34.30  Aligned_cols=42  Identities=12%  Similarity=0.092  Sum_probs=35.2

Q ss_pred             CHHHHHHHHHHHhhcC-------------CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         14 SPVVKLLAVLRFYATG-------------NFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        14 ~~~~~l~~~L~~L~~~-------------~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ++..+|+-+|..|+..             .++.++|...|+|+.||+++++++.+
T Consensus         1 Dv~~Rla~~Ll~l~~~~g~~~~~~~i~l~lt~~~lA~~~G~sRetvsr~L~~l~~   55 (69)
T d1i5za1           1 DVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLED   55 (69)
T ss_dssp             CHHHHHHHHHHHGGGSTTCCCCSSSCEEECCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHcCCCCCCCeeecCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3678999999998732             47889999999999999999987654

>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=93.88  E-value=0.097  Score=32.59  Aligned_cols=47  Identities=9%  Similarity=0.080  Sum_probs=38.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ++.+++.++=.  |.+++.|.+..++|...|+|.+||..++.++..-+.
T Consensus         2 ~p~LT~rE~~v--l~l~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~   48 (67)
T d1fsea_           2 KPLLTKREREV--FELLVQDKTTKEIASELFISEKTVRNHISNAMQKLG   48 (67)
T ss_dssp             CCCCCHHHHHH--HHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHH--HHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            34677766554  455899999999999999999999999998877765

>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=93.22  E-value=0.066  Score=33.44  Aligned_cols=45  Identities=20%  Similarity=0.208  Sum_probs=37.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .+++.+.  -+|.+++.|.+..++|...|+|.+||...+.++..-+.
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            4666553  34567899999999999999999999999998887775

>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=93.14  E-value=0.15  Score=31.17  Aligned_cols=48  Identities=13%  Similarity=0.095  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHHHHHh---hcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFY---ATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L---~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ..++..++-.+.++|-   ....++.++|..+|||+..|+.+-++.+.-|-
T Consensus         7 ~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR   57 (61)
T d1ku3a_           7 SKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK   57 (61)
T ss_dssp             TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            4588999999999993   34468999999999999999999988876653

>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=93.01  E-value=0.1  Score=35.77  Aligned_cols=46  Identities=7%  Similarity=0.081  Sum_probs=40.4

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHHh
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELAK   59 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~~   59 (286)
                      +|+.++-++.|+|+ .+.++..+|...|+|++||...+++....|-.
T Consensus        19 Lpe~QR~vl~L~~~-e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~   64 (106)
T d1xsva_          19 LTNKQRNYLELFYL-EDYSLSEIADTFNVSRQAVYDNIRRTGDLVED   64 (106)
T ss_dssp             SCHHHHHHHHHHHT-SCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH-hCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            77888888887765 67999999999999999999999999988865

>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=92.96  E-value=0.076  Score=32.91  Aligned_cols=45  Identities=13%  Similarity=0.177  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .+++.++=  .|.+++.|.+..++|...++|.+||..++.++..-|.
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            45555443  3567999999999999999999999999998877765

>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=92.85  E-value=0.096  Score=33.82  Aligned_cols=42  Identities=10%  Similarity=-0.032  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHhhc--------------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         15 PVVKLLAVLRFYAT--------------GNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        15 ~~~~l~~~L~~L~~--------------~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ++++|+-+|.+|+.              ..+..++|...|+|+.||++.++.+.+.
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            57899999998864              2468899999999999999999887665

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=92.38  E-value=0.12  Score=32.76  Aligned_cols=44  Identities=9%  Similarity=0.004  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHhhcC--------CChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATG--------NFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~--------~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ..+++++|+-+|..+...        .+.+++|...|+|+.|+++.++.+.+
T Consensus         2 T~dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~lg~sr~tvsr~l~~l~~   53 (73)
T d1zyba1           2 TLDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQD   53 (73)
T ss_dssp             CCSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            457899999998766542        38889999999999999999987654

>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=92.28  E-value=0.15  Score=32.74  Aligned_cols=42  Identities=17%  Similarity=0.304  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHhhc--------------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         15 PVVKLLAVLRFYAT--------------GNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        15 ~~~~l~~~L~~L~~--------------~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      +..+|+-+|..|+.              ..+++++|...|+|+.||+++++++.+.
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            67889999988862              2367899999999999999999988765

>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=92.01  E-value=0.17  Score=32.56  Aligned_cols=42  Identities=12%  Similarity=0.041  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHhhc-------------CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         15 PVVKLLAVLRFYAT-------------GNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        15 ~~~~l~~~L~~L~~-------------~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      ++++|+-+|.+|+.             ..+..++|...|+|+.||+++++++.+.
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            57888888888873             2478899999999999999999887654

>d2ofya1 a.35.1.3 (A:3-84) Putative transcriptional regulator RHA1_ro04071 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcriptional regulator RHA1 ro04071
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=91.77  E-value=0.15  Score=33.11  Aligned_cols=35  Identities=17%  Similarity=0.050  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      +++.-.|..++.+.++.++|..-|||.+|++++=+
T Consensus        13 ~~lG~~ir~~R~~~t~~eLA~~~Gvs~~~ls~iE~   47 (82)
T d2ofya1          13 QRLGELLRSARGDMSMVTVAFDAGISVETLRKIET   47 (82)
T ss_dssp             HHHHHHHHHHHTTSCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHcCCHHHHHHHHc
Confidence            57888999999999999999999999999998754

>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=91.77  E-value=0.1  Score=32.87  Aligned_cols=45  Identities=11%  Similarity=0.062  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      .+++.+.-.  |.+|+.|.+..++|...|+|.+||...+.++..-|.
T Consensus        12 ~LT~rE~~v--l~~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   56 (70)
T d1yioa1          12 SLTGREQQV--LQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQKLN   56 (70)
T ss_dssp             TSCHHHHHH--HHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             cCCHHHHHH--HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            355655443  445889999999999999999999999988876664

>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=91.68  E-value=0.24  Score=32.53  Aligned_cols=48  Identities=15%  Similarity=0.246  Sum_probs=40.4

Q ss_pred             CCCCHHHHHHHHHHH-hh--cCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRF-YA--TGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~-L~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ..+++.++..+.++| |.  ...++.++|..||||+..|..+-.+.+.-|-
T Consensus        17 ~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~kLr   67 (87)
T d1ttya_          17 KTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLR   67 (87)
T ss_dssp             TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHB
T ss_pred             hcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence            358899999999998 43  3469999999999999999999888877774

>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=90.98  E-value=0.22  Score=30.46  Aligned_cols=32  Identities=13%  Similarity=0.237  Sum_probs=25.3

Q ss_pred             HHHHhhcCC--ChHhhhhhccccHhHHHHHHHHH
Q psy13113         22 VLRFYATGN--FQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        22 ~L~~L~~~~--~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      .|..|..+.  +..+||..||||++||.+.+...
T Consensus        10 iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L   43 (63)
T d1biaa1          10 LIALLANGEFHSGEQLGETLGMSRAAINKHIQTL   43 (63)
T ss_dssp             HHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            444555554  78899999999999999988654

>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=90.90  E-value=0.31  Score=27.21  Aligned_cols=41  Identities=17%  Similarity=0.204  Sum_probs=30.7

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      ++.+.++.++    .......|..-..+|...|||++||++++++
T Consensus         1 GRk~~Id~~~----V~~L~~~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1           1 GRKRKIDRDA----VLNMWQQGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             SSCCCSCHHH----HHHHHHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             CCCCccCHHH----HHHHHHcCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            3555666653    2233468889999999999999999998863

>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=90.69  E-value=0.22  Score=31.08  Aligned_cols=48  Identities=17%  Similarity=0.112  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHHHHHh-h--cCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113         11 VIHSPVVKLLAVLRFY-A--TGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus        11 ~~~~~~~~l~~~L~~L-~--~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ..+++.++-.+.++|- .  ...++.++|..+|||+..|..+-.+.+.-|-
T Consensus         4 ~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr   54 (68)
T d2p7vb1           4 AGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR   54 (68)
T ss_dssp             CCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGG
T ss_pred             hcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            3588999999999884 3  3359999999999999999998887666553

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

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: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=90.38  E-value=0.076  Score=32.06  Aligned_cols=23  Identities=22%  Similarity=0.212  Sum_probs=20.4

Q ss_pred             CCChHhhhhhccccHhHHHHHHH
Q psy13113         29 GNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        29 ~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      +.+.+++|...|||.+||+++++
T Consensus         1 NvTi~dvA~~agvS~~TVSr~Ln   23 (57)
T d2hsga1           1 NVTIYDVAREASVSMATVSRVVN   23 (57)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CcCHHHHHHHHCcCHHHHHHHhC
Confidence            35678999999999999999886

>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=90.37  E-value=0.081  Score=31.93  Aligned_cols=22  Identities=18%  Similarity=0.282  Sum_probs=19.6

Q ss_pred             ChHhhhhhccccHhHHHHHHHH
Q psy13113         31 FQIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        31 ~~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      +.+++|...|||.+||+++++.
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            5689999999999999998863

>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=90.12  E-value=0.34  Score=31.72  Aligned_cols=48  Identities=23%  Similarity=0.171  Sum_probs=38.9

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSEELA   58 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~l~   58 (286)
                      ....+++.+.=  +|.+|+.|.+..++|..+++|.+||...+..+..-|.
T Consensus        19 ~~~~LT~rE~~--vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~   66 (87)
T d1p4wa_          19 GDKRLSPKESE--VLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG   66 (87)
T ss_dssp             SSSSCCHHHHH--HHHHHHHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            34567776643  4556899999999999999999999999988877664

>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=89.68  E-value=0.12  Score=31.58  Aligned_cols=28  Identities=14%  Similarity=-0.154  Sum_probs=24.2

Q ss_pred             HHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         24 RFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        24 ~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      .+-+.|.++.++|...|||.+|+++|=+
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            3456789999999999999999998754

>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=88.84  E-value=0.36  Score=30.10  Aligned_cols=32  Identities=9%  Similarity=0.130  Sum_probs=26.1

Q ss_pred             HhhcCCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         25 FYATGNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        25 ~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      +-....+..+||...|+|.+||++++.+.++.
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            33456799999999999999999998866543

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), 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: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.66  E-value=0.1  Score=31.63  Aligned_cols=22  Identities=27%  Similarity=0.394  Sum_probs=19.8

Q ss_pred             CChHhhhhhccccHhHHHHHHH
Q psy13113         30 NFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        30 ~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      .+..++|...|||.+||+++++
T Consensus         3 ~Ti~diA~~agvS~sTVSr~l~   24 (59)
T d1efaa1           3 VTLYDVAEYAGVSYQTVSRVVN   24 (59)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHC
Confidence            4678999999999999999885

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), 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: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.53  E-value=0.11  Score=31.55  Aligned_cols=21  Identities=10%  Similarity=0.067  Sum_probs=19.0

Q ss_pred             ChHhhhhhccccHhHHHHHHH
Q psy13113         31 FQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        31 ~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      +..++|...|||.+||+++++
T Consensus         2 Tl~diA~~agvS~sTVSrvLn   22 (59)
T d1uxda_           2 KLDEIARLAGVSRTTASYVIN   22 (59)
T ss_dssp             CHHHHHHHHTSCTTHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHc
Confidence            568999999999999999886

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=88.41  E-value=0.17  Score=31.50  Aligned_cols=27  Identities=7%  Similarity=-0.044  Sum_probs=24.1

Q ss_pred             HHhhcCCChHhhhhhccccHhHHHHHH
Q psy13113         24 RFYATGNFQIDSEDYHDISQSTICRLV   50 (286)
Q Consensus        24 ~~L~~~~~~~~l~~~Fgvs~stv~~~~   50 (286)
                      ++.+.|.++.++|...|||+.|+++|=
T Consensus         9 ~R~~~gltQ~elA~~LGvs~~ti~~yE   35 (67)
T d2auwa1           9 WMHRNNLSLTTAAEALGISRRMVSYYR   35 (67)
T ss_dssp             HHHHTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            567789999999999999999999863

>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=88.07  E-value=0.25  Score=33.71  Aligned_cols=39  Identities=18%  Similarity=0.131  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         17 VKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        17 ~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      -+++..|+.-....+..++|..+|++++|+++.+++..+
T Consensus        24 ~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~   62 (109)
T d2d1ha1          24 VAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIE   62 (109)
T ss_dssp             HHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHH
Confidence            344555544333469999999999999999999887654

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=87.50  E-value=0.44  Score=32.76  Aligned_cols=42  Identities=19%  Similarity=-0.034  Sum_probs=35.0

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      |..++|-+.-...-..+..|.+..++|..+|+|.++|++++.
T Consensus        11 R~~L~p~e~A~a~~~l~~~g~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_          11 RNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             TTCCCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             ccCCCHHHHHHHHHHHHHhCCCHHHHHHHHCCcHHHHHHHHH
Confidence            456777776666666777889999999999999999999875

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.41  E-value=0.47  Score=29.02  Aligned_cols=38  Identities=13%  Similarity=0.137  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHhhc---CCChHhhhhhccccHhHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYAT---GNFQIDSEDYHDISQSTICRLVAKV   53 (286)
Q Consensus        16 ~~~l~~~L~~L~~---~~~~~~l~~~Fgvs~stv~~~~~~v   53 (286)
                      .+++.-.|..|..   ..+-.+||..||||..||.+.+...
T Consensus         6 ~eR~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L   46 (65)
T d1j5ya1           6 QERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYL   46 (65)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            4566666666653   2478899999999999999988653

>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=87.25  E-value=0.36  Score=33.16  Aligned_cols=50  Identities=18%  Similarity=0.096  Sum_probs=42.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhcc-ccHhHHHHHHHHHHHHHH
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHD-ISQSTICRLVAKVSEELA   58 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fg-vs~stv~~~~~~v~~~l~   58 (286)
                      |...+...-++++.|.+--++.++.++|..|| -+.+||...++.+-..|.
T Consensus        39 R~~~vv~aR~ia~yL~r~~t~~sl~~IG~~fg~rdHsTV~~a~kki~~~~~   89 (110)
T d1l8qa1          39 RNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKK   89 (110)
T ss_dssp             CCSSSHHHHHHHHHHHHHHHCCCHHHHHHHSSCCCSTHHHHHHHHHHHTTC
T ss_pred             CcHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCCccHHHHHHHHHHHHHH
Confidence            44567777889999988889999999999996 899999999988876654

>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=87.03  E-value=0.43  Score=31.70  Aligned_cols=51  Identities=12%  Similarity=0.017  Sum_probs=43.8

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCChHhhhhhcc-ccHhHHHHHHHHHHHHHHh
Q psy13113          9 RGVIHSPVVKLLAVLRFYATGNFQIDSEDYHD-ISQSTICRLVAKVSEELAK   59 (286)
Q Consensus         9 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fg-vs~stv~~~~~~v~~~l~~   59 (286)
                      |...+....++++.|.+=-++.++.++|..|| -+.|||...++.+-..+..
T Consensus        26 R~~~iv~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHsTV~~a~kki~~~~~~   77 (94)
T d1j1va_          26 RSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREE   77 (94)
T ss_dssp             CCHHHHHHHHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHHHHHHhCCCHHHHHHHhCCCCchHHHHHHHHHHHHHHh
Confidence            45556677899999999999999999999995 7999999999988887753

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=85.86  E-value=0.76  Score=27.76  Aligned_cols=28  Identities=14%  Similarity=0.165  Sum_probs=23.8

Q ss_pred             cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         28 TGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        28 ~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ...+-.++|..+|||.+||++.+++..+
T Consensus        20 ~~v~~~~iA~~L~vs~~SVs~mikrL~~   47 (61)
T d2ev0a1          20 GYARVSDIAEALAVHPSSVTKMVQKLDK   47 (61)
T ss_dssp             SSCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHhCCCchhHHHHHHHHHH
Confidence            3458889999999999999999987654

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=84.32  E-value=0.81  Score=32.29  Aligned_cols=42  Identities=5%  Similarity=0.007  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         13 HSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        13 ~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ++..+-..+...+-..+.+..++|..++++++|+++++++..
T Consensus        30 lt~~q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v~~L~   71 (140)
T d2etha1          30 MKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLE   71 (140)
T ss_dssp             SBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            455444444333444557999999999999999999887554

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=84.10  E-value=0.64  Score=30.37  Aligned_cols=36  Identities=17%  Similarity=0.082  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHhh--cCCChHhhhhhccccHhHHHHHHH
Q psy13113         16 VVKLLAVLRFYA--TGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        16 ~~~l~~~L~~L~--~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      ...|+..|..++  .|.+++++|...|+|++|++++.+
T Consensus         9 k~~l~~~i~~~r~~~gltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1           9 KLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHc
Confidence            345666666666  588999999999999999999875

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.56  E-value=0.4  Score=28.04  Aligned_cols=26  Identities=12%  Similarity=-0.027  Sum_probs=23.2

Q ss_pred             CCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         29 GNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        29 ~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..+..++|..+|+|.+++++.|++..
T Consensus        19 ~itl~~lA~~~~~S~~~l~r~Fk~~~   44 (54)
T d1d5ya1          19 PLSLDNVAAKAGYSKWHLQRMFKDVT   44 (54)
T ss_dssp             SCCCHHHHTTTSSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            35888999999999999999999765

>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=83.42  E-value=0.81  Score=28.78  Aligned_cols=41  Identities=15%  Similarity=0.220  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHhhc---CCChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         16 VVKLLAVLRFYAT---GNFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        16 ~~~l~~~L~~L~~---~~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      -++.+-.|..++.   +.+..+++...|++++|+++++...++.
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            3455556666653   4589999999999999999998766543

>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=83.37  E-value=1.2  Score=31.45  Aligned_cols=46  Identities=13%  Similarity=-0.059  Sum_probs=33.3

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ...+++.+--.+....-..+.+..+++...+++++|+++++++...
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            3456765554444444455679999999999999999998876543

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.79  E-value=1.2  Score=27.01  Aligned_cols=38  Identities=13%  Similarity=0.141  Sum_probs=27.7

Q ss_pred             HHHHHHHHhh---cCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113         18 KLLAVLRFYA---TGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus        18 ~l~~~L~~L~---~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      .-+-+++.|.   ...+-.++|..+|||.+||++.+++..+
T Consensus         9 dYL~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mvkrL~~   49 (63)
T d2isya1           9 MYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMER   49 (63)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHhCCCchhHHHHHHHHHH
Confidence            3344444443   3357889999999999999999887654

>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=82.51  E-value=1.2  Score=31.27  Aligned_cols=43  Identities=12%  Similarity=0.076  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         12 IHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        12 ~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      .+++.+-.++...+-..+.+..++|...|++++|++++++...
T Consensus        27 glt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~   69 (139)
T d2a61a1          27 GITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLE   69 (139)
T ss_dssp             TCCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHHHHH
Confidence            3566554444444445578999999999999999999887544

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=81.92  E-value=1.3  Score=27.26  Aligned_cols=35  Identities=20%  Similarity=0.287  Sum_probs=26.7

Q ss_pred             HHHHhhcC--CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         22 VLRFYATG--NFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        22 ~L~~L~~~--~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      .|..+...  .+-.+++...|+|.+||++++...++.
T Consensus        10 Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~   46 (70)
T d1z6ra1          10 VYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEA   46 (70)
T ss_dssp             HHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34444443  578899999999999999999876554

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=81.91  E-value=1.3  Score=29.21  Aligned_cols=28  Identities=14%  Similarity=0.109  Sum_probs=24.0

Q ss_pred             HHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         24 RFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        24 ~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      ..+..|.+..++|..+|.|+++|+..++
T Consensus        14 ~L~e~g~t~~~iA~~~Gks~~~V~~~Lr   41 (93)
T d1vz0a1          14 ALLEMGLTQEEVARRVGKARSTVANALR   41 (93)
T ss_dssp             HHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHccchHHHHHHHH
Confidence            3346789999999999999999998775

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=81.87  E-value=0.62  Score=28.44  Aligned_cols=28  Identities=14%  Similarity=-0.022  Sum_probs=24.2

Q ss_pred             HHhhcCCChHhhhhhccccHhHHHHHHH
Q psy13113         24 RFYATGNFQIDSEDYHDISQSTICRLVA   51 (286)
Q Consensus        24 ~~L~~~~~~~~l~~~Fgvs~stv~~~~~   51 (286)
                      .+...|.++.++|...|||++|++++.+
T Consensus         9 lR~~~g~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_           9 IREKKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHcCCCHHHHHHhcccCHHHHHHHHc
Confidence            3456889999999999999999998764

>d2oa4a1 a.4.12.3 (A:1-93) Uncharacterized protein SPO1678 {Silicibacter pomeroyi [TaxId: 89184]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: SPO1678-like
domain: Uncharacterized protein SPO1678
species: Silicibacter pomeroyi [TaxId: 89184]

Probab=81.65  E-value=2.9  Score=27.26  Aligned_cols=48  Identities=13%  Similarity=-0.005  Sum_probs=42.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHHH
Q psy13113          8 ARGVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVSE   55 (286)
Q Consensus         8 ~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~~   55 (286)
                      ........+.+..+++--+..-.+..+++..+++|++-+..|...+..
T Consensus        29 ~~trRWva~RKaaVV~av~~Gl~S~~EAcrrY~LS~eEf~~W~~a~~~   76 (93)
T d2oa4a1          29 ANTRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAE   76 (93)
T ss_dssp             SCCSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHC
T ss_pred             cccccccHHHHHHHHHHHHcCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            456678999999999999999999999999999999999988877654

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=81.62  E-value=1.1  Score=31.45  Aligned_cols=45  Identities=7%  Similarity=-0.034  Sum_probs=33.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         10 GVIHSPVVKLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        10 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ...+++.+-.++...+-..+.+..+++...+++++|++++++...
T Consensus        28 ~~gLt~~q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i~~L~   72 (137)
T d1z91a1          28 KLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRME   72 (137)
T ss_dssp             TTCCCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             HcCcCHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence            345777655555544456678999999999999999999886543

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=80.97  E-value=0.67  Score=26.97  Aligned_cols=35  Identities=11%  Similarity=0.088  Sum_probs=27.0

Q ss_pred             HHHHHHhh----cCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         20 LAVLRFYA----TGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        20 ~~~L~~L~----~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      --++.|+.    ...+..++|..+|+|++++++.|++..
T Consensus         6 ~~v~~yI~~~~~~~~tl~~lA~~~~~s~~~l~r~Fk~~~   44 (54)
T d1bl0a1           6 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKET   44 (54)
T ss_dssp             HHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            33444444    345888999999999999999998765

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=80.88  E-value=1.2  Score=29.69  Aligned_cols=60  Identities=12%  Similarity=0.101  Sum_probs=40.3

Q ss_pred             HHHHHHHHHhhc---------------CCChHhhhhhcccc-HhHHHHHHHHHHHH-HHhhcccccCCch--hHHHHHH
Q psy13113         17 VKLLAVLRFYAT---------------GNFQIDSEDYHDIS-QSTICRLVAKVSEE-LAKCHQQWIHFPE--DLQTAKN   76 (286)
Q Consensus        17 ~~l~~~L~~L~~---------------~~~~~~l~~~Fgvs-~stv~~~~~~v~~~-l~~~~~~~i~~P~--~~~~~~~   76 (286)
                      -+|+.+|..|+.               ..+++++|...|+| +.||+++++++... +.+.....|..++  .+++++.
T Consensus         4 G~va~~Ll~La~~~G~~~~~g~~i~~~~lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~~~~~i~I~D~~~L~~~A~   82 (100)
T d2bgca1           4 GSICSQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAP   82 (100)
T ss_dssp             HHHHHHHHHHHHHHEEEETTEEEECCSCCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEEETTEEEESCHHHHHHHCH
T ss_pred             cHHHHHHHHHHHHhCCCCCCCeEEeccccCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEEcCCEEEEeCHHHHHHHhc
Confidence            356777777772               25789999999997 89999999988765 4443333333333  4444443

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=80.86  E-value=1  Score=26.91  Aligned_cols=27  Identities=15%  Similarity=0.148  Sum_probs=23.2

Q ss_pred             CChHhhhhhccccHhHHHHHHHHHHHH
Q psy13113         30 NFQIDSEDYHDISQSTICRLVAKVSEE   56 (286)
Q Consensus        30 ~~~~~l~~~Fgvs~stv~~~~~~v~~~   56 (286)
                      .++.++|...|+|++||.+-+++..+.
T Consensus        18 ~s~~~lA~~~gls~~~v~~Ri~~L~~~   44 (60)
T d1i1ga1          18 TPFTEIAKKLGISETAVRKRVKALEEK   44 (60)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            499999999999999999988766543

>d1j9ia_ a.6.1.5 (A:) Terminase gpNU1 subunit domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: Terminase gpNU1 subunit domain
domain: Terminase gpNU1 subunit domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=80.85  E-value=0.23  Score=30.79  Aligned_cols=21  Identities=19%  Similarity=0.085  Sum_probs=17.7

Q ss_pred             hHhhhhhccccHhHHHHHHHH
Q psy13113         32 QIDSEDYHDISQSTICRLVAK   52 (286)
Q Consensus        32 ~~~l~~~Fgvs~stv~~~~~~   52 (286)
                      -.++|..||||.+|+..|+.+
T Consensus         5 k~~lA~iFGVS~~TI~~W~~~   25 (68)
T d1j9ia_           5 KKQLADIFGASIRTIQNWQEQ   25 (68)
T ss_dssp             HHHHHHHTTCCHHHHHHHTTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHC
Confidence            467999999999999987643

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=80.85  E-value=1.2  Score=31.52  Aligned_cols=36  Identities=8%  Similarity=0.125  Sum_probs=26.8

Q ss_pred             HHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         19 LLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        19 l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ++..|.....+.+..+|+..+|++++|++++++...
T Consensus        39 vL~~L~~~~g~~t~~~La~~~~~~~~~vs~~i~~L~   74 (145)
T d2hr3a1          39 VLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELE   74 (145)
T ss_dssp             HHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            334444333346899999999999999999887554

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=80.17  E-value=1.3  Score=31.18  Aligned_cols=44  Identities=14%  Similarity=0.119  Sum_probs=30.8

Q ss_pred             CCCCHHH-HHHHHHHHhhcCCChHhhhhhccccHhHHHHHHHHHH
Q psy13113         11 VIHSPVV-KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS   54 (286)
Q Consensus        11 ~~~~~~~-~l~~~L~~L~~~~~~~~l~~~Fgvs~stv~~~~~~v~   54 (286)
                      ..++..+ .++..|.....+.+..+++..++++++++++++++..
T Consensus        27 ~glt~~~~~~L~~l~~~~~~~t~~~la~~l~i~~~~vs~~l~~L~   71 (140)
T d3deua1          27 LELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLE   71 (140)
T ss_dssp             TTCCHHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHcCCCccHHHHHHHHCCCHhHHHHHHHHHH
Confidence            3455554 3444444444457999999999999999999887554