Psyllid ID: psy14923

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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
Protein Sequence
MALFKLTTGVFTGGNVFNLRSCLMPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGKSYM
Secondary Structure (PSIPRED)
cccccHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEcccccccccccHHHcccccccccccccHHHccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHcHccccccccc
Coil and Loop (DISEMBL)
malfklttgvftggnvFNLRSclmphlnsvttaglkqqtsqplsipekpkkpltpyfkFQGQIRNKImernpnikiiEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRetgkpkkpgnsfyLFIKdnidkkeyegksym
Flexible Loop (DISEMBL)
malfklttgvftggNVFNLRSCLMPHLNSVTTAGLkqqtsqplsipekpkkpltpYFKFQGQIrnkimernpnikiievtklvseEWKKIGEAEkkrleneyakEKEIYAQNVKKYHDELTPEAIEFlrkekevkkqkkekremkklfretgkpkkpgnsfylfikdnidkkeyegksym
Low Complexity Region (SEG)
MALFKLTTGVFTGGNVFNLRSCLMPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRkekevkkqkkekremkkLFRETGKPKKPGNSFYLFIKDNIDKKEYEGKSYM
Disordered region (IsUnstruct)
**LFKLTTGVFTGGNVFNLRSCLMPHLNSVTT**********************PYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIG***************EIYAQNVKKYHD******************************************FYLFIKDN************
Disordered Region (DISOPRED)
*****************************************************TPYFKFQGQIRNK****NPNIKIIEVTKLVSEEWKK*G***KKRLENEYAKEKEIYAQNVKK********************************************SFYLF****************
Disordered Region (DISEMBL)
MALFKLTTGVFTGGNVFNLRSCLMPHLNSVTTA************PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRKEK**********EMKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGKSYM
Disordered Region (DISPRO)
*ALFKLTTGVFTGGNVFNLRSCLM*****************PLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDNID**********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MALFKLTTGVFTGGNVFNLRSCLMPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWxxxxxxxxxxxxxxxxxxxxxxxxxxxxYHDELTPEAxxxxxxxxxxxxxxxxxxxxxxxxxxTGKPKKPGNSFYLFIKDNIDKKEYEGKSYM
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	180	2.2.26 [Sep-21-2011]
Q91ZW1	244	Transcription factor A, m	yes	N/A	0.877	0.647	0.275	4e-13
Q5D144	246	Transcription factor A, m	yes	N/A	0.916	0.670	0.3	3e-11
P40630	243	Transcription factor A, m	yes	N/A	0.905	0.670	0.254	4e-11
Q0II87	246	Transcription factor A, m	yes	N/A	0.688	0.504	0.298	5e-10
Q00059	246	Transcription factor A, m	yes	N/A	0.577	0.422	0.264	6e-10
Q4H0T5	246	Transcription factor A, m	N/A	N/A	0.661	0.483	0.252	5e-09
Q32L68	317	SWI/SNF-related matrix-as	no	N/A	0.4	0.227	0.361	2e-08
P11873	100	High mobility group prote	N/A	N/A	0.427	0.77	0.363	4e-08
Q9Z104	317	SWI/SNF-related matrix-as	no	N/A	0.405	0.230	0.369	7e-08
Q9P0W2	317	SWI/SNF-related matrix-as	no	N/A	0.4	0.227	0.347	8e-08

>sp|Q91ZW1|TFAM_RAT Transcription factor A, mitochondrial OS=Rattus norvegicus GN=Tfam PE=2 SV=1

 Score = 74.3 bits (181), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 49/178 (27%), Positives = 91/178 (51%), Gaps = 20/178 (11%)

Query: 1   MALFKLTTGVFTGGNVFNLRSCLMPHLNSVTTAGLKQQTSQPLS---IPEK-------PK 50
           MALF+   GV        +  C          AG   +   P+S   IP+        PK
Sbjct: 1   MALFRGMWGVLRTLGRTGVEMC----------AGCGGRIPSPVSLICIPKCFSSLGNYPK 50

Query: 51  KPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYA 110
           KP++ Y +F  +   K   ++P+ K+ E+ + ++  W+++ EAEKK  E ++  E ++Y 
Sbjct: 51  KPMSSYLRFSTEQLPKFKAKHPDAKVSELIRKIAAMWRELPEAEKKVYEADFKAEWKVYK 110

Query: 111 QNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDN 168
           + V KY ++LTP  +  L KE   K+ KK+ +  ++     GKPK+P +++ +++ ++
Sbjct: 111 EAVSKYKEQLTPSQLMGLEKEARQKRLKKKAQIKRRELILLGKPKRPRSAYNIYVSES 168

Isoform Mitochondrial binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. Required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. Promotes transcription initiation from the HSP1 and the light strand promoter by binding immediately upstream of transcriptional start sites. Is able to unwind and bend DNA. Required for maintenance of normal levels of mitochondrial DNA. May play a role in organizing and compacting mitochondrial DNA (By similarity). Isoform Nuclear may also function as a transcriptional activator or may have a structural role in the compaction of nuclear DNA during spermatogenesis. Associates with mitochondrial DNA.
Rattus norvegicus (taxid: 10116)

>sp|Q5D144|TFAM_PIG Transcription factor A, mitochondrial OS=Sus scrofa GN=TFAM PE=2 SV=1

 Score = 68.2 bits (165), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 51/170 (30%), Positives = 90/170 (52%), Gaps = 5/170 (2%)

Query: 1   MALFKLTTGVFT--GGNVFNLRSCLMPHLNS-VTTAGLKQQTSQPLSIPEKPKKPLTPYF 57
           MAL +   GV +  G +  +L +     L S  + A + +  S  LS    PKKP+T Y 
Sbjct: 1   MALLRGVWGVLSALGKSGADLCAVCGSRLRSPFSFAYVPRWFSSTLS--GFPKKPMTSYV 58

Query: 58  KFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH 117
           +F  +       +NP+ K  E+ K ++E W+++ ++EKK  E+ Y  + ++Y + V +  
Sbjct: 59  RFSKEQLPIFKAQNPDAKNSELIKKIAELWRELPDSEKKIYEDAYRADWQVYKEEVNRIQ 118

Query: 118 DELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKD 167
           ++LTP  +  L KE   K+ KK+    K+     GKPK+P +++ +FI +
Sbjct: 119 EQLTPSQMVSLEKEIMQKRLKKKALIKKRELTMLGKPKRPRSAYNIFIAE 168

Binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. Required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. Promotes transcription initiation from the HSP1 and the light strand promoter by binding immediately upstream of transcriptional start sites. Is able to unwind and bend DNA. Required for maintenance of normal levels of mitochondrial DNA. May play a role in organizing and compacting mitochondrial DNA. Associates with mitochondrial DNA.

Sus scrofa (taxid: 9823)

>sp|P40630|TFAM_MOUSE Transcription factor A, mitochondrial OS=Mus musculus GN=Tfam PE=1 SV=2

 Score = 67.8 bits (164), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 90/173 (52%), Gaps = 10/173 (5%)

Query: 1   MALFKLTTGVFTGGNVFNLRSCL-----MPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTP 55
           MALF+    V        +  C      +P  +S++   + +  S   S+   PKKP++ 
Sbjct: 1   MALFRGMWSVLKALGRTGVEMCAGCGGRIP--SSISLVCIPKCFS---SMGSYPKKPMSS 55

Query: 56  YFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKK 115
           Y +F  +   K   ++P+ K+ E+ + ++  W+++ EAEKK  E ++  E + Y + V K
Sbjct: 56  YLRFSTEQLPKFKAKHPDAKLSELVRKIAALWRELPEAEKKVYEADFKAEWKAYKEAVSK 115

Query: 116 YHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDN 168
           Y ++LTP  +  + KE   ++ KK+    ++     GKPK+P +++ +++ ++
Sbjct: 116 YKEQLTPSQLMGMEKEARQRRLKKKALVKRRELILLGKPKRPRSAYNIYVSES 168

Isoform Mitochondrial binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. Required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. Promotes transcription initiation from the HSP1 and the light strand promoter by binding immediately upstream of transcriptional start sites. Is able to unwind and bend DNA. Required for maintenance of normal levels of mitochondrial DNA. May play a role in organizing and compacting mitochondrial DNA. Isoform Nuclear may also function as a transcriptional activator or may have a structural role in the compaction of nuclear DNA during spermatogenesis. Associates with mitochondrial DNA.

Mus musculus (taxid: 10090)

>sp|Q0II87|TFAM_BOVIN Transcription factor A, mitochondrial OS=Bos taurus GN=TFAM PE=2 SV=1

 Score = 63.9 bits (154), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 37/124 (29%), Positives = 71/124 (57%)

Query: 44  SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYA 103
           S+   PKKP+T Y +F  +       +NP+ K  E+ K +++ W+++ ++EKK  E+ Y 
Sbjct: 45  SLSGYPKKPMTSYVRFSKEQLPIFKAQNPDAKNSELIKKIAKLWRELPDSEKKIYEDAYR 104

Query: 104 KEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYL 163
            + ++Y + + +  ++LTP  +  L KE   K+ KK+    K+     GKPK+P +++ +
Sbjct: 105 ADWQVYKEEINRIQEQLTPSQMVSLEKEIMQKRLKKKALIKKRELTMLGKPKRPRSAYNI 164

Query: 164 FIKD 167
           FI +
Sbjct: 165 FIAE 168

Binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. Required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. Promotes transcription initiation from the HSP1 and the light strand promoter by binding immediately upstream of transcriptional start sites. Is able to unwind and bend DNA. Required for maintenance of normal levels of mitochondrial DNA. May play a role in organizing and compacting mitochondrial DNA. Associates with mitochondrial DNA.

Bos taurus (taxid: 9913)

>sp|Q00059|TFAM_HUMAN Transcription factor A, mitochondrial OS=Homo sapiens GN=TFAM PE=1 SV=1

 Score = 63.5 bits (153), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 32/121 (26%), Positives = 69/121 (57%)

Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PKKP++ Y +F  +       +NP+ K  E+ + +++ W+++ +++KK  ++ Y  E ++
Sbjct: 50  PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQV 109

Query: 109 YAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDN 168
           Y + + ++ ++LTP  I  L KE   K  K++    KK     GKPK+P +++ +++ + 
Sbjct: 110 YKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAER 169

Query: 169 I 169
            
Sbjct: 170 F 170

Binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. Required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. Promotes transcription initiation from the HSP1 and the light strand promoter by binding immediately upstream of transcriptional start sites. Is able to unwind and bend DNA. Required for maintenance of normal levels of mitochondrial DNA. May play a role in organizing and compacting mitochondrial DNA. target DNA. Interacts with TFB1M and TFB2M. Associates with mitochondrial DNA.

Homo sapiens (taxid: 9606)

>sp|Q4H0T5|TFAM_TRACR Transcription factor A, mitochondrial OS=Trachypithecus cristatus GN=TFAM PE=2 SV=1

 Score = 60.8 bits (146), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 69/119 (57%)

Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PKKP++ Y +F  +        NP+ K  E+ + +++ W+++ +++KK  ++ Y  + ++
Sbjct: 50  PKKPVSSYLRFSKEQLPIFKAENPDAKPTELIRRIAKLWRELPDSKKKIYQDAYRADWQV 109

Query: 109 YAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKD 167
           Y + + ++ ++LTP  I  L KE   K  K++    +K   + GKPK+P +++ +++ +
Sbjct: 110 YKEKISRFKEQLTPSQITSLEKEIMDKHLKRKAMTKRKELTQLGKPKRPRSAYNVYVAE 168

Binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. Required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. Promotes transcription initiation from the HSP1 and the light strand promoter by binding immediately upstream of transcriptional start sites. Is able to unwind and bend DNA. Required for maintenance of normal levels of mitochondrial DNA. May play a role in organizing and compacting mitochondrial DNA. Associates with mitochondrial DNA.

Trachypithecus cristatus (taxid: 122765)

>sp|Q32L68|HM20B_BOVIN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related OS=Bos taurus GN=HMG20B PE=2 SV=1

 Score = 58.5 bits (140), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 45/72 (62%)

Query: 45  IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
           +P  PK P+T Y +F  + R +I  R+P++   E+TK++  EW K+  AEK+R  +E  +
Sbjct: 66  LPNGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAER 125

Query: 105 EKEIYAQNVKKY 116
           EK+ Y + ++ Y
Sbjct: 126 EKQQYMKELRAY 137

Required for correct progression through G2 phase of the cell cycle and entry into mitosis. Required for RCOR1/CoREST mediated repression of neuronal specific gene promoters.

Bos taurus (taxid: 9913)

>sp|P11873|HMGC_TETTH High mobility group protein C OS=Tetrahymena thermophila PE=1 SV=1

 Score = 57.8 bits (138), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 49/77 (63%)

Query: 40  SQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLE 99
           S+  S P  PK+PL+ +F F+     ++ + NPN KI E+T +++E+WK +GE EKK+ E
Sbjct: 3   SKDDSKPAPPKRPLSAFFLFKQHNYEQVKKENPNAKITELTSMIAEKWKAVGEKEKKKYE 62

Query: 100 NEYAKEKEIYAQNVKKY 116
              ++ K  Y ++++ Y
Sbjct: 63  TLQSEAKAKYEKDMQAY 79

Tetrahymena thermophila (taxid: 5911)

>sp|Q9Z104|HM20B_MOUSE SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related OS=Mus musculus GN=Hmg20b PE=1 SV=1

 Score = 56.6 bits (135), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 44/73 (60%)

Query: 45  IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
           +P  PK P+T Y +F  + R +I  R+P++   E+TK++  EW K+  AEK+R  +E  K
Sbjct: 66  LPNGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEK 125

Query: 105 EKEIYAQNVKKYH 117
           EK+ Y + +  Y 
Sbjct: 126 EKQQYLKELWAYQ 138

Required for correct progression through G2 phase of the cell cycle and entry into mitosis. Required for RCOR1/CoREST mediated repression of neuronal specific gene promoters.

Mus musculus (taxid: 10090)

>sp|Q9P0W2|HM20B_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related OS=Homo sapiens GN=HMG20B PE=1 SV=1

 Score = 56.6 bits (135), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 44/72 (61%)

Query: 45  IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
           +P  PK P+T Y +F  + R +I  R+P++   E+TK++  EW K+   EK+R  +E  +
Sbjct: 66  LPNGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPTEKQRYLDEAER 125

Query: 105 EKEIYAQNVKKY 116
           EK+ Y + ++ Y
Sbjct: 126 EKQQYMKELRAY 137

Required for correct progression through G2 phase of the cell cycle and entry into mitosis. Required for RCOR1/CoREST mediated repression of neuronal specific gene promoters.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	180
195449721	256	GK22718 [Drosophila willistoni] gi|19416	0.872	0.613	0.320	8e-19
224924366	256	mitochondrial transcription factor A [St	0.888	0.625	0.317	2e-18
195060651	252	GH14163 [Drosophila grimshawi] gi|193891	0.883	0.630	0.318	2e-18
198449964	256	GA18041 [Drosophila pseudoobscura pseudo	0.883	0.621	0.318	3e-18
118788729	277	AGAP008499-PA [Anopheles gambiae str. PE	0.833	0.541	0.303	4e-18
157136745	255	mitochondrial transcription factor A, pu	0.722	0.509	0.350	7e-18
157107110	255	mitochondrial transcription factor A, pu	0.722	0.509	0.350	8e-18
195390660	256	GJ24186 [Drosophila virilis] gi|19415207	0.683	0.480	0.357	1e-17
194744166	257	GF18333 [Drosophila ananassae] gi|190627	0.866	0.607	0.319	1e-17
195158925	256	GL13929 [Drosophila persimilis] gi|19411	0.883	0.621	0.318	2e-17

>gi|195449721|ref|XP_002072195.1| GK22718 [Drosophila willistoni] gi|194168280|gb|EDW83181.1| GK22718 [Drosophila willistoni]

 Score = 98.6 bits (244), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 52/162 (32%), Positives = 92/162 (56%), Gaps = 5/162 (3%)

Query: 6   LTTGVFTGGNVFNLRSCLMPHLNSVTTAGLKQQTS--QPLSIPEKPKKPLTPYFKFQGQI 63
           L+ G   G  +  +R        S++ + ++Q  +  + + +P +PKKPLTPYF++  ++
Sbjct: 8   LSRGSLIGSLINKVRPLAA---ASISNSPVQQSKTVEEQVGLPPRPKKPLTPYFRYMREM 64

Query: 64  RNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPE 123
           R K++  NPNI  +E  + +S+ W  +    K RL++EY K+KE Y     KY   +T E
Sbjct: 65  RPKLIAANPNISTVEAVRQLSKSWVVVDAKLKDRLQDEYRKDKETYIAQRAKYDATVTDE 124

Query: 124 AIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFI 165
               +R+ K+     KE+R+++K  +E G+PKKP ++F  F+
Sbjct: 125 QRAEIRQIKQDLVDAKERRQLRKRVKELGRPKKPASAFLRFV 166

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|224924366|gb|ACN69133.1| mitochondrial transcription factor A [Stomoxys calcitrans]

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 54/170 (31%), Positives = 96/170 (56%), Gaps = 10/170 (5%)

Query: 6   LTTGVFTGGNVFN--LRSC--LMPHLN------SVTTAGLKQQTSQPLSIPEKPKKPLTP 55
           LT  +F  G+     +  C  L P  N          A  K    + + +P +PKKPLTP
Sbjct: 3   LTVSLFNKGSFLGSLINKCRPLAPPANISLRGPPSVAASTKVTIEEKVGLPIRPKKPLTP 62

Query: 56  YFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKK 115
           YF+F  ++R KI+  NP + ++++ + VS++W+ +  + K+RL+ EY KE++ Y +   K
Sbjct: 63  YFRFMKELRPKIVASNPKMSLVDIVRQVSKKWESVDPSLKQRLQEEYKKEQQEYVEKRTK 122

Query: 116 YHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFI 165
           Y  ++T E    +++ K+ K + KE+R M++  ++ G+PKKP ++F   I
Sbjct: 123 YESKITDEQRNQIKELKQEKVEAKERRMMRRRIKDLGRPKKPASAFIRLI 172

Source: Stomoxys calcitrans

Species: Stomoxys calcitrans

Genus: Stomoxys

Family: Muscidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195060651|ref|XP_001995833.1| GH14163 [Drosophila grimshawi] gi|193891625|gb|EDV90491.1| GH14163 [Drosophila grimshawi]

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 51/160 (31%), Positives = 92/160 (57%), Gaps = 1/160 (0%)

Query: 6   LTTGVFTGGNVFNLRSCLMPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRN 65
           LT G   G  +  +R      +++ +    +    Q + +P +PKKPLTPYF+F  ++R 
Sbjct: 4   LTRGSIIGSLISKVRPLGAAGISNSSVLQARTPEEQ-IGLPPRPKKPLTPYFRFMREMRP 62

Query: 66  KIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAI 125
           K++ ++P I  IEV + +S+ W  +    K+RL++EY  ++EIY     KY  +LT E  
Sbjct: 63  KLIAKDPKISTIEVVRQLSKNWVSVDPKMKERLQSEYKIDQEIYLDQRTKYDAKLTDEQR 122

Query: 126 EFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFI 165
             +++ K+     KE+++++K  +E G+PKKP ++F  F+
Sbjct: 123 AEIKQMKQDISDAKERKQLRKRVKELGRPKKPASAFLRFV 162

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198449964|ref|XP_001357800.2| GA18041 [Drosophila pseudoobscura pseudoobscura] gi|198130831|gb|EAL26935.2| GA18041 [Drosophila pseudoobscura pseudoobscura]

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 51/160 (31%), Positives = 94/160 (58%), Gaps = 1/160 (0%)

Query: 6   LTTGVFTGGNVFNLRSCLMPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRN 65
           L+ G   G  +  +R   + +L++ +   L +   + + +P +PKKPLTPYF+F  ++R 
Sbjct: 8   LSRGSIIGSLINKVRPLAVANLSN-SPVQLSKTVEEQVGLPPRPKKPLTPYFRFMREMRP 66

Query: 66  KIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAI 125
           K++  NP I  IEV + +++ W       K+RL+ E+ K++++Y +   KY   LT E  
Sbjct: 67  KLIATNPTITTIEVVRQLAKSWVDADTNLKERLQVEFKKDQQVYLEQRTKYDATLTDEQR 126

Query: 126 EFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFI 165
             +++ K+   + KE+R+++K  +E G+PKKP ++F  FI
Sbjct: 127 AGIKQLKKDIGEAKERRQLRKRVKELGRPKKPASAFLRFI 166

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|118788729|ref|XP_316944.3| AGAP008499-PA [Anopheles gambiae str. PEST] gi|116122885|gb|EAA12238.3| AGAP008499-PA [Anopheles gambiae str. PEST]

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 47/155 (30%), Positives = 88/155 (56%), Gaps = 5/155 (3%)

Query: 14  GNVFNLRSCLMPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPN 73
           G++ ++ SC +    ++  AG   +     S+PEKPK+P+  Y +F   IR+ +   NP 
Sbjct: 23  GSLSSVPSCGLHATATLNDAGTATK-----SVPEKPKRPMNTYIRFAQSIRSSLASANPQ 77

Query: 74  IKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRKEKE 133
               +++KL + +W+ + +A K +LE EY +E+ ++ Q   KY  +LT      ++ E++
Sbjct: 78  ASPTDISKLAAVKWQSLDQATKAKLEEEYKREQAVWLQKNAKYLSQLTDAQKAEIKLERQ 137

Query: 134 VKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDN 168
            + + K KRE K++ +E G+PK+P N++  F   N
Sbjct: 138 QRNEGKVKREQKRMLKELGRPKRPMNAYLRFCAQN 172

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157136745|ref|XP_001663824.1| mitochondrial transcription factor A, putative [Aedes aegypti] gi|108869859|gb|EAT34084.1| AAEL013643-PA [Aedes aegypti]

 Score = 95.5 bits (236), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 47/134 (35%), Positives = 82/134 (61%), Gaps = 4/134 (2%)

Query: 44  SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYA 103
           ++PEKPK+P+  Y +F   +R  ++ +NP     +++KL + +W+ +  A K +LE+EY 
Sbjct: 48  ALPEKPKRPVNAYIRFLQSVRPSLLAKNPKASPTDISKLAAAQWQVLDPASKSKLEDEYK 107

Query: 104 KEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYL 163
           KE+ ++ Q   KY  +LT +  + +R+ +  K ++K KRE KK  +E G+PK+P N F L
Sbjct: 108 KEQTVWLQKNAKYLSQLTDQQKQDIRQARTEKTEEKAKREYKKKVKELGRPKRPLNGFLL 167

Query: 164 FIKD----NIDKKE 173
           +  D    N+ K+E
Sbjct: 168 YCADKKPKNLSKEE 181

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157107110|ref|XP_001649627.1| mitochondrial transcription factor A, putative [Aedes aegypti] gi|157107112|ref|XP_001649628.1| mitochondrial transcription factor A, putative [Aedes aegypti] gi|108868738|gb|EAT32963.1| AAEL014794-PA [Aedes aegypti] gi|108868739|gb|EAT32964.1| AAEL014794-PB [Aedes aegypti]

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 47/134 (35%), Positives = 82/134 (61%), Gaps = 4/134 (2%)

Query: 44  SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYA 103
           ++PEKPK+P+  Y +F   +R  ++ +NP     +++KL + +W+ +  A K +LE+EY 
Sbjct: 48  ALPEKPKRPVNAYIRFLQSVRPSLLAKNPKASPTDISKLAAAQWQVLDPASKSKLEDEYK 107

Query: 104 KEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYL 163
           KE+ ++ Q   KY  +LT +  + +R+ +  K ++K KRE KK  +E G+PK+P N F L
Sbjct: 108 KEQTVWLQKNAKYLSQLTDQQKQDIRQARTEKTEEKAKREYKKKVKELGRPKRPLNGFLL 167

Query: 164 FIKD----NIDKKE 173
           +  D    N+ K+E
Sbjct: 168 YCADKKPKNLSKEE 181

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195390660|ref|XP_002053986.1| GJ24186 [Drosophila virilis] gi|194152072|gb|EDW67506.1| GJ24186 [Drosophila virilis]

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/123 (35%), Positives = 80/123 (65%)

Query: 43  LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEY 102
           + +P +PKKPLTPYF+F  ++R K++ ++P I  +EV + +S+ W  +    K+RL++EY
Sbjct: 44  IGLPPRPKKPLTPYFRFMREMRPKMLAKDPKITTVEVVRQLSKSWVDVDPKLKERLQSEY 103

Query: 103 AKEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFY 162
            K++EIY +   KY   LT +    +++ K+     KE+++++K  +E G+PKKP ++F 
Sbjct: 104 KKDQEIYLEQRTKYDATLTDQQRAEIKQMKQDINDAKERKQLRKRIKELGRPKKPASAFL 163

Query: 163 LFI 165
            F+
Sbjct: 164 RFV 166

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194744166|ref|XP_001954566.1| GF18333 [Drosophila ananassae] gi|190627603|gb|EDV43127.1| GF18333 [Drosophila ananassae]

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 53/166 (31%), Positives = 93/166 (56%), Gaps = 10/166 (6%)

Query: 7   TTGVFTGGNVFNLRSCLMPHLNSVTTAGLK-------QQTSQPLSIPEKPKKPLTPYFKF 59
           TT + + G++F     LM  +  +  AG+        +   + + +P +PKKPLTPYF+F
Sbjct: 5   TTMLSSRGSLFG---SLMGKVRPLAAAGISNSPVTQSKTLEEQVGLPPRPKKPLTPYFRF 61

Query: 60  QGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE 119
               R K++  NP +  I+  + +S+ W +     K+RL+ EY K+++IY +   KY   
Sbjct: 62  MRDQRPKLIAANPKLSTIDAVRQLSKSWSEADVKLKERLQTEYKKDQQIYLEQRTKYDAT 121

Query: 120 LTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFI 165
           LT E    +++ K+   + KE+R+++K  +E G+PKKP ++F  FI
Sbjct: 122 LTDEQRAEIKQLKQDIVEAKERRQLRKRVKELGRPKKPASAFLRFI 167

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195158925|ref|XP_002020334.1| GL13929 [Drosophila persimilis] gi|194117103|gb|EDW39146.1| GL13929 [Drosophila persimilis]

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 51/160 (31%), Positives = 92/160 (57%), Gaps = 1/160 (0%)

Query: 6   LTTGVFTGGNVFNLRSCLMPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRN 65
           L+ G   G  +  +R   + ++++      K    Q + +P +PKKPLTPYF+F  ++R 
Sbjct: 8   LSRGSIIGSLINKVRPLAVANISNSPVQQSKTVEEQ-VGLPPRPKKPLTPYFRFMREMRP 66

Query: 66  KIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAI 125
           K++  NP I  IEV + +++ W       K+RL+ E+ K++++Y +   KY   LT E  
Sbjct: 67  KLIATNPTITTIEVVRQLAKSWVDADTNLKERLQVEFKKDQQVYLEQRTKYDATLTDEQR 126

Query: 126 EFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFI 165
             +++ K+   + KE+R+++K  +E G+PKKP ++F  FI
Sbjct: 127 AGIKQLKKDIGEAKERRQLRKRVKELGRPKKPASAFLRFI 166

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

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	180
FB|FBgn0038805	284	TFAM "mitochondrial transcript	0.838	0.531	0.302	3.2e-17
RGD|620682	244	Tfam "transcription factor A,	0.733	0.540	0.25	7.1e-13
UNIPROTKB|Q5D144	246	TFAM "Transcription factor A,	0.716	0.524	0.261	6.4e-12
MGI|MGI:107810	243	Tfam "transcription factor A,	0.711	0.526	0.242	8.2e-12
UNIPROTKB|E1BA21	246	TFAM "Transcription factor A,	0.744	0.544	0.244	2.2e-11
UNIPROTKB|Q0II87	246	TFAM "Transcription factor A,	0.744	0.544	0.244	2.2e-11
UNIPROTKB|J3QR61	153	SMARCE1 "SWI/SNF-related matri	0.694	0.816	0.261	2.8e-11
UNIPROTKB|F1RXE6	194	SMARCE1 "Uncharacterized prote	0.694	0.644	0.261	2.8e-11
ZFIN|ZDB-GENE-040426-1159	719	ubtfl "upstream binding transc	0.444	0.111	0.345	4.3e-11
UNIPROTKB|Q00059	246	TFAM "Transcription factor A,	0.711	0.520	0.223	5.1e-11

FB|FBgn0038805 TFAM "mitochondrial transcription factor A" [Drosophila melanogaster (taxid:7227)]

 Score = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 46/152 (30%), Positives = 77/152 (50%)

Query:    29 SVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWK 88
             S T A   +   + L +P +PKKPLTPYF+F  + R K+   NP I  +EV + +S+ W 
Sbjct:    58 SNTPAVPSKTLEEQLGLPPRPKKPLTPYFRFMREQRPKLKAANPQITTVEVVRQLSKNWS 117

Query:    89 KIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLF 148
                   K+RL+ E+ ++++IY +   KY   LT E    ++                   
Sbjct:   118 DADAQLKERLQAEFKRDQQIYVEERTKYDATLTEEQRAEIKQLKQDLVDAKERRQLRKRV 177

Query:   149 RETGKPKKPGNSFYLFI-KDNIDKKEYEGKSY 179
             +E G+PKKP ++F  FI  + I+  + + ++Y
Sbjct:   178 KELGRPKKPASAFLRFIASERINTPQGDKQTY 209

GO:0005739 "mitochondrion" evidence=ISS;IDA;NAS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;NAS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=NAS

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

GO:0006264 "mitochondrial DNA replication" evidence=NAS

GO:0005813 "centrosome" evidence=IDA

GO:0005694 "chromosome" evidence=IDA

RGD|620682 Tfam "transcription factor A, mitochondrial" [Rattus norvegicus (taxid:10116)]

 Score = 170 (64.9 bits), Expect = 7.1e-13, P = 7.1e-13
 Identities = 33/132 (25%), Positives = 68/132 (51%)

Query:    44 SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYA 103
             S+   PKKP++ Y +F  +   K   ++P+ K+ E+ + ++  W+++ EAEKK  E ++ 
Sbjct:    44 SLGNYPKKPMSSYLRFSTEQLPKFKAKHPDAKVSELIRKIAAMWRELPEAEKKVYEADFK 103

Query:   104 KEKEIYAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYL 163
              E ++Y + V KY ++LTP  +  L                       GKPK+P +++ +
Sbjct:   104 AEWKVYKEAVSKYKEQLTPSQLMGLEKEARQKRLKKKAQIKRRELILLGKPKRPRSAYNI 163

Query:   164 FIKDNIDKKEYE 175
             ++ ++  + + E
Sbjct:   164 YVSESFQEAKDE 175

GO:0003677 "DNA binding" evidence=IDA

GO:0003682 "chromatin binding" evidence=ISO;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISO;IMP;TAS

GO:0005634 "nucleus" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISO;IDA

GO:0006264 "mitochondrial DNA replication" evidence=TAS

GO:0006390 "transcription from mitochondrial promoter" evidence=ISO;IMP;TAS

GO:0006391 "transcription initiation from mitochondrial promoter" evidence=ISO;ISS

GO:0008301 "DNA binding, bending" evidence=ISO;ISS

GO:0031072 "heat shock protein binding" evidence=IPI

GO:0033108 "mitochondrial respiratory chain complex assembly" evidence=IEA;ISO

GO:0042645 "mitochondrial nucleoid" evidence=ISO;ISS

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO;ISS

GO:0070363 "mitochondrial light strand promoter sense binding" evidence=ISO;ISS

UNIPROTKB|Q5D144 TFAM "Transcription factor A, mitochondrial" [Sus scrofa (taxid:9823)]

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 34/130 (26%), Positives = 65/130 (50%)

Query:    49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
             PKKP+T Y +F  +       +NP+ K  E+ K ++E W+++ ++EKK  E+ Y  + ++
Sbjct:    50 PKKPMTSYVRFSKEQLPIFKAQNPDAKNSELIKKIAELWRELPDSEKKIYEDAYRADWQV 109

Query:   109 YAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYLFIKDN 168
             Y + V +  ++LTP  +  L                       GKPK+P +++ +FI + 
Sbjct:   110 YKEEVNRIQEQLTPSQMVSLEKEIMQKRLKKKALIKKRELTMLGKPKRPRSAYNIFIAER 169

Query:   169 IDKKEYEGKS 178
               + + +G S
Sbjct:   170 FQEAK-DGPS 178

GO:0008301 "DNA binding, bending" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006390 "transcription from mitochondrial promoter" evidence=ISS

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

GO:0042645 "mitochondrial nucleoid" evidence=ISS

GO:0003682 "chromatin binding" evidence=ISS

GO:0006391 "transcription initiation from mitochondrial promoter" evidence=ISS

GO:0070363 "mitochondrial light strand promoter sense binding" evidence=ISS

GO:0033108 "mitochondrial respiratory chain complex assembly" evidence=IEA

MGI|MGI:107810 Tfam "transcription factor A, mitochondrial" [Mus musculus (taxid:10090)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 31/128 (24%), Positives = 65/128 (50%)

Query:    44 SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYA 103
             S+   PKKP++ Y +F  +   K   ++P+ K+ E+ + ++  W+++ EAEKK  E ++ 
Sbjct:    44 SMGSYPKKPMSSYLRFSTEQLPKFKAKHPDAKLSELVRKIAALWRELPEAEKKVYEADFK 103

Query:   104 KEKEIYAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYL 163
              E + Y + V KY ++LTP  +  +                       GKPK+P +++ +
Sbjct:   104 AEWKAYKEAVSKYKEQLTPSQLMGMEKEARQRRLKKKALVKRRELILLGKPKRPRSAYNI 163

Query:   164 FIKDNIDK 171
             ++ ++  +
Sbjct:   164 YVSESFQE 171

GO:0003677 "DNA binding" evidence=ISO

GO:0003682 "chromatin binding" evidence=ISO

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISO;TAS

GO:0005634 "nucleus" evidence=IEA

GO:0005667 "transcription factor complex" evidence=TAS

GO:0005739 "mitochondrion" evidence=ISO;IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0006390 "transcription from mitochondrial promoter" evidence=ISO

GO:0006391 "transcription initiation from mitochondrial promoter" evidence=ISO

GO:0008301 "DNA binding, bending" evidence=ISO

GO:0031072 "heat shock protein binding" evidence=ISO

GO:0033108 "mitochondrial respiratory chain complex assembly" evidence=IMP

GO:0042645 "mitochondrial nucleoid" evidence=ISO

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO

GO:0070363 "mitochondrial light strand promoter sense binding" evidence=ISO

UNIPROTKB|E1BA21 TFAM "Transcription factor A, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 33/135 (24%), Positives = 66/135 (48%)

Query:    44 SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYA 103
             S+   PKKP+T Y +F  +       +NP+ K  E+ K +++ W+++ ++EKK  E+ Y 
Sbjct:    45 SLSGYPKKPMTSYVRFSKEQLPIFKAQNPDAKNSELIKKIAKLWRELPDSEKKIYEDAYR 104

Query:   104 KEKEIYAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYL 163
              + ++Y + + +  ++LTP  +  L                       GKPK+P +++ +
Sbjct:   105 ADWQVYKEEINRIQEQLTPSQMVSLEKEIMQKRLKKKALIKKRELTMLGKPKRPRSAYNI 164

Query:   164 FIKDNIDKKEYEGKS 178
             FI +   +   +G S
Sbjct:   165 FIAERFQEAR-DGTS 178

GO:0070363 "mitochondrial light strand promoter sense binding" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA

GO:0042645 "mitochondrial nucleoid" evidence=IEA

GO:0033108 "mitochondrial respiratory chain complex assembly" evidence=IEA

GO:0006391 "transcription initiation from mitochondrial promoter" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

UNIPROTKB|Q0II87 TFAM "Transcription factor A, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 33/135 (24%), Positives = 66/135 (48%)

Query:    44 SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYA 103
             S+   PKKP+T Y +F  +       +NP+ K  E+ K +++ W+++ ++EKK  E+ Y 
Sbjct:    45 SLSGYPKKPMTSYVRFSKEQLPIFKAQNPDAKNSELIKKIAKLWRELPDSEKKIYEDAYR 104

Query:   104 KEKEIYAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYL 163
              + ++Y + + +  ++LTP  +  L                       GKPK+P +++ +
Sbjct:   105 ADWQVYKEEINRIQEQLTPSQMVSLEKEIMQKRLKKKALIKKRELTMLGKPKRPRSAYNI 164

Query:   164 FIKDNIDKKEYEGKS 178
             FI +   +   +G S
Sbjct:   165 FIAERFQEAR-DGTS 178

GO:0008301 "DNA binding, bending" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006390 "transcription from mitochondrial promoter" evidence=ISS

GO:0042645 "mitochondrial nucleoid" evidence=ISS

GO:0003682 "chromatin binding" evidence=ISS

GO:0006391 "transcription initiation from mitochondrial promoter" evidence=ISS

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

GO:0070363 "mitochondrial light strand promoter sense binding" evidence=ISS

UNIPROTKB|J3QR61 SMARCE1 "SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1" [Homo sapiens (taxid:9606)]

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 34/130 (26%), Positives = 62/130 (47%)

Query:    25 PHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVS 84
             P  NS  TA       +P   P+ P KPL PY ++  ++ +++   NP++K+ E+ K++ 
Sbjct:    27 PGTNSRVTASSGITIPKP---PKPPDKPLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIG 83

Query:    85 EEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXX 144
               W+ + + EK+   NEY  EK  Y +++K YH+  +P  + ++                
Sbjct:    84 GMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHN--SPAYLAYINAKSRAEAALEEESRQ 141

Query:   145 XXLFRETGKP 154
                  E G+P
Sbjct:   142 RQSRMEKGEP 151

GO:0016514 "SWI/SNF complex" evidence=IEA

GO:0071564 "npBAF complex" evidence=IEA

GO:0071565 "nBAF complex" evidence=IEA

UNIPROTKB|F1RXE6 SMARCE1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 34/130 (26%), Positives = 62/130 (47%)

Query:    25 PHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVS 84
             P  NS  TA       +P   P+ P KPL PY ++  ++ +++   NP++K+ E+ K++ 
Sbjct:    45 PGTNSRVTASSGITIPKP---PKPPDKPLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIG 101

Query:    85 EEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXX 144
               W+ + + EK+   NEY  EK  Y +++K YH+  +P  + ++                
Sbjct:   102 GMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHN--SPAYLAYINAKSRAEAALEEESRQ 159

Query:   145 XXLFRETGKP 154
                  E G+P
Sbjct:   160 RQSRMEKGEP 169

GO:0071565 "nBAF complex" evidence=IEA

GO:0071564 "npBAF complex" evidence=IEA

GO:0047485 "protein N-terminus binding" evidence=IEA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0016922 "ligand-dependent nuclear receptor binding" evidence=IEA

GO:0016514 "SWI/SNF complex" evidence=IEA

GO:0008080 "N-acetyltransferase activity" evidence=IEA

GO:0006338 "chromatin remodeling" evidence=IEA

GO:0006337 "nucleosome disassembly" evidence=IEA

ZFIN|ZDB-GENE-040426-1159 ubtfl "upstream binding transcription factor, like" [Danio rerio (taxid:7955)]

 Score = 153 (58.9 bits), Expect = 4.3e-11, Sum P(2) = 4.3e-11
 Identities = 28/81 (34%), Positives = 56/81 (69%)

Query:    46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
             P+ PKKPLTPYF+F  + R K  + +P +  +++TK++S+++K++ E +K +   E+ +E
Sbjct:   111 PDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQRE 170

Query:   106 KEIYAQNVKKYHDELTPEAIE 126
             KE + +N+ ++ ++  P+ IE
Sbjct:   171 KESFEKNMARFKED-HPDLIE 190

GO:0003682 "chromatin binding" evidence=IEA

UNIPROTKB|Q00059 TFAM "Transcription factor A, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 153 (58.9 bits), Expect = 5.1e-11, P = 5.1e-11
 Identities = 29/130 (22%), Positives = 66/130 (50%)

Query:    49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
             PKKP++ Y +F  +       +NP+ K  E+ + +++ W+++ +++KK  ++ Y  E ++
Sbjct:    50 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQV 109

Query:   109 YAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYLFIKDN 168
             Y + + ++ ++LTP  I  L                       GKPK+P +++ +++ + 
Sbjct:   110 YKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAER 169

Query:   169 IDKKEYEGKS 178
                +E +G S
Sbjct:   170 F--QEAKGDS 177

GO:0031072 "heat shock protein binding" evidence=IEA

GO:0033108 "mitochondrial respiratory chain complex assembly" evidence=IEA

GO:0070363 "mitochondrial light strand promoter sense binding" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0006391 "transcription initiation from mitochondrial promoter" evidence=IDA;TAS

GO:0003682 "chromatin binding" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IMP

GO:0006390 "transcription from mitochondrial promoter" evidence=IMP;TAS

GO:0008301 "DNA binding, bending" evidence=IDA

GO:0006356 "regulation of transcription from RNA polymerase I promoter" evidence=TAS

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

GO:0005759 "mitochondrial matrix" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0042645 "mitochondrial nucleoid" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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	180
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	4e-12
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	2e-11
smart00398	70	smart00398, HMG, high mobility group	1e-09
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	2e-09
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	6e-07
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	0.003
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	0.004

>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

 Score = 58.0 bits (141), Expect = 4e-12
 Identities = 27/61 (44%), Positives = 42/61 (68%)

Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PK+PL+ YF F  + R K+ + NP+  + EVTK++ E+WK++ E EKK+ E +  K+KE 
Sbjct: 1   PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKER 60

Query: 109 Y 109
           Y
Sbjct: 61  Y 61

These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

 Score = 56.1 bits (136), Expect = 2e-11
 Identities = 24/66 (36%), Positives = 41/66 (62%)

Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PK+PL+ YF F  + R ++   NP + + E++K++ E WK + E EKK+ E +  K+KE 
Sbjct: 1   PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKER 60

Query: 109 YAQNVK 114
           Y + + 
Sbjct: 61  YEKEMP 66

HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

>gnl|CDD|197700 smart00398, HMG, high mobility group

 Score = 51.5 bits (124), Expect = 1e-09
 Identities = 24/69 (34%), Positives = 40/69 (57%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
           KPK+P++ +  F  + R KI   NP++   E++K + E WK + E EK   E +  K+KE
Sbjct: 1   KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60

Query: 108 IYAQNVKKY 116
            Y + + +Y
Sbjct: 61  RYEEEMPEY 69

Length = 70

>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box

 Score = 51.1 bits (123), Expect = 2e-09
 Identities = 26/68 (38%), Positives = 40/68 (58%)

Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PK+PL+ +F F  + R K+   NP +K  E++K++ E+WK + E EKK  E +  KEK  
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEKAR 60

Query: 109 YAQNVKKY 116
           Y +    Y
Sbjct: 61  YEKAYPAY 68

Length = 69

>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

 Score = 47.2 bits (112), Expect = 6e-07
 Identities = 32/110 (29%), Positives = 56/110 (50%), Gaps = 1/110 (0%)

Query: 45  IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
            P  PK+PL+ YF +  + R++I + NP +   EV KL+SE+WK++ + EK+    E   
Sbjct: 67  DPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANS 126

Query: 105 EKEIYAQNVKKYHDELTP-EAIEFLRKEKEVKKQKKEKREMKKLFRETGK 153
           ++E Y +  ++Y+ +L     I    + +   + K E     K   E  K
Sbjct: 127 DRERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETK 176

Length = 211

>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIK--IIEVTKLVSEEWKKIGEAEKKRLENE-- 101
           P  PK+ L+ Y  F  + R +I+  NP +   +  V K+V E W K+ E EK   E +  
Sbjct: 20  PNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQ 79

Query: 102 -----YAKEKEIYAQ 111
                Y KEK  YA+
Sbjct: 80  EDKVRYEKEKAEYAK 94

Length = 94

>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898)

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNI-KIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
           P KPK     YF F   +R ++    P +  + E +KL SE+WK + E EK++ E +  +
Sbjct: 1   PNKPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKARE 60

Query: 105 EKEIYAQ 111
           +K+ Y +
Sbjct: 61  DKKRYDR 67

This domain is predominantly found in Maelstrom homolog proteins. It has no known function. Length = 69

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	180
PTZ00199	94	high mobility group protein; Provisional	99.9
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.83
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.82
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.82
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.81
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.8
smart00398	70	HMG high mobility group.	99.79
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.79
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.73
KOG0381|consensus	96		99.72
KOG0527|consensus	331		99.69
KOG0526|consensus	615		99.59
KOG4715|consensus	410		99.59
KOG3248|consensus	421		99.24
KOG0528|consensus	511		99.07
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	98.46
PTZ00199	94	high mobility group protein; Provisional	98.38
KOG2746|consensus	683		98.21
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	97.48
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	97.43
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	97.35
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	97.25
smart00398	70	HMG high mobility group.	97.23
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.15
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	97.14
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	97.13
KOG0526|consensus	615		97.09
COG5648	211	NHP6B Chromatin-associated proteins containing the	97.06
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	96.78
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	96.25
KOG0381|consensus	96		96.14
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	92.24
KOG3248|consensus	421		91.13
KOG0527|consensus	331		90.49
PF11304	107	DUF3106: Protein of unknown function (DUF3106); In	89.97
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	88.99
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	86.13
cd00225	159	API3 Ascaris pepsin inhibitor-3 (API3); protein in	83.27
PRK15117	211	ABC transporter periplasmic binding protein MlaC;	82.99

>PTZ00199 high mobility group protein; Provisional

Probab=99.90  E-value=3.8e-23  Score=145.72  Aligned_cols=83  Identities=29%  Similarity=0.555  Sum_probs=77.3

Q ss_pred             cccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHH
Q psy14923         35 LKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIK--IIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQN  112 (180)
Q Consensus        35 ~k~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~--~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~  112 (180)
                      .+++..++.+||+.|++|+|||++|+.++|..|..+||+++  +++|+++||++|+.||++||.+|+++|++++++|..+
T Consensus         9 ~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e   88 (94)
T PTZ00199          9 LVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKE   88 (94)
T ss_pred             cccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence            34455567899999999999999999999999999999986  8999999999999999999999999999999999999


Q ss_pred             HHhhh
Q psy14923        113 VKKYH  117 (180)
Q Consensus       113 ~~~y~  117 (180)
                      |.+|.
T Consensus        89 ~~~Y~   93 (94)
T PTZ00199         89 KAEYA   93 (94)
T ss_pred             HHHHh
Confidence            99995

>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=99.83  E-value=1.9e-20  Score=127.10  Aligned_cols=72  Identities=17%  Similarity=0.335  Sum_probs=69.5

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         48 KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        48 ~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .|+||+|||+||+++.|..++.+||++++.+|+++||++|+.||+++|++|.++|++++++|..++++|.-.
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~   72 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYT   72 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCccc
Confidence            478999999999999999999999999999999999999999999999999999999999999999999863

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=99.82  E-value=3.4e-20  Score=145.19  Aligned_cols=85  Identities=31%  Similarity=0.606  Sum_probs=81.3

Q ss_pred             cccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy14923         37 QQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKY  116 (180)
Q Consensus        37 ~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y  116 (180)
                      +..+++.+||+.||||+|||++|+.++|.++..++|++++.+|.+++|++|++|+|+||++|...|..++++|..++..|
T Consensus        59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y  138 (211)
T COG5648          59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEY  138 (211)
T ss_pred             HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhh
Confidence            45567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhCC
Q psy14923        117 HDELT  121 (180)
Q Consensus       117 ~~~~~  121 (180)
                      ...++
T Consensus       139 ~~k~~  143 (211)
T COG5648         139 NKKLP  143 (211)
T ss_pred             hcccC
Confidence            99876

>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=99.82  E-value=6.8e-20  Score=122.93  Aligned_cols=69  Identities=23%  Similarity=0.456  Sum_probs=67.1

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy14923         49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH  117 (180)
Q Consensus        49 PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~  117 (180)
                      .|||+|||++|++++|..++.+||++++.+|+++||++|+.||+++|++|.++|+.++++|.+++++|+
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            479999999999999999999999999999999999999999999999999999999999999999885

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.

>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin

Probab=99.81  E-value=1.6e-19  Score=119.42  Aligned_cols=69  Identities=32%  Similarity=0.641  Sum_probs=65.8

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy14923         49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH  117 (180)
Q Consensus        49 PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~  117 (180)
                      |+||+|||++|+.+.+..++.+||+++..+|+++||++|++||+++|.+|.+.|++++.+|.+++.+|+
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            899999999999999999999999999999999999999999999999999999999999999999985

HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....

>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

Probab=99.80  E-value=4.3e-19  Score=116.35  Aligned_cols=65  Identities=42%  Similarity=0.806  Sum_probs=63.7

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHH
Q psy14923         49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNV  113 (180)
Q Consensus        49 PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~  113 (180)
                      ||+|+|||++|+.+.|..++.+||++++.+|++.||++|++||+++|++|.+.|++++++|..+|
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            89999999999999999999999999999999999999999999999999999999999999887

These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.

>smart00398 HMG high mobility group

Probab=99.79  E-value=7.6e-19  Score=116.04  Aligned_cols=70  Identities=34%  Similarity=0.665  Sum_probs=67.9

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy14923         48 KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH  117 (180)
Q Consensus        48 ~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~  117 (180)
                      +|++|+|||++|+++.|..+..+||++++.+|++.||++|+.||+++|++|.+.|++++++|..++..|.
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            5899999999999999999999999999999999999999999999999999999999999999999874

>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins

Probab=99.79  E-value=7.1e-19  Score=118.26  Aligned_cols=72  Identities=33%  Similarity=0.621  Sum_probs=63.8

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHh-CCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy14923         46 PEKPKKPLTPYFKFQGQIRNKIMER-NPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH  117 (180)
Q Consensus        46 p~~PKrP~say~lF~~e~r~~~~~~-~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~  117 (180)
                      |++||+|+|||+||+.+.+..++.. ++.....|+++.|+..|++||++||.+|+++|++++++|..+|..|.
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            6899999999999999999999888 77788999999999999999999999999999999999999999984

It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....

>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

Probab=99.73  E-value=3e-17  Score=107.15  Aligned_cols=65  Identities=37%  Similarity=0.753  Sum_probs=63.1

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHH
Q psy14923         49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNV  113 (180)
Q Consensus        49 PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~  113 (180)
                      |++|+|||++|+++.+..++.++|+++..+|++.||++|+.|++++|.+|.+.|++++.+|.+++
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            78999999999999999999999999999999999999999999999999999999999998775

HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member

>KOG0381|consensus

Probab=99.72  E-value=8.2e-17  Score=113.30  Aligned_cols=76  Identities=37%  Similarity=0.681  Sum_probs=72.3

Q ss_pred             CC--CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHH-hhhhhC
Q psy14923         45 IP--EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVK-KYHDEL  120 (180)
Q Consensus        45 ~p--~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~-~y~~~~  120 (180)
                      +|  +.|++|+|||++|+.+.+..++.+||++++.+|++++|++|++|++++|.+|+..+..++++|..+|. .|+..+
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~~   95 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL   95 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            56  59999999999999999999999999999999999999999999999999999999999999999999 887754

>KOG0527|consensus

Probab=99.69  E-value=1e-16  Score=135.21  Aligned_cols=79  Identities=20%  Similarity=0.413  Sum_probs=74.2

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhC
Q psy14923         42 PLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDEL  120 (180)
Q Consensus        42 ~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  120 (180)
                      ........||||||||+|.++.|.+|..+||++.+.||+|.||.+|+.|+|+||.+|+++|++.+..|++++.+|+-.-
T Consensus        56 ~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYRP  134 (331)
T KOG0527|consen   56 DKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYRP  134 (331)
T ss_pred             CCCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCccccc
Confidence            3344578999999999999999999999999999999999999999999999999999999999999999999999753

>KOG0526|consensus

Probab=99.59  E-value=2e-15  Score=131.73  Aligned_cols=81  Identities=26%  Similarity=0.490  Sum_probs=75.8

Q ss_pred             cccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy14923         35 LKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVK  114 (180)
Q Consensus        35 ~k~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~  114 (180)
                      .+++..|+.+||++|||++||||+|++..|..|+.+  ++++++|++.+|++|+.||+  |.+|++.|+.++++|+.+|.
T Consensus       522 ~~~k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~  597 (615)
T KOG0526|consen  522 EKKKKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMK  597 (615)
T ss_pred             ccccCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHH
Confidence            344777889999999999999999999999999887  89999999999999999999  99999999999999999999


Q ss_pred             hhhhh
Q psy14923        115 KYHDE  119 (180)
Q Consensus       115 ~y~~~  119 (180)
                      +|+..
T Consensus       598 ~yk~g  602 (615)
T KOG0526|consen  598 EYKNG  602 (615)
T ss_pred             hhcCC
Confidence            99954

>KOG4715|consensus

Probab=99.59  E-value=1.8e-14  Score=118.81  Aligned_cols=111  Identities=30%  Similarity=0.516  Sum_probs=96.5

Q ss_pred             cCCCCCCCCccc------ccccCCCCCcccccccccccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHH
Q psy14923          6 LTTGVFTGGNVF------NLRSCLMPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEV   79 (180)
Q Consensus         6 ~~~~~~~~~~~~------~~~~~~~p~~~~~~~~~~k~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei   79 (180)
                      .-|+-|+|++.|      |.+.++.+++++++....-   ....+-|.+|-+|+-+||.|.+..|++|++.||++...||
T Consensus        19 ~st~g~~g~~~~~h~~y~n~r~~~~~~T~sr~~~~~~---~t~pkpPkppekpl~pymrySrkvWd~VkA~nPe~kLWei   95 (410)
T KOG4715|consen   19 PSTPGFGGYNPYTHLAYSNYRLPGNPATNSRVFQNSS---ITRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEI   95 (410)
T ss_pred             CCCCCCCCCCcchhhhccCcCCCCCCCCccccccccc---ccCCCCCCCCCcccchhhHHhhhhhhhhhccCcchHHHHH
Confidence            446668888877      7777778887777666533   2344567889999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         80 TKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        80 ~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      -++||.+|..|+|+||+.|.+.++.++..|++.|..|..+
T Consensus        96 GK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~s  135 (410)
T KOG4715|consen   96 GKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNS  135 (410)
T ss_pred             HHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            9999999999999999999999999999999999999884

>KOG3248|consensus

Probab=99.24  E-value=1.7e-11  Score=102.15  Aligned_cols=73  Identities=15%  Similarity=0.337  Sum_probs=67.8

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .-.|+|+|||+||++|.|++|.+++.-....+|.++||.+|..||.||..+|.++|.++++.+.+-+..|-+.
T Consensus       190 phiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSAR  262 (421)
T KOG3248|consen  190 PHIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSAR  262 (421)
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchh
Confidence            3568999999999999999999998756689999999999999999999999999999999999999999874

>KOG0528|consensus

Probab=99.07  E-value=8.6e-11  Score=101.99  Aligned_cols=80  Identities=19%  Similarity=0.380  Sum_probs=72.3

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy14923         42 PLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELT  121 (180)
Q Consensus        42 ~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~  121 (180)
                      ....+.-.||||||||+|.+|.|.+|...+||+.+..|+++||.+|+.||-.||++|.++-...-..|.+.+++|+-.-.
T Consensus       319 ~~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPR  398 (511)
T KOG0528|consen  319 RASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPR  398 (511)
T ss_pred             cCCCCccccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCC
Confidence            33445667999999999999999999999999999999999999999999999999999999988899999999986543

>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A

Probab=98.46  E-value=1.1e-06  Score=58.79  Aligned_cols=74  Identities=15%  Similarity=0.277  Sum_probs=61.7

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhCCH
Q psy14923         48 KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTP  122 (180)
Q Consensus        48 ~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~~  122 (180)
                      -|..|-+|--+|.+.....+.+.++.....+ .+.+...|.+|++.+|.+|+..|.++..+|+.+|.+|+..+++
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~   76 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRNDRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPAD   76 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTSTHHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHhHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence            4778889999999999999999998877666 4589999999999999999999999999999999999987663

>PTZ00199 high mobility group protein; Provisional

Probab=98.38  E-value=1.5e-07  Score=66.13  Aligned_cols=36  Identities=19%  Similarity=0.333  Sum_probs=30.5

Q ss_pred             HHHhhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        142 REMKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       142 ~~~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ++.++..+|++.||+|+|||++||.++|..+..+|.
T Consensus        11 k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P   46 (94)
T PTZ00199         11 RKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENP   46 (94)
T ss_pred             cccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCc
Confidence            344567899999999999999999999998877663

>KOG2746|consensus

Probab=98.21  E-value=1.5e-06  Score=78.63  Aligned_cols=69  Identities=20%  Similarity=0.409  Sum_probs=63.6

Q ss_pred             CCCCCCCCCCChHHHHHHHHH--HHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHH
Q psy14923         44 SIPEKPKKPLTPYFKFQGQIR--NKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQN  112 (180)
Q Consensus        44 ~~p~~PKrP~say~lF~~e~r--~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~  112 (180)
                      .+..-..+|||+|++|++.+|  ..+...||+..+.-|+++||++|-.|.+.||+.|.++|.+.++.|-++
T Consensus       177 r~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  177 RDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             CcchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            344567899999999999999  888899999999999999999999999999999999999999998776

>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins

Probab=97.48  E-value=8.1e-05  Score=49.54  Aligned_cols=25  Identities=32%  Similarity=0.591  Sum_probs=20.7

Q ss_pred             cCCCCCCCchHHHHHHHhhhhhhhc
Q psy14923        151 TGKPKKPGNSFYLFIKDNIDKKEYE  175 (180)
Q Consensus       151 ~~~PKrP~say~lF~~e~r~~~~~~  175 (180)
                      |++||+|+|||+||+.+++..+..+
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~   25 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEE   25 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHh
Confidence            5689999999999999999998766

It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....

>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

Probab=97.43  E-value=0.0001  Score=47.47  Aligned_cols=24  Identities=29%  Similarity=0.605  Sum_probs=22.0

Q ss_pred             CCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        154 PKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       154 PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ||+|+|||++|+++.|..+..+|.
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p   24 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENP   24 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCc
Confidence            899999999999999999987764

These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.

>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ]

Probab=97.35  E-value=0.0005  Score=53.21  Aligned_cols=49  Identities=22%  Similarity=0.383  Sum_probs=43.5

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCC
Q psy14923         43 LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIG   91 (180)
Q Consensus        43 ~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls   91 (180)
                      .+-|.+-.|-+|||..|+++....|++.+|+++..|....++..|...+
T Consensus       116 ~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  116 NKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             cCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence            3445566678999999999999999999999999999999999998765

>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin

Probab=97.25  E-value=0.00021  Score=46.51  Aligned_cols=24  Identities=42%  Similarity=0.668  Sum_probs=20.1

Q ss_pred             CCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        154 PKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       154 PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      |+||+|||+|||.+.+..+..+|.
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p   24 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENP   24 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHST
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhc
Confidence            899999999999999999987765

HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....

>smart00398 HMG high mobility group

Probab=97.23  E-value=0.00024  Score=46.03  Aligned_cols=25  Identities=40%  Similarity=0.635  Sum_probs=22.2

Q ss_pred             CCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        153 KPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       153 ~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +|++|+|||++|+++.+..+..+|.
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~   25 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENP   25 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCc
Confidence            4899999999999999999877663

>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta

Probab=97.15  E-value=0.0011  Score=51.41  Aligned_cols=49  Identities=18%  Similarity=0.379  Sum_probs=42.7

Q ss_pred             CChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHH
Q psy14923         53 LTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE  105 (180)
Q Consensus        53 ~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~  105 (180)
                      -+||+-|+.+.+.    .|.+++..|+....+..|..||+++|..|..++...
T Consensus        83 nnaYLNFLReFRr----kh~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~~  131 (183)
T PF06382_consen   83 NNAYLNFLREFRR----KHCGLSPQDLIQRAARAWCRLSEAEKNRYRRMAPSV  131 (183)
T ss_pred             chHHHHHHHHHHH----HccCCCHHHHHHHHHHHHHhCCHHHHHHHHhhcchh
Confidence            4679999999875    567999999999999999999999999998865543

The function of this family is unknown.

>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=97.14  E-value=0.00035  Score=46.89  Aligned_cols=25  Identities=28%  Similarity=0.452  Sum_probs=21.8

Q ss_pred             CCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        153 KPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       153 ~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .||||+|||+||+++.+..+..++.
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p   25 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENP   25 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCC
Confidence            3899999999999999998876654

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.

>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

Probab=97.13  E-value=0.00035  Score=44.73  Aligned_cols=24  Identities=25%  Similarity=0.593  Sum_probs=21.7

Q ss_pred             CCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        154 PKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       154 PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ||+|+|||++|+++.+..+..+|.
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~   24 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENP   24 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCc
Confidence            799999999999999999877764

HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member

>KOG0526|consensus

Probab=97.09  E-value=0.00029  Score=62.72  Aligned_cols=36  Identities=17%  Similarity=0.368  Sum_probs=31.2

Q ss_pred             HHhhhhhccCCCCCCCchHHHHHHHhhhhhhhcCCC
Q psy14923        143 EMKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGKS  178 (180)
Q Consensus       143 ~~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~~  178 (180)
                      +..++.|||++|||++||||+|....|.+++..+-+
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~dgi~  560 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKEDGIS  560 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhcCch
Confidence            345788999999999999999999999999877643

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=97.06  E-value=0.00053  Score=54.42  Aligned_cols=68  Identities=29%  Similarity=0.546  Sum_probs=61.3

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVK  114 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~  114 (180)
                      .+++.|..+|+-+-.+.+..+...+|+....+++++++..|++|++.-|.+|.+.+..++++|...++
T Consensus       142 ~~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         142 LPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             cCCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            57778888888888888888888899999999999999999999999999999999999999877654

>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=96.78  E-value=0.0011  Score=43.98  Aligned_cols=24  Identities=38%  Similarity=0.358  Sum_probs=20.8

Q ss_pred             CCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        154 PKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       154 PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .|||+|||++||++.|..+..+|.
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p   25 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYP   25 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCC
Confidence            589999999999999998876653

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.

>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases []

Probab=96.25  E-value=0.0062  Score=38.38  Aligned_cols=40  Identities=25%  Similarity=0.551  Sum_probs=36.3

Q ss_pred             CChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCH
Q psy14923         53 LTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGE   92 (180)
Q Consensus        53 ~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~   92 (180)
                      ++.|-+|.+..|+.+.+.||++....+...++.+|++-++
T Consensus        13 lt~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~~   52 (55)
T PF08073_consen   13 LTNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQE   52 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHHh
Confidence            4568899999999999999999999999999999997654

; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>KOG0381|consensus

Probab=96.14  E-value=0.0047  Score=42.89  Aligned_cols=28  Identities=29%  Similarity=0.554  Sum_probs=24.8

Q ss_pred             cc--CCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        150 ET--GKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       150 ~~--~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      |+  +.||+|+|||++|+.+.+..+..+|.
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p   46 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENP   46 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCC
Confidence            55  59999999999999999999888775

>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function

Probab=92.24  E-value=0.21  Score=36.71  Aligned_cols=45  Identities=20%  Similarity=0.453  Sum_probs=39.9

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCH
Q psy14923         48 KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGE   92 (180)
Q Consensus        48 ~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~   92 (180)
                      |-+|---||.-|...+.+.++.++|++..+++...|-.+|..-++
T Consensus        72 PErR~KAAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPe  116 (122)
T PF06244_consen   72 PERRMKAAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPE  116 (122)
T ss_pred             cchhHHHHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCC
Confidence            344445789999999999999999999999999999999988765

>KOG3248|consensus

Probab=91.13  E-value=0.12  Score=44.08  Aligned_cols=23  Identities=39%  Similarity=0.478  Sum_probs=20.0

Q ss_pred             CCCCCCchHHHHHHHhhhhhhhc
Q psy14923        153 KPKKPGNSFYLFIKDNIDKKEYE  175 (180)
Q Consensus       153 ~PKrP~say~lF~~e~r~~~~~~  175 (180)
                      -.|+|+|||+||++|+|.++-.+
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaE  213 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAE  213 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999988654

>KOG0527|consensus

Probab=90.49  E-value=0.17  Score=43.32  Aligned_cols=30  Identities=20%  Similarity=0.277  Sum_probs=25.5

Q ss_pred             hhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        148 FRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       148 ~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .+..+..|||+||||+|++..|.++-.++.
T Consensus        57 k~~~~hIKRPMNAFMVWSq~~RRkma~qnP   86 (331)
T KOG0527|consen   57 KTSTDRIKRPMNAFMVWSQGQRRKLAKQNP   86 (331)
T ss_pred             CCCccccCCCcchhhhhhHHHHHHHHHhCc
Confidence            355678999999999999999999877764

>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed

Probab=89.97  E-value=3  Score=29.82  Aligned_cols=53  Identities=11%  Similarity=0.349  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHhhcCCHHHHHHHHHHHHH-------HHHHHHHHHHhhhhhCCHHHHHHHHH
Q psy14923         77 IEVTKLVSEEWKKIGEAEKKRLENEYAK-------EKEIYAQNVKKYHDELTPEAIEFLRK  130 (180)
Q Consensus        77 ~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~-------~k~~y~~~~~~y~~~~~~~~~~~~~~  130 (180)
                      .++..-++..|..|+++.+..+.+.+..       +..+....|..|.. ++|+++..+..
T Consensus        10 q~~L~pl~~~W~~l~~~qr~k~l~~a~r~~~mspeqq~r~~~rm~~W~~-LspeqR~~~R~   69 (107)
T PF11304_consen   10 QQALAPLAERWNSLPPEQRRKWLQIAERWPSMSPEQQQRLRERMRRWAA-LSPEQRQQARE   69 (107)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHh-CCHHHHHHHHH
Confidence            4556678888888888888887777754       67777788887776 67777655443

Currently no function is known.

>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT)

Probab=88.99  E-value=1.4  Score=35.09  Aligned_cols=55  Identities=22%  Similarity=0.345  Sum_probs=41.4

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q psy14923         43 LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYA  103 (180)
Q Consensus        43 ~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~  103 (180)
                      ......++||+|+|+.|..=.-    ...|+....+++..|+..|..=+-  |..|.-.|.
T Consensus        38 ~~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~Qk~~S~~l~~lW~~dp~--k~~W~l~ak   92 (201)
T PF04769_consen   38 KRSPEKAKRPLNGFMAFRSYYS----PIFPPLPQKELSGILTKLWEKDPF--KNKWSLMAK   92 (201)
T ss_pred             cccccccccchhHHHHHHHHHH----hhcCCcCHHHHHHHHHHHHhCCcc--HhHHHHHhh
Confidence            3445678999999999976664    456788899999999999987432  566655543

MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=86.13  E-value=2.1  Score=33.94  Aligned_cols=46  Identities=13%  Similarity=0.443  Sum_probs=38.8

Q ss_pred             CCCHHHHHH-HHHHHhhcCCHHHHHHHHHHHHH-HHHHHHHHHHhhhh
Q psy14923         73 NIKIIEVTK-LVSEEWKKIGEAEKKRLENEYAK-EKEIYAQNVKKYHD  118 (180)
Q Consensus        73 ~~~~~ei~k-~l~~~Wk~Ls~~eK~~y~~~a~~-~k~~y~~~~~~y~~  118 (180)
                      -.++..+++ .+|.-|+.+|+++++.|.+.... ....|-..+..|..
T Consensus        63 ~~Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~  110 (198)
T TIGR03481        63 AFDLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAG  110 (198)
T ss_pred             hCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            467777766 58999999999999999999988 66778888888865

The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.

>cd00225 API3 Ascaris pepsin inhibitor-3 (API3); protein inhibitor that reversibly inhibits aspartic proteinase cathepsin E, and gastric enzymes pepsin and gastricsin

Probab=83.27  E-value=1.9  Score=32.67  Aligned_cols=29  Identities=17%  Similarity=0.402  Sum_probs=19.1

Q ss_pred             HHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhC
Q psy14923         84 SEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDEL  120 (180)
Q Consensus        84 ~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  120 (180)
                      |-.|+.|+.+|.+.        ...|..+..+|+..+
T Consensus        25 g~~lReLt~~Eq~e--------l~~y~~d~~~yK~~~   53 (159)
T cd00225          25 GFPLRELTPDEQQE--------LAQYVEDVADYKEEV   53 (159)
T ss_pred             CceeeeCCHHHHHH--------HHHHHHHHHHHHHHH
Confidence            34699999999443        345666666666543

>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional

Probab=82.99  E-value=4  Score=32.63  Aligned_cols=48  Identities=17%  Similarity=0.358  Sum_probs=39.1

Q ss_pred             CCCCHHHHHH-HHHHHhhcCCHHHHHHHHHHHHHH-HHHHHHHHHhhhhh
Q psy14923         72 PNIKIIEVTK-LVSEEWKKIGEAEKKRLENEYAKE-KEIYAQNVKKYHDE  119 (180)
Q Consensus        72 p~~~~~ei~k-~l~~~Wk~Ls~~eK~~y~~~a~~~-k~~y~~~~~~y~~~  119 (180)
                      |-.++..+++ .+|.-|+.+|+++++.|.+....- ...|-..+..|...
T Consensus        66 p~~Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~q  115 (211)
T PRK15117         66 PYVQVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHGQ  115 (211)
T ss_pred             ccCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence            4567777766 689999999999999999988874 45788888888753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	180
3tmm_A	238	Tfam Imposes A U-Turn On Mitochondrial Dna Length =		1e-08
3tq6_A	214	Crystal Structure Of Human Mitochondrial Transcript		2e-08
2crj_A	92	Solution Structure Of The Hmg Domain Of Mouse Hmg D		4e-08
1k99_A	99	Solution Structure Of The First Hmg Box In Human Up		3e-07
2yqi_A	81	Solution Structure Of The Second Hmg-Box Domain Fro		5e-06
1e7j_A	74	Hmg-D Complexed To A Bulge Dna Length = 74		1e-05
1qrv_A	73	Crystal Structure Of The Complex Of Hmg-D And Dna L		2e-05
1hma_A	73	The Solution Structure And Dynamics Of The Dna Bind		2e-05
3nm9_A	73	Hmgd(M13a)-Dna Complex Length = 73		3e-05
2co9_A	102	Solution Structure Of The Hmg_box Domain Of Thymus		2e-04
1j3c_A	79	Solution Structure Of The C-Terminal Domain Of The		3e-04
1j3d_A	78	Solution Structure Of The C-Terminal Domain Of The		4e-04
1wxl_A	73	Solution Structure Of The Hmg-Box Domain In The Ssr		4e-04

>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna Length = 238

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/117 (23%), Positives = 62/117 (52%)
Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PKKP++ Y +F  +       +NP+ K  E+ + +++ W+++ +++KK  ++ Y  E ++
Sbjct: 42  PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQV 101
Query: 109 YAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYLFI 165
           Y + + ++ ++LTP  I  L                       GKPK+P +++ +++
Sbjct: 102 YKEEISRFKEQLTPSQIXSLEKEIXDKHLKRKAXTKKKELTLLGKPKRPRSAYNVYV 158

>pdb|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription Factor A, Tfam Or Mttfa, Bound To The Light Strand Promoter Lsp Length = 214

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/117 (22%), Positives = 60/117 (51%)
Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PKKP++ Y +F  +       +NP+ K  E+ + +++ W+++ +++KK  ++ Y  E ++
Sbjct: 10  PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQV 69
Query: 109 YAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYLFI 165
           Y + + ++ ++LTP  I  L                       GKPK+P +++ +++
Sbjct: 70  YKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYV 126

>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain Protein Hmgx2 Length = 92

Iteration: 1
 Score = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 42/69 (60%)
Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PK P+T Y +F  + R +I  R+P++   E+TK++  EW K+  AEK+R  +E  KEK+ 
Sbjct: 8   PKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQ 67
Query: 109 YAQNVKKYH 117
           Y + +  Y 
Sbjct: 68  YLKELWAYQ 76

>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream Binding Factor Length = 99

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 56/81 (69%), Gaps = 1/81 (1%)
Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P+ PKKPLTPYF+F  + R K  + +P +  +++TK++S+++K++ E +K +   ++ +E
Sbjct: 8   PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQRE 67
Query: 106 KEIYAQNVKKYHDELTPEAIE 126
           K+ + +N+ ++ ++  P+ I+
Sbjct: 68  KQEFERNLARFRED-HPDLIQ 87

>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High Mobility Group Protein B3 Length = 81

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 38/68 (55%)
Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PK+P + +F F  + R KI   NP I I +V K + E W  + ++EK+    + AK KE 
Sbjct: 10  PKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEK 69
Query: 109 YAQNVKKY 116
           Y ++V  Y
Sbjct: 70  YEKDVADY 77

>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna Length = 74

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 45  IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
           + +KPK+PL+ Y  +    R  I   NP IK+ EV K   E W+ +   +K   E + AK
Sbjct: 1   MSDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAK 58
Query: 105 EKEIYAQNVKKYH 117
            K+ Y + VK++ 
Sbjct: 59  AKDDYDRAVKEFE 71

>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna Length = 73

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 47  EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
           +KPK+PL+ Y  +    R  I   NP IK+ EV K   E W+ +   +K   E + AK K
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 107 EIYAQNVKKYH 117
           + Y + VK++ 
Sbjct: 60  DDYDRAVKEFE 70

>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding Domain Of Hmg-D From Drosophila Melanogaster Length = 73

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 47  EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
           +KPK+PL+ Y  +    R  I   NP IK+ EV K   E W+ +   +K   E + AK K
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 107 EIYAQNVKKYH 117
           + Y + VK++ 
Sbjct: 60  DDYDRAVKEFE 70

>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex Length = 73

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 47  EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
           +KPK+PL+ Y  +    R  I   NP IK+ EV K   E W+ +   +K   E + AK K
Sbjct: 2   DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 107 EIYAQNVKKYH 117
           + Y + VK++ 
Sbjct: 60  DDYDRAVKEFE 70

>pdb|2CO9|A Chain A, Solution Structure Of The Hmg_box Domain Of Thymus High Mobility Group Box Protein Tox From Mouse Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 39/76 (51%)
Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P +P+KP++ Y  F    +  I  +NPN    EV+K+V+  W  +GE +K+  + +    
Sbjct: 15  PNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAA 74
Query: 106 KEIYAQNVKKYHDELT 121
           K+ Y + +  Y   L 
Sbjct: 75  KKEYLKQLAAYRASLV 90

>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 79

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 37/72 (51%)
Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P  PK+P + +F F  + R KI   +P + I +  K + E W +    +K+  E + AK 
Sbjct: 6   PNAPKRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKL 65
Query: 106 KEIYAQNVKKYH 117
           KE Y +++  Y 
Sbjct: 66  KEKYEKDIAAYR 77

>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 37/71 (52%)
Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P  PK+P + +F F  + R KI   +P + I +  K + E W +    +K+  E + AK 
Sbjct: 5   PNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKL 64
Query: 106 KEIYAQNVKKY 116
           KE Y +++  Y
Sbjct: 65  KEKYEKDIAAY 75

>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1 Subunit Of Fact Length = 73

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 12/79 (15%)
Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
           PK+  T +  +    R  I   NP IK+ E+ K   E WK++   +K + E+  AK+K+ 
Sbjct: 4   PKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQ- 60
Query: 109 YAQNVKKYHDELT---PEA 124
                 +YHDE+    PEA
Sbjct: 61  ------RYHDEMRNYKPEA 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	180
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-16
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-08
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	7e-16
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	8e-16
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	5e-15
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-08
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	7e-15
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	7e-14
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	9e-14
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	8e-13
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	3e-12
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	3e-07
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	6e-12
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	7e-12
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	9e-12
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	1e-11
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	2e-11
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	4e-08
1ckt_A	71	High mobility group 1 protein; high-mobility group	3e-11
1wgf_A	90	Upstream binding factor 1; transcription factor, D	7e-11
2lhj_A	97	High mobility group protein homolog NHP1; structur	1e-10
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	2e-10
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	3e-10
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	2e-06
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	1e-05
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	6e-05
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	8e-04

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214

 Score = 73.3 bits (179), Expect = 1e-16
 Identities = 32/130 (24%), Positives = 72/130 (55%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
              PKKP++ Y +F  +       +NP+ K  E+ + +++ W+++ +++KK  ++ Y  E
Sbjct: 7   ASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAE 66

Query: 106 KEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFI 165
            ++Y + + ++ ++LTP  I  L KE   K  K++    KK     GKPK+P +++ +++
Sbjct: 67  WQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYV 126

Query: 166 KDNIDKKEYE 175
            +   + + +
Sbjct: 127 AERFQEAKGD 136

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214

 Score = 51.3 bits (122), Expect = 1e-08
 Identities = 21/110 (19%), Positives = 46/110 (41%), Gaps = 4/110 (3%)

Query: 36  KQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEK 95
                + L++  KPK+P + Y  +  +   +    +P     E  K V E WK + ++EK
Sbjct: 102 AMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEK 157

Query: 96  KRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMK 145
           +       +++  Y   +K + +++     + L +    K++K    E  
Sbjct: 158 ELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTIKKQRKYGAEECL 207

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Length = 92

 Score = 68.2 bits (167), Expect = 7e-16
 Identities = 26/72 (36%), Positives = 42/72 (58%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
              PK P+T Y +F  + R +I  R+P++   E+TK++  EW K+  AEK+R  +E  KE
Sbjct: 5   SSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKE 64

Query: 106 KEIYAQNVKKYH 117
           K+ Y + +  Y 
Sbjct: 65  KQQYLKELWAYQ 76

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99

 Score = 68.2 bits (167), Expect = 8e-16
 Identities = 24/88 (27%), Positives = 54/88 (61%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P+ PKKPLTPYF+F  + R K  + +P +  +++TK++S+++K++ E +K +   ++ +E
Sbjct: 8   PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQRE 67

Query: 106 KEIYAQNVKKYHDELTPEAIEFLRKEKE 133
           K+ + +N+ ++ ++         + E  
Sbjct: 68  KQEFERNLARFREDHPDLIQNAKKLEHH 95

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238

 Score = 69.5 bits (169), Expect = 5e-15
 Identities = 34/148 (22%), Positives = 77/148 (52%)

Query: 28  NSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEW 87
            +  T G +        +   PKKP++ Y +F  +       +NP+ K  E+ + +++ W
Sbjct: 21  MASMTGGQQMGRGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRW 80

Query: 88  KKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKL 147
           +++ +++KK  ++ Y  E ++Y + + ++ ++LTP  I  L KE   K  K++    KK 
Sbjct: 81  RELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKE 140

Query: 148 FRETGKPKKPGNSFYLFIKDNIDKKEYE 175
               GKPK+P +++ +++ +   + + +
Sbjct: 141 LTLLGKPKRPRSAYNVYVAERFQEAKGD 168

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238

 Score = 51.8 bits (123), Expect = 1e-08
 Identities = 21/120 (17%), Positives = 47/120 (39%), Gaps = 4/120 (3%)

Query: 24  MPHLNSVTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLV 83
              +             + L++  KPK+P + Y  +  +   +    +P     E  K V
Sbjct: 122 EKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTV 177

Query: 84  SEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKRE 143
            E WK + ++EK+       +++  Y   +K + +++     + L +    K++K    E
Sbjct: 178 KENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTIKKQRKYGAEE 237

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 102

 Score = 65.9 bits (161), Expect = 7e-15
 Identities = 22/79 (27%), Positives = 41/79 (51%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P +P+KP++ Y  F    +  I  +NPN    EV+K+V+  W  +GE +K+  + +    
Sbjct: 15  PNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAA 74

Query: 106 KEIYAQNVKKYHDELTPEA 124
           K+ Y + +  Y   L  ++
Sbjct: 75  KKEYLKQLAAYRASLVSKS 93

>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Length = 77

 Score = 62.7 bits (153), Expect = 7e-14
 Identities = 23/71 (32%), Positives = 37/71 (52%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P  PK+P + +F F  + R KI   +P + I +V K + E W      +K+  E + AK 
Sbjct: 4   PNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 63

Query: 106 KEIYAQNVKKY 116
           KE Y +++  Y
Sbjct: 64  KEKYEKDIAAY 74

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Length = 93

 Score = 62.7 bits (153), Expect = 9e-14
 Identities = 25/88 (28%), Positives = 45/88 (51%)

Query: 30  VTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKK 89
           VT    K++T++    P  PK+ L+ Y  F  + R+ +   NP+I   +V K + E+WK 
Sbjct: 2   VTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKA 61

Query: 90  IGEAEKKRLENEYAKEKEIYAQNVKKYH 117
           +   EK+  E +   +K+ Y    + Y+
Sbjct: 62  LTPEEKQPYEAKAQADKKRYESEKELYN 89

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92

 Score = 60.1 bits (146), Expect = 8e-13
 Identities = 19/71 (26%), Positives = 32/71 (45%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
               KKP++    F    R + +  NP   + + T  + E WK + E EK + E +  K+
Sbjct: 5   SSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKD 64

Query: 106 KEIYAQNVKKY 116
            E Y   +K+ 
Sbjct: 65  LERYNSQMKRA 75

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173

 Score = 60.8 bits (147), Expect = 3e-12
 Identities = 23/71 (32%), Positives = 37/71 (52%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P  PK+P + +F F  + R KI   +P + I +V K + E W      +K+  E + AK 
Sbjct: 99  PNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 158

Query: 106 KEIYAQNVKKY 116
           KE Y +++  Y
Sbjct: 159 KEKYEKDIAAY 169

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173

 Score = 47.3 bits (112), Expect = 3e-07
 Identities = 33/140 (23%), Positives = 58/140 (41%), Gaps = 23/140 (16%)

Query: 34  GLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKI--IEVTKLVSEEWKKIG 91
           G    +      P+KP+  ++ Y  F    R +  +++P+  +   E +K  SE WK + 
Sbjct: 1   GSSGSSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS 60

Query: 92  EAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEKREMKKLFRET 151
             EK + E+    +K  Y + +K Y                        K E KK F++ 
Sbjct: 61  AKEKGKFEDMAKADKARYEREMKTYIP---------------------PKGETKKKFKDP 99

Query: 152 GKPKKPGNSFYLFIKDNIDK 171
             PK+P ++F+LF  +   K
Sbjct: 100 NAPKRPPSAFFLFCSEYRPK 119

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83

 Score = 57.7 bits (140), Expect = 6e-12
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKII--EVTKLVSEEWKKIGEAEKKRLENEYA 103
           P+KP+  ++ Y  F    R +  +++P+  +   E +K  SE WK +   EK + E+   
Sbjct: 5   PKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 64

Query: 104 KEKEIYAQNVKKYH 117
            +K  Y + +K Y 
Sbjct: 65  ADKARYEREMKTYI 78

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A 1qrv_A* Length = 73

 Score = 57.3 bits (139), Expect = 7e-12
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
           KPK+PL+ Y  +    R  I   NP IK+ EV K   E W+ +   +K   E + AK K+
Sbjct: 3   KPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAKD 60

Query: 108 IYAQNVKKY 116
            Y + VK++
Sbjct: 61  DYDRAVKEF 69

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73

 Score = 56.9 bits (138), Expect = 9e-12
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
            PK+  T +  +    R  I   NP IK+ E+ K   E WK++   +K + E+  AK+K+
Sbjct: 3   MPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQ 60

Query: 108 IYAQNVKKY 116
            Y   ++ Y
Sbjct: 61  RYHDEMRNY 69

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86

 Score = 57.0 bits (138), Expect = 1e-11
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKII--EVTKLVSEEWKKIGEAEKKRLENEYA 103
           P+KPK  ++ Y  F    R +  ++NP + +   E +K  SE WK +   EK + +    
Sbjct: 13  PKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAK 72

Query: 104 KEKEIYAQNVKKY 116
            +K  Y + +K Y
Sbjct: 73  ADKVRYDREMKDY 85

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Length = 159

 Score = 58.3 bits (141), Expect = 2e-11
 Identities = 17/73 (23%), Positives = 36/73 (49%)

Query: 45  IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
           + ++ K+P+  +  +    R K+   NP ++  E++K +  +WK + EAEK     E  K
Sbjct: 1   VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQK 60

Query: 105 EKEIYAQNVKKYH 117
            + ++ +    Y 
Sbjct: 61  LQAMHREKYPNYK 73

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Length = 159

 Score = 49.5 bits (118), Expect = 4e-08
 Identities = 24/80 (30%), Positives = 40/80 (50%)

Query: 37  QQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKK 96
            +T +    P  PK+P + +F F  + R KI   +P + I +V K + E W      +K+
Sbjct: 77  GETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQ 136

Query: 97  RLENEYAKEKEIYAQNVKKY 116
             E + AK KE Y +++  Y
Sbjct: 137 PYEKKAAKLKEKYEKDIAAY 156

>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A Length = 71

 Score = 55.5 bits (134), Expect = 3e-11
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKII--EVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           KP+  ++ Y  F    R +  +++P+  +   E +K  SE WK +   EK + E+    +
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 106 KEIYAQNVKKY 116
           K  Y + +K Y
Sbjct: 61  KARYEREMKTY 71

>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 90

 Score = 55.1 bits (133), Expect = 7e-11
 Identities = 18/71 (25%), Positives = 34/71 (47%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
            EKPK+P++  F F  + R ++ E  P +   E+T+L++  W  + E +K + +   A  
Sbjct: 18  SEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAAL 77

Query: 106 KEIYAQNVKKY 116
           K    +     
Sbjct: 78  KAQSERKSGPS 88

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Length = 97

 Score = 54.7 bits (132), Expect = 1e-10
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNI--KIIEVTKLVSEEWKKIGEAEKKRLENEYA 103
           P  PK+ L+ Y  F  + R +I+  NP I   +  + K++   W  + + EKK  E    
Sbjct: 20  PNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSD 79

Query: 104 KEKEIYAQNVKKY 116
           +++  Y +   +Y
Sbjct: 80  EDRVRYEREKAEY 92

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67

 Score = 53.1 bits (128), Expect = 2e-10
 Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 4/69 (5%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
           KPK+P + Y  +  +   +    +P     E  K V E WK + ++EK+       +++ 
Sbjct: 2   KPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDET 57

Query: 108 IYAQNVKKY 116
            Y   +K +
Sbjct: 58  RYHNEMKSW 66

>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Length = 101

 Score = 53.8 bits (129), Expect = 3e-10
 Identities = 14/93 (15%), Positives = 40/93 (43%), Gaps = 2/93 (2%)

Query: 49  PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
            K P+  Y KF  ++ +     +  +K  E    +   W++I +++K+  +    +++  
Sbjct: 9   KKPPMNGYQKFSQELLSNGELNHLPLK--ERMVEIGSRWQRISQSQKEHYKKLAEEQQRQ 66

Query: 109 YAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEK 141
           Y  ++  +   L+P+     ++    K++    
Sbjct: 67  YKVHLDLWVKSLSPQDRAAYKEYISNKRKSGPS 99

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 15/96 (15%), Positives = 37/96 (38%), Gaps = 4/96 (4%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
               K P   Y  +  ++   + +        E   L S++WK + + EK     +  ++
Sbjct: 15  GRPTKPPPNSYSLYCAELMANMKDVPST----ERMVLCSQQWKLLSQKEKDAYHKKCDQK 70

Query: 106 KEIYAQNVKKYHDELTPEAIEFLRKEKEVKKQKKEK 141
           K+ Y   + ++ + L  E  + +  E+++       
Sbjct: 71  KKDYEVELLRFLESLPEEEQQRVLGEEKMLNISGPS 106

>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Length = 87

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 13/66 (19%), Positives = 28/66 (42%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P K K+P+  +  F  + R +  +  P      ++ ++ + WKK+   E++    E    
Sbjct: 15  PNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKAL 74

Query: 106 KEIYAQ 111
            E   +
Sbjct: 75  AEEQKR 80

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Length = 82

 Score = 38.7 bits (91), Expect = 6e-05
 Identities = 10/66 (15%), Positives = 32/66 (48%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
               ++P+  +  F  + R+ + + +P +     TK++++ W  +   EK++  +   + 
Sbjct: 5   SSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEY 64

Query: 106 KEIYAQ 111
           K+ + +
Sbjct: 65  KDAFMK 70

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71

 Score = 35.6 bits (83), Expect = 8e-04
 Identities = 13/64 (20%), Positives = 34/64 (53%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
             ++P+  +  +    R ++ ++NP++   E++K++ + WK +  AEK+    E  + + 
Sbjct: 2   SIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRV 61

Query: 108 IYAQ 111
            + Q
Sbjct: 62  QHMQ 65

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	180
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	100.0
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.98
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.96
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.94
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.91
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.91
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.91
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.9
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.9
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.89
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.89
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.89
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.89
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.89
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.88
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.88
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.88
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.88
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.87
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.87
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.87
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.86
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.86
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.86
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.86
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.86
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.86
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.85
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.85
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.85
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.84
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.84
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.83
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.83
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.81
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.78
2cto_A	93	Novel protein; high mobility group box domain, hel	99.77
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.71
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.69
1wgf_A	90	Upstream binding factor 1; transcription factor, D	98.32
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	98.28
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	98.25
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	98.24
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	98.22
2lhj_A	97	High mobility group protein homolog NHP1; structur	98.19
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	98.19
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	98.19
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	98.17
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	98.09
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	98.07
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	98.07
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	98.05
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	98.02
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	98.01
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	97.97
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	97.96
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	97.87
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	97.86
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	97.81
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	97.79
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	97.78
1ckt_A	71	High mobility group 1 protein; high-mobility group	97.73
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	97.72
2cto_A	93	Novel protein; high mobility group box domain, hel	97.7
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	97.67
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	97.65
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	97.63
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	97.6
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	97.31
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	97.09

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}

Probab=100.00  E-value=5.6e-33  Score=224.72  Aligned_cols=134  Identities=24%  Similarity=0.521  Sum_probs=118.6

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhCCH
Q psy14923         43 LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTP  122 (180)
Q Consensus        43 ~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~~  122 (180)
                      ..+|++||+|+|||++||+++|..++.+||++++.||+++||++|+.||++||.+|+++|+.++++|+++|..|...++|
T Consensus        36 ~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~~p  115 (238)
T 3tmm_A           36 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTP  115 (238)
T ss_dssp             CHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCH
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCchHHHHHHHhhhhhhhcC
Q psy14923        123 EAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEG  176 (180)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~k~~~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~  176 (180)
                      .++..++.........++..++++..+|++.||||+|||+|||+++|..+.-+|
T Consensus       116 ~~~~~~~~~~~~k~~krk~~~kkk~~kdp~~PKrP~say~lF~~e~r~~~k~~~  169 (238)
T 3tmm_A          116 SQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDS  169 (238)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCHHHHHHHHHTTTSCCSS
T ss_pred             HHHHHHHHHHhhhhhhhhcccchhhhcccCCCCCCCcHHHHHHHHHHHHHhccC
Confidence            998776655544444443334456789999999999999999999998876443

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}

Probab=99.98  E-value=5.7e-32  Score=215.67  Aligned_cols=131  Identities=24%  Similarity=0.533  Sum_probs=116.3

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhCCHHHH
Q psy14923         46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAI  125 (180)
Q Consensus        46 p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~~~~~  125 (180)
                      |++||+|+|||++||+++|..++.+||+++++||+++||++|++||++||.+|+++|..++++|..+|..|..+++|.++
T Consensus         7 p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~tp~q~   86 (214)
T 3tq6_A            7 ASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQI   86 (214)
T ss_dssp             HHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhcccCCHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCchHHHHHHHhhhhhhhcC
Q psy14923        126 EFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEG  176 (180)
Q Consensus       126 ~~~~~~~~~~~~~~~k~~~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~  176 (180)
                      ..++.........++..++++..+|++.||||+|||+|||++.|..+.-+|
T Consensus        87 ~~~~~~~~~~~~krk~~kkkk~~kdp~~PKrP~say~lF~~e~r~~~k~~~  137 (214)
T 3tq6_A           87 MSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDS  137 (214)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCHHHHHHHHHTTTSSCSS
T ss_pred             HHHHHHHHHHHhhhcchhhhhhhccccCcccccchhhhhHHHHHHhhccCC
Confidence            877665544443333334456789999999999999999999998875443

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.96  E-value=9.9e-30  Score=196.37  Aligned_cols=116  Identities=27%  Similarity=0.475  Sum_probs=105.9

Q ss_pred             CCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCC--CCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy14923         41 QPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPN--IKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHD  118 (180)
Q Consensus        41 k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~--~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  118 (180)
                      ...+||++|++|+|||+|||+++|..++.+||+  +++.||+++||++|++||++||++|+++|++++++|..+|..|..
T Consensus         8 ~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   87 (173)
T 2yrq_A            8 MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP   87 (173)
T ss_dssp             SSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence            456899999999999999999999999999999  589999999999999999999999999999999999999999998


Q ss_pred             hCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        119 ELTPEAIEFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~k~~~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ..+.                     .++..+|++.||||+|||+|||+++|..+..+|.
T Consensus        88 ~~~~---------------------~kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p  125 (173)
T 2yrq_A           88 PKGE---------------------TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHP  125 (173)
T ss_dssp             CCCC---------------------SSCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCS
T ss_pred             hhhh---------------------hcccccCCccccCcccHHHHHHHHHHHHHHHHCC
Confidence            7641                     1345679999999999999999999998876653

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1

Probab=99.94  E-value=4.6e-27  Score=178.95  Aligned_cols=111  Identities=26%  Similarity=0.455  Sum_probs=101.6

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhCCHHHH
Q psy14923         46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEAI  125 (180)
Q Consensus        46 p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~~~~~  125 (180)
                      |+.|+||++||++|+.+.+..|..+||++++.||+++||++|++||++||++|.++|+.++++|..+|..|.....    
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~k~----   77 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKG----   77 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCCCC----
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccccccc----
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999987531    


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        126 EFLRKEKEVKKQKKEKREMKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       126 ~~~~~~~~~~~~~~~k~~~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                                       +.++..+|++.||||+|||+|||++.|..+..+|.
T Consensus        78 -----------------~~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p  112 (159)
T 2gzk_A           78 -----------------ETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHP  112 (159)
T ss_dssp             -----------------CCGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCS
T ss_pred             -----------------cccccccccccccccccccchhhHhhHHHHHHhCC
Confidence                             22456789999999999999999999999877664

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.91  E-value=4.4e-24  Score=151.55  Aligned_cols=83  Identities=27%  Similarity=0.497  Sum_probs=79.1

Q ss_pred             cCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy14923         39 TSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHD  118 (180)
Q Consensus        39 ~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  118 (180)
                      ..++.+||++|+||+|||+|||+++|..|+.+||++++.+|+++||++|++||+++|++|+++|++++++|..+|.+|..
T Consensus         8 ~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~   87 (102)
T 2co9_A            8 KKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRA   87 (102)
T ss_dssp             SCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34677899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hCC
Q psy14923        119 ELT  121 (180)
Q Consensus       119 ~~~  121 (180)
                      .+.
T Consensus        88 ~~~   90 (102)
T 2co9_A           88 SLV   90 (102)
T ss_dssp             HHT
T ss_pred             hcc
Confidence            764

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1

Probab=99.91  E-value=1.8e-24  Score=152.87  Aligned_cols=83  Identities=28%  Similarity=0.597  Sum_probs=79.4

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         40 SQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        40 ~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .++.+||++||||+|||+|||++.|..++.+||+++++||+++||++|++||++||++|+++|++++++|..+|.+|...
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~   81 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCH
Q psy14923        120 LTP  122 (180)
Q Consensus       120 ~~~  122 (180)
                      +++
T Consensus        82 ~P~   84 (99)
T 1k99_A           82 HPD   84 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            763

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.91  E-value=9.4e-24  Score=145.35  Aligned_cols=77  Identities=27%  Similarity=0.487  Sum_probs=73.7

Q ss_pred             CCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy14923         41 QPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIK--IIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH  117 (180)
Q Consensus        41 k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~--~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~  117 (180)
                      +..+||++||||+|||++||+++|..++.+||+++  +.||+++||++|++||++||++|+++|++++++|..+|.+|+
T Consensus         8 ~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y~   86 (86)
T 2eqz_A            8 MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG   86 (86)
T ss_dssp             CSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            46689999999999999999999999999999986  699999999999999999999999999999999999999984

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A

Probab=99.90  E-value=1.7e-24  Score=151.26  Aligned_cols=86  Identities=27%  Similarity=0.474  Sum_probs=80.6

Q ss_pred             ccccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHH
Q psy14923         34 GLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNV  113 (180)
Q Consensus        34 ~~k~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~  113 (180)
                      ..+++..++.+||+.|+||+|||+|||+++|..++.+||++++.||+++||++|++||++||++|+++|++++++|..+|
T Consensus         6 ~~k~~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~   85 (93)
T 1cg7_A            6 EPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEK   85 (93)
T ss_dssp             CCCCCCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHH
T ss_pred             CCCcccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455567789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhhhh
Q psy14923        114 KKYHDE  119 (180)
Q Consensus       114 ~~y~~~  119 (180)
                      .+|..+
T Consensus        86 ~~Y~~~   91 (93)
T 1cg7_A           86 ELYNAT   91 (93)
T ss_dssp             HHHHHH
T ss_pred             HHHHHc
Confidence            999875

>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A

Probab=99.90  E-value=1e-23  Score=142.05  Aligned_cols=76  Identities=30%  Similarity=0.571  Sum_probs=73.7

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy14923         43 LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHD  118 (180)
Q Consensus        43 ~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  118 (180)
                      .+||++|+||+|||+||++++|..++.+||++++++|+++||++|++||++||++|.++|++++++|..+|.+|..
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3789999999999999999999999999999999999999999999999999999999999999999999999975

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=2.4e-23  Score=145.07  Aligned_cols=78  Identities=26%  Similarity=0.385  Sum_probs=75.7

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy14923         44 SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELT  121 (180)
Q Consensus        44 ~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~  121 (180)
                      .+|++||||+|||++|++++|..++.+||++++.||+++||++|++||++||++|+++|++++++|..+|.+|...++
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~~   80 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQES   80 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTTT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            578999999999999999999999999999999999999999999999999999999999999999999999999765

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus}

Probab=99.89  E-value=3.7e-23  Score=144.09  Aligned_cols=77  Identities=35%  Similarity=0.606  Sum_probs=74.8

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         43 LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        43 ~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .+||++||||+|||+||++++|..++.+||++++.+|+++||++|++||+++|++|.++|++++++|..+|.+|...
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~   78 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQS   78 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999974

>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.89  E-value=3.4e-24  Score=148.84  Aligned_cols=82  Identities=23%  Similarity=0.383  Sum_probs=75.8

Q ss_pred             ccccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHH
Q psy14923         34 GLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNV  113 (180)
Q Consensus        34 ~~k~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~  113 (180)
                      ..+++..++.+||++|+||+|||+|||+++|..++.+||++++.||+++||++|++||++||++|+++|++++++|..+|
T Consensus         6 ~~k~k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~   85 (90)
T 1wgf_A            6 SGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKS   85 (90)
T ss_dssp             CCSSCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCC
T ss_pred             CCCCCcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556667889999999999999999999999999999999999999999999999999999999999999999998776


Q ss_pred             Hh
Q psy14923        114 KK  115 (180)
Q Consensus       114 ~~  115 (180)
                      ..
T Consensus        86 ~~   87 (90)
T 1wgf_A           86 GP   87 (90)
T ss_dssp             SS
T ss_pred             HH
Confidence            54

>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens}

Probab=99.89  E-value=3.8e-23  Score=142.65  Aligned_cols=77  Identities=17%  Similarity=0.286  Sum_probs=73.9

Q ss_pred             CCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy14923         41 QPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH  117 (180)
Q Consensus        41 k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~  117 (180)
                      ++.+||+.|+||+|||+|||+++|..++.+||++++.+|+++||++|++||++||++|+++|++++++|.+++++|+
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            46689999999999999999999999999999999999999999999999999999999999999999999998875

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis}

Probab=99.89  E-value=4.9e-24  Score=149.97  Aligned_cols=86  Identities=22%  Similarity=0.468  Sum_probs=80.6

Q ss_pred             ccccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHH
Q psy14923         34 GLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIK--IIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQ  111 (180)
Q Consensus        34 ~~k~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~--~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~  111 (180)
                      ..+++..++.+||++|+||+|||+|||+++|..++.+||+++  +.+|+++||++|++||++||++|+++|++++++|..
T Consensus         8 ~~k~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~   87 (97)
T 2lhj_A            8 TGVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYER   87 (97)
T ss_dssp             SSCCCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHH
T ss_pred             ccccccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence            445556678899999999999999999999999999999999  999999999999999999999999999999999999


Q ss_pred             HHHhhhhh
Q psy14923        112 NVKKYHDE  119 (180)
Q Consensus       112 ~~~~y~~~  119 (180)
                      +|.+|..+
T Consensus        88 e~~~y~~~   95 (97)
T 2lhj_A           88 EKAEYAQR   95 (97)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhc
Confidence            99999874

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.88  E-value=1.8e-22  Score=144.62  Aligned_cols=86  Identities=17%  Similarity=0.335  Sum_probs=80.1

Q ss_pred             cCCCCCCCCCC-CCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy14923         39 TSQPLSIPEKP-KKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH  117 (180)
Q Consensus        39 ~~k~~~~p~~P-KrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~  117 (180)
                      ..++.+||+.| |||+|||++||+++|..++    ++++.||+++||++|++||++||++|+++|++++++|..+|.+|.
T Consensus         7 ~~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~   82 (108)
T 1v64_A            7 GQLKDKFDGRPTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFL   82 (108)
T ss_dssp             CCSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34677899999 9999999999999999876    789999999999999999999999999999999999999999999


Q ss_pred             hhCCHHHHHHH
Q psy14923        118 DELTPEAIEFL  128 (180)
Q Consensus       118 ~~~~~~~~~~~  128 (180)
                      ..+++++++++
T Consensus        83 ~~~~~~~r~~~   93 (108)
T 1v64_A           83 ESLPEEEQQRV   93 (108)
T ss_dssp             HHSCHHHHHHH
T ss_pred             hhCCHHHHHHH
Confidence            99998887654

>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A*

Probab=99.88  E-value=4.4e-23  Score=138.64  Aligned_cols=74  Identities=23%  Similarity=0.432  Sum_probs=70.2

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy14923         45 IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHD  118 (180)
Q Consensus        45 ~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  118 (180)
                      ||+.||||+|||+||++++|..++.+||++++++|+++||++|++||+++|++|.++|++++++|..++.+|+-
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky   74 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999998864

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1

Probab=99.88  E-value=2.3e-23  Score=142.39  Aligned_cols=77  Identities=26%  Similarity=0.469  Sum_probs=73.6

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         43 LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIK--IIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        43 ~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~--~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .+||++||||+|||++||+++|..++.+||+++  +.+|+++||++|++||++||++|+++|++++++|..+|.+|...
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~   80 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP   80 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            379999999999999999999999999999986  59999999999999999999999999999999999999999875

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A*

Probab=99.88  E-value=1.9e-22  Score=134.69  Aligned_cols=72  Identities=35%  Similarity=0.610  Sum_probs=69.5

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        46 p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      +++||||+|||+|||+++|..++.+||+++++||+++||++|++||+  |++|+++|++++++|.++|++|.++
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~k   72 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999999999999999998  9999999999999999999999864

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster}

Probab=99.87  E-value=2.1e-22  Score=134.43  Aligned_cols=72  Identities=31%  Similarity=0.595  Sum_probs=69.7

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        46 p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      |++||||+|||++|++++|..++.+||+++++||+++||++|++|  ++|++|+++|++++++|..+|.+|..+
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~~   72 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            689999999999999999999999999999999999999999999  889999999999999999999999864

>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A

Probab=99.87  E-value=3.7e-22  Score=137.07  Aligned_cols=75  Identities=23%  Similarity=0.425  Sum_probs=72.6

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         45 IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        45 ~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .|+.|+||+|||+|||+++|..++.+||++++++|+++||++|++||++||++|.++|++++++|..++.+|...
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~   75 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccC
Confidence            378999999999999999999999999999999999999999999999999999999999999999999999874

>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A

Probab=99.87  E-value=3.5e-22  Score=132.44  Aligned_cols=69  Identities=28%  Similarity=0.536  Sum_probs=66.5

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCH--HHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy14923         48 KPKKPLTPYFKFQGQIRNKIMERNPNIKI--IEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKY  116 (180)
Q Consensus        48 ~PKrP~say~lF~~e~r~~~~~~~p~~~~--~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y  116 (180)
                      +||||+|||++|++++|..++.+||++++  ++|+++||++|++||+++|++|.++|++++++|..+|.+|
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            59999999999999999999999999965  9999999999999999999999999999999999999876

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus}

Probab=99.86  E-value=1.6e-22  Score=137.82  Aligned_cols=76  Identities=16%  Similarity=0.358  Sum_probs=73.2

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         44 SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        44 ~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .++++|+||+|||+||++++|..++.+||++++.+|+++||++|++||++||++|.++|++++++|..+|.+|...
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~   78 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSG   78 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcC
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999999764

>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.86  E-value=1.9e-21  Score=137.80  Aligned_cols=85  Identities=14%  Similarity=0.307  Sum_probs=76.9

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhCCHHH
Q psy14923         45 IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEA  124 (180)
Q Consensus        45 ~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~~~~  124 (180)
                      ...+||||+|||++||++++.  ..+++++++.||+++||++|++|+++||++|+++|++++++|..+|.+|...+++++
T Consensus         5 ~~~~PKrP~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~~~   82 (101)
T 1v63_A            5 SSGPKKPPMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQD   82 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTH
T ss_pred             CCCCCCCCCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHHH
Confidence            457999999999999999975  235566889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q psy14923        125 IEFLRKE  131 (180)
Q Consensus       125 ~~~~~~~  131 (180)
                      +.++...
T Consensus        83 ~~~~~~~   89 (101)
T 1v63_A           83 RAAYKEY   89 (101)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8877654

>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A

Probab=99.86  E-value=7.5e-22  Score=134.71  Aligned_cols=75  Identities=19%  Similarity=0.451  Sum_probs=69.4

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         45 IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        45 ~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .++.|+||+|||+|||+++|..++.+||++++++|+++||++|++||++||++|+++|++++++|..++++|+-.
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~   77 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYR   77 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCeeC
Confidence            467899999999999999999999999999999999999999999999999999999999999999999999864

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0

Probab=99.86  E-value=4.4e-22  Score=131.85  Aligned_cols=71  Identities=20%  Similarity=0.465  Sum_probs=63.4

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH  117 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~  117 (180)
                      +.||||+|||+||++++|..++.+||++++++|+++||++|++||+++|++|+++|++++++|..++++|+
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            46899999999999999999999999999999999999999999999999999999999999999998884

>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B

Probab=99.86  E-value=9.8e-22  Score=133.30  Aligned_cols=73  Identities=22%  Similarity=0.485  Sum_probs=70.6

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      +.|+||+|||+||++++|..++.+||++++.+|+++||++|++||++||++|.++|++++++|..+|++|...
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~   73 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYR   73 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccC
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999864

>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens}

Probab=99.86  E-value=1.1e-21  Score=140.01  Aligned_cols=78  Identities=17%  Similarity=0.372  Sum_probs=71.0

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         42 PLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        42 ~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      ..++|+.|+||+|||+|||+++|..++.++|++++.+|+++||++|++||++||++|+++|++++++|..++++|+-.
T Consensus        23 ~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky~  100 (106)
T 4euw_A           23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQ  100 (106)
T ss_dssp             -----CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC-
T ss_pred             ccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCcC
Confidence            457789999999999999999999999999999999999999999999999999999999999999999999999864

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1

Probab=99.85  E-value=4.5e-21  Score=145.72  Aligned_cols=79  Identities=29%  Similarity=0.554  Sum_probs=75.9

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy14923         40 SQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHD  118 (180)
Q Consensus        40 ~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  118 (180)
                      .++.+||+.||||+|||++||+++|..++.+||++++++|+++||++|++||+++|++|+++|++++++|..+|.+|..
T Consensus        80 kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  158 (159)
T 2gzk_A           80 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  158 (159)
T ss_dssp             GGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3567899999999999999999999999999999999999999999999999999999999999999999999999975

>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.85  E-value=3e-21  Score=132.69  Aligned_cols=73  Identities=14%  Similarity=0.322  Sum_probs=70.5

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhC
Q psy14923         48 KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDEL  120 (180)
Q Consensus        48 ~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  120 (180)
                      .|+||+|||+||++++|..++.+||++++++|+++||++|++||++||++|.++|++++++|..+|++|....
T Consensus         2 ~pKRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p   74 (86)
T 2lef_A            2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARD   74 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999998643

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1

Probab=99.85  E-value=2.2e-21  Score=131.11  Aligned_cols=73  Identities=21%  Similarity=0.408  Sum_probs=70.3

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      +.||||+|||+|||+++|..++.+||++++++|+++||++|++||++||++|+++|++++++|..++++|+-.
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky~   73 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYR   73 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeC
Confidence            4689999999999999999999999999999999999999999999999999999999999999999999863

>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.84  E-value=1.6e-21  Score=132.57  Aligned_cols=74  Identities=19%  Similarity=0.398  Sum_probs=68.8

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        46 p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      ++.|+||+|||+||++++|..++.+||++++.+|+++||++|++||++||++|.++|++++++|..++++|.-.
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~   75 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYK   75 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC---
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCeec
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999863

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens}

Probab=99.84  E-value=6.4e-21  Score=125.13  Aligned_cols=67  Identities=24%  Similarity=0.440  Sum_probs=62.6

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYH  117 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~  117 (180)
                      +.||||+|||++||+++|..++..||    ++|+++||++|++||++||.+|+++|++++++|..+|.+|.
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y~   67 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWA   67 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            57999999999999999999986665    79999999999999999999999999999999999999883

>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A

Probab=99.83  E-value=1.2e-20  Score=130.57  Aligned_cols=73  Identities=15%  Similarity=0.261  Sum_probs=70.7

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhC
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDEL  120 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  120 (180)
                      +.|+||+|||++|+++.|..++.++|+ ++++|++.||++|++||++||++|+++|++++++|+++|.+|....
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~   75 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPP   75 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence            689999999999999999999999999 9999999999999999999999999999999999999999998754

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=1.9e-20  Score=144.17  Aligned_cols=80  Identities=29%  Similarity=0.552  Sum_probs=76.5

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         40 SQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        40 ~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .++.+||+.|+||+|||+|||+++|..++.+||++++.+|+++||++|++||+++|++|+++|++++++|..+|.+|...
T Consensus        93 kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~k  172 (173)
T 2yrq_A           93 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK  172 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            35667999999999999999999999999999999999999999999999999999999999999999999999999864

>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=3.3e-20  Score=126.31  Aligned_cols=62  Identities=18%  Similarity=0.272  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHhhcCCHHHHHHHHHHHHHH
Q psy14923         44 SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIK-IIEVTKLVSEEWKKIGEAEKKRLENEYAKE  105 (180)
Q Consensus        44 ~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~-~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~  105 (180)
                      ++++.||||+|||+|||+++|..|+.+||+++ ++||+++||++|++||++||++|+++|+.+
T Consensus         1 ~~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A            1 GSSGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999998 999999999999999999999999999887

>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=99.78  E-value=8.6e-21  Score=131.29  Aligned_cols=71  Identities=8%  Similarity=0.089  Sum_probs=65.4

Q ss_pred             cccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHH
Q psy14923         37 QQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIK--IIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQ  111 (180)
Q Consensus        37 ~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~--~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~  111 (180)
                      +...++.+||++||||+|||+|||+++|.+|+.+||+++  ++||+    ++|++|+++||++|+++|++++++|..
T Consensus        11 ~~~~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~   83 (90)
T 2yuk_A           11 RSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRI   83 (90)
T ss_dssp             CCHHHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence            334566689999999999999999999999999999999  99988    999999999999999999999999864

>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=2.5e-19  Score=124.87  Aligned_cols=70  Identities=16%  Similarity=0.246  Sum_probs=65.5

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHH---HHHhhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy14923         43 LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLV---SEEWKKIGEAEKKRLENEYAKEKEIYAQNVK  114 (180)
Q Consensus        43 ~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l---~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~  114 (180)
                      ..+++.||||+|||++||+++|.+++.+  +++++||+++|   |++|++|+++||++|+++|++++++|.+++.
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~~   77 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR--GLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPG   77 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH--TCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhcccc
Confidence            3567999999999999999999999988  79999999999   9999999999999999999999999988764

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}

Probab=99.71  E-value=2.4e-18  Score=136.83  Aligned_cols=77  Identities=21%  Similarity=0.403  Sum_probs=70.2

Q ss_pred             CCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhC
Q psy14923         41 QPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDEL  120 (180)
Q Consensus        41 k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  120 (180)
                      +..+||+.||||+|||++||+++|..++.++    +.+|+++||++|++||+++|++|+++|++++++|..+|.+|...+
T Consensus       107 k~~kdp~~PKrP~say~lF~~e~r~~~k~~~----p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~~~  182 (214)
T 3tq6_A          107 KELTLLGKPKRPRSAYNVYVAERFQEAKGDS----PQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQM  182 (214)
T ss_dssp             HHHHHTTCCCCCCCHHHHHHHHHTTTSSCSS----HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhccccCcccccchhhhhHHHHHHhhccCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            3457899999999999999999998886554    459999999999999999999999999999999999999999976


Q ss_pred             C
Q psy14923        121 T  121 (180)
Q Consensus       121 ~  121 (180)
                      +
T Consensus       183 ~  183 (214)
T 3tq6_A          183 I  183 (214)
T ss_dssp             H
T ss_pred             c
Confidence            4

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}

Probab=99.69  E-value=4.4e-18  Score=137.35  Aligned_cols=77  Identities=22%  Similarity=0.447  Sum_probs=70.2

Q ss_pred             CCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhC
Q psy14923         41 QPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDEL  120 (180)
Q Consensus        41 k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  120 (180)
                      +..+||+.||||+|||+|||+++|..++.+||    .+|+++||++|++|++++|++|+++|++++++|..+|.+|...+
T Consensus       139 k~~kdp~~PKrP~say~lF~~e~r~~~k~~~p----~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~k~  214 (238)
T 3tmm_A          139 KELTLLGKPKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQM  214 (238)
T ss_dssp             HHHHHTTCCCCCCCHHHHHHHHHTTTSCCSSH----HHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhcccCCCCCCCcHHHHHHHHHHHHHhccCH----HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            34578999999999999999999988865554    59999999999999999999999999999999999999999976


Q ss_pred             C
Q psy14923        121 T  121 (180)
Q Consensus       121 ~  121 (180)
                      .
T Consensus       215 ~  215 (238)
T 3tmm_A          215 I  215 (238)
T ss_dssp             H
T ss_pred             c
Confidence            3

>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1

Probab=98.32  E-value=1.2e-07  Score=65.00  Aligned_cols=34  Identities=18%  Similarity=0.300  Sum_probs=29.9

Q ss_pred             HhhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        144 MKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       144 ~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .++..+|++.||||+|||+|||+++|..+..+|.
T Consensus        11 ~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P   44 (90)
T 1wgf_A           11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERP   44 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCT
T ss_pred             cCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            3566789999999999999999999999887764

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.28  E-value=1.9e-07  Score=63.38  Aligned_cols=33  Identities=12%  Similarity=0.218  Sum_probs=28.9

Q ss_pred             hhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        145 KKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       145 kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ++..+|++.||||+|||+|||++.|..+..+|.
T Consensus         7 ~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p   39 (86)
T 2eqz_A            7 GMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNP   39 (86)
T ss_dssp             SCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCC
Confidence            455789999999999999999999999877664

>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=98.25  E-value=1.3e-07  Score=64.95  Aligned_cols=32  Identities=16%  Similarity=-0.006  Sum_probs=28.8

Q ss_pred             hhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        146 KLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       146 k~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +..+|+++||||+|||||||.+.|+.+..+|.
T Consensus        15 k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP   46 (90)
T 2yuk_A           15 KWEKEEALGEMATVAPVLYTNINFPNLKEEFP   46 (90)
T ss_dssp             HHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCC
T ss_pred             hccCCCCCCCCCccHHHHHHHHhHHHHHHHCc
Confidence            44679999999999999999999999998875

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1

Probab=98.24  E-value=3.7e-07  Score=63.64  Aligned_cols=33  Identities=27%  Similarity=0.353  Sum_probs=28.8

Q ss_pred             hhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        145 KKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       145 kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ++..+|++.||||+|||+|||++.|..+..++.
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P   34 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHP   34 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCT
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            345689999999999999999999999877654

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1

Probab=98.22  E-value=6e-07  Score=60.32  Aligned_cols=29  Identities=14%  Similarity=0.345  Sum_probs=26.5

Q ss_pred             hccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        149 RETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       149 k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +|+++||||+|||+|||+++|..+..+|.
T Consensus         3 kdp~~PKrP~say~lF~~~~r~~~~~~~p   31 (83)
T 1aab_A            3 GDPKKPRGKMSSYAFFVQTSREEHKKKHP   31 (83)
T ss_dssp             CCTTCCCCCCCHHHHHHHHHHHHHTTSCT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            69999999999999999999999887664

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis}

Probab=98.19  E-value=2.9e-07  Score=63.83  Aligned_cols=34  Identities=21%  Similarity=0.287  Sum_probs=29.8

Q ss_pred             HhhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        144 MKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       144 ~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .++..+|++.||||+|||+|||++.|..+..+|.
T Consensus        13 ~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p   46 (97)
T 2lhj_A           13 PRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENP   46 (97)
T ss_dssp             TTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCT
T ss_pred             cccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            3567789999999999999999999999877654

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.19  E-value=4.2e-07  Score=63.63  Aligned_cols=33  Identities=24%  Similarity=0.440  Sum_probs=29.0

Q ss_pred             hhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        145 KKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       145 kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ++..+|++.||||+|||+|||+++|..+..+|.
T Consensus         9 kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P   41 (102)
T 2co9_A            9 KKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNP   41 (102)
T ss_dssp             CSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCT
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            456689999999999999999999999877664

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A

Probab=98.19  E-value=2.8e-07  Score=63.47  Aligned_cols=34  Identities=18%  Similarity=0.340  Sum_probs=29.4

Q ss_pred             HhhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        144 MKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       144 ~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .++..+|++.|+||+|||+|||++.|..+..+|.
T Consensus        11 ~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P   44 (93)
T 1cg7_A           11 TTRKKKDPNAPKRALSAYMFFANENRDIVRSENP   44 (93)
T ss_dssp             CCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCT
T ss_pred             cCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            3566789999999999999999999998876653

>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A

Probab=98.17  E-value=7.7e-07  Score=58.86  Aligned_cols=29  Identities=28%  Similarity=0.543  Sum_probs=26.2

Q ss_pred             hccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        149 RETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       149 k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +|++.||||+|||+|||++.|..+..+|.
T Consensus         2 kdp~~pKrP~saf~lf~~~~r~~~~~~~p   30 (77)
T 1hme_A            2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHP   30 (77)
T ss_dssp             CCSSCCCCCCCTTHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            68999999999999999999999876654

>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens}

Probab=98.09  E-value=1.2e-06  Score=59.45  Aligned_cols=32  Identities=25%  Similarity=0.149  Sum_probs=28.1

Q ss_pred             hhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        146 KLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       146 k~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +..+|++.||||+|||+|||+++|..+..+|.
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P   41 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYP   41 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCT
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            35689999999999999999999999887654

>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.07  E-value=2e-06  Score=57.86  Aligned_cols=28  Identities=14%  Similarity=0.413  Sum_probs=25.4

Q ss_pred             ccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        150 ETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       150 ~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +++.||||+|||+|||++.|..+..+|.
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P   29 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNP   29 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            5789999999999999999999988764

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus}

Probab=98.07  E-value=1.8e-06  Score=59.16  Aligned_cols=30  Identities=13%  Similarity=0.275  Sum_probs=26.7

Q ss_pred             hhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        148 FRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       148 ~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .+|++.||||+|||+|||++.|..+..+|.
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p   31 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHP   31 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            368999999999999999999999887654

>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A*

Probab=98.05  E-value=2.2e-06  Score=56.46  Aligned_cols=28  Identities=25%  Similarity=0.412  Sum_probs=23.5

Q ss_pred             ccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        150 ETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       150 ~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      |++.||||+|||+|||++.|..+..+|.
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p   28 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENP   28 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCS
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCc
Confidence            5789999999999999999999877653

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A*

Probab=98.02  E-value=2.9e-06  Score=55.55  Aligned_cols=26  Identities=23%  Similarity=0.480  Sum_probs=23.6

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ++||||+|||+|||+++|..+..+|.
T Consensus         2 ~~PKrP~say~lf~~~~r~~~~~~~p   27 (73)
T 3nm9_A            2 DKPKRPLSAYALWLNSARESIKRENP   27 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSS
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            68999999999999999999887764

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster}

Probab=98.01  E-value=3e-06  Score=55.49  Aligned_cols=27  Identities=22%  Similarity=0.461  Sum_probs=24.3

Q ss_pred             cCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        151 TGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       151 ~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      |++||||+|||+|||++.|..+..+|.
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p   27 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENP   27 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHST
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            578999999999999999999887764

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens}

Probab=97.97  E-value=3.4e-06  Score=54.29  Aligned_cols=25  Identities=20%  Similarity=0.683  Sum_probs=22.0

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEG  176 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~  176 (180)
                      |+||||+|||+|||++.|..+.-.|
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~   25 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDS   25 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSS
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcC
Confidence            6899999999999999999876544

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1

Probab=97.96  E-value=2.1e-06  Score=60.79  Aligned_cols=29  Identities=24%  Similarity=0.419  Sum_probs=25.6

Q ss_pred             hhhhhccCCC-CCCCchHHHHHHHhhhhhh
Q psy14923        145 KKLFRETGKP-KKPGNSFYLFIKDNIDKKE  173 (180)
Q Consensus       145 kk~~k~~~~P-KrP~say~lF~~e~r~~~~  173 (180)
                      .++.+|++.| |||+|||+|||++.|..+.
T Consensus         8 ~kk~kd~~~P~KrP~say~lF~~e~r~~~k   37 (108)
T 1v64_A            8 QLKDKFDGRPTKPPPNSYSLYCAELMANMK   37 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHHCT
T ss_pred             ccccCCCCCCCCCCCCHHHHHHHHHHHHHh
Confidence            3567899999 9999999999999999764

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.87  E-value=6.8e-06  Score=56.26  Aligned_cols=29  Identities=24%  Similarity=0.245  Sum_probs=25.7

Q ss_pred             hccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        149 RETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       149 k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .++++||||+|||+|||+++|..+..+|.
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p   31 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENP   31 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            46889999999999999999999887664

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus}

Probab=97.86  E-value=8e-06  Score=54.59  Aligned_cols=29  Identities=24%  Similarity=0.347  Sum_probs=25.5

Q ss_pred             hccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        149 RETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       149 k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .+++.||||+|||+|||++.|..+..+|.
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p   31 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHP   31 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            46889999999999999999998877653

>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens}

Probab=97.81  E-value=1e-05  Score=56.97  Aligned_cols=31  Identities=16%  Similarity=0.173  Sum_probs=23.6

Q ss_pred             hhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        147 LFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       147 ~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ..++++.||||+|||+|||++.|..+..++.
T Consensus        23 ~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P   53 (106)
T 4euw_A           23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYP   53 (106)
T ss_dssp             -----CCCCCCCCHHHHHHHHHHHHHHHHCT
T ss_pred             ccCCCCcCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            4678899999999999999999998876654

>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A

Probab=97.79  E-value=1.2e-05  Score=54.07  Aligned_cols=27  Identities=26%  Similarity=0.450  Sum_probs=24.1

Q ss_pred             cCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        151 TGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       151 ~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ++.||||+|||+|||+++|..+..+|.
T Consensus         2 p~~pKRP~~af~lf~~~~r~~~~~~~P   28 (85)
T 1j46_A            2 QDRVKRPMNAFIVWSRDQRRKMALENP   28 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHST
T ss_pred             cCcCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            689999999999999999999876654

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0

Probab=97.78  E-value=9.9e-06  Score=52.41  Aligned_cols=26  Identities=23%  Similarity=0.478  Sum_probs=19.9

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      |.||||+|||+|||++.|..+..+|.
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p   26 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNP   26 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            57999999999999999999887664

>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A

Probab=97.73  E-value=1.6e-05  Score=51.46  Aligned_cols=25  Identities=16%  Similarity=0.355  Sum_probs=22.4

Q ss_pred             CCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        153 KPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       153 ~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +||||+|||+|||++.|..+..+|.
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p   25 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHP   25 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCT
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCC
Confidence            5999999999999999999877664

>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A

Probab=97.72  E-value=1.5e-05  Score=53.21  Aligned_cols=28  Identities=21%  Similarity=0.385  Sum_probs=21.9

Q ss_pred             ccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        150 ETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       150 ~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .++.||||+|||+|||++.|..+..+|.
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p   30 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNP   30 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            4568999999999999999999887664

>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.70  E-value=1.9e-05  Score=54.41  Aligned_cols=28  Identities=21%  Similarity=0.498  Sum_probs=24.5

Q ss_pred             hccCCCCCCCchHHHHHHHhhhhhhhcC
Q psy14923        149 RETGKPKKPGNSFYLFIKDNIDKKEYEG  176 (180)
Q Consensus       149 k~~~~PKrP~say~lF~~e~r~~~~~~~  176 (180)
                      .+.++||||+|||+|||++.|+.+..++
T Consensus         6 ~~~~~PKRP~sAf~lF~~e~R~~ik~e~   33 (93)
T 2cto_A            6 SGMPNRKASRNAYYFFVQEKIPELRRRG   33 (93)
T ss_dssp             CCCCCCCSSCCHHHHHHHTTHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHcC
Confidence            4678999999999999999999987653

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1

Probab=97.67  E-value=2.5e-05  Score=51.63  Aligned_cols=26  Identities=23%  Similarity=0.305  Sum_probs=23.1

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      |.||||+|||+|||++.|..+..+|.
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p   26 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSP   26 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTST
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCc
Confidence            67999999999999999999877654

>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1

Probab=97.65  E-value=2.7e-05  Score=51.85  Aligned_cols=27  Identities=26%  Similarity=0.262  Sum_probs=23.0

Q ss_pred             cCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        151 TGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       151 ~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .+.||||+|||+|||++.|..+..++.
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p   28 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFP   28 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCS
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            368999999999999999998876653

>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B

Probab=97.63  E-value=3e-05  Score=51.44  Aligned_cols=26  Identities=23%  Similarity=0.393  Sum_probs=22.8

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +.||||+|||+|||++.|..+..+|.
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p   26 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENP   26 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTST
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            47999999999999999999876654

>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1

Probab=97.60  E-value=3.4e-05  Score=51.96  Aligned_cols=26  Identities=31%  Similarity=0.354  Sum_probs=22.9

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      |.|+||+|||+|||++.|..+..+|.
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P   26 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAEST   26 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCC
Confidence            57999999999999999999876653

>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1

Probab=97.31  E-value=0.00011  Score=51.16  Aligned_cols=25  Identities=24%  Similarity=0.432  Sum_probs=20.8

Q ss_pred             ccCCCCCCCchHHHHHHHhhhhhhh
Q psy14923        150 ETGKPKKPGNSFYLFIKDNIDKKEY  174 (180)
Q Consensus       150 ~~~~PKrP~say~lF~~e~r~~~~~  174 (180)
                      ..++||||+|||+|||++.+.+...
T Consensus         5 ~~~~PKrP~say~lF~~e~~~~p~~   29 (101)
T 1v63_A            5 SSGPKKPPMNGYQKFSQELLSNGEL   29 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHhCCCC
Confidence            4678999999999999999875443

>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A

Probab=97.09  E-value=0.00027  Score=48.36  Aligned_cols=26  Identities=15%  Similarity=0.095  Sum_probs=23.0

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +.|+||+|||+||+++.|..+...+.
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p   28 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFK   28 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcC
Confidence            58999999999999999998877653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	180
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	7e-12
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	6e-10
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-09
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	1e-09
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	3e-09
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	4e-09
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	5e-09
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	9e-09
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	6e-08
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	8e-08
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-07
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	4e-07

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Hamster (Cricetulus griseus) [TaxId: 10029]

 Score = 56.4 bits (136), Expect = 7e-12
 Identities = 24/77 (31%), Positives = 40/77 (51%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
            PK+P + +F F  + R KI   +P + I +V K + E W      +K+  E + AK KE
Sbjct: 2   APKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 61

Query: 108 IYAQNVKKYHDELTPEA 124
            Y +++  Y  +  P+A
Sbjct: 62  KYEKDIAAYRAKGKPDA 78

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.8 bits (124), Expect = 6e-10
 Identities = 14/92 (15%), Positives = 40/92 (43%), Gaps = 2/92 (2%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
             K P+  Y KF  ++ +     +  +K  E    +   W++I +++K+  +    +++ 
Sbjct: 8   PKKPPMNGYQKFSQELLSNGELNHLPLK--ERMVEIGSRWQRISQSQKEHYKKLAEEQQR 65

Query: 108 IYAQNVKKYHDELTPEAIEFLRKEKEVKKQKK 139
            Y  ++  +   L+P+     ++    K++  
Sbjct: 66  QYKVHLDLWVKSLSPQDRAAYKEYISNKRKSG 97

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.1 bits (122), Expect = 1e-09
 Identities = 18/71 (25%), Positives = 34/71 (47%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
            EKPK+P++  F F  + R ++ E  P +   E+T+L++  W  + E +K + +   A  
Sbjct: 18  SEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAAL 77

Query: 106 KEIYAQNVKKY 116
           K    +     
Sbjct: 78  KAQSERKSGPS 88

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 50.7 bits (121), Expect = 1e-09
 Identities = 26/91 (28%), Positives = 46/91 (50%)

Query: 30  VTTAGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKK 89
           VT    K++T++    P  PK+ L+ Y  F  + R+ +   NP+I   +V K + E+WK 
Sbjct: 2   VTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKA 61

Query: 90  IGEAEKKRLENEYAKEKEIYAQNVKKYHDEL 120
           +   EK+  E +   +K+ Y    + Y+  L
Sbjct: 62  LTPEEKQPYEAKAQADKKRYESEKELYNATL 92

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 49.1 bits (117), Expect = 3e-09
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKII--EVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           KP+  ++ Y  F    R +  +++P+  +   E +K  SE WK +   EK + E+    +
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 106 KEIYAQNVKKY 116
           K  Y + +K Y
Sbjct: 61  KARYEREMKTY 71

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: HMG-D
species: Drosophila melanogaster [TaxId: 7227]

 Score = 49.0 bits (117), Expect = 4e-09
 Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
           KPK+PL+ Y  +    R  I   NP IK+ EV K   E W+     +K   E + AK K+
Sbjct: 3   KPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRA--MKDKSEWEAKAAKAKD 60

Query: 108 IYAQNVKKYH 117
            Y + VK++ 
Sbjct: 61  DYDRAVKEFE 70

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.6 bits (116), Expect = 5e-09
 Identities = 16/71 (22%), Positives = 36/71 (50%)

Query: 47  EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
           ++ K+P+  +  +    R K+ + NP +   E++K +  EWK + E EK+   +E  + +
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 60

Query: 107 EIYAQNVKKYH 117
            ++ +    Y 
Sbjct: 61  ALHMKEHPDYK 71

>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.4 bits (115), Expect = 9e-09
 Identities = 23/71 (32%), Positives = 50/71 (70%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
           P+ PKKPLTPYF+F  + R K  + +P +  +++TK++S+++K++ E +K +   ++ +E
Sbjct: 8   PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQRE 67

Query: 106 KEIYAQNVKKY 116
           K+ + +N+ ++
Sbjct: 68  KQEFERNLARF 78

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 6e-08
 Identities = 17/71 (23%), Positives = 35/71 (49%)

Query: 47  EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
           ++ K+P+  +  +    R K+   NP ++  E++K +  +WK + EAEK     E  K +
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62

Query: 107 EIYAQNVKKYH 117
            ++ +    Y 
Sbjct: 63  AMHREKYPNYK 73

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.2 bits (107), Expect = 8e-08
 Identities = 14/69 (20%), Positives = 32/69 (46%)

Query: 48  KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
             K+P+  +  +    R KI++  P++    ++K++   WK +   EK+    E A+  +
Sbjct: 2   HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSK 61

Query: 108 IYAQNVKKY 116
            + +    Y
Sbjct: 62  QHLEKYPDY 70

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.7 bits (108), Expect = 1e-07
 Identities = 15/91 (16%), Positives = 37/91 (40%), Gaps = 4/91 (4%)

Query: 46  PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
               K P   Y  +  ++   + +        E   L S++WK + + EK     +  ++
Sbjct: 15  GRPTKPPPNSYSLYCAELMANMKDVPST----ERMVLCSQQWKLLSQKEKDAYHKKCDQK 70

Query: 106 KEIYAQNVKKYHDELTPEAIEFLRKEKEVKK 136
           K+ Y   + ++ + L  E  + +  E+++  
Sbjct: 71  KKDYEVELLRFLESLPEEEQQRVLGEEKMLN 101

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Lymphoid enhancer-binding factor, LEF1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.1 bits (104), Expect = 4e-07
 Identities = 15/92 (16%), Positives = 38/92 (41%), Gaps = 9/92 (9%)

Query: 50  KKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIY 109
           KKPL  +  +  ++R  ++  +   +   + +++   W  +   E+ +      KE++++
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLH 63

Query: 110 AQNVKKYHDELTPEAIEFLRKEKEVKKQKKEK 141
            Q    +                + KK+K+EK
Sbjct: 64  MQLYPGWS---------ARDNYGKKKKRKREK 86

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	180
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.91
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.88
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.88
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.86
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.85
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.85
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.85
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.84
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.83
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.83
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.82
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	98.15
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	98.08
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	97.99
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	97.94
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	97.91
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	97.78
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	97.77
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	97.69
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	97.64
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	97.4
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	97.24
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	96.87
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	96.71

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.91  E-value=4.5e-24  Score=147.45  Aligned_cols=88  Identities=27%  Similarity=0.476  Sum_probs=82.1

Q ss_pred             cccccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHH
Q psy14923         33 AGLKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQN  112 (180)
Q Consensus        33 ~~~k~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~  112 (180)
                      ...++...++.++|++||+|+|||++|+.++|..++.+||++++.+|++.||++|++||++||..|.+.|++++++|..+
T Consensus         5 ~~~~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e   84 (93)
T d1lwma_           5 REPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE   84 (93)
T ss_dssp             CCTTSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            33555666778899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhC
Q psy14923        113 VKKYHDEL  120 (180)
Q Consensus       113 ~~~y~~~~  120 (180)
                      |.+|+.++
T Consensus        85 ~~~y~~~l   92 (93)
T d1lwma_          85 KELYNATL   92 (93)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhcc
Confidence            99999865

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.88  E-value=1.9e-23  Score=140.03  Aligned_cols=75  Identities=29%  Similarity=0.539  Sum_probs=72.6

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhCC
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELT  121 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~  121 (180)
                      |+||||+|||++|+.++|..|+.+||++++++|+++||++|++||++||.+|.+.|.+++++|..+|.+|.....
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~~   75 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGK   75 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence            689999999999999999999999999999999999999999999999999999999999999999999988654

>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=4.4e-23  Score=141.76  Aligned_cols=83  Identities=28%  Similarity=0.597  Sum_probs=79.7

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         40 SQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        40 ~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      .+..+||+.|++|+|||++|++++|..++.+||++++.+|++.||+.|+.||+++|.+|.++|++++.+|..+|.+|...
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~   81 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46778999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCH
Q psy14923        120 LTP  122 (180)
Q Consensus       120 ~~~  122 (180)
                      +++
T Consensus        82 ~pe   84 (91)
T d1k99a_          82 HPD   84 (91)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            763

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=3e-22  Score=134.57  Aligned_cols=73  Identities=22%  Similarity=0.485  Sum_probs=70.5

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      +.||||+||||||++++|..++.+||++++++|+++||++|++||++||++|+++|.+++++|..+|++|...
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~   73 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYR   73 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCC
Confidence            4789999999999999999999999999999999999999999999999999999999999999999999753

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=7.4e-22  Score=134.02  Aligned_cols=73  Identities=23%  Similarity=0.426  Sum_probs=71.1

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      +.||||+|||+||++++|..|+.+||+++++||+++||++|++||++||.+|+++|.+++++|..+|++|...
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~   75 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999864

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.85  E-value=1.6e-21  Score=127.94  Aligned_cols=69  Identities=28%  Similarity=0.549  Sum_probs=65.8

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCC--CCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy14923         48 KPKKPLTPYFKFQGQIRNKIMERNPN--IKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKY  116 (180)
Q Consensus        48 ~PKrP~say~lF~~e~r~~~~~~~p~--~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y  116 (180)
                      +||||+|||++|+.++|..++.+||+  +++++|+++||++|++||+++|++|.++|++++++|..+|.+|
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            58999999999999999999999997  5578999999999999999999999999999999999999876

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: HMG-D
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.85  E-value=2.8e-21  Score=127.51  Aligned_cols=71  Identities=35%  Similarity=0.635  Sum_probs=68.0

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy14923         47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDE  119 (180)
Q Consensus        47 ~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  119 (180)
                      ++||||+|||++|+.++|..|+.+||++++.+|+++||++|++|++  |++|+++|++++++|..+|..|..+
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~~~e--K~~y~~~a~~~k~~y~~~~~~y~~~   72 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcChhH--HHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            7899999999999999999999999999999999999999999864  8999999999999999999999864

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=6.3e-22  Score=129.68  Aligned_cols=69  Identities=20%  Similarity=0.432  Sum_probs=65.6

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy14923         48 KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKY  116 (180)
Q Consensus        48 ~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y  116 (180)
                      .+|||+|||+|||++.|..|+.+||++++++|+++||++|++||+++|++|.++|++++++|.+++++|
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            468999999999999999999999999999999999999999999999999999999999998877665

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=1e-20  Score=133.72  Aligned_cols=84  Identities=17%  Similarity=0.275  Sum_probs=76.3

Q ss_pred             cCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy14923         39 TSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHD  118 (180)
Q Consensus        39 ~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  118 (180)
                      ..+...++.+||+|+|||+||++++|.+    ++++++.||+++||++|++||++||++|.++|++++++|..+|.+|..
T Consensus         8 ~~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~   83 (108)
T d1v64a_           8 QLKDKFDGRPTKPPPNSYSLYCAELMAN----MKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLE   83 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHH----CTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCcHHHHHHHHHHHH----ccCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4456678889999999999999998864    689999999999999999999999999999999999999999999999


Q ss_pred             hCCHHHHH
Q psy14923        119 ELTPEAIE  126 (180)
Q Consensus       119 ~~~~~~~~  126 (180)
                      ++++.++.
T Consensus        84 ~~~~~~k~   91 (108)
T d1v64a_          84 SLPEEEQQ   91 (108)
T ss_dssp             HSCHHHHH
T ss_pred             hCCHHHHH
Confidence            99976654

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=7.3e-21  Score=130.22  Aligned_cols=78  Identities=24%  Similarity=0.413  Sum_probs=70.9

Q ss_pred             cccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHH
Q psy14923         35 LKQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQN  112 (180)
Q Consensus        35 ~k~~~~k~~~~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~  112 (180)
                      .+.......++++.||||+|||+|||.++|..++.+||++++.+|+++|+++|+.|+++||++|.++|++++++|.++
T Consensus         7 ~k~~~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_           7 GKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             CSSCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             CCCCccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            444445567889999999999999999999999999999999999999999999999999999999999998888643

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=1.8e-20  Score=130.82  Aligned_cols=81  Identities=15%  Similarity=0.310  Sum_probs=73.2

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhCCHHH
Q psy14923         45 IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDELTPEA  124 (180)
Q Consensus        45 ~p~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~~~~  124 (180)
                      ..++||||+|||+|||.++|..+...  ++++.||+++||++|++||++||++|.++|++++++|..+|.+|...+++.+
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~--~~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~~~~~~   82 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELN--HLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQD   82 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTT--TSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHH
Confidence            34789999999999999999987654  5689999999999999999999999999999999999999999999998766


Q ss_pred             HHH
Q psy14923        125 IEF  127 (180)
Q Consensus       125 ~~~  127 (180)
                      ...
T Consensus        83 ~~~   85 (101)
T d1v63a_          83 RAA   85 (101)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Lymphoid enhancer-binding factor, LEF1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=1.4e-20  Score=127.87  Aligned_cols=72  Identities=14%  Similarity=0.324  Sum_probs=69.1

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhC
Q psy14923         49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHDEL  120 (180)
Q Consensus        49 PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  120 (180)
                      .|||+|||+||+++.|..|..+||++++++|+++||++|++||++||++|.++|++++++|..++++|....
T Consensus         3 ikRP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~~   74 (86)
T d2lefa_           3 IKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARD   74 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCCC
Confidence            479999999999999999999999999999999999999999999999999999999999999999997643

>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.15  E-value=3.9e-07  Score=60.71  Aligned_cols=33  Identities=27%  Similarity=0.353  Sum_probs=29.2

Q ss_pred             hhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        145 KKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       145 kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ++..+||+.|+||+|||+|||++.|..+..+|.
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p   34 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHP   34 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCT
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCC
Confidence            356789999999999999999999999887764

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.08  E-value=3.9e-07  Score=61.10  Aligned_cols=34  Identities=18%  Similarity=0.340  Sum_probs=29.4

Q ss_pred             HhhhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        144 MKKLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       144 ~kk~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ..+..++++.||||+|||+|||.+.|..+..+|.
T Consensus        11 ~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p   44 (93)
T d1lwma_          11 TTRKKKDPNAPKRALSAYMFFANENRDIVRSENP   44 (93)
T ss_dssp             CCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCT
T ss_pred             cccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCC
Confidence            3456789999999999999999999999887664

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: HMG-D
species: Drosophila melanogaster [TaxId: 7227]

Probab=97.99  E-value=1.7e-06  Score=55.28  Aligned_cols=26  Identities=23%  Similarity=0.506  Sum_probs=23.9

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ++||||+|||+|||.++|..+..+|.
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p   27 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENP   27 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTST
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcC
Confidence            58999999999999999999988775

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.94  E-value=2.2e-06  Score=56.84  Aligned_cols=32  Identities=19%  Similarity=0.316  Sum_probs=28.2

Q ss_pred             hhhhccCCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        146 KLFRETGKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       146 k~~k~~~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ...++++.||||+|||+|||.++|..+..+|.
T Consensus        13 ~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p   44 (90)
T d1wgfa_          13 GGKGGSEKPKRPVSAMFIFSEEKRRQLQEERP   44 (90)
T ss_dssp             CCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCT
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCC
Confidence            34578999999999999999999999988774

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Hamster (Cricetulus griseus) [TaxId: 10029]

Probab=97.91  E-value=2.4e-06  Score=55.27  Aligned_cols=26  Identities=31%  Similarity=0.535  Sum_probs=23.5

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      ++||||+|||+|||.++|..+..+|.
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p   26 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHP   26 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCC
Confidence            57999999999999999999987764

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.78  E-value=5.7e-06  Score=52.29  Aligned_cols=25  Identities=16%  Similarity=0.355  Sum_probs=22.8

Q ss_pred             CCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        153 KPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       153 ~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      +||||+|||++||.+.|..+..+|.
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p   25 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHP   25 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCT
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCC
Confidence            4999999999999999999988764

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.77  E-value=5.4e-06  Score=55.96  Aligned_cols=29  Identities=21%  Similarity=0.347  Sum_probs=25.1

Q ss_pred             ccCCCCCCCchHHHHHHHhhhhhhhcCCC
Q psy14923        150 ETGKPKKPGNSFYLFIKDNIDKKEYEGKS  178 (180)
Q Consensus       150 ~~~~PKrP~say~lF~~e~r~~~~~~~~~  178 (180)
                      ..++||||+|||+|||.|+|..+...|.+
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~~~~   33 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELNHLP   33 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTTSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhcCCC
Confidence            46789999999999999999998877753

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.69  E-value=1.2e-05  Score=52.24  Aligned_cols=27  Identities=22%  Similarity=0.380  Sum_probs=23.8

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGKS  178 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~~  178 (180)
                      +.||||+|||+||++++|..+..+|..
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~   27 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPK   27 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCC
Confidence            469999999999999999999877754

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.64  E-value=1.3e-05  Score=52.54  Aligned_cols=27  Identities=26%  Similarity=0.448  Sum_probs=24.2

Q ss_pred             CCCCCCCchHHHHHHHhhhhhhhcCCC
Q psy14923        152 GKPKKPGNSFYLFIKDNIDKKEYEGKS  178 (180)
Q Consensus       152 ~~PKrP~say~lF~~e~r~~~~~~~~~  178 (180)
                      +.||||+|||+|||+++|..+..+|..
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~   29 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPR   29 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhcc
Confidence            579999999999999999999887753

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.40  E-value=4.1e-05  Score=48.13  Aligned_cols=25  Identities=28%  Similarity=0.284  Sum_probs=22.0

Q ss_pred             CCCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        153 KPKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       153 ~PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .+|||+|||+|||+++|..+..+|.
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p   26 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFP   26 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCS
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhc
Confidence            4689999999999999999887764

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.24  E-value=5.4e-05  Score=51.55  Aligned_cols=26  Identities=19%  Similarity=0.211  Sum_probs=20.9

Q ss_pred             hhhccCCCCCCCchHHHHHHHhhhhh
Q psy14923        147 LFRETGKPKKPGNSFYLFIKDNIDKK  172 (180)
Q Consensus       147 ~~k~~~~PKrP~say~lF~~e~r~~~  172 (180)
                      ...++.+||+|+|||+|||+++|..+
T Consensus        11 ~~~~~~p~K~P~~ay~lF~~~~r~~~   36 (108)
T d1v64a_          11 DKFDGRPTKPPPNSYSLYCAELMANM   36 (108)
T ss_dssp             CCTTTSCCCCCSSHHHHHHHHHHHHC
T ss_pred             ccCCCCCCCCCCcHHHHHHHHHHHHc
Confidence            34556667888999999999999865

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Lymphoid enhancer-binding factor, LEF1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.87  E-value=0.00025  Score=46.13  Aligned_cols=24  Identities=33%  Similarity=0.423  Sum_probs=21.7

Q ss_pred             CCCCCchHHHHHHHhhhhhhhcCC
Q psy14923        154 PKKPGNSFYLFIKDNIDKKEYEGK  177 (180)
Q Consensus       154 PKrP~say~lF~~e~r~~~~~~~~  177 (180)
                      .|||+|||+||+++.|..+..+|.
T Consensus         3 ikRP~naf~lF~~~~r~~~~~~~P   26 (86)
T d2lefa_           3 IKKPLNAFMLYMKEMRANVVAEST   26 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCC
Confidence            589999999999999999988775

>d1l8ya_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.71  E-value=0.0088  Score=37.23  Aligned_cols=70  Identities=16%  Similarity=0.279  Sum_probs=55.9

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy14923         48 KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYAQNVKKYHD  118 (180)
Q Consensus        48 ~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  118 (180)
                      -|..|.+|--+|.+.....+.+.+-. +-.-..+.+..-|++|...||.+|...|.+|..+|+.++-+.+.
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~-DR~KaqkaMeatW~~meKkEki~wikkaaedqkryerel~emr~   72 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRA   72 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHh-hHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence            35667788888888888877776633 33444567788899999999999999999999999988877654