Psyllid ID: psy16970

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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-------
Protein Sequence
MRIASGASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELSIRNQRARSRKVENVVLKPVLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPSLKMLGVSPQYL
Secondary Structure (PSIPRED)
ccccccccccccEEEEEEEEcccHHHHHHHHHHHHHHccEEcHHHHHHHccccccccccccccccccccccccccccccEEEEcccccEEEEEEEcccccccccEEEEEccccccccEEEEEcccccccccEEccccccccccEEccEEEEEccEEEEccEEEccccccEEEEEEcccccccccEEEccccccccccccccccEEEEEccccccEEEEcEEEEEEccccccEEEEEccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEccccccccHHHHHHHHHcHHHHHHHHHHHHHHHccEEEccccEEEEEcccccccccccccccccHHHHHHHHHccccEEEEccccEEEEEEccHccccccccEEEEEEcEEEccccEEcccccccccccEcccccccccccccEEEEEEccEEEEEccEEccccccEEEEEccccccccccEEcccccccccccccccccEEEEEcccccEEEEEEEEEEEEEEEEccccEEEccccccccccHHHcccccccc
Coil and Loop (DISEMBL)
mriasgasmndrFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIrlnennltakrlhrapelsirnqRARSRKVENVVLKPVLGQIYIYIYHMhwtpaqqanvlfsdeprvnfgdvripkgfdfprpqkigqlagvhgvssdpivIVDAQtllvpnfsydgeapdakfwvgtgphpspqgirvpdengkeeplrrynrKTIVltlpgeltvfeighfgvwceaftvdfghiqipanvnmppslkmlgvspqyl
Flexible Loop (DISEMBL)
mriasgasmndrfiVSQVLRNCFATALEVRQELQDVrkvhlnegtvrirlnennltakrlhrapelsirnqrarsrkvenvvlkPVLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGphpspqgirvpdengkeeplrrynrKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPanvnmppslkmlgvspqyl
Low Complexity Region (SEG)
MRIASGASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELSIRNQRARSRKVENVVLKPVLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPSLKMLGVSPQYL
Disordered region (IsUnstruct)
***********RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA*******************KVENVVLKPVLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVG***********************RYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVN***************
Disordered Region (DISOPRED)
************FIVSQVLRNCFATALEVRQELQDVRKVHLNE********************************RKVENVVLKPVLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPS****************RRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPSLKM********
Disordered Region (DISEMBL)
********MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELSIRNQRARSRKVENVVLKPVLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPSLKMLGVSPQYL
Disordered Region (DISPRO)
********MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELSIRNQRARSRKVENVVLKPVLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPSLKMLGV*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRIASGASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELSIRNQRARSRKVENVVLKPVLGQIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPSLKMLGVSPQYL
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	257	2.2.26 [Sep-21-2011]
Q9GPJ1	1503	Protein Skeletor, isoform	no	N/A	0.540	0.092	0.763	3e-64
Q9VGY6	784	Protein Skeletor, isoform	no	N/A	0.540	0.177	0.763	3e-64

>sp|Q9GPJ1|SKEL2_DROME Protein Skeletor, isoforms D/E OS=Drosophila melanogaster GN=Skeletor PE=1 SV=3

 Score =  245 bits (625), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 113/148 (76%), Positives = 127/148 (85%)

Query: 108 LFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEA 167
           ++ DE  VNFGDV IP   DFPRPQKI  L GVHGVSSD IVIVDAQTLLVPNFSYDGEA
Sbjct: 128 VWCDEFAVNFGDVSIPPNLDFPRPQKISALRGVHGVSSDNIVIVDAQTLLVPNFSYDGEA 187

Query: 168 PDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEA 227
           PDAKFWVG G  P+  G+R+PDENGKE PLRRY RKTIVLTLP +LT+F+IGHFGVWCEA
Sbjct: 188 PDAKFWVGRGQRPTSDGLRIPDENGKENPLRRYERKTIVLTLPEDLTIFDIGHFGVWCEA 247

Query: 228 FTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           FTVDFGH+++P  +N+PPSLKMLG+SPQ
Sbjct: 248 FTVDFGHVRLPEGLNVPPSLKMLGISPQ 275

Provides structural support to stabilize and organize the microtubule spindle during mitosis (within embryonic somatic cells) and meiosis (within spermatocytes). The role in mitosis regulation depends on the Ran pathway.
Drosophila melanogaster (taxid: 7227)

>sp|Q9VGY6|SKEL1_DROME Protein Skeletor, isoforms B/C OS=Drosophila melanogaster GN=Skeletor PE=1 SV=2

 Score =  244 bits (624), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 113/148 (76%), Positives = 127/148 (85%)

Query: 108 LFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEA 167
           ++ DE  VNFGDV IP   DFPRPQKI  L GVHGVSSD IVIVDAQTLLVPNFSYDGEA
Sbjct: 128 VWCDEFAVNFGDVSIPPNLDFPRPQKISALRGVHGVSSDNIVIVDAQTLLVPNFSYDGEA 187

Query: 168 PDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEA 227
           PDAKFWVG G  P+  G+R+PDENGKE PLRRY RKTIVLTLP +LT+F+IGHFGVWCEA
Sbjct: 188 PDAKFWVGRGQRPTSDGLRIPDENGKENPLRRYERKTIVLTLPEDLTIFDIGHFGVWCEA 247

Query: 228 FTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           FTVDFGH+++P  +N+PPSLKMLG+SPQ
Sbjct: 248 FTVDFGHVRLPEGLNVPPSLKMLGISPQ 275

Provides structural support to stabilize and organize the microtubule spindle during mitosis (within embryonic somatic cells) and meiosis (within spermatocytes). The role in mitosis regulation depends on the Ran pathway.

Drosophila melanogaster (taxid: 7227)

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	257
270013011	1351	hypothetical protein TcasGA2_TC010675 [T	0.575	0.109	0.817	3e-69
189241000	1205	PREDICTED: similar to AGAP003513-PA [Tri	0.575	0.122	0.817	3e-69
340725449	1320	PREDICTED: DOMON domain-containing prote	0.579	0.112	0.791	2e-68
350415097	1320	PREDICTED: DOMON domain-containing prote	0.579	0.112	0.791	2e-68
383858511	1543	PREDICTED: uncharacterized protein LOC10	0.579	0.096	0.785	6e-68
307176630	1406	DOMON domain-containing protein CG14681	0.575	0.105	0.770	1e-67
328783620	866	PREDICTED: DOMON domain-containing prote	0.579	0.172	0.778	5e-67
380024195	1387	PREDICTED: LOW QUALITY PROTEIN: protein	0.579	0.107	0.771	2e-66
332021656	1494	DOMON domain-containing protein [Acromyr	0.568	0.097	0.777	2e-66
242009471	894	conserved hypothetical protein [Pediculu	0.568	0.163	0.790	6e-66

>gi|270013011|gb|EFA09459.1| hypothetical protein TcasGA2_TC010675 [Tribolium castaneum]

 Score =  267 bits (682), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 121/148 (81%), Positives = 136/148 (91%)

Query: 108 LFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEA 167
           ++ +E  VNFGDV+IP+GFD+P+PQKI  L GVH +SSDPIVIVDAQTLLVPN SYDGEA
Sbjct: 116 VWCEEFEVNFGDVKIPRGFDYPKPQKIEPLKGVHAISSDPIVIVDAQTLLVPNLSYDGEA 175

Query: 168 PDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEA 227
           PDAKFWVG GP PSPQGIRVPDENGK EPLRRY+RKT+VLTLPG+LTVF+IGHFG+WCEA
Sbjct: 176 PDAKFWVGRGPKPSPQGIRVPDENGKMEPLRRYDRKTVVLTLPGDLTVFDIGHFGIWCEA 235

Query: 228 FTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           FTVDFGH+QIP NVN+PPSLKMLGVSPQ
Sbjct: 236 FTVDFGHVQIPQNVNVPPSLKMLGVSPQ 263

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189241000|ref|XP_968712.2| PREDICTED: similar to AGAP003513-PA [Tribolium castaneum]

 Score =  267 bits (682), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 121/148 (81%), Positives = 136/148 (91%)

Query: 108 LFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEA 167
           ++ +E  VNFGDV+IP+GFD+P+PQKI  L GVH +SSDPIVIVDAQTLLVPN SYDGEA
Sbjct: 116 VWCEEFEVNFGDVKIPRGFDYPKPQKIEPLKGVHAISSDPIVIVDAQTLLVPNLSYDGEA 175

Query: 168 PDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEA 227
           PDAKFWVG GP PSPQGIRVPDENGK EPLRRY+RKT+VLTLPG+LTVF+IGHFG+WCEA
Sbjct: 176 PDAKFWVGRGPKPSPQGIRVPDENGKMEPLRRYDRKTVVLTLPGDLTVFDIGHFGIWCEA 235

Query: 228 FTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           FTVDFGH+QIP NVN+PPSLKMLGVSPQ
Sbjct: 236 FTVDFGHVQIPQNVNVPPSLKMLGVSPQ 263

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340725449|ref|XP_003401082.1| PREDICTED: DOMON domain-containing protein CG14681-like [Bombus terrestris]

 Score =  265 bits (676), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 118/149 (79%), Positives = 136/149 (91%)

Query: 107 VLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGE 166
            ++ DE  VNFGDVRIP+GFD+P+PQK+  L GVHGVSS+PIV+VDAQTLL+P+FSYDGE
Sbjct: 128 AVWCDEFSVNFGDVRIPRGFDYPKPQKLAALNGVHGVSSEPIVVVDAQTLLIPSFSYDGE 187

Query: 167 APDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCE 226
           APDAKFWVG GP PSPQGIRVPDENGKE+PLRRY+RK IVLTLPG+LT+ +IGHFGVWCE
Sbjct: 188 APDAKFWVGAGPSPSPQGIRVPDENGKEQPLRRYDRKAIVLTLPGDLTIHQIGHFGVWCE 247

Query: 227 AFTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           AFTVDFGH+QIP  +N+PPSLKMLGVSPQ
Sbjct: 248 AFTVDFGHVQIPQGLNVPPSLKMLGVSPQ 276

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350415097|ref|XP_003490532.1| PREDICTED: DOMON domain-containing protein CG14681-like [Bombus impatiens]

 Score =  265 bits (676), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 118/149 (79%), Positives = 136/149 (91%)

Query: 107 VLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGE 166
            ++ DE  VNFGDVRIP+GFD+P+PQK+  L GVHGVSS+PIV+VDAQTLL+P+FSYDGE
Sbjct: 128 AVWCDEFSVNFGDVRIPRGFDYPKPQKLAALNGVHGVSSEPIVVVDAQTLLIPSFSYDGE 187

Query: 167 APDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCE 226
           APDAKFWVG GP PSPQGIRVPDENGKE+PLRRY+RK IVLTLPG+LT+ +IGHFGVWCE
Sbjct: 188 APDAKFWVGAGPSPSPQGIRVPDENGKEQPLRRYDRKAIVLTLPGDLTIHQIGHFGVWCE 247

Query: 227 AFTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           AFTVDFGH+QIP  +N+PPSLKMLGVSPQ
Sbjct: 248 AFTVDFGHVQIPQGLNVPPSLKMLGVSPQ 276

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858511|ref|XP_003704744.1| PREDICTED: uncharacterized protein LOC100877328 [Megachile rotundata]

 Score =  263 bits (671), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 117/149 (78%), Positives = 136/149 (91%)

Query: 107 VLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGE 166
            ++ DE  VNFGDVRIP+GFD+P+PQK+  L+GVHGVSS+PIV+VDAQTLL+PNFSYDGE
Sbjct: 191 AVWCDEYAVNFGDVRIPRGFDYPKPQKLAALSGVHGVSSEPIVVVDAQTLLIPNFSYDGE 250

Query: 167 APDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCE 226
           APDAKFWVG GP PSPQGIR+PDENGK  PLRRY+RKTIVLTLP +LT+ +IGHFGVWCE
Sbjct: 251 APDAKFWVGAGPTPSPQGIRIPDENGKVVPLRRYDRKTIVLTLPSDLTIHQIGHFGVWCE 310

Query: 227 AFTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           AFTVDFGH+QIP ++N+PPSLKMLGVSPQ
Sbjct: 311 AFTVDFGHVQIPQSLNVPPSLKMLGVSPQ 339

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307176630|gb|EFN66098.1| DOMON domain-containing protein CG14681 [Camponotus floridanus]

 Score =  262 bits (669), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 114/148 (77%), Positives = 136/148 (91%)

Query: 108 LFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEA 167
           ++ DE  VNFGDVRIP+GFD+P+PQK+  L+G+HGV+S+P+VIVDAQTLL+P+FSYDGEA
Sbjct: 234 VWCDEFSVNFGDVRIPRGFDYPKPQKLKSLSGIHGVNSEPVVIVDAQTLLIPSFSYDGEA 293

Query: 168 PDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEA 227
           PDAKFW+GTGP PS QGIR+PDENGKE+PLRRY+RKTIVLTLPG+LTV + GHFGVWCEA
Sbjct: 294 PDAKFWIGTGPTPSSQGIRIPDENGKEQPLRRYDRKTIVLTLPGDLTVHQFGHFGVWCEA 353

Query: 228 FTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           F VDFGH+QIP  +N+PPSLKMLGVSPQ
Sbjct: 354 FAVDFGHVQIPQGLNIPPSLKMLGVSPQ 381

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328783620|ref|XP_003250319.1| PREDICTED: DOMON domain-containing protein CG14681-like [Apis mellifera]

 Score =  259 bits (663), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 116/149 (77%), Positives = 135/149 (90%)

Query: 107 VLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGE 166
            ++ DE  VNFGDVRIP+GFD+P+PQK+  L GVHGVSS+PIV+VDAQTLL+P+FSYDGE
Sbjct: 128 AVWCDEFSVNFGDVRIPRGFDYPKPQKLAALNGVHGVSSEPIVVVDAQTLLIPSFSYDGE 187

Query: 167 APDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCE 226
           APDAKFWVG GP PSPQGIRVPDENGKE+PLRRY+RK IVLTLPG++T+ +IGHFGVWCE
Sbjct: 188 APDAKFWVGAGPTPSPQGIRVPDENGKEQPLRRYDRKAIVLTLPGDVTIHQIGHFGVWCE 247

Query: 227 AFTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           AF VDFGH+QIP  +N+PPSLKMLGVSPQ
Sbjct: 248 AFAVDFGHVQIPQGLNVPPSLKMLGVSPQ 276

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380024195|ref|XP_003695891.1| PREDICTED: LOW QUALITY PROTEIN: protein Skeletor, isoforms D/E-like [Apis florea]

 Score =  258 bits (658), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 115/149 (77%), Positives = 134/149 (89%)

Query: 107 VLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGE 166
            ++ DE  VNFGDVRIP+GFD+P+PQK+  L GVHGVSS+PIV+VDAQTLL+P+FSYDGE
Sbjct: 191 AVWCDEFSVNFGDVRIPRGFDYPKPQKLAALNGVHGVSSEPIVVVDAQTLLIPSFSYDGE 250

Query: 167 APDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCE 226
           APDAKFWVG G  PSPQGIRVPDENGKE+PLRRY+RK IVLTLPG++T+ +IGHFGVWCE
Sbjct: 251 APDAKFWVGAGATPSPQGIRVPDENGKEQPLRRYDRKAIVLTLPGDVTIHQIGHFGVWCE 310

Query: 227 AFTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           AF VDFGH+QIP  +N+PPSLKMLGVSPQ
Sbjct: 311 AFAVDFGHVQIPQGLNVPPSLKMLGVSPQ 339

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332021656|gb|EGI62015.1| DOMON domain-containing protein [Acromyrmex echinatior]

 Score =  258 bits (658), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 115/148 (77%), Positives = 134/148 (90%)

Query: 108 LFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEA 167
           ++ DE  VNFGDVRIP+GFD+P+PQK+  L+G+HGVSS+PIVIVDAQTLL+P FSYDGEA
Sbjct: 173 VWCDEFSVNFGDVRIPRGFDYPKPQKLKALSGIHGVSSEPIVIVDAQTLLIPRFSYDGEA 232

Query: 168 PDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEA 227
           PDAKFWVG G  PS QGIRVPDENGKE+PLRRY+RKTIVLTLP +LTV ++GHFGVWCEA
Sbjct: 233 PDAKFWVGAGSTPSSQGIRVPDENGKEQPLRRYDRKTIVLTLPADLTVHQLGHFGVWCEA 292

Query: 228 FTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           F VDFGH+QIP ++N+PPSLKMLGVSPQ
Sbjct: 293 FAVDFGHVQIPHSLNIPPSLKMLGVSPQ 320

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242009471|ref|XP_002425509.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212509364|gb|EEB12771.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  256 bits (654), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 117/148 (79%), Positives = 133/148 (89%)

Query: 108 LFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEA 167
           ++ DE  VNFGDV+I +  DFP+PQKI  L GVHGVSS+PIVIVDAQTLL+PNFSYDGEA
Sbjct: 128 VWCDEFSVNFGDVKISRSLDFPKPQKISGLNGVHGVSSEPIVIVDAQTLLIPNFSYDGEA 187

Query: 168 PDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEA 227
           PDAKFWVG G  P+PQGIR+PDENGKE PLRRY+RKTIVLTLPG+LT+F+IGHFGVWCEA
Sbjct: 188 PDAKFWVGPGLKPTPQGIRIPDENGKEVPLRRYDRKTIVLTLPGDLTIFDIGHFGVWCEA 247

Query: 228 FTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
           FTVDFGH+QIP  +N+PPSLKMLGVSPQ
Sbjct: 248 FTVDFGHVQIPKGLNIPPSLKMLGVSPQ 275

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

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	257
FB|FBgn0262717	1503	Skeletor "Skeletor" [Drosophil	0.575	0.098	0.763	6.7e-60
FB|FBgn0001321	689	knk "knickkopf" [Drosophila me	0.513	0.191	0.428	2.1e-25
WB|WBGene00020921	511	W01C8.5 [Caenorhabditis elegan	0.610	0.307	0.254	5e-09
UNIPROTKB|Q48AN7	309	CPS_0108 "Putative uncharacter	0.357	0.297	0.302	0.00029
TIGR_CMR|CPS_0108	309	CPS_0108 "hypothetical protein	0.357	0.297	0.302	0.00029

FB|FBgn0262717 Skeletor "Skeletor" [Drosophila melanogaster (taxid:7227)]

 Score = 626 (225.4 bits), Expect = 6.7e-60, P = 6.7e-60
 Identities = 113/148 (76%), Positives = 127/148 (85%)

Query:   108 LFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGEA 167
             ++ DE  VNFGDV IP   DFPRPQKI  L GVHGVSSD IVIVDAQTLLVPNFSYDGEA
Sbjct:   128 VWCDEFAVNFGDVSIPPNLDFPRPQKISALRGVHGVSSDNIVIVDAQTLLVPNFSYDGEA 187

Query:   168 PDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEA 227
             PDAKFWVG G  P+  G+R+PDENGKE PLRRY RKTIVLTLP +LT+F+IGHFGVWCEA
Sbjct:   188 PDAKFWVGRGQRPTSDGLRIPDENGKENPLRRYERKTIVLTLPEDLTIFDIGHFGVWCEA 247

Query:   228 FTVDFGHIQIPANVNMPPSLKMLGVSPQ 255
             FTVDFGH+++P  +N+PPSLKMLG+SPQ
Sbjct:   248 FTVDFGHVRLPEGLNVPPSLKMLGISPQ 275

GO:0016363 "nuclear matrix" evidence=IDA

GO:0005694 "chromosome" evidence=IDA;NAS

GO:0005652 "nuclear lamina" evidence=IDA

GO:0005198 "structural molecule activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005700 "polytene chromosome" evidence=IDA

GO:0005819 "spindle" evidence=IDA

GO:0006997 "nucleus organization" evidence=NAS

GO:0051225 "spindle assembly" evidence=IDA

GO:0006584 "catecholamine metabolic process" evidence=TAS

GO:0004500 "dopamine beta-monooxygenase activity" evidence=TAS

FB|FBgn0001321 knk "knickkopf" [Drosophila melanogaster (taxid:7227)]

 Score = 297 (109.6 bits), Expect = 2.1e-25, P = 2.1e-25
 Identities = 57/133 (42%), Positives = 84/133 (63%)

Query:   116 NFGDVRIPKGFDFPRPQKIGQLAG-VHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWV 174
             NFGDV IP+ FD P  Q  G  +   H VSS  + I+D++T+ + +F+YDG      FW 
Sbjct:   143 NFGDVYIPEEFDPPMSQLGGTFSKRSHNVSSSSVEILDSKTIRIKDFTYDGRGKRTFFWT 202

Query:   175 GTGPHPSPQGIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGH 234
             G GP PS +G ++PDE G  +P+R+YN++TI L LPG+ T+F+I    V+  A   ++GH
Sbjct:   203 GVGPQPSSRGSKLPDERGYLDPIRQYNKETIELELPGDKTIFDIDWISVYDVADNENYGH 262

Query:   235 IQIPANVNMPPSL 247
             +     +N+PPSL
Sbjct:   263 VLFNDKLNVPPSL 275

GO:0007362 "terminal region determination" evidence=IGI

GO:0008293 "torso signaling pathway" evidence=IGI

GO:0035151 "regulation of tube size, open tracheal system" evidence=IMP

GO:0007424 "open tracheal system development" evidence=IMP

GO:0008362 "chitin-based embryonic cuticle biosynthetic process" evidence=IMP

GO:0035158 "regulation of tube diameter, open tracheal system" evidence=IMP

GO:0006031 "chitin biosynthetic process" evidence=IMP

GO:0035152 "regulation of tube architecture, open tracheal system" evidence=IMP

GO:0006035 "cuticle chitin biosynthetic process" evidence=IMP

GO:0001838 "embryonic epithelial tube formation" evidence=IMP

GO:0060439 "trachea morphogenesis" evidence=IMP

WB|WBGene00020921 W01C8.5 [Caenorhabditis elegans (taxid:6239)]

 Score = 158 (60.7 bits), Expect = 5.0e-09, P = 5.0e-09
 Identities = 43/169 (25%), Positives = 82/169 (48%)

Query:    89 QIYIYIYHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIG-QLAGV-HGVSSD 146
             ++ +++   H     ++  ++S +   +   V  P+    P+  K+  + +G  + + S 
Sbjct:   106 RVVVHVPEKHRIDEFKSFSIYSFKTDKSMASVVFPENVKIPKSVKLSTEFSGKRYQLRSG 165

Query:   147 PIVIVDAQTLLVPNFSYDG-EAPDAKFWVGTGPHPS-PQGIRVP----DENGKEEPLRRY 200
             P+ ++D +T+ V  F+++G +AP   F+ G G   S   G++V     DE    E    Y
Sbjct:   166 PLYVIDRRTIKVYGFTFEGNKAPKTYFYAGRGASVSYSSGVKVAIRGKDEKEISEISENY 225

Query:   201 NR-KTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPAN---VNMPP 245
                K I+L LP    +F I    V+C  + V+FG + +P +   VN+PP
Sbjct:   226 RGGKDIILELPENYDIFHIDWISVYCYKYRVNFGSVLVPTDDTLVNLPP 274

GO:0040010 "positive regulation of growth rate" evidence=IMP

UNIPROTKB|Q48AN7 CPS_0108 "Putative uncharacterized protein" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 114 (45.2 bits), Expect = 0.00029, P = 0.00029
 Identities = 29/96 (30%), Positives = 44/96 (45%)

Query:   141 HGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRY 200
             H VS    +I D  T+ +  FSYDG  PD  F+ G   H        P   G++   + Y
Sbjct:   215 HNVSGKATIIDDC-TIEISQFSYDGGGPDVYFY-GAIDHEYTSVDAFP--MGQKLNGKIY 270

Query:   201 NRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQ 236
             N   I + LP   ++ ++    VWC  F  +FG ++
Sbjct:   271 NNARIFIKLPQNKSLDDLNGLSVWCTEFEANFGQVE 306

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|CPS_0108 CPS_0108 "hypothetical protein" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 114 (45.2 bits), Expect = 0.00029, P = 0.00029
 Identities = 29/96 (30%), Positives = 44/96 (45%)

Query:   141 HGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQGIRVPDENGKEEPLRRY 200
             H VS    +I D  T+ +  FSYDG  PD  F+ G   H        P   G++   + Y
Sbjct:   215 HNVSGKATIIDDC-TIEISQFSYDGGGPDVYFY-GAIDHEYTSVDAFP--MGQKLNGKIY 270

Query:   201 NRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQ 236
             N   I + LP   ++ ++    VWC  F  +FG ++
Sbjct:   271 NNARIFIKLPQNKSLDDLNGLSVWCTEFEANFGQVE 306


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.139   0.423    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      257       257   0.00086  114 3  11 22  0.44    33
                                                     32  0.48    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  5
  No. of states in DFA:  593 (63 KB)
  Total size of DFA:  190 KB (2109 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.43u 0.07s 22.50t   Elapsed:  00:00:09
  Total cpu time:  22.44u 0.07s 22.51t   Elapsed:  00:00:09
  Start:  Thu Aug 15 13:35:54 2013   End:  Thu Aug 15 13:36:03 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	257
smart00686	108	smart00686, DM13, Domain present in fly proteins (	1e-48
pfam10517	107	pfam10517, DM13, Electron transfer DM13	6e-28
pfam01498	72	pfam01498, HTH_Tnp_Tc3_2, Transposase	0.003

>gnl|CDD|128929 smart00686, DM13, Domain present in fly proteins (CG14681, CG12492, CG6217), worm H06A10

 Score =  155 bits (394), Expect = 1e-48
 Identities = 59/107 (55%), Positives = 72/107 (67%), Gaps = 1/107 (0%)

Query: 139 GVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQ-GIRVPDENGKEEPL 197
             HGVSSDP+ IVDA+TL +PNFSYDG  PDA FWVG G  P  + G +VPDE G   PL
Sbjct: 2   LQHGVSSDPVEIVDAKTLRIPNFSYDGSGPDAYFWVGAGSRPDNEGGKKVPDEYGYCNPL 61

Query: 198 RRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMP 244
           RRY+ + IVL LP  LT+ +I  F VWC     +FGH+  P N+N+P
Sbjct: 62  RRYHNEDIVLRLPESLTIDDIKWFSVWCLKTAHNFGHVLFPENLNIP 108

1 and Arabidopsis thaliana MBG8.9. Length = 108

>gnl|CDD|220794 pfam10517, DM13, Electron transfer DM13

 Score =  102 bits (257), Expect = 6e-28
 Identities = 35/109 (32%), Positives = 54/109 (49%), Gaps = 5/109 (4%)

Query: 132 QKIGQLAGVHGVSSDPIVIVDAQTLLVPNFSYDGE-APDAKFWVGTGPHPSPQG-IRVPD 189
           +  G L+G H  S   + IVD +TLLV  F +     PD K ++G G  P+ +G  R  D
Sbjct: 2   EFSGDLSGSHWTSGT-VTIVDGKTLLVLEFDFAPSGGPDYKVYLGPGFVPTEEGFKRPKD 60

Query: 190 ENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIP 238
           E  +  PL+ +     +  LP  + + +     VWCE F+V FG  ++ 
Sbjct: 61  EYVELGPLKTFGD--QIYELPAGVDIDDYTSVSVWCEKFSVFFGSAKLR 107

The DM13 domain is a component of a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins. It contains a nearly absolutely conserved cysteine, which could be involved in a redox reaction, either as a naked thiol group or through binding a prosthetic group like heme. Length = 107

>gnl|CDD|216533 pfam01498, HTH_Tnp_Tc3_2, Transposase

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 22/64 (34%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELSIRN 70
          DR I+  V  N   T  ++  ELQ++ K  ++  T+R RL++  L A++  + P LS +N
Sbjct: 1  DRRILRLVRENPRITLRDLANELQEIGKS-VSRSTIRRRLHKAGLKARKPRKKPLLSAKN 59

Query: 71 QRAR 74
          ++AR
Sbjct: 60 KKAR 63

Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in. Tc3 is a member of the Tc1/mariner family of transposable elements. Length = 72

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	257
smart00686	108	DM13 Domain present in fly proteins (CG14681, CG12	100.0
KOG4731|consensus	512		99.96
PF10517	108	DM13: Electron transfer DM13; InterPro: IPR019545	99.94
KOG4731|consensus	512		99.94
PF01498	72	HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Tr	99.62
PF13592	60	HTH_33: Winged helix-turn helix	96.25
PF13551	112	HTH_29: Winged helix-turn helix	94.96
cd00131	128	PAX Paired Box domain	94.6
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	94.36
PF13565	77	HTH_32: Homeodomain-like domain	94.27
PF13276	60	HTH_21: HTH-like domain	93.97
smart00351	125	PAX Paired Box domain.	91.68
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	91.65
TIGR01529	146	argR_whole arginine repressor. This model includes	91.51
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	91.34
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	90.75
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	90.48
PRK11169	164	leucine-responsive transcriptional regulator; Prov	90.17
PF01316	70	Arg_repressor: Arginine repressor, DNA binding dom	89.14
PRK00441	149	argR arginine repressor; Provisional	87.64
COG3415	138	Transposase and inactivated derivatives [DNA repli	87.11
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	86.97
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	86.86
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	86.5
PRK03341	168	arginine repressor; Provisional	86.29
PRK05066	156	arginine repressor; Provisional	86.25
PHA02517	277	putative transposase OrfB; Reviewed	85.75
PRK04280	148	arginine repressor; Provisional	85.31
COG1438	150	ArgR Arginine repressor [Transcription]	84.92
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	84.3
PF07592	311	DDE_Tnp_ISAZ013: Rhodopirellula transposase DDE do	83.49
PRK09462	148	fur ferric uptake regulator; Provisional	81.71
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	81.65

>smart00686 DM13 Domain present in fly proteins (CG14681, CG12492, CG6217), worm H06A10

Probab=100.00  E-value=3.3e-41  Score=270.35  Aligned_cols=106  Identities=56%  Similarity=1.021  Sum_probs=102.3

Q ss_pred             cccccccccEEEEeCceEEecCeeccCCCCceEEEecCCCCCCCC-CceecCCCCCCCcCccccCceEEEEcCCCceeec
Q psy16970        139 GVHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQ-GIRVPDENGKEEPLRRYNRKTIVLTLPGELTVFE  217 (257)
Q Consensus       139 ~~H~v~sg~V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~-G~~vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~d  217 (257)
                      .+||++|++|+|+|+|||+|.+|+|||+|||||||+|.++.|+.. |+++|||.|.+++|++|+||+|+|+||+++||+|
T Consensus         2 ~~h~v~g~~V~i~d~~Tl~I~~FsydG~~pD~yF~~g~~~~p~~~~G~~v~de~g~~~~l~~y~~e~ivl~LP~~~ti~d   81 (108)
T smart00686        2 LQHGVSSDPVEIVDAKTLRIPNFSYDGSGPDAYFWVGAGSRPDNEGGKKVPDEYGYCNPLRRYHNEDIVLRLPESLTIDD   81 (108)
T ss_pred             CcccccceeEEEEeCCEEEEcceeccCCCCcEEEEeccCCCCCCcCCeEcCCccCCcccccceeCCEEEEECCCCCeEec
Confidence            479998777999999999999999999999999999999999986 9999999998888999999999999999999999


Q ss_pred             cCeEEEeccccccCeeeEEcCCCCCCC
Q psy16970        218 IGHFGVWCEAFTVDFGHIQIPANVNMP  244 (257)
Q Consensus       218 i~w~SVwc~~~~~nFG~V~ip~~~~~P  244 (257)
                      |+||||||.++++|||||.||+++++|
T Consensus        82 i~w~SV~~~~~~~nFG~V~ip~~~~~p  108 (108)
T smart00686       82 IKWFSVWCLKTAHNFGHVLFPENLNIP  108 (108)
T ss_pred             CCEEEEEccccCCcceeEEccCCCCCC
Confidence            999999999999999999999999998

1 and Arabidopsis thaliana MBG8.9.

>KOG4731|consensus

Probab=99.96  E-value=3.5e-29  Score=238.98  Aligned_cols=159  Identities=37%  Similarity=0.590  Sum_probs=143.2

Q ss_pred             ccCChhhhccccccCCCccccceeEeCCCCCCCCCcccccccc-ccccccccEEEEeCceEEecCeeccCCCC-ceEEEe
Q psy16970         97 MHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKIGQLAG-VHGVSSDPIVIVDAQTLLVPNFSYDGEAP-DAKFWV  174 (257)
Q Consensus        97 ~~w~~~~w~~vvwsdEsk~~fGsVwrp~ge~~Pkpq~Ig~l~~-~H~v~sg~V~ivD~~Tl~i~~FsydG~gP-d~yfw~  174 (257)
                      +.|+..+|. .||+.++..+||+|..|.+.+.|+.+..++++. .||++|++++|+|++||+|.+|+|+|+++ +-||.+
T Consensus       117 ~t~de~kw~-sv~~l~ta~nfg~Vv~pee~d~P~~es~~~~s~~~~~v~SdnieviDarTlki~~Fsy~g~~~~~~y~~A  195 (512)
T KOG4731|consen  117 KTIDEIKWF-SVWDLPTASNFGDVVIPEESDTPKAESPPSFSNGVYGVSSDNIEVIDARTLKIPCFSYDGKYRPRWYFNA  195 (512)
T ss_pred             ceeeheeeE-EEEEccCCCcccceeccCCCCCccccCCcccccCccccccCCeeEeccceeeeccccccCccCCceEEec
Confidence            557777774 789999999999988999999999999999964 89999999999999999999999999755 555555


Q ss_pred             cCCCCCCCCCce------ecCCCCCCCcCccccCceEEEEcCCCceeeccCeEEEeccccccCeeeEEcCCCCCCCCccc
Q psy16970        175 GTGPHPSPQGIR------VPDENGKEEPLRRYNRKTIVLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPSLK  248 (257)
Q Consensus       175 g~~~~p~~~G~~------vpde~g~~~~L~~Y~~~~i~l~LP~~~ti~di~w~SVwc~~~~~nFG~V~ip~~~~~P~~~~  248 (257)
                      |.|+.|+.+|-+      .+++.|+..+|+.|+++||+|+||++.||+||.||||||..+.+|||||.+|.++++|++.+
T Consensus       196 G~G~~~s~~s~kk~ai~~~~~~~~~~~sl~~~n~k~Ivl~Lped~tIfDI~wIsV~c~ky~~dfGhv~v~~d~n~e~~~~  275 (512)
T KOG4731|consen  196 GRGDIPSSASGKKLAIMAFDDEKGYETSLRMYNAKDIVLELPEDGTIFDIDWISVYCVKYVVDFGHVLVPPDLNVEPSPP  275 (512)
T ss_pred             cccCcccccccceeeeecccccccCCchhHhhccceEEEECCCCCcEEeeceEEEEEEEEeeccceeecCCccccCcCCC
Confidence            999999987665      68999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cCCCCCCC
Q psy16970        249 MLGVSPQY  256 (257)
Q Consensus       249 ~~~~~~~~  256 (257)
                      .++.-+++
T Consensus       276 ~v~si~~s  283 (512)
T KOG4731|consen  276 YVPSINNS  283 (512)
T ss_pred             ccCccccc
Confidence            88655543

>PF10517 DM13: Electron transfer DM13; InterPro: IPR019545 This domain of unknown function is present in proteins of Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana

Probab=99.94  E-value=2.6e-27  Score=188.76  Aligned_cols=99  Identities=42%  Similarity=0.899  Sum_probs=91.1

Q ss_pred             cccccccccccEEEEeCceEEecCeeccCC-CCceEEEecCCCCCCCCCceec-CCCCCCCcCccccCceEEEEcCCCce
Q psy16970        137 LAGVHGVSSDPIVIVDAQTLLVPNFSYDGE-APDAKFWVGTGPHPSPQGIRVP-DENGKEEPLRRYNRKTIVLTLPGELT  214 (257)
Q Consensus       137 l~~~H~v~sg~V~ivD~~Tl~i~~FsydG~-gPd~yfw~g~~~~p~~~G~~vp-de~g~~~~L~~Y~~~~i~l~LP~~~t  214 (257)
                      ++..|++ +|+|+|+|+||+.+.+|+|+|. |||+|||++++..|+..|++++ ++.+...+|+.| +++++++||++++
T Consensus         7 ~~~~h~v-sG~v~i~d~~t~~i~~f~f~~~~gPD~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~LP~~~~   84 (108)
T PF10517_consen    7 LSGGHGV-SGTVTIVDGKTFLIFNFNFDGSQGPDLYFWLGKGPSPTPDGFIIPSDEYVSLGPLKSY-NGDQTYTLPAGVD   84 (108)
T ss_pred             cCCCcee-eEEEEEeCCCeEEEecccccCCCCCCEEEEEECCCCCCCcccccccccceeeeccccc-CCCEEEECCCCCC
Confidence            3446888 5899999999999999999995 8999999999988888888877 677788999999 8999999999999


Q ss_pred             eeccCeEEEeccccccCeeeEEc
Q psy16970        215 VFEIGHFGVWCEAFTVDFGHIQI  237 (257)
Q Consensus       215 i~di~w~SVwc~~~~~nFG~V~i  237 (257)
                      ++||+||||||++|+++||||.|
T Consensus        85 ~~d~~~v~IwC~~f~~~FG~a~l  107 (108)
T PF10517_consen   85 LDDYKWVSIWCEKFSVNFGHAPL  107 (108)
T ss_pred             HHHCCEEEEEehhcCceeeEEEe
Confidence            99999999999999999999987

In some proteins it is found in either one or two copies, N-terminal to the DOMON domain. Proteins with the DM13 and DOMON domains include Skeletor, which is part of a macromolecular complex that forms the spindle matrix []. The DM13 domain is also a component of a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins []. It contains a nearly absolutely conserved cysteine, which could be involved in a redox reaction, either as a naked thiol group or through binding a prosthetic group like heme [].

>KOG4731|consensus

Probab=99.94  E-value=1.1e-26  Score=221.88  Aligned_cols=117  Identities=34%  Similarity=0.612  Sum_probs=108.2

Q ss_pred             CCCcccccccc-ccccccccEEEEeCceEEecCeeccCCCCceEEEecCCCCCCCCC-ceecCCCCCCCcC-ccccCceE
Q psy16970        129 PRPQKIGQLAG-VHGVSSDPIVIVDAQTLLVPNFSYDGEAPDAKFWVGTGPHPSPQG-IRVPDENGKEEPL-RRYNRKTI  205 (257)
Q Consensus       129 Pkpq~Ig~l~~-~H~v~sg~V~ivD~~Tl~i~~FsydG~gPd~yfw~g~~~~p~~~G-~~vpde~g~~~~L-~~Y~~~~i  205 (257)
                      ..-.++|+|+. +|+++ |.|++||+|||+|.+|+|+|.+||+|||+|.+.+|+..| +..++|+|++..| ++|+|+++
T Consensus        31 y~G~~lGels~lehqVs-G~Vf~Vns~t~qI~nF~~~~~~~d~~fw~~~sn~psn~gi~~~~~e~G~t~~l~~~~~N~~~  109 (512)
T KOG4731|consen   31 YYGVYLGELSSLEHQVS-GDVFAVNSTTFQIVNFNYDGGPPDVFFWGGMSNRPSNEGIRHNDDEYGSTQSLNRTYKNKDF  109 (512)
T ss_pred             ccceeeeeccccccccc-eeEEEEeeeEEEEEEeccCCCCCceEEEeccCCCCCCccccccccccccccccceecccccE
Confidence            34567888976 78885 899999999999999999999999999999999999999 6678999999987 78999999


Q ss_pred             EEEcCCCceeeccCeEEEeccccccCeeeEEcCCCCCCCCc
Q psy16970        206 VLTLPGELTVFEIGHFGVWCEAFTVDFGHIQIPANVNMPPS  246 (257)
Q Consensus       206 ~l~LP~~~ti~di~w~SVwc~~~~~nFG~V~ip~~~~~P~~  246 (257)
                      +|+||+++||++|+|+||||..++.|||||.||.+++.|.+
T Consensus       110 ~v~lp~~~t~de~kw~sv~~l~ta~nfg~Vv~pee~d~P~~  150 (512)
T KOG4731|consen  110 TVRLPENKTIDEIKWFSVWDLPTASNFGDVVIPEESDTPKA  150 (512)
T ss_pred             EEEcCCCceeeheeeEEEEEccCCCcccceeccCCCCCccc
Confidence            99999999999999999999999999999999999999944

>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition

Probab=99.62  E-value=2.2e-16  Score=116.41  Aligned_cols=72  Identities=33%  Similarity=0.451  Sum_probs=42.5

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccCCCcchHHHHhhhhhhhccccccccchh
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELSIRNQRARSRKVENVVLKPVLGQI   90 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~p~l~~~~~~~r~~~~~~~~~~~~~~~~   90 (257)
                      +|+|++.+.+||+.|+.+|+.+|++. |..||..||+|.|++.|++++...++|+||+.|+++|++              
T Consensus         1 ~r~I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L~~~g~~~~~~~~kP~Ls~~~~~~Rl~--------------   65 (72)
T PF01498_consen    1 DRRIVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRLREAGLKKRKARKKPFLSPKHKKKRLE--------------   65 (72)
T ss_dssp             ---------------HHHHHHHT----T--S-HHHHHHHHHHT-EEEETTEEEES--HHHHHHHHH--------------
T ss_pred             CcHHHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHHHHcCccccccccCCCCCHHHHHHHHH--------------
Confidence            58899999999999999999999998 899999999999999999999999999999999999999              


Q ss_pred             hhhhhccc
Q psy16970         91 YIYIYHMH   98 (257)
Q Consensus        91 ~~a~~h~~   98 (257)
                       ||++|+|
T Consensus        66 -fA~~h~~   72 (72)
T PF01498_consen   66 -FAKEHLD   72 (72)
T ss_dssp             -HH-----
T ss_pred             -HhhhccC
Confidence             9999985

This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.

>PF13592 HTH_33: Winged helix-turn helix

Probab=96.25  E-value=0.0083  Score=42.94  Aligned_cols=43  Identities=12%  Similarity=0.007  Sum_probs=39.2

Q ss_pred             CcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccC
Q psy16970         21 NCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRA   63 (257)
Q Consensus        21 ~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~   63 (257)
                      +.+-|+.+|+..+....|+.+|.++|++.|++.|+..++++..
T Consensus         2 ~~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~r~G~s~~kp~~~   44 (60)
T PF13592_consen    2 GGRWTLKEIAAYIEEEFGVKYSPSGVYRLLKRLGFSYQKPRPR   44 (60)
T ss_pred             CCcccHHHHHHHHHHHHCCEEcHHHHHHHHHHcCCccccCCCC
Confidence            4567899999999999999999999999999999999888765

>PF13551 HTH_29: Winged helix-turn helix

Probab=94.96  E-value=0.062  Score=41.35  Aligned_cols=48  Identities=15%  Similarity=0.104  Sum_probs=39.7

Q ss_pred             CchhhHHHHHHHhhCc-----ccCHHHHHHHH-HhccCccccHHHHHHHHHhcC
Q psy16970          7 ASMNDRFIVSQVLRNC-----FATALEVRQEL-QDVRKVHLNEGTVRIRLNENN   54 (257)
Q Consensus         7 ~~~~~r~i~r~v~~~~-----~~ta~~i~~~l-~~~~g~~~s~~Tvrr~L~~~~   54 (257)
                      ++.+...|+..+.++|     ..|..+|+..| ....|+.+|.+||+|.|++.|
T Consensus        59 ~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~G  112 (112)
T PF13551_consen   59 SEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRAG  112 (112)
T ss_pred             CHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHCc
Confidence            3445567777777777     57899999987 888889999999999999986

>cd00131 PAX Paired Box domain

Probab=94.60  E-value=0.077  Score=43.65  Aligned_cols=45  Identities=16%  Similarity=-0.054  Sum_probs=36.9

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccC----ccccHHHHHHHHHh
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRK----VHLNEGTVRIRLNE   52 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g----~~~s~~Tvrr~L~~   52 (257)
                      ....+.|+..+.++|.+|+.|++++|.+.+.    +.+|.+||.|.|+.
T Consensus        78 ~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~  126 (128)
T cd00131          78 PEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN  126 (128)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence            3456778888999999999999999876531    36799999999875

>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=94.36  E-value=0.1  Score=35.02  Aligned_cols=38  Identities=32%  Similarity=0.337  Sum_probs=31.4

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ..|+.|++...+|+..+..+|.+++      .+|+.||++|+++
T Consensus         3 ~~D~~Il~~Lq~d~r~s~~~la~~l------glS~~~v~~Ri~r   40 (42)
T PF13404_consen    3 ELDRKILRLLQEDGRRSYAELAEEL------GLSESTVRRRIRR   40 (42)
T ss_dssp             HHHHHHHHHHHH-TTS-HHHHHHHH------TS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHHH------CcCHHHHHHHHHH
Confidence            4689999999999999999999987      5899999999875

...

>PF13565 HTH_32: Homeodomain-like domain

Probab=94.27  E-value=0.08  Score=38.67  Aligned_cols=43  Identities=16%  Similarity=0.097  Sum_probs=37.3

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccc--cHHHHHHHH
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHL--NEGTVRIRL   50 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~--s~~Tvrr~L   50 (257)
                      +.....|+..+..+|.-|..+|+..|....|+.+  |.+||+|.|
T Consensus        33 ~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L   77 (77)
T PF13565_consen   33 PEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL   77 (77)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence            4445788888899999999999999999888766  999999976

>PF13276 HTH_21: HTH-like domain

Probab=93.97  E-value=0.17  Score=35.76  Aligned_cols=50  Identities=18%  Similarity=0.141  Sum_probs=40.9

Q ss_pred             HHHHHHHhhC-cccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccc
Q psy16970         12 RFIVSQVLRN-CFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLH   61 (257)
Q Consensus        12 r~i~r~v~~~-~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~   61 (257)
                      ..|......+ +..-+..|..+|+..+|..+|..||+|.+++.||.++..+
T Consensus         8 ~~I~~i~~~~~~~yG~rri~~~L~~~~~~~v~~krV~RlM~~~gL~~~~rr   58 (60)
T PF13276_consen    8 ELIKEIFKESKPTYGYRRIWAELRREGGIRVSRKRVRRLMREMGLRSKRRR   58 (60)
T ss_pred             HHHHHHHHHcCCCeehhHHHHHHhccCcccccHHHHHHHHHHcCCcccCCC
Confidence            3455555555 7788899999999998899999999999999999986544

>smart00351 PAX Paired Box domain

Probab=91.68  E-value=0.29  Score=39.89  Aligned_cols=43  Identities=19%  Similarity=0.018  Sum_probs=35.8

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccc-----cHHHHHHHHH
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHL-----NEGTVRIRLN   51 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~-----s~~Tvrr~L~   51 (257)
                      .....+|+..+.++|..|+.||+++|.+. |+.+     |.+||.+.|.
T Consensus        78 ~~~~~~I~~~~~~~p~~t~~el~~~L~~~-gv~~~~~~Ps~sti~~~l~  125 (125)
T smart00351       78 PKVVKKIADYKQENPGIFAWEIRDRLLSE-GVCDKDNVPSVSSINRILR  125 (125)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHc-CCCcCCCCCChhhHHHhhC
Confidence            45567888889999999999999999864 4666     9999998873

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

Probab=91.65  E-value=0.63  Score=34.07  Aligned_cols=55  Identities=22%  Similarity=0.192  Sum_probs=38.4

Q ss_pred             HHHHHh-hCcccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCcccccccCCCcchH
Q psy16970         14 IVSQVL-RNCFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLTAKRLHRAPELSIR   69 (257)
Q Consensus        14 i~r~v~-~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~~~~~~~~p~l~~~   69 (257)
                      |.+.+. .+--+++.+|.+.|+.. |..+|+.||||+|+.   .|+..++...--.||.+
T Consensus         3 IL~~L~~~~~P~g~~~l~~~L~~~-g~~~se~avRrrLr~me~~Glt~~~g~~G~~iT~~   61 (66)
T PF08461_consen    3 ILRILAESDKPLGRKQLAEELKLR-GEELSEEAVRRRLRAMERDGLTRKVGRQGRIITEK   61 (66)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhc-ChhhhHHHHHHHHHHHHHCCCccccCCcccccCHH
Confidence            444443 34459999999999988 699999999999985   55555444444445543

>TIGR01529 argR_whole arginine repressor

Probab=91.51  E-value=0.42  Score=40.28  Aligned_cols=42  Identities=19%  Similarity=0.163  Sum_probs=37.0

Q ss_pred             HHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCc
Q psy16970         14 IVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLT   56 (257)
Q Consensus        14 i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~   56 (257)
                      |...+..++..|+.||.+.|+..+ ..+|..||+|-|++.|+-
T Consensus         7 i~~Li~~~~i~tqeeL~~~L~~~G-~~vsqaTIsRdL~elglv   48 (146)
T TIGR01529         7 IKEIITEEKISTQEELVALLKAEG-IEVTQATVSRDLRELGAV   48 (146)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHhC-CCcCHHHHHHHHHHcCCE
Confidence            555668889999999999998764 999999999999999985

This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.

>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=91.34  E-value=0.57  Score=31.35  Aligned_cols=38  Identities=24%  Similarity=0.225  Sum_probs=31.2

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ..++.|+..+..+|..|..||++.+      .+|.+||++.|++
T Consensus         3 ~~~~~Il~~l~~~~~~t~~ela~~~------~is~~tv~~~l~~   40 (48)
T PF13412_consen    3 ETQRKILNYLRENPRITQKELAEKL------GISRSTVNRYLKK   40 (48)
T ss_dssp             HHHHHHHHHHHHCTTS-HHHHHHHH------TS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHh------CCCHHHHHHHHHH
Confidence            3578899999999999999999987      4799999988875

...

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=90.75  E-value=0.48  Score=39.62  Aligned_cols=39  Identities=21%  Similarity=0.377  Sum_probs=34.9

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ...|+.|+.+..+|+..|..+|+++|      .+|+.||++|+++
T Consensus         8 D~~D~~Il~~Lq~d~R~s~~eiA~~l------glS~~tV~~Ri~r   46 (153)
T PRK11179          8 DNLDRGILEALMENARTPYAELAKQF------GVSPGTIHVRVEK   46 (153)
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence            35799999999999999999999998      5899999988765

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

Probab=90.48  E-value=0.55  Score=37.86  Aligned_cols=46  Identities=22%  Similarity=0.153  Sum_probs=39.0

Q ss_pred             hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccc
Q psy16970         10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLH   61 (257)
Q Consensus        10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~   61 (257)
                      +...|...|..+|.+|..|++..|      .||.+||.+.|++.|+..++..
T Consensus        58 d~~~L~~~v~~~pd~tl~Ela~~l------~Vs~~ti~~~Lkrlg~t~KK~~  103 (119)
T PF01710_consen   58 DRDELKALVEENPDATLRELAERL------GVSPSTIWRALKRLGITRKKKT  103 (119)
T ss_pred             cHHHHHHHHHHCCCcCHHHHHHHc------CCCHHHHHHHHHHcCchhccCc
Confidence            455688888999999999999876      3799999999999999976554

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 [].

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=90.17  E-value=0.5  Score=40.00  Aligned_cols=40  Identities=15%  Similarity=0.194  Sum_probs=35.0

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      ...|+.|+++..+|+..|..||.+++      .+|+.||++|+++.
T Consensus        13 D~~D~~IL~~Lq~d~R~s~~eiA~~l------glS~~tv~~Ri~rL   52 (164)
T PRK11169         13 DRIDRNILNELQKDGRISNVELSKRV------GLSPTPCLERVRRL   52 (164)
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHH------CcCHHHHHHHHHHH
Confidence            34699999999999999999999987      58999999887753

>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []

Probab=89.14  E-value=0.93  Score=33.88  Aligned_cols=46  Identities=13%  Similarity=0.198  Sum_probs=33.6

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      ...|...+..++..|=.||...|... |+.++..||.|-|++.|+..
T Consensus         7 ~~~I~~li~~~~i~sQ~eL~~~L~~~-Gi~vTQaTiSRDLkeL~~vK   52 (70)
T PF01316_consen    7 QELIKELISEHEISSQEELVELLEEE-GIEVTQATISRDLKELGAVK   52 (70)
T ss_dssp             HHHHHHHHHHS---SHHHHHHHHHHT-T-T--HHHHHHHHHHHT-EE
T ss_pred             HHHHHHHHHHCCcCCHHHHHHHHHHc-CCCcchhHHHHHHHHcCcEE
Confidence            34567777889999999999999997 59999999999999999764

The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....

>PRK00441 argR arginine repressor; Provisional

Probab=87.64  E-value=1.2  Score=37.65  Aligned_cols=46  Identities=20%  Similarity=0.230  Sum_probs=40.8

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      ...|.+.+.++...|-.|+.+.|+..| ..+|..||||=|++.++..
T Consensus         6 ~~~I~~ll~~~~~~~q~eL~~~L~~~G-~~vSqaTisRDl~~L~lvK   51 (149)
T PRK00441          6 HAKILEIINSKEIETQEELAEELKKMG-FDVTQATVSRDIKELKLIK   51 (149)
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHhcC-CCcCHHHHHHHHHHcCcEE
Confidence            456778888899999999999999875 9999999999999999774

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

Probab=87.11  E-value=1.6  Score=36.77  Aligned_cols=55  Identities=27%  Similarity=0.161  Sum_probs=45.5

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccCCC
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPE   65 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~p~   65 (257)
                      ...++..+.+...-|..+++..|+...|+.++.+.|++.||+.||..++++..+.
T Consensus        68 q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~~v~~~l~~~GlsykK~~~~~~  122 (138)
T COG3415          68 QLEILLERLREKDWTLKELVEELGLEFGVWYHASAVRRLLHELGLSYKKPRWTPA  122 (138)
T ss_pred             HHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHHHHHHHHHHcCCCcCCCCCCcc
Confidence            3455556656666999999999998889999999999999999999887776653

>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=86.97  E-value=1.3  Score=30.27  Aligned_cols=35  Identities=26%  Similarity=0.222  Sum_probs=25.9

Q ss_pred             HHHHHH-hhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970         13 FIVSQV-LRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus        13 ~i~r~v-~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      .|+... ..+...|+.+++++|      .||.+||++-++..
T Consensus         4 ~il~~L~~~~~~it~~eLa~~l------~vS~rTi~~~i~~L   39 (55)
T PF08279_consen    4 QILKLLLESKEPITAKELAEEL------GVSRRTIRRDIKEL   39 (55)
T ss_dssp             HHHHHHHHTTTSBEHHHHHHHC------TS-HHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCcCHHHHHHHh------CCCHHHHHHHHHHH
Confidence            344444 556669999999987      58999999988764

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 ....

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=86.86  E-value=1  Score=34.80  Aligned_cols=40  Identities=20%  Similarity=0.266  Sum_probs=34.7

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcC
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENN   54 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~   54 (257)
                      ..|+.|++.+.+++..|..+|..++      .+|+.||++++++..
T Consensus         3 ~~D~~il~~L~~~~~~~~~~la~~l------~~s~~tv~~~l~~L~   42 (108)
T smart00344        3 EIDRKILEELQKDARISLAELAKKV------GLSPSTVHNRVKRLE   42 (108)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHH------CcCHHHHHHHHHHHH
Confidence            4689999999999999999999987      589999999887643

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

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

Probab=86.50  E-value=1.6  Score=34.15  Aligned_cols=46  Identities=24%  Similarity=0.229  Sum_probs=35.1

Q ss_pred             hhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970         10 NDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT   56 (257)
Q Consensus        10 ~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~   56 (257)
                      ++..|+..+.. +...||.||.+.|+..+ ..+|..||+|.|.   +.|+-
T Consensus         2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~-~~i~~~TVYR~L~~L~~~Gli   51 (116)
T cd07153           2 QRLAILEVLLESDGHLTAEEIYERLRKKG-PSISLATVYRTLELLEEAGLV   51 (116)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHhcC-CCCCHHHHHHHHHHHHhCCCE
Confidence            45566777755 45699999999998865 7899999999765   45554

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>PRK03341 arginine repressor; Provisional

Probab=86.29  E-value=1.5  Score=37.94  Aligned_cols=46  Identities=20%  Similarity=0.226  Sum_probs=40.7

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      ...|.+.+.+++..|-.||...|+..| +.+|..||+|-|++.++..
T Consensus        17 ~~~I~~li~~~~i~tQ~eL~~~L~~~G-i~vTQaTiSRDl~eL~~~K   62 (168)
T PRK03341         17 QARIVAILSRQSVRSQAELAALLADEG-IEVTQATLSRDLDELGAVK   62 (168)
T ss_pred             HHHHHHHHHHCCCccHHHHHHHHHHcC-CcccHHHHHHHHHHhcCEe
Confidence            456778888999999999999999875 9999999999999998764

>PRK05066 arginine repressor; Provisional

Probab=86.25  E-value=1.7  Score=37.20  Aligned_cols=46  Identities=15%  Similarity=0.148  Sum_probs=40.8

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCcc-ccHHHHHHHHHhcCCcc
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVH-LNEGTVRIRLNENNLTA   57 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~-~s~~Tvrr~L~~~~l~~   57 (257)
                      +..|.+.+..++..|=.||.+.|+..| .. ++..||.|-|++.|+..
T Consensus        11 ~~~I~~iI~~~~I~tQeeL~~~L~~~G-i~~vTQATiSRDikeL~lvK   57 (156)
T PRK05066         11 VKAFKALLKEEKFGSQGEIVTALQEQG-FDNINQSKVSRMLTKFGAVR   57 (156)
T ss_pred             HHHHHHHHhhCCCCCHHHHHHHHHHCC-CCeecHHHHHHHHHHcCCEE
Confidence            356778888899999999999999985 88 99999999999999874

>PHA02517 putative transposase OrfB; Reviewed

Probab=85.75  E-value=1.6  Score=39.32  Aligned_cols=48  Identities=15%  Similarity=0.030  Sum_probs=38.7

Q ss_pred             HHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCccccc
Q psy16970         12 RFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRL   60 (257)
Q Consensus        12 r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~   60 (257)
                      ..|++...+ ++...+..|..+|+.. |..+|..||+|.|++.||.+...
T Consensus        33 ~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~gl~~~~~   81 (277)
T PHA02517         33 SEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKELGLAGVLR   81 (277)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHcCCceEec
Confidence            445555544 5788999999999876 58999999999999999986543

>PRK04280 arginine repressor; Provisional

Probab=85.31  E-value=1.9  Score=36.55  Aligned_cols=46  Identities=20%  Similarity=0.183  Sum_probs=40.9

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      ...|.+.+..++..|=.||.+.|+..| ..++..||.|-|++.|+-.
T Consensus         6 ~~~I~~iI~~~~I~tQeeL~~~L~~~G-i~vTQATiSRDikeL~lvK   51 (148)
T PRK04280          6 HIKIREIITNNEIETQDELVDRLREEG-FNVTQATVSRDIKELHLVK   51 (148)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHcC-CCeehHHHHHHHHHcCCEE
Confidence            346778888899999999999999985 9999999999999999774

>COG1438 ArgR Arginine repressor [Transcription]

Probab=84.92  E-value=1.9  Score=36.86  Aligned_cols=47  Identities=21%  Similarity=0.217  Sum_probs=41.6

Q ss_pred             hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      -...|.+.+.++...|=.||...|++.| ..++..||.|-|++.|+..
T Consensus         7 R~~~Ik~iI~~~~i~TQ~Elv~~L~~~G-i~vTQaTvSRDlkelglvK   53 (150)
T COG1438           7 RLELIKEIITEEKISTQEELVELLQEEG-IEVTQATVSRDLKELGLVK   53 (150)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHcC-CeEehHHHHHHHHHcCCEE
Confidence            3467778889999999999999999987 7799999999999999875

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

Probab=84.30  E-value=2.2  Score=30.01  Aligned_cols=36  Identities=22%  Similarity=0.239  Sum_probs=30.9

Q ss_pred             HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970         12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus        12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      ..|+..+..+...|..|+.+.+      .+|..||||=|+..
T Consensus         3 ~~Il~~l~~~~~~s~~ela~~~------~VS~~TiRRDl~~L   38 (57)
T PF08220_consen    3 QQILELLKEKGKVSVKELAEEF------GVSEMTIRRDLNKL   38 (57)
T ss_pred             HHHHHHHHHcCCEEHHHHHHHH------CcCHHHHHHHHHHH
Confidence            4678888999999999999987      58999999988753

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

>PF07592 DDE_Tnp_ISAZ013: Rhodopirellula transposase DDE domain; InterPro: IPR011518 These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces

Probab=83.49  E-value=1.3  Score=41.97  Aligned_cols=44  Identities=16%  Similarity=0.095  Sum_probs=36.7

Q ss_pred             ccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccCCCcc
Q psy16970         23 FATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELS   67 (257)
Q Consensus        23 ~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~p~l~   67 (257)
                      ..|+.+|+++|... |..+|..||++.|++.||.-+..+|.-+.+
T Consensus        24 ~~S~~~la~~L~~~-G~~vS~~tV~~lL~~lGYsLq~n~Kt~~g~   67 (311)
T PF07592_consen   24 RKSTRKLAEELRRQ-GHPVSARTVARLLNRLGYSLQANRKTKEGK   67 (311)
T ss_pred             eccHHHHHHHHHHc-CCCccHHHHHHHHHHcCcchhhhhcccCCC
Confidence            37889999999665 599999999999999999988777654443

More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK09462 fur ferric uptake regulator; Provisional

Probab=81.71  E-value=3.2  Score=34.39  Aligned_cols=44  Identities=18%  Similarity=0.170  Sum_probs=35.3

Q ss_pred             chhhHHHHHHHhhC--cccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          8 SMNDRFIVSQVLRN--CFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         8 ~~~~r~i~r~v~~~--~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ..++..|+..+...  ...||.||-+.|+..+ ..+|..||+|.|..
T Consensus        16 T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~-~~i~~aTVYR~L~~   61 (148)
T PRK09462         16 TLPRLKILEVLQEPDNHHVSAEDLYKRLIDMG-EEIGLATVYRVLNQ   61 (148)
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhC-CCCCHHHHHHHHHH
Confidence            35667777777653  4799999999998866 78999999999864

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

Probab=81.65  E-value=2.5  Score=33.47  Aligned_cols=47  Identities=21%  Similarity=0.145  Sum_probs=33.8

Q ss_pred             hhhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970          9 MNDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT   56 (257)
Q Consensus         9 ~~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~   56 (257)
                      .++..|+..+.. +...||.||.+.|+..+ ..+|..||+|.|.   +.|+-
T Consensus         8 ~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~-~~is~~TVYR~L~~L~e~Gli   58 (120)
T PF01475_consen    8 PQRLAILELLKESPEHLTAEEIYDKLRKKG-PRISLATVYRTLDLLEEAGLI   58 (120)
T ss_dssp             HHHHHHHHHHHHHSSSEEHHHHHHHHHHTT-TT--HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHhhhcc-CCcCHHHHHHHHHHHHHCCeE
Confidence            355666666644 45899999999999654 8999999999876   45544

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	257
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05

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

 Score = 48.7 bits (115), Expect = 8e-07
 Identities = 36/270 (13%), Positives = 79/270 (29%), Gaps = 80/270 (29%)

Query: 17  QVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAPELSIRNQRARSR 76
            V  + F    +  +++QD+ K  L++  +   +   +       R     +  Q     
Sbjct: 23  SVFEDAFVDNFDC-KDVQDMPKSILSKEEIDHIIMSKD-AVSGTLRLFWTLLSKQ----- 75

Query: 77  KVENVV---LKPVLGQIYIYIYH-MHWTPAQQA--NVLFSDEPRVNFGDVRIPKGFDFPR 130
             E +V   ++ VL   Y ++   +     Q +    ++ ++    + D ++   ++  R
Sbjct: 76  --EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSR 133

Query: 131 PQKIGQL-AGVHGVSSDPIVIVD-----------AQTLLVPNFSYDGEAPDAKFWVGTGP 178
            Q   +L   +  +     V++D               L  ++    +     FW+    
Sbjct: 134 LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCL--SYKVQCKMDFKIFWLNLKN 191

Query: 179 HPSP-------------------------QGIRVPDENGKEEPLRR------YNRKTIVL 207
             SP                           I++   + + E LRR      Y    +VL
Sbjct: 192 CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE-LRRLLKSKPYENCLLVL 250

Query: 208 TLPGELTVFEIGHFGVW----CEAFTVDFG 233
                          V       AF  +  
Sbjct: 251 L-------------NVQNAKAWNAF--NLS 265

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

 Score = 44.1 bits (103), Expect = 3e-05
 Identities = 26/120 (21%), Positives = 38/120 (31%), Gaps = 28/120 (23%)

Query: 28  EVRQELQDVRKVHL-----NEGTVRI-----RLNENNLTAKRLHRAPELSIRNQRARSRK 77
           +V   +  + K  L      E T+ I      L         LHR    SI +     + 
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR----SIVDHYNIPKT 458

Query: 78  VENVVLKPVLGQIYIY--I-YHMHWTPAQQANVLFSDEPRVNFGDVRIPKGFDFPRPQKI 134
            ++  L P     Y Y  I +H+     +      +    V F D      F F   QKI
Sbjct: 459 FDSDDLIPPYLDQYFYSHIGHHL--KNIEHPE-RMTLFRMV-FLD------FRFLE-QKI 507

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	257
3hot_A	345	Transposable element mariner, complete CDS; protei	99.02
1u78_A	141	TC3 transposase, transposable element TC3 transpos	98.66
2f7t_A	227	MOS1 transposase; RNAse-H like fold, DDD motif, DN	97.64
3f2k_A	226	Histone-lysine N-methyltransferase setmar; histone	97.38
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	95.25
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	93.78
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	92.45
2k27_A	159	Paired box protein PAX-8; paired domain, solution	92.2
1b4a_A	149	Arginine repressor; helix turn helix; 2.50A {Geoba	91.96
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	90.79
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	89.63
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	88.36
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	88.28
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	88.16
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	87.08
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	85.81
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	85.73
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	85.34
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	84.52
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	83.96
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	83.85
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	83.61
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	83.17
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	82.99
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	82.78
2w57_A	150	Ferric uptake regulation protein; gene regulation,	82.72
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	82.53
3lap_A	170	Arginine repressor; arginine repressor, DNA bindin	81.59
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	81.49
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	81.14
4ets_A	162	Ferric uptake regulation protein; metal binding pr	80.77
3v4g_A	180	Arginine repressor; vibrio vulnificus CMCP6, virul	80.65
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	80.43
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	80.32
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	80.22

>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A*

Probab=99.02  E-value=2.9e-10  Score=102.72  Aligned_cols=100  Identities=17%  Similarity=0.142  Sum_probs=85.8

Q ss_pred             hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcccccccCC-CcchHHHHhhhhhhhccccccccc
Q psy16970         10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTAKRLHRAP-ELSIRNQRARSRKVENVVLKPVLG   88 (257)
Q Consensus        10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~~~~~~~p-~l~~~~~~~r~~~~~~~~~~~~~~   88 (257)
                      ++..|...+..+|..|..+|+++|      .+|.+||+|.|++.|+..+..+++| .|++.++++|++            
T Consensus        73 ~~~~i~~~v~~~~~~t~~~ia~~l------~vs~~tV~r~L~~~g~~~k~~~~~~~~l~~~~~~~r~~------------  134 (345)
T 3hot_A           73 EDAELQALLDEDDAQTQKQLAEQL------EVSQQAVSNRLREMGKIQKVGRWVPHELNERQMERRKN------------  134 (345)
T ss_dssp             CHHHHHHHHHHCSCCCHHHHHHHT------TSCHHHHHHHHHHTTCEEEECCEESSCCCHHHHHHHHH------------
T ss_pred             cHHHHHHHHHhCccchHHHHHHHH------CCCHHHHHHHHHHhCCeeeccccccccCChhhhhhhHH------------
Confidence            346777788899999999999988      4899999999999999987777766 999999999999            


Q ss_pred             hhhhhhhcccCC--hhhhccccccCCCccccce-----eEeCCCCCCCC
Q psy16970         89 QIYIYIYHMHWT--PAQQANVLFSDEPRVNFGD-----VRIPKGFDFPR  130 (257)
Q Consensus        89 ~~~~a~~h~~w~--~~~w~~vvwsdEsk~~fGs-----Vwrp~ge~~Pk  130 (257)
                         ||..|+++.  .++|..++|+||+.++++.     +|.+.|+..+.
T Consensus       135 ---~~~~~l~~~~~~~~~~~Iv~~DE~~~~~~~~~~~~~w~~~g~~~~~  180 (345)
T 3hot_A          135 ---TCEILLSRYKRKSFLHRIVTGDEKWIFFVNPKRKKSYVDPGQPATS  180 (345)
T ss_dssp             ---HHHHHHHHHHHSCCGGGEEEEEEEEEESCCCCCCEEEECSSSCCCC
T ss_pred             ---HHHHHHHhhCCcchHHhhhcccceeEEecCccceeeeccCCCCCCC
Confidence               999999874  3578999999999998642     99999876543

>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=98.66  E-value=1.4e-08  Score=80.22  Aligned_cols=74  Identities=20%  Similarity=0.264  Sum_probs=34.9

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCC-cccccccCCCcchHHHHhhhhhhhccccccc
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNL-TAKRLHRAPELSIRNQRARSRKVENVVLKPV   86 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l-~~~~~~~~p~l~~~~~~~r~~~~~~~~~~~~   86 (257)
                      +.+...|++. ..+|..|+.+|..+|    |+.+|.+||+|.|++.|+ ..+++.++|.|++.|+++|++          
T Consensus        63 ~~~~~~i~~~-~~~~~~s~~~i~~~l----g~~~s~~tV~r~l~~~g~~~~~k~~~~~~l~~~~~~~R~~----------  127 (141)
T 1u78_A           63 VRDERNVIRA-ASNSCKTARDIRNEL----QLSASKRTILNVIKRSGVIVRQKLRPAPLLSADHKLKRLE----------  127 (141)
T ss_dssp             HHHHHHHHHH-HHHCCCCHHHHHHHT----TCCSCHHHHHHHHHHTC---------------------------------
T ss_pred             HHHHHHHHHH-HhCCCCCHHHHHHHH----CCCccHHHHHHHHHHCCCceeeecCCCCCCCHHHHHHHHH----------
Confidence            3455666666 667889999999988    468999999999999999 888899999999999999999          


Q ss_pred             cchhhhhhhcccCCh
Q psy16970         87 LGQIYIYIYHMHWTP  101 (257)
Q Consensus        87 ~~~~~~a~~h~~w~~  101 (257)
                           ||..|++|+.
T Consensus       128 -----~~~~~~~~~~  137 (141)
T 1u78_A          128 -----FAKNNMGTHH  137 (141)
T ss_dssp             ---------------
T ss_pred             -----HHHHHccccc
Confidence                 9999999874

>2f7t_A MOS1 transposase; RNAse-H like fold, DDD motif, DNA binding protein; 2.25A {Drosophila mauritiana}

Probab=97.64  E-value=8.1e-06  Score=70.27  Aligned_cols=50  Identities=16%  Similarity=0.137  Sum_probs=37.3

Q ss_pred             CCCcchHHHHhhhhhhhccccccccchhhhhhhcccC--ChhhhccccccCCCccccc-----eeEeCCCCC
Q psy16970         63 APELSIRNQRARSRKVENVVLKPVLGQIYIYIYHMHW--TPAQQANVLFSDEPRVNFG-----DVRIPKGFD  127 (257)
Q Consensus        63 ~p~l~~~~~~~r~~~~~~~~~~~~~~~~~~a~~h~~w--~~~~w~~vvwsdEsk~~fG-----sVwrp~ge~  127 (257)
                      .|+||++|+++|++               ||..|++|  +.++|.+++|+||+.++..     .+|.+.|+.
T Consensus         3 p~~Lt~~~k~~R~~---------------~~~~~l~~~~~~~f~~~Ivf~DE~~f~~~~~~~~~~W~~~ge~   59 (227)
T 2f7t_A            3 PHELNERQMERRKN---------------TCEILLSRYKRKSFLHRIVTGDEKWIFFVNPKRKKSYVDPGQP   59 (227)
T ss_dssp             CCCCCHHHHHHHHH---------------HHHHHHHHHHHSCCGGGEEEEEEEEEEBCCCC-----------
T ss_pred             CccCCHHHHHHHHH---------------HHHHHHhccCCcchhhheEeccCCEEEecCccccccccCCCCC
Confidence            47999999999999               99999998  6788999999999999752     289888874

>3f2k_A Histone-lysine N-methyltransferase setmar; histone-lysine N-methyltransferase setmar, SET domain and mariner transposase fusion; 1.85A {Homo sapiens} PDB: 3k9k_A 3k9j_A

Probab=97.38  E-value=2e-05  Score=68.28  Aligned_cols=75  Identities=11%  Similarity=0.062  Sum_probs=48.2

Q ss_pred             CCcchHHHHhhhhhhhccccccccchhhhhhhcccCCh--hhhccccccCCCccccce-----eEeCCCCCCCCCccccc
Q psy16970         64 PELSIRNQRARSRKVENVVLKPVLGQIYIYIYHMHWTP--AQQANVLFSDEPRVNFGD-----VRIPKGFDFPRPQKIGQ  136 (257)
Q Consensus        64 p~l~~~~~~~r~~~~~~~~~~~~~~~~~~a~~h~~w~~--~~w~~vvwsdEsk~~fGs-----Vwrp~ge~~Pkpq~Ig~  136 (257)
                      .+||++++++|++               ||..|+.+..  ++|.++||+||+.+.++.     +|++.|+..+.  .   
T Consensus         4 ~~Lt~~~k~~R~~---------------~~~~ll~~~~~~~f~~~iv~~DE~~~~~~n~~~~~~W~~~ge~~~~--~---   63 (226)
T 3f2k_A            4 HELTENQKNRRFE---------------VSSSLILRNHNEPFLDRIVTCDEKWILYDNRRRSAQWLDQEEAPKH--F---   63 (226)
T ss_dssp             CCCCHHHHHHHHH---------------HHHHHHHHHHHSCCGGGEEEEEEEEEESBCC---------------------
T ss_pred             ccCCHHHHHHHHH---------------HHHHHHhhhcccchhHhEEEeccceEEEecccceeeecCCCCCCcc--c---
Confidence            3699999999999               9999998864  789999999999997642     89888874221  1   


Q ss_pred             ccc-ccccccccEEEEeCceEEecCeeccCCCC
Q psy16970        137 LAG-VHGVSSDPIVIVDAQTLLVPNFSYDGEAP  168 (257)
Q Consensus       137 l~~-~H~v~sg~V~ivD~~Tl~i~~FsydG~gP  168 (257)
                      ... .|+   +.|+|       +.+|+++|.++
T Consensus        64 ~~~~~~~---~~vmv-------~~~~s~~G~~~   86 (226)
T 3f2k_A           64 PKPILHP---KKVMV-------TIWWSAAGLIH   86 (226)
T ss_dssp             -----CC---CEEEE-------EEEEETTEEEE
T ss_pred             cccccCC---cceEE-------EEEeecCCcEE
Confidence            112 343   34665       58999988764

>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=95.25  E-value=0.034  Score=37.84  Aligned_cols=42  Identities=21%  Similarity=0.186  Sum_probs=34.9

Q ss_pred             HHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCc
Q psy16970         14 IVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLT   56 (257)
Q Consensus        14 i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~   56 (257)
                      |...+..+...|+.||.+.|...+ ..+|..||+|-|++.|+-
T Consensus        10 i~~ll~~~~~~t~~el~~~l~~~~-~~vs~~Tv~R~L~~lg~v   51 (64)
T 2p5k_A           10 IREIITSNEIETQDELVDMLKQDG-YKVTQATVSRDIKELHLV   51 (64)
T ss_dssp             HHHHHHHSCCCSHHHHHHHHHHTT-CCCCHHHHHHHHHHHTCE
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHhC-CCcCHHHHHHHHHHcCCE
Confidence            344556688999999999998764 789999999999988765

>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=93.78  E-value=0.057  Score=40.60  Aligned_cols=45  Identities=11%  Similarity=-0.019  Sum_probs=34.4

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCc-----cccHHHHHHHHHhcC
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKV-----HLNEGTVRIRLNENN   54 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~-----~~s~~Tvrr~L~~~~   54 (257)
                      .....|.+.+..+|..|+.+|+.+|... |+     .+|.+||+|.|++.|
T Consensus        79 ~~~~~i~~~~~~~~~~s~~~i~~~l~~~-g~~~~~~~~s~~tv~r~l~~~~  128 (128)
T 1pdn_C           79 EIENRIEEYKRSSPGMFSWEIREKLIRE-GVCDRSTAPSVSAISRLVRGRD  128 (128)
T ss_dssp             THHHHHHHTTTTCTTCCHHHHHHHHHHT-SSSCSTTCCCHHHHHHHC----
T ss_pred             HHHHHHHHHHHhCcchHHHHHHHHHHHc-CCccccCCcCHHHHHHHHHhcC
Confidence            3556677777788999999999999876 56     699999999998754

>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=92.45  E-value=0.19  Score=39.62  Aligned_cols=46  Identities=15%  Similarity=0.024  Sum_probs=38.0

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhcc----CccccHHHHHHHHHhcC
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVR----KVHLNEGTVRIRLNENN   54 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~----g~~~s~~Tvrr~L~~~~   54 (257)
                      .....|.+.+..+|..|+.+|+.+|.+..    |..+|.+||+|.|++..
T Consensus        94 ~~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~~~  143 (149)
T 1k78_A           94 KVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKV  143 (149)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC-
T ss_pred             HHHHHHHHHHHhCcchhHHHHHHHHHHhcccccCCCcCHHHHHHHHHHHh
Confidence            35667888888899999999999997764    67899999999998643

>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=92.20  E-value=0.25  Score=39.51  Aligned_cols=49  Identities=12%  Similarity=-0.045  Sum_probs=39.9

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhcc----CccccHHHHHHHHHhcCCc
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVR----KVHLNEGTVRIRLNENNLT   56 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~----g~~~s~~Tvrr~L~~~~l~   56 (257)
                      ......|.+.+.++|..|+.+|..+|...+    +..+|.+||+|.|++..-.
T Consensus        86 ~~~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~~~~  138 (159)
T 2k27_A           86 PKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQ  138 (159)
T ss_dssp             TTHHHHHHHHHHHCSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHCccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHHhCC
Confidence            345677888888899999999999998655    5789999999999875433

>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A

Probab=91.96  E-value=0.25  Score=40.62  Aligned_cols=47  Identities=19%  Similarity=0.222  Sum_probs=41.3

Q ss_pred             hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      -...|...+.+++..|-.|+.+.|+..| ..+|..||+|-|++.|+..
T Consensus         6 R~~~I~~li~~~~~~tq~eL~~~L~~~G-~~VtqaTisRDL~eL~~vK   52 (149)
T 1b4a_A            6 RHIKIREIIMSNDIETQDELVDRLREAG-FNVTQATVSRDIKEMQLVK   52 (149)
T ss_dssp             HHHHHHHHHHHSCCCSHHHHHHHHHHTT-CCCCHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHHHCCCccHHHHHHHHHHcC-CCcCHHHHHHHHHHcCCeE
Confidence            3456778889999999999999999885 9999999999999988764

>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=90.79  E-value=0.2  Score=37.01  Aligned_cols=38  Identities=13%  Similarity=0.045  Sum_probs=32.6

Q ss_pred             hhhHHHHHHHhhCc---ccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          9 MNDRFIVSQVLRNC---FATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         9 ~~~r~i~r~v~~~~---~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ..++.|+..+..++   ..|+.||+++|.      +|++||+++|.+
T Consensus        10 ~~~~~IL~~L~~~~pg~~~t~~eLA~~Lg------vsr~tV~~~L~~   50 (81)
T 1qbj_A           10 DQEQRILKFLEELGEGKATTAHDLSGKLG------TPKKEINRVLYS   50 (81)
T ss_dssp             HHHHHHHHHHHHHCTTCCBCHHHHHHHHT------CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHC------cCHHHHHHHHHH
Confidence            45778889999999   999999999984      799999998765

>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=89.63  E-value=0.28  Score=35.62  Aligned_cols=39  Identities=13%  Similarity=0.018  Sum_probs=32.6

Q ss_pred             hhhHHHHHHHhhCc---ccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970          9 MNDRFIVSQVLRNC---FATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus         9 ~~~r~i~r~v~~~~---~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      ..++.|+..+..++   ..|+.||++.|.      ++.+||+++|.+.
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lg------vs~~tV~~~L~~L   55 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLG------TPKKEINRVLYSL   55 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHC------CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHC------cCHHHHHHHHHHH
Confidence            34678888888899   999999999984      7899999987653

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=88.36  E-value=0.58  Score=37.54  Aligned_cols=47  Identities=21%  Similarity=0.168  Sum_probs=37.3

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT   56 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~   56 (257)
                      .+++.|+..+......||.||.+.|...+ ..+|..||+|.|+   +.|+-
T Consensus        19 ~qR~~Il~~l~~~~h~ta~ei~~~l~~~~-~~is~~TVYR~L~~L~e~Glv   68 (145)
T 3eyy_A           19 PQRQLVLEAVDTLEHATPDDILGEVRKTA-SGINISTVYRTLELLEELGLV   68 (145)
T ss_dssp             HHHHHHHHHHHHHSSBCHHHHHHHHHTTC-TTCCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHhhC-CCCCHhHHHHHHHHHHHCCcE
Confidence            46677777776655899999999998764 7899999999886   45554

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=88.28  E-value=0.56  Score=37.99  Aligned_cols=39  Identities=13%  Similarity=0.157  Sum_probs=34.5

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      ..|+.|++...+|+..|..+|.+.|      .+|+.||+++|++.
T Consensus         3 ~~d~~il~~L~~~~~~s~~~la~~l------g~s~~tv~~rl~~L   41 (162)
T 3i4p_A            3 RLDRKILRILQEDSTLAVADLAKKV------GLSTTPCWRRIQKM   41 (162)
T ss_dssp             HHHHHHHHHHTTCSCSCHHHHHHHH------TCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHH------CcCHHHHHHHHHHH
Confidence            4688999999999999999999987      58999999987764

>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=88.16  E-value=0.51  Score=29.75  Aligned_cols=41  Identities=5%  Similarity=0.007  Sum_probs=28.2

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      .+.+.++..... . .|..+|+..+      .+|..||++.|++.++..
T Consensus         9 ~~~~~i~~l~~~-g-~s~~~ia~~l------gvs~~Tv~r~l~~~~~~~   49 (52)
T 1jko_C            9 HEQEQISRLLEK-G-HPRQQLAIIF------GIGVSTLYRYFPASSIKK   49 (52)
T ss_dssp             THHHHHHHHHHT-T-CCHHHHHHTT------SCCHHHHHHHSCTTC---
T ss_pred             HHHHHHHHHHHc-C-CCHHHHHHHH------CCCHHHHHHHHHHccccc
Confidence            344556665443 3 7888888775      489999999999888754

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

Probab=87.08  E-value=1  Score=32.03  Aligned_cols=44  Identities=18%  Similarity=0.170  Sum_probs=34.1

Q ss_pred             chhhHHHHHHHhhC--cccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          8 SMNDRFIVSQVLRN--CFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         8 ~~~~r~i~r~v~~~--~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ...+..|+..+...  ...|+.||.+.|...+ ..+|..||+|.|+.
T Consensus        16 t~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~-~~is~~TVyR~L~~   61 (83)
T 2fu4_A           16 TLPRLKILEVLQEPDNHHVSAEDLYKRLIDMG-EEIGLATVYRVLNQ   61 (83)
T ss_dssp             CHHHHHHHHHHTSGGGSSBCHHHHHHHHHHTT-CCCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhC-CCCCHhhHHHHHHH
Confidence            34556677777654  5799999999998754 67999999998874

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

Probab=85.81  E-value=0.73  Score=34.42  Aligned_cols=38  Identities=16%  Similarity=0.079  Sum_probs=31.9

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      ...+.|+...++++ .|+.||+.+|      .+|+++|+++|+..
T Consensus        17 ~~~~~IL~lL~~~g-~sa~eLAk~L------giSk~aVr~~L~~L   54 (82)
T 1oyi_A           17 EIVCEAIKTIGIEG-ATAAQLTRQL------NMEKREVNKALYDL   54 (82)
T ss_dssp             HHHHHHHHHHSSST-EEHHHHHHHS------SSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcC-CCHHHHHHHH------CcCHHHHHHHHHHH
Confidence            45678888888888 9999999997      48999999998754

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=85.73  E-value=1.2  Score=35.08  Aligned_cols=48  Identities=17%  Similarity=0.122  Sum_probs=36.9

Q ss_pred             chhhHHHHHHHhhC--cccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCc
Q psy16970          8 SMNDRFIVSQVLRN--CFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLT   56 (257)
Q Consensus         8 ~~~~r~i~r~v~~~--~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~   56 (257)
                      ..+++.|+..+...  ...||.||.+.|+..+ ..+|..||+|.|+.   .|+-
T Consensus        17 T~qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~-~~is~aTVYR~L~~L~e~Glv   69 (136)
T 1mzb_A           17 TLPRVKILQMLDSAEQRHMSAEDVYKALMEAG-EDVGLATVYRVLTQFEAAGLV   69 (136)
T ss_dssp             CHHHHHHHHHHHCC-CCSBCHHHHHHHHHHTT-CCCCHHHHHHHHHHHHHHTSE
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHCCcE
Confidence            34567777777654  4799999999998864 68999999998864   5544

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=85.34  E-value=0.86  Score=38.57  Aligned_cols=41  Identities=22%  Similarity=0.216  Sum_probs=36.1

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      ...|+..+.++++.|..||.+.|      .+|+.||||=|.+.+...
T Consensus        14 ~~~i~~~l~~~~~~~~~~la~~~------~vs~~TiRrDl~eL~~~~   54 (190)
T 4a0z_A           14 REAIRQQIDSNPFITDHELSDLF------QVSIQTIRLDRTYLNIPE   54 (190)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHH------TSCHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHCCCEeHHHHHHHH------CCCHHHHHHHHHHhcCcc
Confidence            46788899999999999999998      489999999999887765

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

Probab=84.52  E-value=1.4  Score=34.55  Aligned_cols=47  Identities=21%  Similarity=0.202  Sum_probs=36.1

Q ss_pred             hhhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHHh---cCCc
Q psy16970          9 MNDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLNE---NNLT   56 (257)
Q Consensus         9 ~~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~---~~l~   56 (257)
                      .++..|+..+.. +...||.||.+.|+..+ ..+|..||+|.|+.   .|+-
T Consensus        11 ~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~-~~is~~TVYR~L~~L~e~Glv   61 (131)
T 2o03_A           11 RQRAAISTLLETLDDFRSAQELHDELRRRG-ENIGLTTVYRTLQSMASSGLV   61 (131)
T ss_dssp             HHHHHHHHHHHHCCSCEEHHHHHHHHHHTT-CCCCHHHHHHHHHHHHTTTSE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhC-CCCCHhhHHHHHHHHHHCCCE
Confidence            456667777754 45799999999998764 68999999998874   5544

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

Probab=83.96  E-value=1.7  Score=34.57  Aligned_cols=49  Identities=18%  Similarity=0.192  Sum_probs=37.5

Q ss_pred             chhhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCcc
Q psy16970          8 SMNDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTA   57 (257)
Q Consensus         8 ~~~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~   57 (257)
                      ..+++.|+..+.. +...||.||.+.|+..+ ..+|..||+|.|+   +.|+-.
T Consensus        21 T~qR~~Il~~L~~~~~~~sa~ei~~~l~~~~-~~is~aTVYR~L~~L~e~Glv~   73 (145)
T 2fe3_A           21 TPQRHAILEYLVNSMAHPTADDIYKALEGKF-PNMSVATVYNNLRVFRESGLVK   73 (145)
T ss_dssp             CHHHHHHHHHHHHCSSCCCHHHHHHHHGGGC-TTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhC-CCCChhhHHHHHHHHHHCCCEE
Confidence            3456677777754 46799999999998764 6899999999876   466543

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=83.85  E-value=1.4  Score=34.99  Aligned_cols=47  Identities=15%  Similarity=0.108  Sum_probs=36.1

Q ss_pred             hhhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCc
Q psy16970          9 MNDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLT   56 (257)
Q Consensus         9 ~~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~   56 (257)
                      .+++.|+..+.. +...||.||.+.|...+ ..+|..||+|.|+   +.|+-
T Consensus        14 ~qR~~Il~~L~~~~~h~sa~eI~~~l~~~~-~~is~aTVYR~L~~L~e~Glv   64 (139)
T 3mwm_A           14 RQRAAVSAALQEVEEFRSAQELHDMLKHKG-DAVGLTTVYRTLQSLADAGEV   64 (139)
T ss_dssp             HHHHHHHHHHTTCSSCEEHHHHHHHHHHTT-CCCCHHHHHHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHCCCE
Confidence            356667777755 35799999999998764 6899999999886   45554

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=83.17  E-value=1.6  Score=31.94  Aligned_cols=38  Identities=11%  Similarity=0.001  Sum_probs=32.3

Q ss_pred             hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970         10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus        10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      .-..|+..+.++..+|..||.++|      .+|+.||||-|.+-
T Consensus         3 ~L~~Il~~L~~~g~vsv~eLa~~l------~VS~~TIRrdL~~L   40 (78)
T 1xn7_A            3 SLIQVRDLLALRGRMEAAQISQTL------NTPQPMINAMLQQL   40 (78)
T ss_dssp             CHHHHHHHHHHSCSBCHHHHHHHT------TCCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCcHHHHHHHH------CcCHHHHHHHHHHH
Confidence            345788889999999999999987      58999999988754

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=82.99  E-value=1.9  Score=34.70  Aligned_cols=48  Identities=17%  Similarity=0.205  Sum_probs=36.6

Q ss_pred             hhhHHHHHHHhh-CcccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCcc
Q psy16970          9 MNDRFIVSQVLR-NCFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTA   57 (257)
Q Consensus         9 ~~~r~i~r~v~~-~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~   57 (257)
                      .++..|+..+.. +...||.||.+.|+..+ ..+|..||+|.|+   +.|+-.
T Consensus        27 ~qR~~IL~~l~~~~~~~sa~ei~~~l~~~~-~~is~aTVYR~L~~L~e~Glv~   78 (150)
T 2xig_A           27 KQREEVVSVLYRSGTHLSPEEITHSIRQKD-KNTSISSVYRILNFLEKENFIS   78 (150)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHHHHS-TTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhC-CCCCHhhHHHHHHHHHHCCcEE
Confidence            456667777755 36799999999998764 6899999999886   455543

>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=82.78  E-value=1.7  Score=34.41  Aligned_cols=40  Identities=20%  Similarity=0.180  Sum_probs=33.9

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      ...++.|+..+.+++..|..||.++|      .+|..||+++|++.
T Consensus         6 d~~~~~il~~L~~~~~~s~~ela~~l------g~s~~tv~~~l~~L   45 (151)
T 2cyy_A            6 DEIDKKIIKILQNDGKAPLREISKIT------GLAESTIHERIRKL   45 (151)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHH------CSCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHH
Confidence            45678899999999999999999988      47999999987653

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=82.72  E-value=1.4  Score=35.41  Aligned_cols=49  Identities=18%  Similarity=0.190  Sum_probs=37.5

Q ss_pred             chhhHHHHHHHhhC--cccCHHHHHHHHHhccCccccHHHHHHHHH---hcCCcc
Q psy16970          8 SMNDRFIVSQVLRN--CFATALEVRQELQDVRKVHLNEGTVRIRLN---ENNLTA   57 (257)
Q Consensus         8 ~~~~r~i~r~v~~~--~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~---~~~l~~   57 (257)
                      ..++..|+..+...  ...||.||.+.|+..+ ..+|..||+|.|+   +.|+-.
T Consensus        16 T~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~-~~is~aTVYR~L~~L~e~Glv~   69 (150)
T 2w57_A           16 TLPRLKILEVLQQPECQHISAEELYKKLIDLG-EEIGLATVYRVLNQFDDAGIVT   69 (150)
T ss_dssp             CHHHHHHHHHHTSGGGSSEEHHHHHHHHHHTT-CCCCHHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHCCcEE
Confidence            35666777777554  4799999999998864 6899999999887   456543

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=82.53  E-value=1.9  Score=34.00  Aligned_cols=39  Identities=18%  Similarity=0.145  Sum_probs=33.4

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ...++.|+..+..++..|..||.+.|      .+|+.||+++|++
T Consensus         8 d~~d~~il~~L~~~~~~s~~ela~~l------g~s~~tv~~~l~~   46 (151)
T 2dbb_A            8 DRVDMQLVKILSENSRLTYRELADIL------NTTRQRIARRIDK   46 (151)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHT------TSCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence            45678899999999999999999987      4799999997765

>3lap_A Arginine repressor; arginine repressor, DNA binding, DNA-canavanine ternary complex; HET: GGB; 2.15A {Mycobacterium tuberculosis} PDB: 3fhz_A* 3ere_D* 3laj_A*

Probab=81.59  E-value=2.1  Score=35.88  Aligned_cols=46  Identities=15%  Similarity=0.107  Sum_probs=41.1

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      ...|.+.+.++...|=.||.+.|+..| ..++..||+|=|++.|+..
T Consensus        22 ~~~I~~iI~~~~I~tQeEL~~~L~~~G-i~vTQATlSRDikEL~lvK   67 (170)
T 3lap_A           22 QARIVAILSSAQVRSQNELAALLAAEG-IEVTQATLSRDLEELGAVK   67 (170)
T ss_dssp             HHHHHHHHHHSCCCSHHHHHHHHHHTT-CCCCHHHHHHHHHHHTCEE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHcC-CCcCchhHHHHHHHcCcEE
Confidence            446788889999999999999999985 9999999999999999764

>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=81.49  E-value=2.2  Score=33.44  Aligned_cols=39  Identities=15%  Similarity=0.210  Sum_probs=33.3

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      ..++.|+..+.+++..|..||.+.|      .+|+.||+++|++.
T Consensus         5 ~~d~~il~~L~~~~~~s~~ela~~l------g~s~~tv~~~l~~L   43 (144)
T 2cfx_A            5 QIDLNIIEELKKDSRLSMRELGRKI------KLSPPSVTERVRQL   43 (144)
T ss_dssp             HHHHHHHHHHHHCSCCCHHHHHHHH------TCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHH
Confidence            4577899999999999999999988      47999999887754

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=81.14  E-value=2.3  Score=33.56  Aligned_cols=39  Identities=18%  Similarity=0.307  Sum_probs=33.3

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ...++.|+..+.+++..|..||.+.+      .+|+.||+++|++
T Consensus         7 d~~d~~il~~L~~~~~~s~~ela~~l------g~s~~tv~~~l~~   45 (152)
T 2cg4_A            7 DNLDRGILEALMGNARTAYAELAKQF------GVSPETIHVRVEK   45 (152)
T ss_dssp             CHHHHHHHHHHHHCTTSCHHHHHHHH------TSCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence            34577899999999999999999988      4799999988765

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=80.77  E-value=2.4  Score=34.63  Aligned_cols=49  Identities=14%  Similarity=0.230  Sum_probs=37.1

Q ss_pred             hhhHHHHHHHhhC-cccCHHHHHHHHHhcc-CccccHHHHHHHHH---hcCCcc
Q psy16970          9 MNDRFIVSQVLRN-CFATALEVRQELQDVR-KVHLNEGTVRIRLN---ENNLTA   57 (257)
Q Consensus         9 ~~~r~i~r~v~~~-~~~ta~~i~~~l~~~~-g~~~s~~Tvrr~L~---~~~l~~   57 (257)
                      .+++.|+..+... ...||.||-+.|.... +..+|..||+|.|+   +.|+-.
T Consensus        33 ~qR~~IL~~L~~~~~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~   86 (162)
T 4ets_A           33 KQREVLLKTLYHSDTHYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVT   86 (162)
T ss_dssp             HHHHHHHHHHHSCCSCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEE
Confidence            4567777777554 6799999999998751 36899999999886   456543

>3v4g_A Arginine repressor; vibrio vulnificus CMCP6, virulence, type secretion system, center for structural genomics of infecti diseases, csgid; 1.60A {Vibrio vulnificus} PDB: 1aoy_A

Probab=80.65  E-value=2.3  Score=36.06  Aligned_cols=47  Identities=15%  Similarity=0.089  Sum_probs=41.6

Q ss_pred             hhHHHHHHHhhCcccCHHHHHHHHHhccCccc-cHHHHHHHHHhcCCcc
Q psy16970         10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHL-NEGTVRIRLNENNLTA   57 (257)
Q Consensus        10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~-s~~Tvrr~L~~~~l~~   57 (257)
                      -...|.+.+.++...|=.||.+.|+..| ..+ +..||.|=|++.|+..
T Consensus        34 r~~~I~eiI~~~~I~TQeEL~~~L~~~G-i~viTQATvSRDIkELglvK   81 (180)
T 3v4g_A           34 LVRAFKALLKEERFGSQGEIVEALKQEG-FENINQSKVSRMLTKFGAVR   81 (180)
T ss_dssp             HHHHHHHHHHHTCCCSHHHHHHHHHHTT-CTTCCHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHhhCCcCCHHHHHHHHHHCC-CcccCHHHHHHHHHHcCCEE
Confidence            3456788889999999999999999985 888 9999999999999875

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=80.43  E-value=1.5  Score=32.91  Aligned_cols=41  Identities=7%  Similarity=-0.057  Sum_probs=33.6

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      -..|+..+.++..+|..||.+.|      .+|+.||||-|.+-.-.+
T Consensus         4 L~~Il~~L~~~g~vsv~eLA~~l------~VS~~TIRrDL~~Le~~G   44 (87)
T 2k02_A            4 LMEVRDMLALQGRMEAKQLSARL------QTPQPLIDAMLERMEAMG   44 (87)
T ss_dssp             THHHHHHHHHSCSEEHHHHHHHT------TCCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHH------CcCHHHHHHHHHHHHHCC
Confidence            45788888999999999999987      589999999887644333

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=80.32  E-value=2.5  Score=33.78  Aligned_cols=39  Identities=21%  Similarity=0.215  Sum_probs=33.1

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ...++.|+..+.+++..|..||.+.+      .+|..||+++|++
T Consensus         9 d~~~~~il~~L~~~~~~s~~ela~~l------g~s~~tv~~~l~~   47 (162)
T 2p5v_A            9 DKTDIKILQVLQENGRLTNVELSERV------ALSPSPCLRRLKQ   47 (162)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHH------TSCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence            34577899999999999999999987      4799999988765

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=80.22  E-value=2.4  Score=34.64  Aligned_cols=39  Identities=23%  Similarity=0.309  Sum_probs=33.9

Q ss_pred             chhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          8 SMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         8 ~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ...++.|+..+.+++..|..||.+.|      .+|+.||+++|++
T Consensus        16 d~~d~~IL~~L~~~~~~s~~eLA~~l------glS~~tv~~~l~~   54 (171)
T 2ia0_A           16 DDLDRNILRLLKKDARLTISELSEQL------KKPESTIHFRIKK   54 (171)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHH------TSCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence            45678999999999999999999988      4899999988765

---

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	257
d1u78a2	50	Transposase tc3a1-65 {Caenorhabditis elegans [TaxI	96.83
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	94.26
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	93.41
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	93.33
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	93.3
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	93.27
d1aoya_	78	Arginine repressor (ArgR), N-terminal DNA-binding	93.08
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	92.94
d2p5ka1	63	Arginine repressor (ArgR), N-terminal DNA-binding	91.57
d1b4aa1	75	Arginine repressor (ArgR), N-terminal DNA-binding	91.35
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	83.91

>d1u78a2 a.4.1.2 (A:55-104) Transposase tc3a1-65 {Caenorhabditis elegans [TaxId: 6239]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Transposase tc3a1-65
species: Caenorhabditis elegans [TaxId: 6239]

Probab=96.83  E-value=0.00077  Score=43.71  Aligned_cols=44  Identities=18%  Similarity=0.209  Sum_probs=38.3

Q ss_pred             CCchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcC
Q psy16970          6 GASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENN   54 (257)
Q Consensus         6 ~~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~   54 (257)
                      -|.++.|.++++... .+.||.+|+.|||.    .+|.+||-+.+.++|
T Consensus         7 ls~rdernviraasn-s~kta~dir~el~l----~~sk~tiln~i~~~g   50 (50)
T d1u78a2           7 LSVRDERNVIRAASN-SCKTARDIRNELQL----SASKRTILNVIKRSG   50 (50)
T ss_dssp             SCHHHHHHHHHHHHH-CCCCHHHHHHHTTC----CSCHHHHHHHHHHTC
T ss_pred             cchHHHHHHHHHHhc-chhhHHHHHHHHhh----hhHHHHHHHHHhhcC
Confidence            478999999999764 67999999999984    899999999998875

>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=94.26  E-value=0.018  Score=43.88  Aligned_cols=44  Identities=9%  Similarity=-0.051  Sum_probs=38.0

Q ss_pred             CchhhHHHHHHHhhCcccCHHHHHHHHHhcc----CccccHHHHHHHH
Q psy16970          7 ASMNDRFIVSQVLRNCFATALEVRQELQDVR----KVHLNEGTVRIRL   50 (257)
Q Consensus         7 ~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~----g~~~s~~Tvrr~L   50 (257)
                      ++..+.+|.+.+..+|.+|+.||+++|...+    +...|.+||+|.|
T Consensus        76 t~~~~~~I~~~~~~~P~~t~~El~~~L~~egv~~~~~~pSvStI~RiL  123 (123)
T d1pdnc_          76 TPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLV  123 (123)
T ss_dssp             CSTHHHHHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC
T ss_pred             CHHHHHHHHHHHHhCCCccHHHHHHHHHHcCCCCCCCCCChhhHhhcC
Confidence            5678899999999999999999999998754    3467899999976

>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=93.41  E-value=0.06  Score=35.82  Aligned_cols=38  Identities=21%  Similarity=0.357  Sum_probs=33.7

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ..|++|++...+|+..|..+|+..+      .+|+.||++++++
T Consensus         3 ~~D~kIl~~L~~n~r~s~~~lA~~~------gls~~~v~~Ri~~   40 (60)
T d1i1ga1           3 ERDKIILEILEKDARTPFTEIAKKL------GISETAVRKRVKA   40 (60)
T ss_dssp             SHHHHHHHHHHHCTTCCHHHHHHHH------TSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence            4689999999999999999999987      5799999988764

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=93.33  E-value=0.062  Score=35.58  Aligned_cols=39  Identities=21%  Similarity=0.181  Sum_probs=34.3

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhc
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNEN   53 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~   53 (257)
                      ..|+.|++...+|+..|..||++.|      .+|+.||.+++++.
T Consensus         3 ~~D~~Il~~L~~n~r~s~~eiA~~l------~ls~~~v~~Ri~~L   41 (60)
T d2cyya1           3 EIDKKIIKILQNDGKAPLREISKIT------GLAESTIHERIRKL   41 (60)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHH------CSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHHH
Confidence            4689999999999999999999997      57999999887653

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=93.30  E-value=0.062  Score=35.98  Aligned_cols=38  Identities=18%  Similarity=0.310  Sum_probs=33.7

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ..|+.|++....|+..|..||+..+      .+|..||++|+++
T Consensus         5 ~~D~~IL~~L~~~~r~s~~eiA~~l------~ls~~~v~~Ri~r   42 (63)
T d2cg4a1           5 NLDRGILEALMGNARTAYAELAKQF------GVSPETIHVRVEK   42 (63)
T ss_dssp             HHHHHHHHHHHHCTTSCHHHHHHHH------TSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence            4689999999999999999999987      5799999988765

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=93.27  E-value=0.072  Score=35.76  Aligned_cols=38  Identities=16%  Similarity=0.241  Sum_probs=34.0

Q ss_pred             hhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970          9 MNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus         9 ~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      ..|+.|+.+..+|+..|..+|+..|      .+|+.||++++++
T Consensus         5 ~~D~~IL~~L~~n~r~s~~~iA~~l------gis~~tv~~Ri~~   42 (63)
T d2cfxa1           5 QIDLNIIEELKKDSRLSMRELGRKI------KLSPPSVTERVRQ   42 (63)
T ss_dssp             HHHHHHHHHHHHCSCCCHHHHHHHH------TCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH------CcCHHHHHHHHHH
Confidence            4689999999999999999999998      5899999988764

>d1aoya_ a.4.5.3 (A:) Arginine repressor (ArgR), N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=93.08  E-value=0.11  Score=36.83  Aligned_cols=57  Identities=16%  Similarity=0.109  Sum_probs=44.4

Q ss_pred             CccccCCchhhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970          1 MRIASGASMNDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus         1 ~~~~~~~~~~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      |+-.+--.+..+.|.+.+..++..|=.||...|...|-..++..||.|-|++.|+..
T Consensus         1 M~k~~kq~~~l~~I~~li~~~~i~tQ~eL~~~L~~~G~~~vTQaTiSRDL~eLg~vK   57 (78)
T d1aoya_           1 MRSSAKQEELVKAFKALLKEEKFSSQGEIVAALQEQGFDNINQSKVSRMLTKFGAVR   57 (78)
T ss_dssp             CCCCCCSTTHHHHHHHHHHTCCCCSHHHHHHHHHHHTCSSCCHHHHHHHHHHHTCEE
T ss_pred             CCchHHHHHHHHHHHHHHHhCCcCCHHHHHHHHHHcCCcchhHHHHHHHHHHhCCEE
Confidence            333333333335677888999999999999999998733599999999999999774

>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=92.94  E-value=0.083  Score=35.48  Aligned_cols=37  Identities=5%  Similarity=0.163  Sum_probs=31.7

Q ss_pred             hhHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970         10 NDRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus        10 ~~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      .+..|+.....+.+.|+.|++++|      .||.+||+|.+.+
T Consensus         6 ~~~~iL~~L~~~~~~s~~eLa~~l------~vS~~ti~r~i~~   42 (63)
T d1biaa1           6 VPLKLIALLANGEFHSGEQLGETL------GMSRAAINKHIQT   42 (63)
T ss_dssp             HHHHHHHHHTTSSCBCHHHHHHHH------TSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCcCCHHHHHHHH------CcCHHHHHHHHHH
Confidence            456788888999999999999998      5899999987654

>d2p5ka1 a.4.5.3 (A:2-64) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=91.57  E-value=0.17  Score=34.41  Aligned_cols=45  Identities=20%  Similarity=0.128  Sum_probs=40.2

Q ss_pred             HHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         12 RFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        12 r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      ..|...+..++..|=.||...|... |+.++..||.|-|++.|+..
T Consensus         7 ~~I~~li~~~~i~tQ~eL~~~L~~~-G~~vTQaTlSRDL~eLg~vK   51 (63)
T d2p5ka1           7 IKIREIITSNEIETQDELVDMLKQD-GYKVTQATVSRDIKELHLVK   51 (63)
T ss_dssp             HHHHHHHHHSCCCSHHHHHHHHHHT-TCCCCHHHHHHHHHHHTCEE
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHc-CCCeeHHHHHHHHHHhCCEE
Confidence            4677778899999999999999998 59999999999999999764

>d1b4aa1 a.4.5.3 (A:4-78) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=91.35  E-value=0.2  Score=35.16  Aligned_cols=46  Identities=20%  Similarity=0.224  Sum_probs=41.2

Q ss_pred             hHHHHHHHhhCcccCHHHHHHHHHhccCccccHHHHHHHHHhcCCcc
Q psy16970         11 DRFIVSQVLRNCFATALEVRQELQDVRKVHLNEGTVRIRLNENNLTA   57 (257)
Q Consensus        11 ~r~i~r~v~~~~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~~~l~~   57 (257)
                      ...|.+.+..++..|=.||...|... |+.++..||.|-|++.|+..
T Consensus         4 ~~~I~~li~~~~i~tQ~eL~~~L~~~-Gi~vTQaTlSRDL~eLg~vK   49 (75)
T d1b4aa1           4 HIKIREIIMSNDIETQDELVDRLREA-GFNVTQATVSRDIKEMQLVK   49 (75)
T ss_dssp             HHHHHHHHHHSCCCSHHHHHHHHHHT-TCCCCHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHc-CCceeHHHHHHHHHHhCCEE
Confidence            35678888999999999999999998 59999999999999999875

>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=83.91  E-value=0.68  Score=30.65  Aligned_cols=34  Identities=15%  Similarity=0.139  Sum_probs=26.7

Q ss_pred             HHHHHHhhC-cccCHHHHHHHHHhccCccccHHHHHHHHHh
Q psy16970         13 FIVSQVLRN-CFATALEVRQELQDVRKVHLNEGTVRIRLNE   52 (257)
Q Consensus        13 ~i~r~v~~~-~~~ta~~i~~~l~~~~g~~~s~~Tvrr~L~~   52 (257)
                      .|+..+.+. .+.|+.+++++|      .||.+||+|-|+.
T Consensus        11 ~Il~~L~~~~~~vs~~~La~~l------~VS~~TI~rdi~~   45 (65)
T d1j5ya1          11 SIVRILERSKEPVSGAQLAEEL------SVSRQVIVQDIAY   45 (65)
T ss_dssp             HHHHHHHHCSSCBCHHHHHHHH------TSCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCcHHHHHHHH------CCCHHHHHHHHHH
Confidence            466666554 569999999998      5899999997654