Citrus Sinensis ID: 031021

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------
Protein Sequence
MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHccccccHHHHHccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHcHHHHHccccHHHHHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHHHHHcccEEccccccccEEEEcccccccccccccccccccccHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHcccccHHHHHHHHccHHHcccHHHHHHHHHHHHHHHccHHHHHHHHHHcHHHHHccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHcccccccHHHHHHHHHHcccEEEccccccEEEEEccccccccccccccEEcccHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MSTQIVARILIKALmampapdfslclflipervqMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHqkancgwilegdqstsqlivlppnefnhpelkknvadsiplehitrifpilg
Flexible Loop (DISEMBL)
MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPElkknvadsiplehitrifpilg
Low Complexity Region (SEG)
MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG
Disordered region (IsUnstruct)
****IVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNH**LKKNVADSIPLEHITRIFPI**
Disordered Region (DISOPRED)
**TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNE*N*****KNVADSIPLEHITRIFPILG
Disordered Region (DISEMBL)
MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG
Disordered Region (DISPRO)
MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	167	2.2.26 [Sep-21-2011]
Q94HF1	226	Eukaryotic translation in	no	no	0.994	0.734	0.772	3e-74
Q9SZA3	226	Eukaryotic translation in	yes	no	0.982	0.725	0.742	2e-71
Q567V6	219	Eukaryotic translation in	yes	no	0.904	0.689	0.312	3e-17
Q3T0V3	218	Eukaryotic translation in	yes	no	0.904	0.692	0.318	1e-16
Q9DBZ5	218	Eukaryotic translation in	yes	no	0.904	0.692	0.318	1e-16
Q9UBQ5	218	Eukaryotic translation in	yes	no	0.904	0.692	0.318	2e-16
A7SGZ5	216	Eukaryotic translation in	N/A	no	0.910	0.703	0.282	5e-15
Q28C65	218	Eukaryotic translation in	yes	no	0.904	0.692	0.293	7e-15
Q6GNI4	218	Eukaryotic translation in	N/A	no	0.904	0.692	0.293	7e-15
Q54EQ1	246	Eukaryotic translation in	yes	no	0.874	0.593	0.306	3e-13

>sp|Q94HF1|EIF3K_ORYSJ Eukaryotic translation initiation factor 3 subunit K OS=Oryza sativa subsp. japonica GN=TIF3K1 PE=2 SV=1

 Score =  276 bits (707), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 129/167 (77%), Positives = 149/167 (89%), Gaps = 1/167 (0%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           +S QIV+RILIKALMAMP PDFSLCLFLIPE VQME+QFKTLIVLSHYLET RFR FWDE
Sbjct: 61  LSVQIVSRILIKALMAMPGPDFSLCLFLIPEHVQMEEQFKTLIVLSHYLETARFRQFWDE 120

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           A+K+RNI++ VPGFEQAIQS+AIHVLSLTYQK+PR VLAEAIN++GL+LDKFLEH  AN 
Sbjct: 121 ASKNRNILDVVPGFEQAIQSYAIHVLSLTYQKVPRPVLAEAINIEGLALDKFLEHHIANS 180

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GW++E   + SQLIVLP NEFNHPELKKN A+++P EH+TRIFP+L 
Sbjct: 181 GWVIEKG-ARSQLIVLPRNEFNHPELKKNTAETVPFEHVTRIFPVLS 226

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SZA3|EIF3K_ARATH Eukaryotic translation initiation factor 3 subunit K OS=Arabidopsis thaliana GN=TIF3K1 PE=2 SV=1

 Score =  268 bits (684), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 124/167 (74%), Positives = 147/167 (88%), Gaps = 3/167 (1%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           M+T IVARIL+KALMAMP PDFSLCLFLIPERVQME+QFK+LIVLSHYLETGRF+ FWDE
Sbjct: 63  MNTHIVARILVKALMAMPTPDFSLCLFLIPERVQMEEQFKSLIVLSHYLETGRFQQFWDE 122

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           AAK+R+I+EAVPGFEQAIQ++A H+LSL+YQK+PR+VLAEA+N+ G SLDKF+E Q  N 
Sbjct: 123 AAKNRHILEAVPGFEQAIQAYASHLLSLSYQKVPRSVLAEAVNMDGASLDKFIEQQVTNS 182

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GWI+E +  +   IVLP NEFNHPELKKN  +++PLEHI RIFPILG
Sbjct: 183 GWIVEKEGGS---IVLPQNEFNHPELKKNTGENVPLEHIARIFPILG 226

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Arabidopsis thaliana (taxid: 3702)

>sp|Q567V6|EIF3K_DANRE Eukaryotic translation initiation factor 3 subunit K OS=Danio rerio GN=eif3k PE=2 SV=1

 Score = 87.8 bits (216), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/160 (31%), Positives = 85/160 (53%), Gaps = 9/160 (5%)

Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
           T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L + LET  F+ FW    
Sbjct: 64  TTVTAQILLKALTNLPHTDFTLCKCMIDQTHQEERPIRQILYLGNLLETCHFQSFWASLE 123

Query: 63  KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
           ++R++++ + GFE++++ F  HV+ +TYQ I   +LAE +   G  LD  ++      GW
Sbjct: 124 ENRDLIDGITGFEESVRKFICHVVGITYQNIEYRLLAEML---GDPLDTQVKVWMNKYGW 180

Query: 123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
               D    Q+ +    E   P   KN+ + I  E ++ I
Sbjct: 181 TENED---GQIFIHNQEESVKP---KNIVEKIDFESVSSI 214

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Danio rerio (taxid: 7955)

>sp|Q3T0V3|EIF3K_BOVIN Eukaryotic translation initiation factor 3 subunit K OS=Bos taurus GN=EIF3K PE=2 SV=1

 Score = 85.9 bits (211), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 51/160 (31%), Positives = 85/160 (53%), Gaps = 9/160 (5%)

Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
           T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct: 63  TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122

Query: 63  KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
           ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  GW
Sbjct: 123 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLTDSQLKVWMSKYGW 179

Query: 123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
               D+S  Q+ +    E   P   KN+ + I  + ++ I
Sbjct: 180 --SADES-GQIFICSQEESIKP---KNIVEKIDFDSVSSI 213

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S preinitiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of posttermination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation.

Bos taurus (taxid: 9913)

>sp|Q9DBZ5|EIF3K_MOUSE Eukaryotic translation initiation factor 3 subunit K OS=Mus musculus GN=Eif3k PE=1 SV=1

 Score = 85.9 bits (211), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 51/160 (31%), Positives = 85/160 (53%), Gaps = 9/160 (5%)

Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
           T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct: 63  TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122

Query: 63  KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
           ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  GW
Sbjct: 123 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLTDNQLKVWMSKYGW 179

Query: 123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
               D+S  Q+ +    E   P   KN+ + I  + ++ I
Sbjct: 180 --SADES-GQVFICSQEESIKP---KNIVEKIDFDSVSSI 213

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S preinitiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of posttermination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation.

Mus musculus (taxid: 10090)

>sp|Q9UBQ5|EIF3K_HUMAN Eukaryotic translation initiation factor 3 subunit K OS=Homo sapiens GN=EIF3K PE=1 SV=1

 Score = 85.1 bits (209), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/160 (31%), Positives = 85/160 (53%), Gaps = 9/160 (5%)

Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
           T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct: 63  TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122

Query: 63  KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
           ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  GW
Sbjct: 123 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLSDSQLKVWMSKYGW 179

Query: 123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
               D+S  Q+ +    E   P   KN+ + I  + ++ I
Sbjct: 180 --SADES-GQIFICSQEESIKP---KNIVEKIDFDSVSSI 213

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S preinitiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of posttermination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation.

Homo sapiens (taxid: 9606)

>sp|A7SGZ5|EIF3K_NEMVE Eukaryotic translation initiation factor 3 subunit K OS=Nematostella vectensis GN=v1g170558 PE=3 SV=1

 Score = 80.1 bits (196), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 46/163 (28%), Positives = 87/163 (53%), Gaps = 11/163 (6%)

Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
           T ++++IL+KALM +P  DF +C  +I + +Q +   K +I+L+  LET  F   W    
Sbjct: 61  TSVISQILLKALMNLPNADFIMCRCVIDDAIQQDLTIKKVILLAERLETCAFTSAWQFIK 120

Query: 63  KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAI-NLKGLSLDKFLEHQKANCG 121
           +  ++V+ V GF  AI+++  +V+ +TYQ I  ++ +E +  L+G  L  +++ +    G
Sbjct: 121 EEASLVDGVTGFHDAIRNYITYVIGVTYQTIEESLASELLGGLQGAQLQDWIKAK----G 176

Query: 122 WILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFP 164
           W+   D +     +   N+  H +  KN+A+ I    +  I  
Sbjct: 177 WMSSDDGT-----IYVTNQEAHIK-SKNIAEKIDFASVANIIA 213

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Nematostella vectensis (taxid: 45351)

>sp|Q28C65|EIF3K_XENTR Eukaryotic translation initiation factor 3 subunit K OS=Xenopus tropicalis GN=eif3k PE=2 SV=1

 Score = 80.1 bits (196), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 47/160 (29%), Positives = 83/160 (51%), Gaps = 9/160 (5%)

Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
           T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct: 63  TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQSFWQALD 122

Query: 63  KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
           ++ ++++ + GFE +++ F  HV+ +TYQ I R +LAE +   G   +  L    +  GW
Sbjct: 123 ENLDLIDGITGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLSEPQLRVWMSKYGW 179

Query: 123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
           +   +    ++ V    E   P   KN+ + I  + ++ I
Sbjct: 180 M---ESENGKIFVCNQEENIKP---KNIVEKIDFDSVSGI 213

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Xenopus tropicalis (taxid: 8364)

>sp|Q6GNI4|EIF3K_XENLA Eukaryotic translation initiation factor 3 subunit K OS=Xenopus laevis GN=eif3k PE=2 SV=1

 Score = 80.1 bits (196), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 47/160 (29%), Positives = 83/160 (51%), Gaps = 9/160 (5%)

Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
           T + A++L+KAL  +P  DF+LC  +I +  Q +   + ++ L   LET  F+ FW    
Sbjct: 63  TTVTAQVLLKALTNLPHTDFTLCKCMIDQAHQEDRPIRQILYLGDLLETCHFQSFWQALD 122

Query: 63  KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
           ++ ++++ V GFE +++ F  HV+ +TYQ I R +LAE +   G   +  L    +  GW
Sbjct: 123 ENLDLIDGVTGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLSEPQLRVWMSKYGW 179

Query: 123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
           I   +    ++ V    E   P   KN+ + I  + ++ I
Sbjct: 180 I---ESENGKIFVCNQEENIKP---KNIVEKIDFDSVSGI 213

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Xenopus laevis (taxid: 8355)

>sp|Q54EQ1|EIF3K_DICDI Eukaryotic translation initiation factor 3 subunit K OS=Dictyostelium discoideum GN=eif3K PE=3 SV=2

 Score = 74.3 bits (181), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 49/160 (30%), Positives = 81/160 (50%), Gaps = 14/160 (8%)

Query: 6   VARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHR 65
           +A++L KALM  P  DF    ++IP  +Q E+    L +L+++LET +F+  W     H 
Sbjct: 96  IAKMLAKALMNFPCNDFLFLSYMIPSIIQKEEPLLKLFILNNFLETCKFKEAWTHINSHS 155

Query: 66  NIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEH-QKANCGWIL 124
              E +P F   I++F   VLS+TYQ I  T+L E +NL   +  + +++ Q     W +
Sbjct: 156 FFSE-IPSFIDNIRNFISGVLSITYQNISITMLGELLNLSDRT--QLVDYIQSKQPTWKI 212

Query: 125 EGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFP 164
               S S + +   N       K+  AD+   + ++RI P
Sbjct: 213 ----SDSTVSLQSDNS------KQKKADTFTFDQLSRILP 242

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Dictyostelium discoideum (taxid: 44689)

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	167
225444609	229	PREDICTED: eukaryotic translation initia	1.0	0.729	0.880	5e-83
224068568	235	predicted protein [Populus trichocarpa]	1.0	0.710	0.856	2e-80
118484167	238	unknown [Populus trichocarpa]	1.0	0.701	0.844	1e-79
449452616	231	PREDICTED: eukaryotic translation initia	0.994	0.718	0.838	2e-78
356547978	229	PREDICTED: eukaryotic translation initia	1.0	0.729	0.838	5e-78
357479317	235	Eukaryotic translation initiation factor	1.0	0.710	0.832	6e-78
388507968	229	unknown [Lotus japonicus]	1.0	0.729	0.832	8e-78
388508942	229	unknown [Lotus japonicus]	1.0	0.729	0.832	1e-77
224142767	243	predicted protein [Populus trichocarpa]	1.0	0.687	0.819	1e-77
255550315	236	Eukaryotic translation initiation factor	1.0	0.707	0.814	2e-77

>gi|225444609|ref|XP_002274986.1| PREDICTED: eukaryotic translation initiation factor 3 subunit K [Vitis vinifera] gi|297738508|emb|CBI27753.3| unnamed protein product [Vitis vinifera]

 Score =  311 bits (797), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 147/167 (88%), Positives = 157/167 (94%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MSTQIVARIL+KALMAMPAPDFSLCLFLIPERVQME+QFKTLIVLSHYLET RFR FWDE
Sbjct: 63  MSTQIVARILVKALMAMPAPDFSLCLFLIPERVQMEEQFKTLIVLSHYLETARFRQFWDE 122

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           AAK+R+IVE VPGFEQAIQ++AIHVLSLTYQK+PRTVLAEAIN++GLSLDKFLEHQ ANC
Sbjct: 123 AAKNRHIVEVVPGFEQAIQAYAIHVLSLTYQKVPRTVLAEAINIEGLSLDKFLEHQVANC 182

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GW+LE  Q   QLIVLPPNEFNHPELKKN ADSIPLEHITRIFPILG
Sbjct: 183 GWVLEKSQGKGQLIVLPPNEFNHPELKKNAADSIPLEHITRIFPILG 229

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224068568|ref|XP_002326147.1| predicted protein [Populus trichocarpa] gi|118488161|gb|ABK95900.1| unknown [Populus trichocarpa] gi|222833340|gb|EEE71817.1| predicted protein [Populus trichocarpa]

 Score =  303 bits (776), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 143/167 (85%), Positives = 154/167 (92%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MSTQIVARIL+KALMAMPAPDFSLCLFLIPERVQME+QFKTLIVLSHYLETGRFR FWDE
Sbjct: 69  MSTQIVARILVKALMAMPAPDFSLCLFLIPERVQMEEQFKTLIVLSHYLETGRFRQFWDE 128

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           AAK R+IVEAVPGFEQAIQ++AIH+LSLTYQK+PR+VLAEAIN++GLSLDKFLE Q ANC
Sbjct: 129 AAKSRHIVEAVPGFEQAIQAYAIHLLSLTYQKVPRSVLAEAINIEGLSLDKFLEQQVANC 188

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GWILE      QLIVLP NEFNHPELKKN ADSIPLEH+ RIFPILG
Sbjct: 189 GWILEKSHGRGQLIVLPSNEFNHPELKKNTADSIPLEHVARIFPILG 235

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118484167|gb|ABK93965.1| unknown [Populus trichocarpa]

 Score =  300 bits (768), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 141/167 (84%), Positives = 154/167 (92%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MSTQIVARILIKALMAMPAPDF LCLFLIPERVQME+QFKTLIVLSHYLETGRFR FWDE
Sbjct: 72  MSTQIVARILIKALMAMPAPDFGLCLFLIPERVQMEEQFKTLIVLSHYLETGRFRQFWDE 131

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           AAK+R+IVEAVPGFEQAIQ++AIH+LSLTYQK+PR++LAEAIN++GLSLDKFLE Q +NC
Sbjct: 132 AAKNRHIVEAVPGFEQAIQTYAIHLLSLTYQKVPRSILAEAINIEGLSLDKFLEQQVSNC 191

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GW LE      QLIVLP NEFNHPELKKN ADSIPLEH+TRIFPILG
Sbjct: 192 GWTLEKGHGQVQLIVLPSNEFNHPELKKNTADSIPLEHVTRIFPILG 238

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452616|ref|XP_004144055.1| PREDICTED: eukaryotic translation initiation factor 3 subunit K-like [Cucumis sativus] gi|449518139|ref|XP_004166101.1| PREDICTED: eukaryotic translation initiation factor 3 subunit K-like [Cucumis sativus]

 Score =  296 bits (757), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 140/167 (83%), Positives = 155/167 (92%), Gaps = 1/167 (0%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MSTQIVARIL+KALMAMPAPDFSLCLFLIPERVQMEDQFKTLI+LSHYLETG+FR FWDE
Sbjct: 66  MSTQIVARILVKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIILSHYLETGKFRQFWDE 125

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           AAK+R+IVEAVPGFEQAIQ++A+HVLSLTYQK+PR+VLAEAIN++GLSLDKFLEHQ AN 
Sbjct: 126 AAKNRHIVEAVPGFEQAIQAYAVHVLSLTYQKVPRSVLAEAINIEGLSLDKFLEHQVANS 185

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GW LE      QLIV+PPNEFNHPELKK  +DSIPL+HITRIFPILG
Sbjct: 186 GWTLEKG-GKGQLIVIPPNEFNHPELKKKSSDSIPLDHITRIFPILG 231

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356547978|ref|XP_003542381.1| PREDICTED: eukaryotic translation initiation factor 3 subunit K-like [Glycine max]

 Score =  295 bits (754), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 140/167 (83%), Positives = 153/167 (91%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MS+QIVARIL+KALMAMPAPDFSLCLFLIPERVQME+QFKTLIVLSHYLETGRFR FWDE
Sbjct: 63  MSSQIVARILVKALMAMPAPDFSLCLFLIPERVQMEEQFKTLIVLSHYLETGRFRQFWDE 122

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           AAK R+IVEAVPGFEQAIQ +AIHVLSLTYQ+IPRTVLAEAIN++GLSLDKFLE+Q AN 
Sbjct: 123 AAKSRHIVEAVPGFEQAIQGYAIHVLSLTYQRIPRTVLAEAINIEGLSLDKFLENQVANN 182

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GW++E  Q  +QLIVLP NEFN P LKKN ADS+PLEHITRIFPIL 
Sbjct: 183 GWVIEKSQGRAQLIVLPRNEFNDPALKKNAADSVPLEHITRIFPILS 229

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357479317|ref|XP_003609944.1| Eukaryotic translation initiation factor 3 subunit K [Medicago truncatula] gi|355510999|gb|AES92141.1| Eukaryotic translation initiation factor 3 subunit K [Medicago truncatula]

 Score =  295 bits (754), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 139/167 (83%), Positives = 151/167 (90%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MS+QIVARIL+KALMAMPAPDFSLCLFLIPERVQME+QFKTLIVLSHYLETGRFR FWDE
Sbjct: 69  MSSQIVARILVKALMAMPAPDFSLCLFLIPERVQMEEQFKTLIVLSHYLETGRFRQFWDE 128

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           A+K R+IVEAVPGFEQAIQ +AIHVLSLTYQKIPRTVLAEAIN++GLSLDKFLEHQ  N 
Sbjct: 129 ASKSRHIVEAVPGFEQAIQGYAIHVLSLTYQKIPRTVLAEAINVEGLSLDKFLEHQVENS 188

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GW++E  Q   QLIVLP NEFN P LKKN ADS+PLEH+TRIFPIL 
Sbjct: 189 GWVIEKSQGKGQLIVLPRNEFNDPILKKNTADSVPLEHVTRIFPILS 235

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507968|gb|AFK42050.1| unknown [Lotus japonicus]

 Score =  294 bits (753), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 139/167 (83%), Positives = 152/167 (91%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MS+QIVARIL+KALMAMPAPDFSLCLFLIPERVQME+QFKTLIVLSHYLETGRFR FWDE
Sbjct: 63  MSSQIVARILVKALMAMPAPDFSLCLFLIPERVQMEEQFKTLIVLSHYLETGRFRQFWDE 122

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           AAK R+IVEAVPGFEQAIQS+A+HV+SLTYQK+PRTVLAEAIN++GLSLDKFLEHQ AN 
Sbjct: 123 AAKSRHIVEAVPGFEQAIQSYAVHVISLTYQKVPRTVLAEAINVEGLSLDKFLEHQVANS 182

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GW +E  Q   QLIV+P NEFN P LKKN ADS+PLEHITRIFPIL 
Sbjct: 183 GWAIEKSQGKGQLIVIPRNEFNDPILKKNTADSVPLEHITRIFPILS 229

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388508942|gb|AFK42537.1| unknown [Lotus japonicus]

 Score =  294 bits (752), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 139/167 (83%), Positives = 152/167 (91%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MS+QIVARIL+KALMAMPAPDFSLCLFLIPERVQME+QFKTLIVLSHYLETGRFR FWDE
Sbjct: 63  MSSQIVARILVKALMAMPAPDFSLCLFLIPERVQMEEQFKTLIVLSHYLETGRFRQFWDE 122

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           AAK R+IVEAVPGFEQAIQS+A+HV+SLTYQK+PRTVLAEAIN++GLSLDKFLEHQ AN 
Sbjct: 123 AAKSRHIVEAVPGFEQAIQSYAVHVISLTYQKVPRTVLAEAINVEGLSLDKFLEHQVANS 182

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GW +E  Q   QLIV+P NEFN P LKKN ADS+PLEHITRIFPIL 
Sbjct: 183 GWAIEKSQGKGQLIVIPRNEFNDPILKKNTADSVPLEHITRIFPILS 229

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142767|ref|XP_002324723.1| predicted protein [Populus trichocarpa] gi|222866157|gb|EEF03288.1| predicted protein [Populus trichocarpa]

 Score =  293 bits (751), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 141/172 (81%), Positives = 154/172 (89%), Gaps = 5/172 (2%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MSTQIVARILIKALMAMPAPDF LCLFLIPERVQME+QFKTLIVLSHYLETGRFR FWDE
Sbjct: 72  MSTQIVARILIKALMAMPAPDFGLCLFLIPERVQMEEQFKTLIVLSHYLETGRFRQFWDE 131

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAE-----AINLKGLSLDKFLEH 115
           AAK+R+IVEAVPGFEQAIQ++AIH+LSLTYQK+PR++LAE     AIN++GLSLDKFLE 
Sbjct: 132 AAKNRHIVEAVPGFEQAIQTYAIHLLSLTYQKVPRSILAEACMWQAINIEGLSLDKFLEQ 191

Query: 116 QKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           Q +NCGW LE      QLIVLP NEFNHPELKKN ADSIPLEH+TRIFPILG
Sbjct: 192 QVSNCGWTLEKGHGQVQLIVLPSNEFNHPELKKNTADSIPLEHVTRIFPILG 243

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255550315|ref|XP_002516208.1| Eukaryotic translation initiation factor 3 subunit, putative [Ricinus communis] gi|223544694|gb|EEF46210.1| Eukaryotic translation initiation factor 3 subunit, putative [Ricinus communis]

 Score =  293 bits (750), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 136/167 (81%), Positives = 152/167 (91%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
           MSTQIVARIL+KALMA+PAPDFSLCLFLIPERVQME+Q K LIVLSH+LETGRFR FWDE
Sbjct: 70  MSTQIVARILVKALMALPAPDFSLCLFLIPERVQMEEQLKNLIVLSHFLETGRFRQFWDE 129

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
           AAK R+IVEAVPGFEQA+Q++AIH+LSLTYQK+PR+VLAEAIN++ LSLDKFLEHQ ANC
Sbjct: 130 AAKSRHIVEAVPGFEQAVQAYAIHLLSLTYQKVPRSVLAEAINVEALSLDKFLEHQVANC 189

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
           GWI+E      QLIVLP NEFNHPELKKN AD+IPLEH+ RIFPILG
Sbjct: 190 GWIIEKGHGKGQLIVLPSNEFNHPELKKNTADTIPLEHVARIFPILG 236

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	167
TAIR|locus:2119131	226	EIF3K "eukaryotic translation	0.982	0.725	0.742	1.4e-64
UNIPROTKB|Q9UBQ5	218	EIF3K "Eukaryotic translation	0.904	0.692	0.325	7.5e-18
UNIPROTKB|Q3T0V3	218	EIF3K "Eukaryotic translation	0.904	0.692	0.318	9.5e-18
UNIPROTKB|E2R4Y6	218	EIF3K "Uncharacterized protein	0.904	0.692	0.318	9.5e-18
MGI|MGI:1921080	218	Eif3k "eukaryotic translation	0.904	0.692	0.318	1.2e-17
ZFIN|ZDB-GENE-050417-45	219	zgc:110726 "zgc:110726" [Danio	0.904	0.689	0.312	1.2e-17
UNIPROTKB|F1RI41	218	EIF3K "Uncharacterized protein	0.904	0.692	0.318	1.6e-17
UNIPROTKB|B7ZAM9	211	EIF3K "Eukaryotic translation	0.874	0.691	0.329	3.2e-17
UNIPROTKB|K7EQM4	170	EIF3K "Eukaryotic translation	0.844	0.829	0.333	1.1e-16
UNIPROTKB|Q28C65	218	eif3k "Eukaryotic translation	0.904	0.692	0.3	2.9e-16

TAIR|locus:2119131 EIF3K "eukaryotic translation initiation factor 3K" [Arabidopsis thaliana (taxid:3702)]

 Score = 658 (236.7 bits), Expect = 1.4e-64, P = 1.4e-64
 Identities = 124/167 (74%), Positives = 147/167 (88%)

Query:     1 MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
             M+T IVARIL+KALMAMP PDFSLCLFLIPERVQME+QFK+LIVLSHYLETGRF+ FWDE
Sbjct:    63 MNTHIVARILVKALMAMPTPDFSLCLFLIPERVQMEEQFKSLIVLSHYLETGRFQQFWDE 122

Query:    61 AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
             AAK+R+I+EAVPGFEQAIQ++A H+LSL+YQK+PR+VLAEA+N+ G SLDKF+E Q  N 
Sbjct:   123 AAKNRHILEAVPGFEQAIQAYASHLLSLSYQKVPRSVLAEAVNMDGASLDKFIEQQVTNS 182

Query:   121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIFPILG 167
             GWI+E +  +   IVLP NEFNHPELKKN  +++PLEHI RIFPILG
Sbjct:   183 GWIVEKEGGS---IVLPQNEFNHPELKKNTGENVPLEHIARIFPILG 226

GO:0003743 "translation initiation factor activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA;ISS

GO:0006413 "translational initiation" evidence=IEA

GO:0006446 "regulation of translational initiation" evidence=IEA

GO:0043022 "ribosome binding" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

GO:0006364 "rRNA processing" evidence=RCA

UNIPROTKB|Q9UBQ5 EIF3K "Eukaryotic translation initiation factor 3 subunit K" [Homo sapiens (taxid:9606)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 52/160 (32%), Positives = 86/160 (53%)

Query:     3 TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct:    63 TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122

Query:    63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
             ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +    LS D  L+   +  GW
Sbjct:   123 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLG--DLS-DSQLKVWMSKYGW 179

Query:   123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
                 D+S  Q+ +    E   P   KN+ + I  + ++ I
Sbjct:   180 --SADES-GQIFICSQEESIKP---KNIVEKIDFDSVSSI 213

GO:0006446 "regulation of translational initiation" evidence=IEA

GO:0043022 "ribosome binding" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IDA

GO:0003743 "translation initiation factor activity" evidence=IC;IDA

GO:0006413 "translational initiation" evidence=IC;IDA;TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q3T0V3 EIF3K "Eukaryotic translation initiation factor 3 subunit K" [Bos taurus (taxid:9913)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 51/160 (31%), Positives = 85/160 (53%)

Query:     3 TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct:    63 TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122

Query:    63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
             ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  GW
Sbjct:   123 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLTDSQLKVWMSKYGW 179

Query:   123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
                 D+S  Q+ +    E   P   KN+ + I  + ++ I
Sbjct:   180 --SADES-GQIFICSQEESIKP---KNIVEKIDFDSVSSI 213

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0043022 "ribosome binding" evidence=IEA

GO:0006446 "regulation of translational initiation" evidence=IEA

UNIPROTKB|E2R4Y6 EIF3K "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 51/160 (31%), Positives = 85/160 (53%)

Query:     3 TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct:    63 TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122

Query:    63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
             ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  GW
Sbjct:   123 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLTDSQLKVWMSKYGW 179

Query:   123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
                 D+S  Q+ +    E   P   KN+ + I  + ++ I
Sbjct:   180 --SADES-GQIFICSQEESIKP---KNIVEKIDFDSVSSI 213

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0043022 "ribosome binding" evidence=IEA

GO:0006446 "regulation of translational initiation" evidence=IEA

MGI|MGI:1921080 Eif3k "eukaryotic translation initiation factor 3, subunit K" [Mus musculus (taxid:10090)]

 Score = 215 (80.7 bits), Expect = 1.2e-17, P = 1.2e-17
 Identities = 51/160 (31%), Positives = 85/160 (53%)

Query:     3 TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct:    63 TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122

Query:    63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
             ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  GW
Sbjct:   123 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLTDNQLKVWMSKYGW 179

Query:   123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
                 D+S  Q+ +    E   P   KN+ + I  + ++ I
Sbjct:   180 --SADES-GQVFICSQEESIKP---KNIVEKIDFDSVSSI 213

GO:0003723 "RNA binding" evidence=RCA

GO:0003743 "translation initiation factor activity" evidence=IDA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISO;IDA

GO:0006412 "translation" evidence=IEA

GO:0006413 "translational initiation" evidence=ISO;IDA

GO:0006446 "regulation of translational initiation" evidence=IEA

GO:0043022 "ribosome binding" evidence=IEA

ZFIN|ZDB-GENE-050417-45 zgc:110726 "zgc:110726" [Danio rerio (taxid:7955)]

 Score = 215 (80.7 bits), Expect = 1.2e-17, P = 1.2e-17
 Identities = 50/160 (31%), Positives = 85/160 (53%)

Query:     3 TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L + LET  F+ FW    
Sbjct:    64 TTVTAQILLKALTNLPHTDFTLCKCMIDQTHQEERPIRQILYLGNLLETCHFQSFWASLE 123

Query:    63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
             ++R++++ + GFE++++ F  HV+ +TYQ I   +LAE +   G  LD  ++      GW
Sbjct:   124 ENRDLIDGITGFEESVRKFICHVVGITYQNIEYRLLAEML---GDPLDTQVKVWMNKYGW 180

Query:   123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
                 D    Q+ +    E   P   KN+ + I  E ++ I
Sbjct:   181 TENED---GQIFIHNQEESVKP---KNIVEKIDFESVSSI 214

GO:0043022 "ribosome binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006446 "regulation of translational initiation" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA;ISS

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA;ISS

GO:0006413 "translational initiation" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|F1RI41 EIF3K "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 51/160 (31%), Positives = 85/160 (53%)

Query:     3 TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct:    63 TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122

Query:    63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
             ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  GW
Sbjct:   123 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLTDGQLKVWMSKYGW 179

Query:   123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
                 D+S  Q+ +    E   P   KN+ + I  + ++ I
Sbjct:   180 --SADES-GQIFICSQEESIKP---KNIVEKIDFDSVSSI 213

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0043022 "ribosome binding" evidence=IEA

GO:0006446 "regulation of translational initiation" evidence=IEA

UNIPROTKB|B7ZAM9 EIF3K "Eukaryotic translation initiation factor 3 subunit K" [Homo sapiens (taxid:9606)]

 Score = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 51/155 (32%), Positives = 83/155 (53%)

Query:     3 TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct:    63 TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122

Query:    63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
             ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +    LS D  L+   +  GW
Sbjct:   123 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLG--DLS-DSQLKVWMSKYGW 179

Query:   123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLE 157
                 D+S  Q+ +    E   P   KN+ + I  +
Sbjct:   180 --SADES-GQIFICSQEESIKP---KNIVEKIDFD 208

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0006446 "regulation of translational initiation" evidence=IEA

GO:0043022 "ribosome binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|K7EQM4 EIF3K "Eukaryotic translation initiation factor 3 subunit K" [Homo sapiens (taxid:9606)]

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 50/150 (33%), Positives = 81/150 (54%)

Query:     3 TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct:    30 TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 89

Query:    63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
             ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +    LS D  L+   +  GW
Sbjct:    90 ENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLG--DLS-DSQLKVWMSKYGW 146

Query:   123 ILEGDQSTSQLIVLPPNEFNHPELKKNVAD 152
                 D+S  Q+ +    E   P   KN+ +
Sbjct:   147 --SADES-GQIFICSQEESIKP---KNIVE 170

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0006446 "regulation of translational initiation" evidence=IEA

GO:0043022 "ribosome binding" evidence=IEA

UNIPROTKB|Q28C65 eif3k "Eukaryotic translation initiation factor 3 subunit K" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 202 (76.2 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 48/160 (30%), Positives = 84/160 (52%)

Query:     3 TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW    
Sbjct:    63 TTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQSFWQALD 122

Query:    63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
             ++ ++++ + GFE +++ F  HV+ +TYQ I R +LAE +    LS +  L    +  GW
Sbjct:   123 ENLDLIDGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLG--DLS-EPQLRVWMSKYGW 179

Query:   123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
             +   +    ++ V    E   P   KN+ + I  + ++ I
Sbjct:   180 M---ESENGKIFVCNQEENIKP---KNIVEKIDFDSVSGI 213

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SZA3	EIF3K_ARATH	No assigned EC number	0.7425	0.9820	0.7256	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_Genewise1_v1.C_280266 SubName- Full=Putative uncharacterized protein; (236 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	167
pfam03399	155	pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p2	5e-20
pfam10075	144	pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN	2e-15
CHL00099	585	CHL00099, ilvB, acetohydroxyacid synthase large su	0.004

>gnl|CDD|217534 pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p25 family

 Score = 80.8 bits (200), Expect = 5e-20
 Identities = 24/99 (24%), Positives = 43/99 (43%), Gaps = 1/99 (1%)

Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
            + +A  L+  L   P  DF   L L+P+ ++ +   +  + L   L  G +  F+    
Sbjct: 54  AEFIAYYLLYLLSNNPISDFHTELELLPDEIRNDPYIQFALELEQALMEGNYHRFFRLLK 113

Query: 63  KHRNIVEAVPG-FEQAIQSFAIHVLSLTYQKIPRTVLAE 100
           K   +   +   F   I+  A+  +S  Y+ IP + LAE
Sbjct: 114 KAPYLYACLLERFLDRIRKEALKAISKAYRSIPLSYLAE 152

This large family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits. Length = 155

>gnl|CDD|220553 pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN8

 Score = 68.5 bits (168), Expect = 2e-15
 Identities = 37/142 (26%), Positives = 57/142 (40%), Gaps = 10/142 (7%)

Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQF-KTLIVLSHYLETGRFRHFW--- 58
           T++   IL+K L      DF L L  IP+ ++  +   + L+ L   L    +  FW   
Sbjct: 4   TELYGLILLKLLTQNDIADFRLLLKRIPQAIKESNPEIQQLLTLGQLLWENDYAKFWQTL 63

Query: 59  DEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKA 118
                  +    + G E  I+     ++   Y  I    LAE   L GLS D+ LE    
Sbjct: 64  RSNDWSEDYTPFIAGLEDTIRDEIAALVGKAYSSISIDDLAE---LLGLSSDEELEKFAK 120

Query: 119 NCGWILEGDQSTSQLIVLPPNE 140
             GW L+ D    +++   P E
Sbjct: 121 KRGWTLDSD---GRILPPNPEE 139

This PCI_Csn8 domain is conserved from plants to humans. It is a signature protein motif found in components of CSN (COP9 signalosome). It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development. Length = 144

>gnl|CDD|214363 CHL00099, ilvB, acetohydroxyacid synthase large subunit

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 21/81 (25%), Positives = 39/81 (48%)

Query: 57  FWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQ 116
           F+ E   H N+ E  P F +  +++ I  L +  +K  ++ L EA++  G  L      +
Sbjct: 497 FYGERYSHSNMEEGAPDFVKLAEAYGIKGLRIKSRKDLKSSLKEALDYDGPVLIDCQVIE 556

Query: 117 KANCGWILEGDQSTSQLIVLP 137
             NC  ++   +S SQ+I + 
Sbjct: 557 DENCYPMVAPGKSNSQMIGIL 577

Length = 585

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	167
KOG3252	217	consensus Uncharacterized conserved protein [Funct	100.0
PF10075	143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	100.0
KOG4414	197	consensus COP9 signalosome, subunit CSN8 [Posttran	99.51
PF03399	204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	99.19
PF01399	105	PCI: PCI domain; InterPro: IPR000717 A homology do	97.76
KOG3151	260	consensus 26S proteasome regulatory complex, subun	97.26
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	96.72
smart00753	88	PAM PCI/PINT associated module.	96.72
KOG1861	540	consensus Leucine permease transcriptional regulat	96.48
KOG2758	432	consensus Translation initiation factor 3, subunit	93.13
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	90.46
KOG2581	493	consensus 26S proteasome regulatory complex, subun	90.28
KOG0687	393	consensus 26S proteasome regulatory complex, subun	86.37
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	84.65
COG5071	439	RPN5 26S proteasome regulatory complex component [	84.05
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	83.42
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	83.18
COG5187	412	RPN7 26S proteasome regulatory complex component,	82.84
COG1654	79	BirA Biotin operon repressor [Transcription]	81.78
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	81.13
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	80.24
PF13730	55	HTH_36: Helix-turn-helix domain	80.19

>KOG3252 consensus Uncharacterized conserved protein [Function unknown]

Probab=100.00  E-value=5.5e-53  Score=329.03  Aligned_cols=157  Identities=40%  Similarity=0.696  Sum_probs=143.7

Q ss_pred             CCHHHHHHHHHHHHHcCCccchhhhhcCCCccccCchhHHHHHHHHHHHHcCChHHHHHHHhhccchhhcccchHHHHHH
Q 031021            1 MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQS   80 (167)
Q Consensus         1 ~~~~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~~~~~i~gFed~IR~   80 (167)
                      ||.+++++|||||||++|||||+||+||||+++|.++++++|+.||++||+|+|+.||++.+.++++++.|+||||+||+
T Consensus        60 ~nt~itaqILlKaL~~lP~tDF~l~kcli~~~~~~ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N~~mle~itGFedsvr~  139 (217)
T KOG3252|consen   60 FNTTITAQILLKALTNLPHTDFTLAKCLIDERVQMEEPFRSIIDLGDYLETCRFQQFWQEADENRDMLEGITGFEDSVRK  139 (217)
T ss_pred             hhhHHHHHHHHHHHhcCCCcchhHHHHhcCHHHhcccchhHHHhHHHHHhhchHHHHhhhhccchHHhcCCCcHHHHHHH
Confidence            68899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCCCccccccccccccCCcccc
Q 031021           81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHIT  160 (167)
Q Consensus        81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~N~~~~~~~i~E~i~f~~~~  160 (167)
                      |+|||||.|||+|+++.|+++||   ...+++++.|++++||..+..   | .+++|.++++  .++|||.|||+||+|+
T Consensus       140 yachvv~iTyQkI~k~lLaellG---~~sDs~le~~~~~~GW~a~e~---G-~ifv~~qE~~--iKtkNi~EkI~fd~Va  210 (217)
T KOG3252|consen  140 YACHVVGITYQKIDKWLLAELLG---GLSDSQLEVWMTKYGWIADES---G-QIFVASQEEE--IKTKNIVEKIDFDHVA  210 (217)
T ss_pred             HHHHheechHhhchHHHHHHhhC---cccHHHHHHHHHHccceecCC---c-eEEEeccccc--cccCCccccCCcchHH
Confidence            99999999999999999999997   444566777779999999843   4 6777777763  3459999999999999


Q ss_pred             cccccC
Q 031021          161 RIFPIL  166 (167)
Q Consensus       161 ~i~~~~  166 (167)
                      ++||.+
T Consensus       211 ~ima~~  216 (217)
T KOG3252|consen  211 SIMASL  216 (217)
T ss_pred             HHHHhc
Confidence            999975

>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8

Probab=100.00  E-value=2.4e-34  Score=218.32  Aligned_cols=131  Identities=33%  Similarity=0.570  Sum_probs=107.7

Q ss_pred             CHHHHHHHHHHHHHcCCccchhhhhcCCCccccC-chhHHHHHHHHHHHHcCChHHHHHHHhhc---cchhhcccchHHH
Q 031021            2 STQIVARILIKALMAMPAPDFSLCLFLIPERVQM-EDQFKTLIVLSHYLETGRFRHFWDEAAKH---RNIVEAVPGFEQA   77 (167)
Q Consensus         2 ~~~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~-~~~i~~i~~L~~lLe~c~F~~FW~~l~~~---~~~~~~i~gFed~   77 (167)
                      ++++++.+|+|+|++.|.+||.+|.++||++.+. +++|+.++.|+++||+|+|++||+.++++   +++.+.|+||+|+
T Consensus         3 ~~~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~   82 (143)
T PF10075_consen    3 NPEIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDT   82 (143)
T ss_dssp             -HHHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHH
T ss_pred             chhHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999987 59999999999999999999999999887   8999999999999


Q ss_pred             HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCC
Q 031021           78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEF  141 (167)
Q Consensus        78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~  141 (167)
                      ||++|+++|+.||++|+.+.+++|||++++++.+++    +++||+++++     .++++.|++
T Consensus        83 iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~----~~~gW~~d~~-----~~~~~~~~~  137 (143)
T PF10075_consen   83 IRERIAHLISKAYSSISLSDLAEMLGLSEEELEKFI----KSRGWTVDGD-----GVLFPPNPE  137 (143)
T ss_dssp             HHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHH----HHHT-EE----------EE---HH
T ss_pred             HHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHH----HHcCCEECCC-----ccEEecCCc
Confidence            999999999999999999999999999988888888    7779999843     455655555

In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.

>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.51  E-value=1.8e-14  Score=109.96  Aligned_cols=130  Identities=17%  Similarity=0.248  Sum_probs=102.1

Q ss_pred             ccchhhhhcC---CCcccc-CchhHHHHHHHHHHHHcCChHHHHHHHhhc---cchhhcccchHHHHHHHHHHHHHHhcc
Q 031021           19 APDFSLCLFL---IPERVQ-MEDQFKTLIVLSHYLETGRFRHFWDEAAKH---RNIVEAVPGFEQAIQSFAIHVLSLTYQ   91 (167)
Q Consensus        19 ~~DF~lc~~L---l~~~~~-~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~---~~~~~~i~gFed~IR~~i~~vV~~tyq   91 (167)
                      +.|..-..+|   ||+... ..+|+..+|.+|+.+|+.+|+..|++++..   ++..+.|..|.|.-|++.+.++.++|+
T Consensus        52 ~dD~dnARfLWKRIP~AIKe~k~El~aaWgiGQkiWq~Df~GiYeaI~~~dWSeeak~imaAf~D~~~kR~FaLl~qAYs  131 (197)
T KOG4414|consen   52 HDDCDNARFLWKRIPPAIKEAKPELGAAWGIGQKIWQHDFAGIYEAINAHDWSEEAKDIMAAFRDATRKRAFALLLQAYS  131 (197)
T ss_pred             hccchhHHHHHHhCCHHHhhcCchhhhhhhhhHHHHhcccchHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444443   566555 378999999999999999999999999876   778889999999999999999999999


Q ss_pred             cccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCCCccccccccccccCCcccccc
Q 031021           92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI  162 (167)
Q Consensus        92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~N~~~~~~~i~E~i~f~~~~~i  162 (167)
                      +|-.+.++.+|||+.++.-+.+    -++||+.|..   ++.+.+|+.+-.       =.-+++|+++.++
T Consensus       132 sI~~~D~A~FlGl~~ddAtk~i----lEnGWqaDaa---sqMasl~kk~V~-------~a~~Vd~nK~~~L  188 (197)
T KOG4414|consen  132 SIIADDFAAFLGLPEDDATKGI----LENGWQADAA---SQMASLKKKAVA-------GALDVDFNKFIPL  188 (197)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHH----HHcccchhhH---HHHhhccchhcc-------cccccchhhceec
Confidence            9999999999999999888888    7889999855   234446543321       2235666665443

>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]

Probab=99.19  E-value=5.4e-11  Score=93.99  Aligned_cols=103  Identities=22%  Similarity=0.346  Sum_probs=83.8

Q ss_pred             CHHHHHHHHHHHHHcCCccchhhhhcCCCccccCchhHHHHHHHHHHHHcCChHHHHHHH--hhccchhhcccc-hHHHH
Q 031021            2 STQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEA--AKHRNIVEAVPG-FEQAI   78 (167)
Q Consensus         2 ~~~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l--~~~~~~~~~i~g-Fed~I   78 (167)
                      ..++++..||..|++-+.+||..++..+|+....++.|+....+...+.+++|..||..+  ++.+.+...+.. |.+.|
T Consensus        98 ~~ef~~y~lL~~l~~~~~~~~~~~l~~l~~~~~~~~~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~i  177 (204)
T PF03399_consen   98 EAEFIAYYLLYLLCQNNIPDFHMELELLPSEILSSPYIQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRI  177 (204)
T ss_dssp             HHHHHHHHHHHTT-T---THHHHHHTTS-HHHHTSHHHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHH
T ss_pred             HHHHHHHHHHHHHHcccchHHHHHHHHCchhhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHH
Confidence            357889999999999999999999999998888899999999999999999999999999  544545444444 99999


Q ss_pred             HHHHHHHHHHhccc-ccHHHHHHHhcC
Q 031021           79 QSFAIHVLSLTYQK-IPRTVLAEAINL  104 (167)
Q Consensus        79 R~~i~~vV~~tyqs-I~~~~L~~~Lgl  104 (167)
                      |..+++.++.||++ |+.+.|+++||+
T Consensus       178 R~~al~~i~~ay~~~i~l~~l~~~L~F  204 (204)
T PF03399_consen  178 RLRALQSISKAYRSSIPLSFLAELLGF  204 (204)
T ss_dssp             HHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence            99999999999999 999999999974

The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.

>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins

Probab=97.76  E-value=0.00058  Score=47.63  Aligned_cols=79  Identities=22%  Similarity=0.281  Sum_probs=65.2

Q ss_pred             HHHHHHHHHHcCChHHHHHHHhhc-------cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHH
Q 031021           41 TLIVLSHYLETGRFRHFWDEAAKH-------RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFL  113 (167)
Q Consensus        41 ~i~~L~~lLe~c~F~~FW~~l~~~-------~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~  113 (167)
                      .+..|-+.+.+++|..|-+.++..       +.+...+..+...+|...+..++..|++|+.+.+++.|+++.++++.++
T Consensus         2 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l   81 (105)
T PF01399_consen    2 PYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESIL   81 (105)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHH
Confidence            356788889999999998887765       3444567778899999999999999999999999999999999999999


Q ss_pred             HHHhhh
Q 031021          114 EHQKAN  119 (167)
Q Consensus       114 ~~~~~~  119 (167)
                      .+.+..
T Consensus        82 ~~~I~~   87 (105)
T PF01399_consen   82 IDLISN   87 (105)
T ss_dssp             HHHHHT
T ss_pred             HHHHHC
Confidence            777543

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.

>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]

Probab=97.26  E-value=0.0012  Score=54.26  Aligned_cols=112  Identities=15%  Similarity=0.232  Sum_probs=89.1

Q ss_pred             HHHHHHcCCccchhhhhcCCCccccCc-hhHHHHHHHHHHHHcCChHHHHHHHhhcc--chhhcccchHHHHHHHHHHHH
Q 031021           10 LIKALMAMPAPDFSLCLFLIPERVQME-DQFKTLIVLSHYLETGRFRHFWDEAAKHR--NIVEAVPGFEQAIQSFAIHVL   86 (167)
Q Consensus        10 LlKaL~~~P~~DF~lc~~Ll~~~~~~~-~~i~~i~~L~~lLe~c~F~~FW~~l~~~~--~~~~~i~gFed~IR~~i~~vV   86 (167)
                      |+--|.+=--+||-.-+-+||.+.+.+ +=|...+.|.+-+=...|...|++.++.+  .+.-=|.=+.+.||..|+..+
T Consensus       107 LL~LLsqNRiaeFHteLe~lp~~~l~~~~~I~~~v~LEq~~MEGaYnKv~~a~~s~p~~~y~~FmdIl~~tiRdEIA~c~  186 (260)
T KOG3151|consen  107 LLYLLSQNRIAEFHTELELLPKKILQHNPYISHPVSLEQSLMEGAYNKVLSAKQSIPSEEYTYFMDILLDTIRDEIAGCI  186 (260)
T ss_pred             HHHHHHhccHHHHHHHHHhccHHHhhccchhhhHHHHHHHHHhhHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444589999999999987654 78899999999999999999999988763  222223334678999999999


Q ss_pred             HHhcccccHHHHHHHhcCCc-hHHHHHHHHHhhhcCceee
Q 031021           87 SLTYQKIPRTVLAEAINLKG-LSLDKFLEHQKANCGWILE  125 (167)
Q Consensus        87 ~~tyqsI~~~~L~~~Lgl~~-~~l~~~~~~~~~~~GW~~~  125 (167)
                      -.+|..|+.+.-+++|+++. .++.++.    .+.+|.++
T Consensus       187 EKsYd~l~~s~a~~~L~f~~~~e~~~~~----~~r~W~l~  222 (260)
T KOG3151|consen  187 EKSYDKLSASDATQMLLFNNDKELKKFA----TERQWPLD  222 (260)
T ss_pred             HHHHhhcCHHHHHHHHhcCChHHHHHHH----HhcCCccc
Confidence            99999999999999999865 4566665    77789987

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

Probab=96.72  E-value=0.0079  Score=41.18  Aligned_cols=65  Identities=15%  Similarity=0.199  Sum_probs=52.3

Q ss_pred             ccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhc--CceeeccCCCceEEEeCC
Q 031021           71 VPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC--GWILEGDQSTSQLIVLPP  138 (167)
Q Consensus        71 i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~--GW~~~~~~~~~~~vv~p~  138 (167)
                      +..+...+|.....-++.+|++|+.+.|++.++++.++++.++.+.+.+.  ..++|..   .+++.+-.
T Consensus         3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~---~~~v~~~~   69 (88)
T smart00088        3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV---NGIVEFEE   69 (88)
T ss_pred             HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc---CCEEEECC
Confidence            45678899999999999999999999999999999999999998876542  3666643   24566643

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.

>smart00753 PAM PCI/PINT associated module

Probab=96.72  E-value=0.0079  Score=41.18  Aligned_cols=65  Identities=15%  Similarity=0.199  Sum_probs=52.3

Q ss_pred             ccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhc--CceeeccCCCceEEEeCC
Q 031021           71 VPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC--GWILEGDQSTSQLIVLPP  138 (167)
Q Consensus        71 i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~--GW~~~~~~~~~~~vv~p~  138 (167)
                      +..+...+|.....-++.+|++|+.+.|++.++++.++++.++.+.+.+.  ..++|..   .+++.+-.
T Consensus         3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~---~~~v~~~~   69 (88)
T smart00753        3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV---NGIVEFEE   69 (88)
T ss_pred             HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc---CCEEEECC
Confidence            45678899999999999999999999999999999999999998876542  3666643   24566643

>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]

Probab=96.48  E-value=0.039  Score=49.59  Aligned_cols=105  Identities=13%  Similarity=0.193  Sum_probs=86.0

Q ss_pred             ccchhhhhcCCCccccCchhHHHHHHHHHHHHcCChHHHHHHHhhccchhh-cccchHHHHHHHHHHHHHHhcc-cccHH
Q 031021           19 APDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVE-AVPGFEQAIQSFAIHVLSLTYQ-KIPRT   96 (167)
Q Consensus        19 ~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~~~~-~i~gFed~IR~~i~~vV~~tyq-sI~~~   96 (167)
                      .+|.+..+.=|.+...+++-|...+.+....-..+|..|+..+..-+.+-. .|.-|.|.-|+.++.++..+|+ +|+.+
T Consensus       403 ~~di~sll~~lt~E~ked~~V~hAL~vR~A~~~GNY~kFFrLY~~AP~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~  482 (540)
T KOG1861|consen  403 YPDILSLLRDLTEEDKEDEAVAHALEVRSAVTLGNYHKFFRLYLTAPNMSGYLMDLFLERERKKALTIICKSYRPTITVD  482 (540)
T ss_pred             chHHHHHHHhccHhhccCHHHHHHHHHHHHHHhccHHHHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHcCCCccHH
Confidence            357777777777778889999999999999999999999999876443333 3556999999999999999999 99999


Q ss_pred             HHHHHhcCCc-hHHHHHHHHHhhhcCceeecc
Q 031021           97 VLAEAINLKG-LSLDKFLEHQKANCGWILEGD  127 (167)
Q Consensus        97 ~L~~~Lgl~~-~~l~~~~~~~~~~~GW~~~~~  127 (167)
                      .+++-|.+.+ +....|+    +.++|+.+..
T Consensus       483 fi~~~laf~~~e~c~~~l----~~~~~~~~~~  510 (540)
T KOG1861|consen  483 FIASELAFDSMEDCVNFL----NEQNLTYDSL  510 (540)
T ss_pred             HHhhhhhhchHHHHHHHH----hccCcccccc
Confidence            9999998866 3344444    8889998754

>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]

Probab=93.13  E-value=0.29  Score=42.57  Aligned_cols=59  Identities=12%  Similarity=0.124  Sum_probs=50.7

Q ss_pred             cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCce
Q 031021           65 RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWI  123 (167)
Q Consensus        65 ~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~  123 (167)
                      .-+++-...|.+.-|.+|+..-..-.|.|+.+.||.-|||++++.+.|+-..++...=.
T Consensus       322 fFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~  380 (432)
T KOG2758|consen  322 FFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERWIVNLIRTARLD  380 (432)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhh
Confidence            44456677899999999999999999999999999999999999999998777655433

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

Probab=90.46  E-value=0.77  Score=28.79  Aligned_cols=48  Identities=13%  Similarity=0.166  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHhccccc-HHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021           76 QAIQSFAIHVLSLTYQKIP-RTVLAEAINLKGLSLDKFLEHQKANCGWIL  124 (167)
Q Consensus        76 d~IR~~i~~vV~~tyqsI~-~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~  124 (167)
                      +.+++.+....-..-+.++ ...|++.+|++...+.+.+..+ .+.||-.
T Consensus         8 ~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L-~~~G~i~   56 (66)
T cd07377           8 DQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALREL-EAEGLVE   56 (66)
T ss_pred             HHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEE
Confidence            3444444433222333455 8999999999999999998777 7899943

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]

Probab=90.28  E-value=0.9  Score=40.56  Aligned_cols=80  Identities=13%  Similarity=0.277  Sum_probs=61.2

Q ss_pred             hhHHHHHHHHHHHHcCChHHHHHHHhhc------cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchH-H
Q 031021           37 DQFKTLIVLSHYLETGRFRHFWDEAAKH------RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLS-L  109 (167)
Q Consensus        37 ~~i~~i~~L~~lLe~c~F~~FW~~l~~~------~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~-l  109 (167)
                      ..+..-+.|.+.....+-..|=+.+.+.      .+....+..+.-.|=+--.+-||.+|++||....|.-||++.++ .
T Consensus       316 ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~  395 (493)
T KOG2581|consen  316 KSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDA  395 (493)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhH
Confidence            3677778999999999999999888776      23333455566666677788999999999999999999997766 4


Q ss_pred             HHHHHHH
Q 031021          110 DKFLEHQ  116 (167)
Q Consensus       110 ~~~~~~~  116 (167)
                      +-.|.+.
T Consensus       396 EyiVakA  402 (493)
T KOG2581|consen  396 EYIVAKA  402 (493)
T ss_pred             HHHHHHH
Confidence            4444433

>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]

Probab=86.37  E-value=12  Score=32.72  Aligned_cols=76  Identities=13%  Similarity=0.173  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHcCChHHHHHHHhhc-------cchhhcccc-hHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHH
Q 031021           40 KTLIVLSHYLETGRFRHFWDEAAKH-------RNIVEAVPG-FEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDK  111 (167)
Q Consensus        40 ~~i~~L~~lLe~c~F~~FW~~l~~~-------~~~~~~i~g-Fed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~  111 (167)
                      +.+.++..-|-.|+|..|+..+...       .-++..... |-.-+|.++-.=+=-+|++.+.+.+|+-.|+|-+=+++
T Consensus       257 ~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDr  336 (393)
T KOG0687|consen  257 PSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDR  336 (393)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHh
Confidence            3445677788899999999987432       122221222 34457777777777899999999999999998765555


Q ss_pred             HHHH
Q 031021          112 FLEH  115 (167)
Q Consensus       112 ~~~~  115 (167)
                      .+.+
T Consensus       337 eL~r  340 (393)
T KOG0687|consen  337 ELGR  340 (393)
T ss_pred             HHHH
Confidence            4433

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=84.65  E-value=4.9  Score=24.04  Aligned_cols=46  Identities=20%  Similarity=0.332  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCce
Q 031021           76 QAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWI  123 (167)
Q Consensus        76 d~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~  123 (167)
                      +..+..|+..+.. -..++...+|+.+|++...+...+++. .+.||-
T Consensus         2 ~~~~~~Il~~l~~-~~~~t~~ela~~~~is~~tv~~~l~~L-~~~g~I   47 (48)
T PF13412_consen    2 DETQRKILNYLRE-NPRITQKELAEKLGISRSTVNRYLKKL-EEKGLI   47 (48)
T ss_dssp             -HHHHHHHHHHHH-CTTS-HHHHHHHHTS-HHHHHHHHHHH-HHTTSE
T ss_pred             CHHHHHHHHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHH-HHCcCc
Confidence            4567777877777 455999999999999999998888776 666763

...

>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

Probab=84.05  E-value=4.1  Score=35.42  Aligned_cols=57  Identities=18%  Similarity=0.289  Sum_probs=42.8

Q ss_pred             HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCC
Q 031021           81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPP  138 (167)
Q Consensus        81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~  138 (167)
                      .=+++|+.-|++|+..+|+.+|++++++.++++... ..+|-....-+-..+++-+-+
T Consensus       342 HN~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISdl-VN~G~~yaKiNrpa~Ii~FEK  398 (439)
T COG5071         342 HNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDL-VNKGHFYAKINRPAQIISFEK  398 (439)
T ss_pred             hhHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHHH-HhcCcEEEEecCccceEEeec
Confidence            346899999999999999999999999999999776 567766532222124555533

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=83.42  E-value=5.8  Score=24.32  Aligned_cols=46  Identities=15%  Similarity=0.211  Sum_probs=33.6

Q ss_pred             HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeecc
Q 031021           81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGD  127 (167)
Q Consensus        81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~  127 (167)
                      .|...+-.+=..++...||+.||+|...+...++.. ++.|..+...
T Consensus         4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L-~~~~~~I~~~   49 (55)
T PF08279_consen    4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKEL-REWGIPIESK   49 (55)
T ss_dssp             HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHH-HHTT-EEEEE
T ss_pred             HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHH-HHCCCeEEee
Confidence            455666444445999999999999999999998877 7778666543

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=83.18  E-value=2.9  Score=25.52  Aligned_cols=33  Identities=15%  Similarity=0.237  Sum_probs=27.8

Q ss_pred             cc-cHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021           92 KI-PRTVLAEAINLKGLSLDKFLEHQKANCGWILE  125 (167)
Q Consensus        92 sI-~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~  125 (167)
                      .+ +...|++.+|++...+.+.++.+ .+.||-..
T Consensus        19 ~l~s~~~la~~~~vs~~tv~~~l~~L-~~~g~i~~   52 (60)
T smart00345       19 KLPSERELAAQLGVSRTTVREALSRL-EAEGLVQR   52 (60)
T ss_pred             cCcCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEE
Confidence            46 79999999999999999998777 67899643

>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]

Probab=82.84  E-value=5.4  Score=34.53  Aligned_cols=78  Identities=13%  Similarity=0.154  Sum_probs=57.0

Q ss_pred             chhHHHHHHHHHHHHcCChHHHHHHHhhc-------cchh-hcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCch
Q 031021           36 EDQFKTLIVLSHYLETGRFRHFWDEAAKH-------RNIV-EAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGL  107 (167)
Q Consensus        36 ~~~i~~i~~L~~lLe~c~F~~FW~~l~~~-------~~~~-~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~  107 (167)
                      .+.+..|..|..-|-.|+|..|+..+...       .-++ .-+.=|-..+|+++-.-+=-+|+..+.+.+|+-.|+|-+
T Consensus       267 ~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~  346 (412)
T COG5187         267 SEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSVE  346 (412)
T ss_pred             hhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHH
Confidence            45678888999999999999888765332       1112 222335556888887778889999999999999999875


Q ss_pred             H----HHHHH
Q 031021          108 S----LDKFL  113 (167)
Q Consensus       108 ~----l~~~~  113 (167)
                      =    |.+|+
T Consensus       347 yvdrDLg~FI  356 (412)
T COG5187         347 YVDRDLGEFI  356 (412)
T ss_pred             HHhhhHHhhC
Confidence            3    44554

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=81.78  E-value=6.3  Score=27.06  Aligned_cols=54  Identities=20%  Similarity=0.189  Sum_probs=42.0

Q ss_pred             HHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCC
Q 031021           85 VLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEF  141 (167)
Q Consensus        85 vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~  141 (167)
                      +.-.++.-+|=+.|++.||+|...+-+.++.+ ++.|-.++...++|.  .+|+.++
T Consensus        12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~L-r~~G~~I~s~~~kGY--~L~~~~~   65 (79)
T COG1654          12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQL-REEGVDIESVRGKGY--LLPQLPD   65 (79)
T ss_pred             HHHcCCCcccHHHHHHHHCccHHHHHHHHHHH-HHhCCceEecCCCce--eccCccc
Confidence            34457778999999999999999999999887 899999987655454  4444443

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

Probab=81.13  E-value=12  Score=26.00  Aligned_cols=62  Identities=15%  Similarity=0.149  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHHHh------cccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCC
Q 031021           76 QAIQSFAIHVLSLT------YQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNE  140 (167)
Q Consensus        76 d~IR~~i~~vV~~t------yqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~  140 (167)
                      -.+.+.+..+...+      .-.++...|++++|++.+.+-+.+.++ .+.||-.-.. + .+.|.+++|.
T Consensus        25 ~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~L-e~~GlI~r~~-~-~~~~~~n~~~   92 (95)
T TIGR01610        25 GREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSL-ARRRIIFRQG-M-MGIVGVNTPL   92 (95)
T ss_pred             HHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHH-HHCCCeeeec-C-CceeecCCCc
Confidence            34445555555433      567889999999999999888888777 7899997432 2 2578886654

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

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=80.24  E-value=9  Score=33.03  Aligned_cols=79  Identities=13%  Similarity=0.172  Sum_probs=67.1

Q ss_pred             CchhHHHHHHHHHHHHcCChHHHHHHHhhc-------cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCch
Q 031021           35 MEDQFKTLIVLSHYLETGRFRHFWDEAAKH-------RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGL  107 (167)
Q Consensus        35 ~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~-------~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~  107 (167)
                      .+|+|.....|-+.-+..+-.+|=+-++++       +-+.+.+..+...||.-++--+-.-|.+|..+-++.-|+++..
T Consensus       300 NdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~~~  379 (440)
T KOG1464|consen  300 NDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVPEA  379 (440)
T ss_pred             CCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCCHH
Confidence            589999999999999999999999888776       3444556677778888888778889999999999999999998


Q ss_pred             HHHHHH
Q 031021          108 SLDKFL  113 (167)
Q Consensus       108 ~l~~~~  113 (167)
                      ++...+
T Consensus       380 dV~~LL  385 (440)
T KOG1464|consen  380 DVESLL  385 (440)
T ss_pred             HHHHHH
Confidence            877765

>PF13730 HTH_36: Helix-turn-helix domain

Probab=80.19  E-value=2.9  Score=25.72  Aligned_cols=28  Identities=11%  Similarity=0.268  Sum_probs=25.2

Q ss_pred             cHHHHHHHhcCCchHHHHHHHHHhhhcCc
Q 031021           94 PRTVLAEAINLKGLSLDKFLEHQKANCGW  122 (167)
Q Consensus        94 ~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW  122 (167)
                      |.+.|++.+|++...+.+.++++ ++.||
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~~L-~~~G~   54 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIKEL-EEKGL   54 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHH-HHCcC
Confidence            78999999999999999999887 77888

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	167
1rz4_A	226	Crystal Structure Of Human Eif3k Length = 226		2e-17

>pdb|1RZ4|A Chain A, Crystal Structure Of Human Eif3k Length = 226

Iteration: 1
 Score = 84.7 bits (208), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 51/160 (31%), Positives = 84/160 (52%), Gaps = 9/160 (5%)
Query: 3   TQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAA 62
           T + A+IL+KAL  +P  DF+LC   I +  Q E   + ++ L   LET  F+ FW    
Sbjct: 63  TTVTAQILLKALTNLPHTDFTLCKCXIDQAHQEERPIRQILYLGDLLETCHFQAFWQALD 122
Query: 63  KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122
           ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  GW
Sbjct: 123 ENXDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEXL---GDLSDSQLKVWXSKYGW 179
Query: 123 ILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
               D+S  Q+ +    E   P   KN+ + I  + ++ I
Sbjct: 180 --SADES-GQIFICSQEESIKP---KNIVEKIDFDSVSSI 213
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	167
1rz4_A	226	Eukaryotic translation initiation factor 3 subuni;	5e-48

>1rz4_A Eukaryotic translation initiation factor 3 subuni; heat analogous motif, winged-helix, biosynthetic protein; 2.10A {Homo sapiens} SCOP: a.4.5.53 a.118.1.18 Length = 226

 Score =  154 bits (390), Expect = 5e-48
 Identities = 49/162 (30%), Positives = 83/162 (51%), Gaps = 9/162 (5%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW  
Sbjct: 61  FQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQA 120

Query: 61  AAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120
             ++ +++E + GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  
Sbjct: 121 LDENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLSDSQLKVWMSKY 177

Query: 121 GWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162
           GW  +      Q+ +    E   P   KN+ + I  + ++ I
Sbjct: 178 GWSADES---GQIFICSQEESIKP---KNIVEKIDFDSVSSI 213

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	167
1rz4_A	226	Eukaryotic translation initiation factor 3 subuni;	100.0
4b0z_A	229	RPN12, 26S proteasome regulatory subunit RPN12; pr	99.32
4b4t_T	274	26S proteasome regulatory subunit RPN12; hydrolase	99.13
3t5v_A	316	Nuclear mRNA export protein SAC3; PCI, mRNA nuclea	98.21
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	98.02
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	97.54
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	96.94
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.54
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	96.12
4b4t_S	523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	91.5
4b4t_O	393	26S proteasome regulatory subunit RPN9; hydrolase,	91.0
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	89.44
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	87.97

>1rz4_A Eukaryotic translation initiation factor 3 subuni; heat analogous motif, winged-helix, biosynthetic protein; 2.10A {Homo sapiens} SCOP: a.4.5.53 a.118.1.18

Probab=100.00  E-value=2e-45  Score=297.75  Aligned_cols=155  Identities=30%  Similarity=0.592  Sum_probs=142.3

Q ss_pred             CCHHHHHHHHHHHHHcCCccchhhhhcCCCccccCchhHHHHHHHHHHHHcCChHHHHHHHhhccchhhcccchHHHHHH
Q 031021            1 MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQS   80 (167)
Q Consensus         1 ~~~~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~~~~~i~gFed~IR~   80 (167)
                      ++.+++++||+||||++|++||.+|+||||++.+.+++|++++.|+++||+|+|++||+.+++++++.+.|+||+|+||+
T Consensus        61 ~~~~ii~~iLlk~L~~~p~~DF~~~l~LIp~~~~~~~~I~~i~~L~~~L~~~~y~~fW~~l~~~~~l~~~i~gf~dsIR~  140 (226)
T 1rz4_A           61 FQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALDENMDLLEGITGFEDSVRK  140 (226)
T ss_dssp             CCHHHHHHHHHHHHHTTTSTHHHHHHHTSCHHHHTSTTHHHHHHHHHHHHTTCHHHHHHHSCTTCHHHHTSTTHHHHHHH
T ss_pred             cchhHHHHHHHHHHHcCCHHHHHHHHHhCChhhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhcChhHHHHHhHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcccccHHHHHHHhc-CCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCCCccccccccccccCCccc
Q 031021           81 FAIHVLSLTYQKIPRTVLAEAIN-LKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHI  159 (167)
Q Consensus        81 ~i~~vV~~tyqsI~~~~L~~~Lg-l~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~N~~~~~~~i~E~i~f~~~  159 (167)
                      +|+++|++||++|+++.+++||| ++++++++|+    +++||+++++   | .+ ++.|.+|+++ +|||+|+|+||++
T Consensus       141 ~I~~~i~~aY~sI~~~~la~lLg~~s~~el~~fi----~~~GW~vd~~---g-~I-~~~n~e~~~k-~~~~~E~i~~~~~  210 (226)
T 1rz4_A          141 FICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWM----SKYGWSADES---G-QI-FICSQEESIK-PKNIVEKIDFDSV  210 (226)
T ss_dssp             HHHHHHHHHCSEECHHHHHHHTTSCCHHHHHHHH----HHHTCEECC------CE-ECCCHHHHTS-CCCSSCCCCHHHH
T ss_pred             HHHHHHHHHHhhCCHHHHHHHHcCCCHHHHHHHH----HHCCCEECCC---c-cE-EeCCCccccc-ceeeeecccHHHH
Confidence            99999999999999999999995 8889999998    6779999743   3 34 5577777766 4999999999999


Q ss_pred             cccccc
Q 031021          160 TRIFPI  165 (167)
Q Consensus       160 ~~i~~~  165 (167)
                      +++|+.
T Consensus       211 ~~~~~~  216 (226)
T 1rz4_A          211 SSIMAS  216 (226)
T ss_dssp             HHHHCC
T ss_pred             HHHHHH
Confidence            999997

>4b0z_A RPN12, 26S proteasome regulatory subunit RPN12; protein binding, proteasome ubitquitin; HET: SGM GOL; 1.58A {Schizosaccharomyces pombe}

Probab=99.32  E-value=1.3e-11  Score=99.27  Aligned_cols=125  Identities=14%  Similarity=0.206  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHcCCccchhhhhcCCCccc--cCchhHHHHHHHHHHHHcCChHHHHHHHhhccc--hhhcccchHHHHHH
Q 031021            5 IVARILIKALMAMPAPDFSLCLFLIPERV--QMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRN--IVEAVPGFEQAIQS   80 (167)
Q Consensus         5 iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~--~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~--~~~~i~gFed~IR~   80 (167)
                      +++--||--|..--.+||...+..+|...  +.++-|+..+.|.+.+...+|..||+.+++.+.  ...-|.-|.+.+|.
T Consensus        99 ~~~~~LL~lL~~~~~~ef~~~le~l~~~~~~~~~~~I~~al~l~~al~~GnY~kff~l~~~~p~~~~~~~~~~l~~~vR~  178 (229)
T 4b0z_A           99 VTGLNLLYLLSENRIAEFHTALESVPDKSLFERDPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVMSMVRN  178 (229)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHCSCTTHHHHCHHHHHHHHHHHHHHTTCHHHHHHHHHTCCCGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCchHHHHHHHhcChHHHhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhcCccchHHHHHHHHHHHHHH
Confidence            33333444454445699999999998763  568999999999999999999999999987632  23456678999999


Q ss_pred             HHHHHHHHhcccccHHHHHHHhcCCc-hHHHHHHHHHhhhcCceeeccCCCceEEEeCC
Q 031021           81 FAIHVLSLTYQKIPRTVLAEAINLKG-LSLDKFLEHQKANCGWILEGDQSTSQLIVLPP  138 (167)
Q Consensus        81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~-~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~  138 (167)
                      .++..+..||.+|+.+.++++||+++ +++.+|+    +++||++++     +.|++|+
T Consensus       179 ~~l~~i~kaY~~i~l~~~~~~L~f~s~~e~~~f~----~~~gw~i~d-----g~i~F~~  228 (229)
T 4b0z_A          179 EIATCAEKVYSEIPLSNATSLLYLENTKETEKLA----EERGWDIRD-----GVIYFPK  228 (229)
T ss_dssp             HHHHHHHHHCSEEEHHHHHHHTTCSSHHHHHHHH----HHHTCEEET-----TEEECC-
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHH----HHcCCEEeC-----CEEecCC
Confidence            99999999999999999999999965 6677777    778999972     4788875

>4b4t_T 26S proteasome regulatory subunit RPN12; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.13  E-value=3.8e-10  Score=93.15  Aligned_cols=119  Identities=15%  Similarity=0.255  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHHHcCCccchhhhhcCCCcc---ccCchhHHHHHHHHHHHHcCChHHHHHHHhhccch----hhcccchHH
Q 031021            4 QIVARILIKALMAMPAPDFSLCLFLIPER---VQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNI----VEAVPGFEQ   76 (167)
Q Consensus         4 ~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~---~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~~----~~~i~gFed   76 (167)
                      .+++-=||-.|..--.+||..-+-.||..   .+.++-|+..+.|.+.|-..+|..||+.+++.+..    .--|.-|.+
T Consensus       104 e~~~~~LLylL~~n~~~efh~~Le~L~~~~~~~~~d~~Ik~al~le~al~eGnY~kff~l~~~~~~p~~~~~~f~d~l~~  183 (274)
T 4b4t_T          104 KLISLYLLNLLSQNNTTKFHSELQYLDKHIKNLEDDSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNISEFDSFTDILKS  183 (274)
T ss_dssp             HHHHHHHHHHHHHHCSTHHHHHHHSSSCSSSTTTCCHHHHHHHHHHHHHHHTCSHHHHHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHhcchhhHhHhcChHHHHHHHHHHHHHcCCHHHHHHHHhcCCCCcHHHHHHHHHHHH
Confidence            45555567777777789999999999864   45689999999999999999999999998875322    224556788


Q ss_pred             HHHHHHHHHHHHhcccccHHHHHHHhcCCc-hHHHHHHHHHhhhcCceeec
Q 031021           77 AIQSFAIHVLSLTYQKIPRTVLAEAINLKG-LSLDKFLEHQKANCGWILEG  126 (167)
Q Consensus        77 ~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~-~~l~~~~~~~~~~~GW~~~~  126 (167)
                      .||..|+..+..||.+|+.+.++++|++++ +++.+|+    +++||++++
T Consensus       184 ~iR~~a~~~i~kaY~~i~l~~~~~~L~F~s~~e~~~F~----~~~gW~~~~  230 (274)
T 4b4t_T          184 AIRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFA----LERNWPIVN  230 (274)
T ss_dssp             HHHHHHHHHHHHHCSSCCHHHHHHHHTCCSHHHHHHHH----HHTTCCCCS
T ss_pred             HHHHHHHHHHHHHHhhcCHHHHHHHhCCCCHHHHHHHH----HHcCCEEeC
Confidence            999999999999999999999999999965 6788887    788999973

>3t5v_A Nuclear mRNA export protein SAC3; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae}

Probab=98.21  E-value=6.3e-06  Score=69.16  Aligned_cols=107  Identities=11%  Similarity=0.180  Sum_probs=86.8

Q ss_pred             cCCccchhhhhcCCCccccCchhHHHHHHHHHHHHc---------------CChHHHHHHHhhc-cch--hhcccchHHH
Q 031021           16 AMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLET---------------GRFRHFWDEAAKH-RNI--VEAVPGFEQA   77 (167)
Q Consensus        16 ~~P~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~---------------c~F~~FW~~l~~~-~~~--~~~i~gFed~   77 (167)
                      ++-.+|+.--+-.+|+....++.|+.-+.+...+.+               .+|..||+.+++. .++  .-.+..|...
T Consensus       126 ~l~~~~~~~~l~~Lp~~i~~~p~Vq~AL~l~~a~~~~~~~e~~~~~~~~~~gNY~rFFrL~~~~~~pyL~aclle~~~~~  205 (316)
T 3t5v_A          126 KIRDPQYDENIQRLPKHIFQDKLVQMALCFRRVISNSAYTERGFVKTENCLNFYARFFQLMQSPSLPLLMGFFLQMHLTD  205 (316)
T ss_dssp             STTCTHHHHHHTTSCHHHHTSHHHHHHHHHHHHHCCTTCCCTTCCCCSSCCCCHHHHHHHHTCTTSCHHHHHHHGGGHHH
T ss_pred             HhccchHHHHHHhCCHHHhcCHHHHHHHHHHHHHHhcccccccccccccccchHHHHHHHHhccCCChHHHHHHHHHHHH
Confidence            344567777777788888889999999999888763               6799999999873 233  2346668889


Q ss_pred             HHHHHHHHHHHhc----ccccHHHHHHHhcCCc-hHHHHHHHHHhhhcCceeec
Q 031021           78 IQSFAIHVLSLTY----QKIPRTVLAEAINLKG-LSLDKFLEHQKANCGWILEG  126 (167)
Q Consensus        78 IR~~i~~vV~~ty----qsI~~~~L~~~Lgl~~-~~l~~~~~~~~~~~GW~~~~  126 (167)
                      +|..++..+..||    .+++.+.|+++|++++ +++.+||    +.+||++.+
T Consensus       206 vR~~AL~~i~kay~~k~~~~pl~~L~~~L~Fds~ee~~~F~----~~~gl~~~~  255 (316)
T 3t5v_A          206 IRFYALRALSHTLNKKHKPIPFIYLENMLLFNNRQEIIEFC----NYYSIEIIN  255 (316)
T ss_dssp             HHHHHHHHHHHHSCTTCCCEEHHHHHHHTTCSSHHHHHHHH----HHTTCCEET
T ss_pred             HHHHHHHHHHHHhccCCCCcCHHHHHHHhCCCCHHHHHHHH----HHCCCeEeC
Confidence            9999999999999    4899999999999964 7777887    888999974

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.02  E-value=3.8e-05  Score=66.22  Aligned_cols=128  Identities=12%  Similarity=0.159  Sum_probs=91.7

Q ss_pred             HHHHHHHHHHHHcCCccchhhhhcCCCcc-----ccCchhHHHHHHHHHHHHcCChHHHHHHHhhc--------cchhhc
Q 031021            4 QIVARILIKALMAMPAPDFSLCLFLIPER-----VQMEDQFKTLIVLSHYLETGRFRHFWDEAAKH--------RNIVEA   70 (167)
Q Consensus         4 ~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~-----~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~--------~~~~~~   70 (167)
                      +++....|.|+..+|.+|+--  -++...     ...+|.+..+..+-..+..|+|..|++.+...        .-+.+.
T Consensus       248 ~~~~y~~l~al~~~~r~~l~~--~v~~~~~~~~~l~~~p~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~d~~l~~h  325 (429)
T 4b4t_R          248 SIATYASVTGLFTLERTDLKS--KVIDSPELLSLISTTAALQSISSLTISLYASDYASYFPYLLETYANVLIPCKYLNRH  325 (429)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHH--SSSSSHHHHHGGGSHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHSTTTTTCTTSTTT
T ss_pred             HHHHHHHHHHHhcCCHHHHHH--HHhcCHHHHhhccCChhHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhccCHHHHHH
Confidence            345555667777777766432  122211     12356788888899999999999999875321        333444


Q ss_pred             ccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcC--ceeeccCCCceEEEe
Q 031021           71 VPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCG--WILEGDQSTSQLIVL  136 (167)
Q Consensus        71 i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G--W~~~~~~~~~~~vv~  136 (167)
                      +..|.+.||......+...|++|+.+.||+.||++.+++++++.+.+..--  =++|..  + +++.+
T Consensus       326 ~~~l~~~ir~~~l~q~~~~Ys~I~l~~mA~~l~~s~~~~E~~L~~lI~~g~l~akID~~--~-giv~~  390 (429)
T 4b4t_R          326 ADFFVREMRRKVYAQLLESYKTLSLKSMASAFGVSVAFLDNDLGKFIPNKQLNCVIDRV--N-GIVET  390 (429)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCSEEEHHHHHHHHTSCHHHHHHHHHHHHHHTSSCEEEETT--T-TEEEE
T ss_pred             HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHcCCeEEEEcCC--C-CEEEE
Confidence            677899999999999999999999999999999999999999877765432  245543  2 46665

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=97.54  E-value=0.0011  Score=56.98  Aligned_cols=128  Identities=11%  Similarity=0.138  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHcCCccchhhhhcCCCc--cccCchhHHHHHHHHHHHHcCChHHHHHHHhhcc-------chhhcccch
Q 031021            4 QIVARILIKALMAMPAPDFSLCLFLIPE--RVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHR-------NIVEAVPGF   74 (167)
Q Consensus         4 ~iv~~ILlKaL~~~P~~DF~lc~~Ll~~--~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~-------~~~~~i~gF   74 (167)
                      ++..-.+|.+|+...-+|+.--..  .+  ....+|++..+..|......|++.+|=+.+....       -+...+..+
T Consensus       221 ~~lkYlvL~aLl~~~r~el~~~l~--~~~~~~~~~pei~~l~~L~~a~~~~dl~~f~~iL~~~~~~l~~D~~l~~h~~~L  298 (394)
T 3txn_A          221 TSLKYMLLCKIMLGQSDDVNQLVS--GKLAITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQAHLGTL  298 (394)
T ss_dssp             HHHHHHHHHHHHTTCGGGHHHHHH--SHHHHTTCSHHHHHHHHHHHHHHTTCHHHHHHHHHHSTTTTTTSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHhc--cccccccCCccHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcChHHHHHHHHH
Confidence            345556677777777777653111  11  0114788999999999999999999988876642       222335667


Q ss_pred             HHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhh---cCceeeccCCCceEEEeC
Q 031021           75 EQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKAN---CGWILEGDQSTSQLIVLP  137 (167)
Q Consensus        75 ed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~---~GW~~~~~~~~~~~vv~p  137 (167)
                      .+.||......+...|++|+.+.+++.||++.+++++.+.+.+..   .| ++|..  + +++.+.
T Consensus       299 ~~~Ir~~~L~~i~~pYsrIsl~~iA~~l~ls~~evE~~L~~lI~dg~I~a-~IDq~--~-giv~~~  360 (394)
T 3txn_A          299 YDTMLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFSG-ILDQG--E-GVLIVF  360 (394)
T ss_dssp             HHHHHHHHHHHHHTTCSEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSCE-EEETT--T-TEEEEC
T ss_pred             HHHHHHHHHHHHhHhhceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCeeE-EEcCC--C-CEEEEC
Confidence            888999999999999999999999999999999999998776544   23 55643  2 466663

>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: a.4.5.47

Probab=96.94  E-value=0.0027  Score=43.14  Aligned_cols=49  Identities=12%  Similarity=0.159  Sum_probs=41.9

Q ss_pred             ccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhh
Q 031021           71 VPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKAN  119 (167)
Q Consensus        71 i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~  119 (167)
                      ..-+.+.|.+.-.+.++..|++|+.+.||++||++.+++++++.+.+..
T Consensus         9 ~~~L~~~v~E~nl~~is~~Y~~Isl~~La~ll~ls~~~vE~~ls~mI~~   57 (84)
T 1ufm_A            9 SSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITE   57 (84)
T ss_dssp             SCCCCHHHHHHHHHHHHHSCSEEEHHHHHHHTTSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHhcCeeeHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence            3456677888888889999999999999999999999999998776544

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.54  E-value=0.03  Score=45.68  Aligned_cols=85  Identities=5%  Similarity=0.051  Sum_probs=66.7

Q ss_pred             CchhHHHHHHHHHHHHcCChHHHHHHHhhc-------cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCch
Q 031021           35 MEDQFKTLIVLSHYLETGRFRHFWDEAAKH-------RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGL  107 (167)
Q Consensus        35 ~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~-------~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~  107 (167)
                      ..+++.....+......+.+..|=..+...       +.+...+..+.+.+|......+...|++|+.+.+++.||++.+
T Consensus       292 ~~~~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~y~~i~l~~la~~l~~~~~  371 (434)
T 4b4t_Q          292 QSRGIDAMKAVAEAYNNRSLLDFNTALKQYEKELMGDELTRSHFNALYDTLLESNLCKIIEPFECVEISHISKIIGLDTQ  371 (434)
T ss_dssp             CCHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHTCSHHHHHHHHHHHHHHHHHHHHHHHSSCSCEEHHHHHHHHTCCHH
T ss_pred             cchhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHhCcCHH
Confidence            356777777888888888887766655443       2233456677888999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhh
Q 031021          108 SLDKFLEHQKAN  119 (167)
Q Consensus       108 ~l~~~~~~~~~~  119 (167)
                      ++++++.+.+..
T Consensus       372 ~~E~~l~~lI~~  383 (434)
T 4b4t_Q          372 QVEGKLSQMILD  383 (434)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC
Confidence            999988765443

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.12  E-value=0.058  Score=46.50  Aligned_cols=100  Identities=10%  Similarity=0.138  Sum_probs=65.9

Q ss_pred             hhHHHHHHHHHHHHc---CChHHHHHHHhhc----cch------hhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhc
Q 031021           37 DQFKTLIVLSHYLET---GRFRHFWDEAAKH----RNI------VEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAIN  103 (167)
Q Consensus        37 ~~i~~i~~L~~lLe~---c~F~~FW~~l~~~----~~~------~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lg  103 (167)
                      +++.....|.....+   .+|+.+.+.++..    +-+      ......+.++|++.-...++.-|++|+.+.|+++||
T Consensus       291 ~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~L~~~v~ehnl~~i~k~Ys~I~l~~la~lL~  370 (445)
T 4b4t_P          291 KKLESQESLVKLFTTNELMRWPIVQKTYEPVLNEDDLAFGGEANKHHWEDLQKRVIEHNLRVISEYYSRITLLRLNELLD  370 (445)
T ss_dssp             HHHHHHHHHHHHHHHCCSSSHHHHHHHTCSSTTTCCSSCCCSCSSHHHHHHHHHHHHHHHHHHHHHEEEEEHHHHHHHHT
T ss_pred             cccHHHHHHHHHHHhchHhhhHHHHHHHHHHhcccchhhhcchhhHHHHHHHHHHHHHHHHHHHHHhceeeHHHHHHHhC
Confidence            445554455555544   4567766665432    111      112355888999999999999999999999999999


Q ss_pred             CCchHHHHHHHHHhhhc---CceeeccCCCceEEEeCCCC
Q 031021          104 LKGLSLDKFLEHQKANC---GWILEGDQSTSQLIVLPPNE  140 (167)
Q Consensus       104 l~~~~l~~~~~~~~~~~---GW~~~~~~~~~~~vv~p~n~  140 (167)
                      ++.+++++++.+.+...   | ++|..  + |+|.+..+.
T Consensus       371 l~~~evE~~ls~mI~~g~i~a-kIDq~--~-giV~F~~~~  406 (445)
T 4b4t_P          371 LTESQTETYISDLVNQGIIYA-KVNRP--A-KIVNFEKPK  406 (445)
T ss_dssp             SCHHHHHHHHHHHHHHTSSCC-EEETT--T-TEEEC----
T ss_pred             cCHHHHHHHHHHHHHCCCEEE-EEcCC--C-CEEEECCCC
Confidence            99999999987665432   3 34533  2 478875544

>4b4t_S RPN3, 26S proteasome regulatory subunit RPN3; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.50  E-value=0.67  Score=41.19  Aligned_cols=103  Identities=14%  Similarity=0.167  Sum_probs=69.9

Q ss_pred             hHHHHHHHHHHHHcCChHHHHHHHhhcc------chhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCC-chHHH
Q 031021           38 QFKTLIVLSHYLETGRFRHFWDEAAKHR------NIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLK-GLSLD  110 (167)
Q Consensus        38 ~i~~i~~L~~lLe~c~F~~FW~~l~~~~------~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~-~~~l~  110 (167)
                      .+..-..|.+.....+..+|=+.+..+.      .....|.....++.+.-++-++.+|++|+...++..|+++ .++.+
T Consensus       341 ~L~pY~~Lv~Avr~GdL~~F~~~L~~h~~~F~~Dgty~LI~rLr~~vir~~irkis~~YsrIsL~dIa~kL~L~s~eeaE  420 (523)
T 4b4t_S          341 SLLPYYHLTKAVKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSEQTVE  420 (523)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHHTTCTHHHHHHHHHHHHHHHHHSCCCSSEECHHHHHHHHHHHHSSCHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHhcceeccCChhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhCCCCHHHHH
Confidence            4555567889999999999999887662      2223345556678888889999999999999999999995 35566


Q ss_pred             HHHHHHhhhcCceeeccCCCceEEEeCCCCC
Q 031021          111 KFLEHQKANCGWILEGDQSTSQLIVLPPNEF  141 (167)
Q Consensus       111 ~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~  141 (167)
                      ..+.+.+.+-...---++.+ +.|++..++|
T Consensus       421 ~iVAkmI~dG~I~A~Idh~~-g~v~ske~~d  450 (523)
T 4b4t_S          421 YMVSRAIRDGVIEAKINHED-GFIETTELLN  450 (523)
T ss_dssp             HHHHHHHHHTSSCCEECTTT-CCEECCSSSC
T ss_pred             HHHHHHHHcCCceEEEecCC-CEEEeCcccc
Confidence            66655544332332222222 4566654444

>4b4t_O 26S proteasome regulatory subunit RPN9; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.00  E-value=1.5  Score=36.93  Aligned_cols=113  Identities=13%  Similarity=0.154  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHcCCccchhhhhcCCC-ccccCchhHHHHHHHHHHHHcCChHHHHHHHhhccchhhcccchHHHHHHHH--
Q 031021            6 VARILIKALMAMPAPDFSLCLFLIP-ERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFA--   82 (167)
Q Consensus         6 v~~ILlKaL~~~P~~DF~lc~~Ll~-~~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~~~~~i~gFed~IR~~i--   82 (167)
                      ...+++.||+.=--..|.--+..-. ......++...+..|=++...+++.+|=+.++.+.+-.+.+....+.+++.+  
T Consensus       214 a~~l~~~all~~~i~~f~eLL~~p~i~~L~~~~~~~~l~~Ll~~f~~g~~~~f~~~~~~~~~~~~~l~~~~~~l~~kirl  293 (393)
T 4b4t_O          214 AYDLSISALLGDKIYNFGELLHHPIMETIVNDSNYDWLFQLLNALTVGDFDKFDSLIKVQISKIPILAQHESFLRQKICL  293 (393)
T ss_dssp             HHHHHHHHHHCCSSCSTHHHHHSCCTTSSCSSSSTTHHHHHHHHHHHTCHHHHHHHCCHHHHHSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCChHHHhCChHHHHhhcCCchHHHHHHHHHHhcCCHHHHHHHHHHhhhhCcchhhhHHHHHHHHHH
Confidence            3445555555322255543333211 1233457778888888999999999986654443222233333333333322  


Q ss_pred             HHHHH----HhcccccHHHHHHHhcCCchHHHHHHHHHhh
Q 031021           83 IHVLS----LTYQKIPRTVLAEAINLKGLSLDKFLEHQKA  118 (167)
Q Consensus        83 ~~vV~----~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~  118 (167)
                      ..++.    ..|++|+-+.+++.||++.++++.++-+.+.
T Consensus       294 l~l~~l~~~~~~~~i~f~~ia~~l~i~~~evE~lli~aI~  333 (393)
T 4b4t_O          294 MTLIETVFVKNIRMLSFEDISKATHLPKDNVEHLVMRAIS  333 (393)
T ss_dssp             HHHHHHHCSSSCCCEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCCcCcHHHHHHHhCcCHHHHHHHHHHHHH
Confidence            22333    3578899999999999999999999876643

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

Probab=89.44  E-value=0.74  Score=29.12  Aligned_cols=48  Identities=13%  Similarity=0.082  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021           76 QAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL  124 (167)
Q Consensus        76 d~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~  124 (167)
                      +..|+.|+.++...=..++...||+.||++...+.+.++.+ ++.|+..
T Consensus         9 ~~~~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L-~~~G~I~   56 (67)
T 2heo_A            9 DNLEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRL-KKEDRVS   56 (67)
T ss_dssp             CHHHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHH-HHTTSEE
T ss_pred             cHHHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHH-HHCCcEe
Confidence            34788999999874456999999999999999999998777 7889943

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

Probab=87.97  E-value=2.5  Score=27.18  Aligned_cols=44  Identities=14%  Similarity=0.138  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021           79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL  124 (167)
Q Consensus        79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~  124 (167)
                      |+.|+..+.. ...++...|++.+|++...+...++.+ .+.|+-.
T Consensus         2 r~~Il~~L~~-~~~~s~~eLa~~lgvs~~tv~r~L~~L-~~~GlI~   45 (81)
T 2htj_A            2 KNEILEFLNR-HNGGKTAEIAEALAVTDYQARYYLLLL-EKAGMVQ   45 (81)
T ss_dssp             HHHHHHHHHH-SCCCCHHHHHHHHTSCHHHHHHHHHHH-HHHTSEE
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHH-HHCCCEE
Confidence            6677777764 367999999999999999999988776 7789986

---

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	167
d1rz4a1	85	a.4.5.53 (A:132-216) Eukaryotic translation initia	2e-28
d1rz4a2	130	a.118.1.18 (A:2-131) Eukaryotic translation initia	2e-26

>d1rz4a1 a.4.5.53 (A:132-216) Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
domain: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 99.0 bits (247), Expect = 2e-28
 Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 9/90 (10%)

Query: 73  GFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQ 132
           GFE +++ F  HV+ +TYQ I R +LAE +   G   D  L+   +  GW  +      Q
Sbjct: 2   GFEDSVRKFICHVVGITYQHIDRWLLAEML---GDLSDSQLKVWMSKYGWSADESG---Q 55

Query: 133 LIVLPPNEFNHPELKKNVADSIPLEHITRI 162
           + +    E   P   KN+ + I  + ++ I
Sbjct: 56  IFICSQEESIKP---KNIVEKIDFDSVSSI 82

>d1rz4a2 a.118.1.18 (A:2-131) Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 130

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain
domain: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 94.8 bits (236), Expect = 2e-26
 Identities = 23/71 (32%), Positives = 40/71 (56%)

Query: 1   MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDE 60
             T + A+IL+KAL  +P  DF+LC  +I +  Q E   + ++ L   LET  F+ FW  
Sbjct: 60  FQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQA 119

Query: 61  AAKHRNIVEAV 71
             ++ +++E +
Sbjct: 120 LDENMDLLEGI 130

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	167
d1rz4a1	85	Eukaryotic translation initiation factor 3 subunit	99.94
d1rz4a2	130	Eukaryotic translation initiation factor 3 subunit	99.93
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	97.5
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	92.72
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	89.2
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	88.85
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	87.79
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	86.86
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	86.71
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	83.56
d1zyba1	73	Probable transcription regulator BT4300, C-termina	83.01

>d1rz4a1 a.4.5.53 (A:132-216) Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
domain: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=3.2e-28  Score=167.23  Aligned_cols=84  Identities=25%  Similarity=0.484  Sum_probs=70.5

Q ss_pred             cchHHHHHHHHHHHHHHhcccccHHHHHHHhcCC-chHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCCCcccccccc
Q 031021           72 PGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLK-GLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNV  150 (167)
Q Consensus        72 ~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~-~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~N~~~~~~~i  150 (167)
                      .||||+||+||||+|++|||+|+++.|++|||+. +.+|++|+    +++||+++++   |  .++|.|++|..++ |||
T Consensus         1 tGFedsIR~~i~~vv~iTyq~I~~~~L~e~LG~~~d~~L~~~i----~~~gW~~~~~---g--~v~v~nqe~~iK~-kni   70 (85)
T d1rz4a1           1 TGFEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWM----SKYGWSADES---G--QIFICSQEESIKP-KNI   70 (85)
T ss_dssp             TTHHHHHHHHHHHHHHHHCSEECHHHHHHHTTSCCHHHHHHHH----HHHTCEECC-------CEECCCHHHHTSC-CCS
T ss_pred             CcHHHHHHHHHHhheeeeeeEEcHHHHHHHhCCCCHHHHHHHH----HHcCCEEcCC---C--EEEecChhhhcCc-cce
Confidence            4999999999999999999999999999999874 45566666    8899999743   2  3477777777665 999


Q ss_pred             ccccCCccccccccc
Q 031021          151 ADSIPLEHITRIFPI  165 (167)
Q Consensus       151 ~E~i~f~~~~~i~~~  165 (167)
                      +|+|+||+++++|..
T Consensus        71 ~EkI~fe~v~~ima~   85 (85)
T d1rz4a1          71 VEKIDFDSVSSIMAS   85 (85)
T ss_dssp             SCCCCHHHHHHHHCC
T ss_pred             eeeccHHHHHHHhcC
Confidence            999999999999963

>d1rz4a2 a.118.1.18 (A:2-131) Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain
domain: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=5.3e-27  Score=172.29  Aligned_cols=71  Identities=32%  Similarity=0.658  Sum_probs=68.2

Q ss_pred             CCHHHHHHHHHHHHHcCCccchhhhhcCCCccccCchhHHHHHHHHHHHHcCChHHHHHHHhhccchhhcc
Q 031021            1 MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAV   71 (167)
Q Consensus         1 ~~~~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~~~~~i   71 (167)
                      ||.++|++||+||||++|++||++|+||||++.|++++|++|.+|+++||+|+|++||+.++++++++++|
T Consensus        60 ~~~~vi~~ILlKALt~~P~~DF~lc~~Li~~~~q~~e~i~~l~~L~~lLE~c~F~~FW~~~~~~~~l~~~v  130 (130)
T d1rz4a2          60 FQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQALDENMDLLEGI  130 (130)
T ss_dssp             CCHHHHHHHHHHHHHTTTSTHHHHHHHTSCHHHHTSTTHHHHHHHHHHHHTTCHHHHHHHSCTTCHHHHTS
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHcChhcCCcHHHHHHHHHHHHHHhCCHHHHHHHHhhCHHHhccC
Confidence            68999999999999999999999999999999999999999999999999999999999999999887754

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.50  E-value=0.00014  Score=48.07  Aligned_cols=70  Identities=11%  Similarity=0.157  Sum_probs=55.0

Q ss_pred             cchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcC--ceeeccCCCceEEEeCCCCCCcc
Q 031021           72 PGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCG--WILEGDQSTSQLIVLPPNEFNHP  144 (167)
Q Consensus        72 ~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G--W~~~~~~~~~~~vv~p~n~~N~~  144 (167)
                      +-|+++|++.-.+.++..|++|+.+.|++.||++.+++++++.+.+.+.-  =++|..   .++|.+..++.+.|
T Consensus        10 t~L~~~i~Ehni~~is~~Y~~Isl~~la~~l~l~~~evE~~l~~mI~~~~i~akIDq~---~g~V~F~~~e~~~~   81 (84)
T d1ufma_          10 SILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQI---DGIVHFETREASGP   81 (84)
T ss_dssp             CCCCHHHHHHHHHHHHHSCSEEEHHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETT---TTEEEECCSSCCCS
T ss_pred             HHHHHHHHHHHHHHHHHhhceeeHHHHHHHHCCCHHHHHHHHHHHHhcCeEEEEEeCC---CCEEEECCCCcCCC
Confidence            34788999999999999999999999999999999999999987765433  234433   25888876666544

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

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

Probab=92.72  E-value=0.098  Score=31.65  Aligned_cols=54  Identities=11%  Similarity=0.099  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCce
Q 031021           77 AIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQ  132 (167)
Q Consensus        77 ~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~  132 (167)
                      ..|..|..++. .-..++-+.||+.||+|...+...++.+ ++.|+.+....|.|.
T Consensus         5 ~~~~~iL~~L~-~~~~~s~~eLa~~l~vS~~ti~r~i~~L-~~~G~~I~~~~g~GY   58 (63)
T d1biaa1           5 TVPLKLIALLA-NGEFHSGEQLGETLGMSRAAINKHIQTL-RDWGVDVFTVPGKGY   58 (63)
T ss_dssp             HHHHHHHHHHT-TSSCBCHHHHHHHHTSCHHHHHHHHHHH-HHTTCCCEEETTTEE
T ss_pred             HHHHHHHHHHH-HCCcCCHHHHHHHHCcCHHHHHHHHHHH-HHCCCcEEEeCCCeE
Confidence            46777888885 4788999999999999999999999887 789998765545443

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.20  E-value=0.44  Score=29.01  Aligned_cols=46  Identities=13%  Similarity=0.152  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeec
Q 031021           79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEG  126 (167)
Q Consensus        79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~  126 (167)
                      +..|++.|- .+..+++..|++.+|||...+-..+.++ .+.||-.+.
T Consensus         7 ~~~Il~~i~-~~g~~sr~eLa~~~gLS~~Tvs~iv~~L-~~~glv~e~   52 (70)
T d1z6ra1           7 AGAVYRLID-QLGPVSRIDLSRLAQLAPASITKIVHEM-LEAHLVQEL   52 (70)
T ss_dssp             HHHHHHHHH-SSCSCCHHHHHHHTTCCHHHHHHHHHHH-HHHTSEEEC
T ss_pred             HHHHHHHHH-HcCCcCHHHHHHHHCcCHHHHHHHHHHH-HHCCCEEee
Confidence            456888887 6999999999999999999998888877 678998763

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=88.85  E-value=0.54  Score=28.15  Aligned_cols=48  Identities=10%  Similarity=0.153  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeecc
Q 031021           79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGD  127 (167)
Q Consensus        79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~  127 (167)
                      +..|+..+...=..|+.+.||+.||+|...+...++.+ ++.|+.+...
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L-~~~G~~I~~~   56 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYL-RSLGYNIVAT   56 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHH-HHHTCCCEEE
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHH-HHCCCeEEEe
Confidence            35677777766556999999999999999999988776 7889987654

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.79  E-value=1.6  Score=25.95  Aligned_cols=33  Identities=15%  Similarity=0.238  Sum_probs=29.4

Q ss_pred             cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021           92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE  125 (167)
Q Consensus        92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~  125 (167)
                      .++.+.||+++|++.+.+-..+.++ ++.||-.-
T Consensus        29 ~lt~~~lA~~~G~sRetvsr~L~~l-~~~glI~~   61 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVGRILKML-EDQNLISA   61 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHHHH-HHTTSEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEE
Confidence            4899999999999999999998888 88999864

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=86.86  E-value=0.62  Score=28.64  Aligned_cols=33  Identities=15%  Similarity=0.012  Sum_probs=28.8

Q ss_pred             cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021           92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE  125 (167)
Q Consensus        92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~  125 (167)
                      .++.+.||.++|++.+.+-..+.++ ++.||-.-
T Consensus        29 ~lt~~eLA~~~G~sretvsr~L~~l-~~~glI~~   61 (81)
T d2gaua1          29 YLSREELATLSNMTVSNAIRTLSTF-VSERMLAL   61 (81)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHH-HHTTSEEE
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEe
Confidence            4688999999999999999998887 88999864

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=86.71  E-value=0.99  Score=27.15  Aligned_cols=45  Identities=18%  Similarity=0.171  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021           79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE  125 (167)
Q Consensus        79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~  125 (167)
                      |..|++++. ....+++..|++.+|++...+...+.+. .+.||-.+
T Consensus         8 ~~~Il~~l~-~~g~~sr~eLa~~~glS~~Tv~~~l~~L-~~~Glv~e   52 (71)
T d1z05a1           8 AGRVYKLID-QKGPISRIDLSKESELAPASITKITREL-IDAHLIHE   52 (71)
T ss_dssp             HHHHHHHHH-HHCSBCHHHHHHHHTCCHHHHHHHHHHH-HHTTSEEE
T ss_pred             HHHHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEE
Confidence            457888885 4789999999999999999988888777 67899764

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=83.56  E-value=1.6  Score=26.74  Aligned_cols=33  Identities=15%  Similarity=0.142  Sum_probs=28.9

Q ss_pred             cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021           92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE  125 (167)
Q Consensus        92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~  125 (167)
                      .++.+.+|.++|++.+.+-..+.++ ++.||-.-
T Consensus        30 ~~t~~eiA~~lG~sretvsr~l~~l-~~~g~I~~   62 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTALNSL-IKEGYISR   62 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHHHHH-HHTTSSEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEE
Confidence            5678999999999999999998887 88999863

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=83.01  E-value=1.1  Score=27.36  Aligned_cols=33  Identities=24%  Similarity=0.263  Sum_probs=29.0

Q ss_pred             cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021           92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE  125 (167)
Q Consensus        92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~  125 (167)
                      .++.+.||+++|++.+.+-..+.++ ++.||-.-
T Consensus        27 ~lt~~elA~~lg~sr~tvsr~l~~l-~~~g~I~~   59 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNISKTLNEL-QDNGLIEL   59 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHH-HHTTSCEE
T ss_pred             ecCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEe
Confidence            4789999999999999999998887 88999864