Citrus Sinensis ID: 025134

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------
Protein Sequence
MFCGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAPQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccEEccccccccccccccccEEEEEEEcccEEEcccccccccccccHHHHHHHHccccccccccccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccEEEEEEcccccHHHHHHHHHHccccccccccEEEEcccccccccccccHHHHcccccEEEEEc
Secondary Structure Prediction (SSPRO)
ccccEEEcccccccccHHHHHHHHHHHccccccccccccccccccccccccEEcccccccccccccccEEEEEEEEcccEEEccccccccccHHHHHHHHHHHcccccHHHHccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccHccccccccccccccccccEEEEEEEccccEEEEEEcccccHHHHHHHHHHHccccccccEEEEEccccccccccccHHHHHccccEEEEEEc
Coil and Loop (DISEMBL)
mfcgmlvqdpskgdpndVDAIFNQAKelgavegplehlspssssrsftgtarllsgetvpsapqqpepivhnivfwangftvndgplrrlddpenaSFLESIkksecpkelepadkrssvHVNLIrrdvkcpepekhhvpfqgvgrtlgssstaaseptvdstpvntasssseglvvdenlpstsVQIRLADGTRLIAHFnlhhtisdihsfidasrpgtarnyqlqmmgfppkvlaDRTQTIEQAGLANSVVIQKF
Flexible Loop (DISEMBL)
mfcgmlvqdpskgdpNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAPQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESikksecpkelepadkrssvhvNLIRRdvkcpepekhhvpfqgvgrtlgSSSTAaseptvdstpvntasssseglvvdenlpSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIeqaglansvviqkf
Low Complexity Region (SEG)
MFCGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLspssssrsFTGTARLLSGETVPSAPQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF
Disordered region (IsUnstruct)
********************************************************************IVHNIVFWANGFTVNDG***************************************************************************************************SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADR***I**************
Disordered Region (DISOPRED)
MFCGML*********************************************************************WANGFTVNDGPLR*******************************VHVNLIRRDVKC**************************************************PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF
Disordered Region (DISEMBL)
MFCGMLVQDPSKGDPNDVDAIFNQAKELGAVEG*****************ARLLSGETVPSAPQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIRRDVKCPEPEKHHVPFQGVGRT***************************LVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF
Disordered Region (DISPRO)
**CGMLVQDPSKGDPNDVDAIFNQAKEL*****************************TVPSAPQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIRRDVKCPEPEKHHVPF***********************************VDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFCGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAPQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	257	2.2.26 [Sep-21-2011]
Q7Y175	421	UBA and UBX domain-contai	no	no	0.968	0.591	0.583	2e-71
Q5RBG3	370	NSFL1 cofactor p47 OS=Pon	yes	no	0.980	0.681	0.356	3e-34
Q9UNZ2	370	NSFL1 cofactor p47 OS=Hom	yes	no	0.980	0.681	0.356	3e-34
Q3SZC4	370	NSFL1 cofactor p47 OS=Bos	yes	no	0.961	0.667	0.345	3e-33
O35987	370	NSFL1 cofactor p47 OS=Rat	yes	no	0.961	0.667	0.342	8e-33
Q9CZ44	370	NSFL1 cofactor p47 OS=Mus	yes	no	0.961	0.667	0.342	8e-33
Q0P3R5	350	UBX domain-containing pro	N/A	no	0.906	0.665	0.354	1e-31
P0C627	331	UBX domain-containing pro	no	no	0.957	0.743	0.340	3e-31
Q5ZK10	369	NSFL1 cofactor p47 OS=Gal	yes	no	0.961	0.669	0.327	9e-31
Q0KL01	331	UBX domain-containing pro	no	no	0.957	0.743	0.333	2e-30

>sp|Q7Y175|UBAX1_ARATH UBA and UBX domain-containing protein At4g15410 OS=Arabidopsis thaliana GN=At4g15410 PE=2 SV=1

 Score =  268 bits (686), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 153/262 (58%), Positives = 188/262 (71%), Gaps = 13/262 (4%)

Query: 3   CGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPS-SSSRSFTGTARLLSGETVPS 61
            GM+VQDP K    DVD +F+QA++  AV+ P+E   PS S+S SFTG ARLLSGE V S
Sbjct: 166 SGMMVQDPKK--VKDVDELFDQARQ-SAVDRPVE---PSRSASTSFTGAARLLSGEAVSS 219

Query: 62  APQQPEP-----IVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADK 116
           +PQQ +      I+H I FW NGFTVNDGPLR   DPENA+F+ SI +SECP ELEPADK
Sbjct: 220 SPQQQQQEQPQRIMHTITFWLNGFTVNDGPLRGFSDPENAAFMNSISRSECPSELEPADK 279

Query: 117 RSSVHVNLIRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTP-VNTASSSSEGL 175
           +  VHV+L+RR     EP K   PFQGVGRTLG+S + +S     S+  +N A + S GL
Sbjct: 280 KIPVHVDLVRRGENFTEPPKPKNPFQGVGRTLGASGSGSSSAPQASSAPMNVAPAPSRGL 339

Query: 176 VVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKV 235
           VVD   P+TS+Q+RLADGTRL++ FN HHT+ D+  FIDASRPG ++ YQL  MGFPPK 
Sbjct: 340 VVDPAAPTTSIQLRLADGTRLVSRFNNHHTVRDVRGFIDASRPGGSKEYQLLTMGFPPKQ 399

Query: 236 LADRTQTIEQAGLANSVVIQKF 257
           L +  QTIEQAG+AN+VVIQKF
Sbjct: 400 LTELDQTIEQAGIANAVVIQKF 421

Arabidopsis thaliana (taxid: 3702)

>sp|Q5RBG3|NSF1C_PONAB NSFL1 cofactor p47 OS=Pongo abelii GN=NSFL1C PE=2 SV=1

 Score =  145 bits (365), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 94/264 (35%), Positives = 138/264 (52%), Gaps = 12/264 (4%)

Query: 6   LVQDPSKGDPND-VDAIFNQAKELGAVEGPLEHLSPSSSS--RSFTGTARLL-------S 55
           +V  P K  PN+ VD +F  AKE GAV       SP  +S  R F G    L       S
Sbjct: 106 IVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAAPEEES 165

Query: 56  GETVPSAPQQPEPIVHNIV-FWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPA 114
                   Q     VH ++  W +GF++++G LR   DP NA FLESI++ E P EL   
Sbjct: 166 AYVAGEKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRL 225

Query: 115 DKRSSVHVNL-IRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSE 173
                V++++   RD    +P+     F G G+ LGS++      +  +      + +S 
Sbjct: 226 AHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLSTSSPAQQAENEAKASS 285

Query: 174 GLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP 233
            +++DE+ P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M  FP 
Sbjct: 286 SILIDESEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFILMTTFPN 345

Query: 234 KVLADRTQTIEQAGLANSVVIQKF 257
           K LAD +QT+++A L N+V++Q+ 
Sbjct: 346 KELADESQTLKEANLLNAVIVQRL 369

Reduces the ATPase activity of VCP. Necessary for the fragmentation of Golgi stacks during mitosis and for VCP-mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER).

Pongo abelii (taxid: 9601)

>sp|Q9UNZ2|NSF1C_HUMAN NSFL1 cofactor p47 OS=Homo sapiens GN=NSFL1C PE=1 SV=2

 Score =  145 bits (365), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 94/264 (35%), Positives = 138/264 (52%), Gaps = 12/264 (4%)

Query: 6   LVQDPSKGDPND-VDAIFNQAKELGAVEGPLEHLSPSSSS--RSFTGTARLL-------S 55
           +V  P K  PN+ VD +F  AKE GAV       SP  +S  R F G    L       S
Sbjct: 106 IVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAAPEEES 165

Query: 56  GETVPSAPQQPEPIVHNIV-FWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPA 114
                   Q     VH ++  W +GF++++G LR   DP NA FLESI++ E P EL   
Sbjct: 166 AYVAGEKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRL 225

Query: 115 DKRSSVHVNL-IRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSE 173
                V++++   RD    +P+     F G G+ LGS++      +  +      + +S 
Sbjct: 226 AHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLSTSSPAQQAENEAKASS 285

Query: 174 GLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP 233
            +++DE+ P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M  FP 
Sbjct: 286 SILIDESEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFILMTTFPN 345

Query: 234 KVLADRTQTIEQAGLANSVVIQKF 257
           K LAD +QT+++A L N+V++Q+ 
Sbjct: 346 KELADESQTLKEANLLNAVIVQRL 369

Reduces the ATPase activity of VCP. Necessary for the fragmentation of Golgi stacks during mitosis and for VCP-mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER) (By similarity). Inhibits the activity of CTSL (in vitro).

Homo sapiens (taxid: 9606)

>sp|Q3SZC4|NSF1C_BOVIN NSFL1 cofactor p47 OS=Bos taurus GN=NSFL1C PE=2 SV=1

 Score =  142 bits (357), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 137/269 (50%), Gaps = 22/269 (8%)

Query: 6   LVQDPSKGDPND-VDAIFNQAKELGAVEGPLEHLSPSSSS--RSFTGTARLLSGETVPSA 62
           +V  P K  PN+ VD +F  AKE GAV       SP  +S  R F G      G  + +A
Sbjct: 106 IVGPPRKRSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAG-----GGYRLGAA 160

Query: 63  PQQPEPIVHN-------------IVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPK 109
           P++    V               +  W  GF++++G LR   DP NA FLESI++ E P 
Sbjct: 161 PEEESAYVAGERRRHSGQDVHVVLKLWKTGFSLDNGELRSYQDPSNAQFLESIRRGEVPA 220

Query: 110 ELEPADKRSSVHVNL-IRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTA 168
           EL        V++++   RD    +P+     F G G+ LGS++      +  +      
Sbjct: 221 ELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQILNTSSPAQQAENE 280

Query: 169 SSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQM 228
           + +S  + +DE+ P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M
Sbjct: 281 AKASSSISIDESQPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLM 340

Query: 229 MGFPPKVLADRTQTIEQAGLANSVVIQKF 257
             FP K LAD  QT+++A L N+V++Q+ 
Sbjct: 341 TTFPNKELADENQTLKEANLLNAVIVQRL 369

Reduces the ATPase activity of VCP. Necessary for the fragmentation of Golgi stacks during mitosis and for VCP-mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER).

Bos taurus (taxid: 9913)

>sp|O35987|NSF1C_RAT NSFL1 cofactor p47 OS=Rattus norvegicus GN=Nsfl1c PE=1 SV=1

 Score =  140 bits (354), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 92/269 (34%), Positives = 137/269 (50%), Gaps = 22/269 (8%)

Query: 6   LVQDPSKGDPND-VDAIFNQAKELGAVEGPLEHLSPSSSS--RSFTGTARLLSGETVPSA 62
           +V  P K  PN+ VD +F  AKE GAV       SP  +S  R F G      G  + +A
Sbjct: 106 IVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAG-----GGYRLGAA 160

Query: 63  PQQPEPIVHN-------------IVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPK 109
           P++    V               +  W  GF++++G LR   DP NA FLESI++ E P 
Sbjct: 161 PEEESAYVAGERRRHSGQDVHVVLKLWKTGFSLDNGDLRSYQDPSNAQFLESIRRGEVPA 220

Query: 110 ELEPADKRSSVHVNL-IRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTA 168
           EL        V++++   RD    +P+     F G G+ LGS++      +  +      
Sbjct: 221 ELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENE 280

Query: 169 SSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQM 228
           + +S  ++++E  P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M
Sbjct: 281 AKASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLM 340

Query: 229 MGFPPKVLADRTQTIEQAGLANSVVIQKF 257
             FP K LAD  QT+++A L N+V++Q+ 
Sbjct: 341 TTFPNKELADENQTLKEANLLNAVIVQRL 369

Reduces the ATPase activity of VCP. Necessary for the fragmentation of Golgi stacks during mitosis and for VCP-mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER).

Rattus norvegicus (taxid: 10116)

>sp|Q9CZ44|NSF1C_MOUSE NSFL1 cofactor p47 OS=Mus musculus GN=Nsfl1c PE=1 SV=1

 Score =  140 bits (353), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 92/269 (34%), Positives = 137/269 (50%), Gaps = 22/269 (8%)

Query: 6   LVQDPSKGDPND-VDAIFNQAKELGAVEGPLEHLSPSSSS--RSFTGTARLLSGETVPSA 62
           +V  P K  PN+ VD +F  AKE GAV       SP  +S  R F G      G  + +A
Sbjct: 106 IVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAG-----GGYRLGAA 160

Query: 63  PQQPEPIVHN-------------IVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPK 109
           P++    V               +  W  GF++++G LR   DP NA FLESI++ E P 
Sbjct: 161 PEEESAYVAGERRRHSGQDVHVVLKLWKTGFSLDNGDLRSYQDPSNAQFLESIRRGEVPA 220

Query: 110 ELEPADKRSSVHVNL-IRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTA 168
           EL        V++++   RD    +P+     F G G+ LGS++      +  +      
Sbjct: 221 ELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENE 280

Query: 169 SSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQM 228
           + +S  ++++E  P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M
Sbjct: 281 AKASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLM 340

Query: 229 MGFPPKVLADRTQTIEQAGLANSVVIQKF 257
             FP K LAD  QT+++A L N+V++Q+ 
Sbjct: 341 TTFPNKELADENQTLKEANLLNAVIVQRL 369

Reduces the ATPase activity of VCP. Necessary for the fragmentation of Golgi stacks during mitosis and for VCP-mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER).

Mus musculus (taxid: 10090)

>sp|Q0P3R5|UBX2B_XENLA UBX domain-containing protein 2B OS=Xenopus laevis GN=ubxn2b PE=2 SV=1

 Score =  137 bits (344), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 91/257 (35%), Positives = 136/257 (52%), Gaps = 24/257 (9%)

Query: 18  VDAIFNQAKELGAVEGPLEHLSPSSSS----RSFTGTARLLSGETVPSAP--------QQ 65
           V+ +F +AKE GA+  P++  S SS +    R+FTG    L   +             +Q
Sbjct: 100 VNELFKEAKEHGAI--PIDDTSKSSGAFYRARTFTGRGYKLGDSSKREFEYMQGEDPFEQ 157

Query: 66  PEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNL- 124
            + I   +  W+NGF+++DG LR   DP NA FLES+KK E P EL+       V++++ 
Sbjct: 158 GQEIQILLKLWSNGFSLDDGELRSYSDPINAEFLESVKKGEIPVELQRLVHGGQVNLDME 217

Query: 125 IRRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLV----VDEN 180
             +D +  +P      F G G+ LGS +     P + STP +        L     +DE+
Sbjct: 218 DHQDQEYIKPRLKFKAFSGEGKKLGSVT-----PEIISTPSSPEEEHKRFLNAEVDLDEH 272

Query: 181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRT 240
           +P+T +QIRLADGTRLI  FNL H I D+  FI  +R   A+     +  FP   L D T
Sbjct: 273 VPTTKIQIRLADGTRLIQRFNLSHRIMDVRQFIIHARSDFAQCDFALLTTFPNVELTDET 332

Query: 241 QTIEQAGLANSVVIQKF 257
           QT+E+A + N+V++Q+ 
Sbjct: 333 QTLEEADILNTVILQRL 349

Adapter protein required for Golgi and endoplasmic reticulum biogenesis. Involved in Golgi and endoplasmic reticulum maintenance during interphase and in their reassembly at the end of mitosis.

Xenopus laevis (taxid: 8355)

>sp|P0C627|UBX2B_RAT UBX domain-containing protein 2B OS=Rattus norvegicus GN=Ubxn2b PE=1 SV=1

 Score =  135 bits (339), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 92/270 (34%), Positives = 143/270 (52%), Gaps = 24/270 (8%)

Query: 2   FCGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSS---SRSFTGTARLLSGET 58
           + G+ +  P  G    V+ +F +A+E GAV  PL   + SSS   ++SFTG    L    
Sbjct: 71  YGGLHIAQPPTG--KIVNELFKEAREHGAV--PLNEATRSSSDDKAKSFTGGGYRLGSSF 126

Query: 59  VPSAP-----QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEP 113
              +       Q + +   +  W+NGF+++DG LR   DP NA FLES+K+ E P EL+ 
Sbjct: 127 YKRSEYIYGENQLQDVQILLRLWSNGFSLDDGELRPYSDPTNAQFLESVKRGEIPLELQR 186

Query: 114 ADKRSSVHVNL-IRRDVKCPEPEKHHVPFQGVGRTLGS-----SSTAASEPTVDSTPVNT 167
               S V +++   +D +  +P      F G G+ LGS      ST +S    D + +N 
Sbjct: 187 LVHGSQVSLDMEDHQDQEYIKPRLRFKAFSGEGQKLGSLTPEIVSTPSSPEEEDKSILNA 246

Query: 168 ASSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQ 227
           A      +++D+++P+T +QIRLADG+RLI  FN  H I D+  FI  SRP  A    + 
Sbjct: 247 A------VLIDDSVPTTKIQIRLADGSRLIQRFNSTHRILDVRDFIVQSRPEFATTDFIL 300

Query: 228 MMGFPPKVLADRTQTIEQAGLANSVVIQKF 257
           +  FP K L D + T++ A + N+V++Q+ 
Sbjct: 301 VTSFPSKELTDESVTLQDADILNTVILQQL 330

Adapter protein required for Golgi and endoplasmic reticulum biogenesis. Involved in Golgi and endoplasmic reticulum maintenance during interphase and in their reassembly at the end of mitosis. The complex formed with VCP has membrane fusion activity; membrane fusion activity requires USO1-GOLGA2 tethering and BET1L. VCPIP1 is also required, but not its deubiquitinating activity.

Rattus norvegicus (taxid: 10116)

>sp|Q5ZK10|NSF1C_CHICK NSFL1 cofactor p47 OS=Gallus gallus GN=NSFL1C PE=2 SV=1

 Score =  134 bits (336), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 136/269 (50%), Gaps = 22/269 (8%)

Query: 6   LVQDPSKGDPND-VDAIFNQAKELGAV--EGPLEHLSPSSSSRSFTGTARLLSGETVPSA 62
           +V  P K  PN+ V+ +F  AKE GAV  +   +    SS  + F G      G  + + 
Sbjct: 105 IVGPPRKKSPNELVEDLFKGAKEHGAVAVDRTAKSSGESSKPKPFAG-----GGYRLGAT 159

Query: 63  PQQPEPIV-----HNIV--------FWANGFTVNDGPLRRLDDPENASFLESIKKSECPK 109
           P++    V     HN V         W  GF+++ G LR   DP NA FL+ I++ E P 
Sbjct: 160 PEEESAYVAGERRHNSVQDVHVVLKLWKTGFSLDSGELRSYQDPSNAQFLDDIRRGEVPA 219

Query: 110 ELEPADKRSSVHVNLI-RRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTA 168
           EL    +   V++++   RD +  +P+     F G G+ LGS++      +  +      
Sbjct: 220 ELRRLARGGQVNLDMEDHRDEEYVKPKSVFKAFTGEGQKLGSTAPQVLSTSSPAQQAENE 279

Query: 169 SSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQM 228
           + +S  + +DE+ P T++QIRLADG RL+  FN +H I DI  FI  +RP  A    + M
Sbjct: 280 AKASSAIAIDESEPVTNIQIRLADGGRLVQKFNHNHRIRDIRLFIVDARPAMAATSFVLM 339

Query: 229 MGFPPKVLADRTQTIEQAGLANSVVIQKF 257
             FP K L D  QT+++A L N+V++Q+ 
Sbjct: 340 TTFPNKELTDENQTLKEANLLNAVIVQRL 368

Reduces the ATPase activity of VCP. Necessary for the fragmentation of Golgi stacks during mitosis and for VCP-mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER).

Gallus gallus (taxid: 9031)

>sp|Q0KL01|UBX2B_MOUSE UBX domain-containing protein 2B OS=Mus musculus GN=Ubxn2b PE=1 SV=2

 Score =  132 bits (333), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 90/270 (33%), Positives = 143/270 (52%), Gaps = 24/270 (8%)

Query: 2   FCGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSS---SSRSFTGTARLLSGET 58
           + G+ +  P  G    V+ +F +A+E GAV  PL   + SS    ++SFTG    L    
Sbjct: 71  YDGLHIVQPPTG--KIVNELFKEAREHGAV--PLNEATRSSREDKTKSFTGGGYRLGNSF 126

Query: 59  VPSAP-----QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEP 113
              +       Q + +   +  W NGF+++DG LR   DP NA FLES+K+ E P EL+ 
Sbjct: 127 YKRSEYIYGENQLQDVQVLLKLWRNGFSLDDGELRPYSDPTNAQFLESVKRGETPLELQR 186

Query: 114 ADKRSSVHVNL-IRRDVKCPEPEKHHVPFQGVGRTLGS-----SSTAASEPTVDSTPVNT 167
               + V++++   +D +  +P      F G G+ LGS      ST +S    D + +N 
Sbjct: 187 LVHGAQVNLDMEDHQDQEYIKPRLRFKAFSGEGQKLGSLTPEIVSTPSSPEEEDKSILNA 246

Query: 168 ASSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQ 227
           A      +++D+++P+T +QIRLADG+RL+  FN  H I D+  FI  SRP  A    + 
Sbjct: 247 A------VLIDDSMPTTKIQIRLADGSRLVQRFNSTHRILDVRDFIVRSRPEFATTDFIL 300

Query: 228 MMGFPPKVLADRTQTIEQAGLANSVVIQKF 257
           +  FP K L D T T+++A + N+V++Q+ 
Sbjct: 301 VTSFPSKELTDETVTLQEADILNTVILQQL 330

Adapter protein required for Golgi and endoplasmic reticulum biogenesis. Involved in Golgi and endoplasmic reticulum maintenance during interphase and in their reassembly at the end of mitosis. The complex formed with VCP has membrane fusion activity; membrane fusion activity requires USO1-GOLGA2 tethering and BET1L. VCPIP1 is also required, but not its deubiquitinating activity.

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	257
255554763	305	NSFL1 cofactor p47, putative [Ricinus co	0.988	0.832	0.827	1e-118
225444462	299	PREDICTED: UBA and UBX domain-containing	0.972	0.836	0.792	1e-112
224115898	305	predicted protein [Populus trichocarpa]	0.980	0.826	0.808	1e-112
224115762	253	predicted protein [Populus trichocarpa]	0.976	0.992	0.8	1e-111
118488401	305	unknown [Populus trichocarpa]	0.980	0.826	0.785	1e-109
224118108	309	predicted protein [Populus trichocarpa]	0.980	0.815	0.757	1e-106
356555700	301	PREDICTED: UBA and UBX domain-containing	0.984	0.840	0.762	1e-105
255638519	301	unknown [Glycine max]	0.984	0.840	0.762	1e-105
356532265	301	PREDICTED: UBA and UBX domain-containing	0.984	0.840	0.743	1e-103
449455377	302	PREDICTED: UBA and UBX domain-containing	0.980	0.834	0.747	1e-101

>gi|255554763|ref|XP_002518419.1| NSFL1 cofactor p47, putative [Ricinus communis] gi|223542264|gb|EEF43806.1| NSFL1 cofactor p47, putative [Ricinus communis]

 Score =  430 bits (1105), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 211/255 (82%), Positives = 235/255 (92%), Gaps = 1/255 (0%)

Query: 4   GMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAP 63
           GMLVQDPSKG+ NDVDAIFNQA++LGAVEGPL+ L PSSSSRSFTGT RLLSGET+PSAP
Sbjct: 51  GMLVQDPSKGNGNDVDAIFNQARQLGAVEGPLDPLRPSSSSRSFTGTGRLLSGETIPSAP 110

Query: 64  QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVN 123
           QQPE ++HNIVFW NGFTVNDGPLRRLDDPENA FLESI+KSECPKEL PAD+RSSVHVN
Sbjct: 111 QQPEAVIHNIVFWTNGFTVNDGPLRRLDDPENAPFLESIRKSECPKELAPADRRSSVHVN 170

Query: 124 LIRRDVKCPEPEKH-HVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLVVDENLP 182
           LIRR+ +CPEPEK  HVPFQGVGRTLGSS TAASEPT +STPVNTA +SS G+VVDE+LP
Sbjct: 171 LIRREEQCPEPEKQRHVPFQGVGRTLGSSCTAASEPTANSTPVNTAPTSSMGVVVDESLP 230

Query: 183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQT 242
           STS+Q+RLADGTR+IAHFN HHT++DI +FIDASRPG A+NYQLQ+MGFPPK+L D TQT
Sbjct: 231 STSIQLRLADGTRMIAHFNYHHTVNDIRAFIDASRPGGAQNYQLQLMGFPPKLLGDPTQT 290

Query: 243 IEQAGLANSVVIQKF 257
           IEQAGLANSVVIQKF
Sbjct: 291 IEQAGLANSVVIQKF 305

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225444462|ref|XP_002272066.1| PREDICTED: UBA and UBX domain-containing protein At4g15410 [Vitis vinifera] gi|147798327|emb|CAN74529.1| hypothetical protein VITISV_031346 [Vitis vinifera] gi|297741768|emb|CBI32997.3| unnamed protein product [Vitis vinifera]

 Score =  410 bits (1055), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 202/255 (79%), Positives = 225/255 (88%), Gaps = 5/255 (1%)

Query: 4   GMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAP 63
           GMLVQDPSKG  NDVDAIFNQA++LGAVEGP+  ++PSSSSRSFTGT RLLSGE VP+AP
Sbjct: 49  GMLVQDPSKG--NDVDAIFNQARQLGAVEGPM--INPSSSSRSFTGTGRLLSGELVPTAP 104

Query: 64  QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVN 123
           QQPE ++HNIVFW+NGFTVNDGPLRRLDDPENASFLESI+KSECPKELEPAD+RSSVHVN
Sbjct: 105 QQPETVIHNIVFWSNGFTVNDGPLRRLDDPENASFLESIRKSECPKELEPADRRSSVHVN 164

Query: 124 LIRRDVKCPEPEKHHVPFQGVGRTLGSSSTAAS-EPTVDSTPVNTASSSSEGLVVDENLP 182
           LIRRD  CPE EK  VPFQGVGRTLGSSS A   EPTV  TP+NTA S + GL+VDE LP
Sbjct: 165 LIRRDENCPESEKTRVPFQGVGRTLGSSSAAPEPEPTVAPTPLNTAPSPNMGLIVDEALP 224

Query: 183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQT 242
           STS+Q+RL+DGTR+IAHFN HHTI+DI +FI+ASRPG + NYQLQMMGFPPK L D  QT
Sbjct: 225 STSIQLRLSDGTRMIAHFNYHHTITDIRAFIEASRPGGSTNYQLQMMGFPPKQLNDPMQT 284

Query: 243 IEQAGLANSVVIQKF 257
           IEQAGLANSVVIQK+
Sbjct: 285 IEQAGLANSVVIQKY 299

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115898|ref|XP_002317152.1| predicted protein [Populus trichocarpa] gi|222860217|gb|EEE97764.1| predicted protein [Populus trichocarpa]

 Score =  410 bits (1055), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 207/256 (80%), Positives = 230/256 (89%), Gaps = 4/256 (1%)

Query: 4   GMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAP 63
           GMLVQDP+KG  NDVDAIFNQA++LGAVEGPLE+++ SSSS SF+GT RLLSGETVPSAP
Sbjct: 52  GMLVQDPTKG--NDVDAIFNQARQLGAVEGPLENINQSSSSSSFSGTGRLLSGETVPSAP 109

Query: 64  QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVN 123
           QQPE +VHNIVFW NGFTVNDGPLR LDDPENASFLESI+KSECPKELEPAD+RSSVHVN
Sbjct: 110 QQPEAVVHNIVFWTNGFTVNDGPLRSLDDPENASFLESIRKSECPKELEPADRRSSVHVN 169

Query: 124 LIRRDVKCPEPEKH-HVPFQGVGRTLGSSSTA-ASEPTVDSTPVNTASSSSEGLVVDENL 181
           LIRRD KCPEPE+  HV FQGVGRTLGSSSTA A+EPT DS P+N+A +   GLVVDE L
Sbjct: 170 LIRRDQKCPEPERQRHVAFQGVGRTLGSSSTALATEPTADSAPLNSAPTPFMGLVVDETL 229

Query: 182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQ 241
           PSTS+Q+RLADGTR++AHFN HHT++DI SFIDASRPG A NYQLQ+MGFPPK+L D TQ
Sbjct: 230 PSTSIQLRLADGTRMVAHFNNHHTVNDIRSFIDASRPGAALNYQLQLMGFPPKLLTDPTQ 289

Query: 242 TIEQAGLANSVVIQKF 257
           TIEQAGLANSVVIQKF
Sbjct: 290 TIEQAGLANSVVIQKF 305

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115762|ref|XP_002317118.1| predicted protein [Populus trichocarpa] gi|222860183|gb|EEE97730.1| predicted protein [Populus trichocarpa]

 Score =  406 bits (1043), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 204/255 (80%), Positives = 229/255 (89%), Gaps = 4/255 (1%)

Query: 5   MLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAPQ 64
           MLVQDP+KG  NDVDAIFNQA++LGAVEGPLE+++ SSSS SF+GT RLLSGETVPSAPQ
Sbjct: 1   MLVQDPTKG--NDVDAIFNQARQLGAVEGPLENINQSSSSSSFSGTGRLLSGETVPSAPQ 58

Query: 65  QPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNL 124
           QPE +VHNIVFW NGFTVNDGPLR LDDPENASF+ESI+KSECPKELEPAD+RSSVHVNL
Sbjct: 59  QPEAVVHNIVFWTNGFTVNDGPLRSLDDPENASFIESIRKSECPKELEPADRRSSVHVNL 118

Query: 125 IRRDVKCPEPEKH-HVPFQGVGRTLGSSSTA-ASEPTVDSTPVNTASSSSEGLVVDENLP 182
           IR+D KCPEPE+  HVPFQGVGRTLGSSSTA A+EPT DS P+N+A +   GLVVDE LP
Sbjct: 119 IRKDQKCPEPERQRHVPFQGVGRTLGSSSTALATEPTADSAPLNSAPTPFMGLVVDETLP 178

Query: 183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQT 242
           STS+Q+RLADGTR++ HFN HHT++DI SFIDASRPG A NYQLQ+MGFPPK+L D TQT
Sbjct: 179 STSIQLRLADGTRMVTHFNNHHTVNDIRSFIDASRPGAALNYQLQLMGFPPKLLTDPTQT 238

Query: 243 IEQAGLANSVVIQKF 257
           IEQAGLANSVVIQKF
Sbjct: 239 IEQAGLANSVVIQKF 253

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118488401|gb|ABK96017.1| unknown [Populus trichocarpa]

 Score =  399 bits (1026), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 201/256 (78%), Positives = 229/256 (89%), Gaps = 4/256 (1%)

Query: 4   GMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAP 63
           GMLVQDP+KG  NDVDAIFNQA++LGAVEGPLE+L+ SSSSRSFTGT RLLSGETVPSAP
Sbjct: 52  GMLVQDPTKG--NDVDAIFNQARQLGAVEGPLENLNQSSSSRSFTGTGRLLSGETVPSAP 109

Query: 64  QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVN 123
           QQPE +VHNIVFW NGFTV+DGPLRRLDDPENASFLESI+KSECPKELEP+D+RSSVHVN
Sbjct: 110 QQPEAVVHNIVFWTNGFTVDDGPLRRLDDPENASFLESIRKSECPKELEPSDRRSSVHVN 169

Query: 124 LIRRDVKCPEPEKH-HVPFQGVGRTLG-SSSTAASEPTVDSTPVNTASSSSEGLVVDENL 181
           LIRRD KCPEPEK  H  FQG+GRTLG SS++ ASEP  DS P+++A +   GLVVDE L
Sbjct: 170 LIRRDQKCPEPEKQRHAAFQGIGRTLGSSSASPASEPPADSAPLSSAPAPLMGLVVDETL 229

Query: 182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQ 241
           PSTS+Q+RLADGTR++AHFN  +T++DI SFIDASRPG ARNYQLQ+MGFPPK+L + TQ
Sbjct: 230 PSTSIQLRLADGTRMVAHFNNSNTVNDIRSFIDASRPGGARNYQLQLMGFPPKLLTEPTQ 289

Query: 242 TIEQAGLANSVVIQKF 257
           TIEQAGL+NSVVIQKF
Sbjct: 290 TIEQAGLSNSVVIQKF 305

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118108|ref|XP_002331560.1| predicted protein [Populus trichocarpa] gi|222873784|gb|EEF10915.1| predicted protein [Populus trichocarpa]

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 197/260 (75%), Positives = 227/260 (87%), Gaps = 8/260 (3%)

Query: 4   GMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAP 63
           GMLVQDP+KG  NDVDAIFNQA++LGAVEGPLE+L+ SSSSRSFTGT RLLSGETVPSAP
Sbjct: 52  GMLVQDPTKG--NDVDAIFNQARQLGAVEGPLENLNQSSSSRSFTGTGRLLSGETVPSAP 109

Query: 64  QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLE-----SIKKSECPKELEPADKRS 118
           QQPE +VHNIVFW NGFTV+DGPLRRLDDPENASFLE     SI+KSECPKELEP+D+RS
Sbjct: 110 QQPEAVVHNIVFWTNGFTVDDGPLRRLDDPENASFLEVIAIKSIRKSECPKELEPSDRRS 169

Query: 119 SVHVNLIRRDVKCPEPEKHHVPFQGVGRTLG-SSSTAASEPTVDSTPVNTASSSSEGLVV 177
           SVHVNLIRRD KCP  ++ H  FQG+GRTLG SS++ ASEP  DS P+++A +   GLVV
Sbjct: 170 SVHVNLIRRDQKCPVKKQRHAAFQGIGRTLGSSSASPASEPPADSAPLSSAPAPLMGLVV 229

Query: 178 DENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA 237
           DE LPSTS+Q+RLADGTR++AHFN  +T++DI SFIDASRPG ARNYQLQ+MGFPPK+L 
Sbjct: 230 DETLPSTSIQLRLADGTRMVAHFNNSNTVNDIRSFIDASRPGGARNYQLQLMGFPPKLLT 289

Query: 238 DRTQTIEQAGLANSVVIQKF 257
           + TQTIEQAGL+NSVVIQKF
Sbjct: 290 EPTQTIEQAGLSNSVVIQKF 309

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356555700|ref|XP_003546168.1| PREDICTED: UBA and UBX domain-containing protein At4g15410-like [Glycine max]

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 196/257 (76%), Positives = 216/257 (84%), Gaps = 4/257 (1%)

Query: 3   CGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSA 62
            GMLVQDPSKG  NDVD IFNQA++LGAVE PL+ L     S SFTGT RLLSGET  S 
Sbjct: 47  SGMLVQDPSKG--NDVDEIFNQARQLGAVERPLDQLQEPPRSTSFTGTGRLLSGETTRST 104

Query: 63  P-QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVH 121
             QQPE +VHNIVFW+NGFTVNDGPLR LDDPENASFLESIKKSECPKELEP D+RSSV+
Sbjct: 105 NNQQPEAVVHNIVFWSNGFTVNDGPLRSLDDPENASFLESIKKSECPKELEPEDRRSSVN 164

Query: 122 VNLIRRDVKCPEPEKHHVPFQGVGRTLGSSSTA-ASEPTVDSTPVNTASSSSEGLVVDEN 180
           VNLIRR+    EPEK HV FQGVGRTLGSSST+ A +P   STP NTA + S GLVVD++
Sbjct: 165 VNLIRRNENYREPEKQHVAFQGVGRTLGSSSTSMAPDPPAASTPPNTAPTPSAGLVVDQS 224

Query: 181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRT 240
           LPSTS+Q+RLADGTRLI+HFN HHTISDI +FIDASRPG  +NYQLQ+MGFPPK+LAD T
Sbjct: 225 LPSTSIQLRLADGTRLISHFNYHHTISDIRAFIDASRPGGRQNYQLQLMGFPPKILADET 284

Query: 241 QTIEQAGLANSVVIQKF 257
           QTIEQAGLANSVVIQKF
Sbjct: 285 QTIEQAGLANSVVIQKF 301

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255638519|gb|ACU19568.1| unknown [Glycine max]

 Score =  388 bits (996), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 196/257 (76%), Positives = 216/257 (84%), Gaps = 4/257 (1%)

Query: 3   CGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSA 62
            GMLVQDPSKG  NDVD IFNQA++LGAVE PL+ L     S SFTGT RLLSGET  S 
Sbjct: 47  SGMLVQDPSKG--NDVDEIFNQARQLGAVERPLDQLREPPRSTSFTGTGRLLSGETTRST 104

Query: 63  P-QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVH 121
             QQPE +VHNIVFW+NGFTVNDGPLR LDDPENASFLESIKKSECPKELEP D+RSSV+
Sbjct: 105 NNQQPEAVVHNIVFWSNGFTVNDGPLRSLDDPENASFLESIKKSECPKELEPEDRRSSVN 164

Query: 122 VNLIRRDVKCPEPEKHHVPFQGVGRTLGSSSTA-ASEPTVDSTPVNTASSSSEGLVVDEN 180
           VNLIRR+    EPEK HV FQGVGRTLGSSST+ A +P   STP NTA + S GLVVD++
Sbjct: 165 VNLIRRNENYREPEKQHVAFQGVGRTLGSSSTSMAPDPPAASTPPNTAPTPSAGLVVDQS 224

Query: 181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRT 240
           LPSTS+Q+RLADGTRLI+HFN HHTISDI +FIDASRPG  +NYQLQ+MGFPPK+LAD T
Sbjct: 225 LPSTSIQLRLADGTRLISHFNYHHTISDIRAFIDASRPGGRQNYQLQLMGFPPKILADET 284

Query: 241 QTIEQAGLANSVVIQKF 257
           QTIEQAGLANSVVIQKF
Sbjct: 285 QTIEQAGLANSVVIQKF 301

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356532265|ref|XP_003534694.1| PREDICTED: UBA and UBX domain-containing protein At4g15410-like [Glycine max]

 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 191/257 (74%), Positives = 212/257 (82%), Gaps = 4/257 (1%)

Query: 3   CGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSA 62
            GMLVQDPSKG  NDVD IFNQA++LGAVE PL+ L     S SFTGT RLLSGET  S 
Sbjct: 47  SGMLVQDPSKG--NDVDEIFNQARQLGAVERPLDQLQEPPRSTSFTGTGRLLSGETTRST 104

Query: 63  P-QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVH 121
             QQPE +VHNIVFW+NGFTVNDGPLR LDDP+NASFLESIKKSECPKELEP D+RSSV+
Sbjct: 105 NNQQPEAVVHNIVFWSNGFTVNDGPLRSLDDPQNASFLESIKKSECPKELEPEDRRSSVN 164

Query: 122 VNLIRRDVKCPEPEKHHVPFQGVGRTLGSSSTA-ASEPTVDSTPVNTASSSSEGLVVDEN 180
           VNLIRR+    EPEK HV FQGVGRTLGSSST+ A +    STP N A + S GLVVD++
Sbjct: 165 VNLIRRNENYREPEKQHVAFQGVGRTLGSSSTSMAPDSPAASTPTNAAPTPSAGLVVDQS 224

Query: 181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRT 240
           LPSTS+Q+RLADGTRLI+HFN HHTISDI +FIDASRPG  +NYQLQ+MGFPPK+L D T
Sbjct: 225 LPSTSIQLRLADGTRLISHFNYHHTISDIRAFIDASRPGGRQNYQLQLMGFPPKILIDET 284

Query: 241 QTIEQAGLANSVVIQKF 257
           QTIEQAGLANSVVIQK 
Sbjct: 285 QTIEQAGLANSVVIQKI 301

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455377|ref|XP_004145429.1| PREDICTED: UBA and UBX domain-containing protein At4g15410-like isoform 1 [Cucumis sativus]

 Score =  374 bits (960), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 192/257 (74%), Positives = 223/257 (86%), Gaps = 5/257 (1%)

Query: 3   CGMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSA 62
            GMLVQDP+KG  NDVD++FNQA+++GAVEGP++H   SS S SFTGT R+LSGETV SA
Sbjct: 49  SGMLVQDPTKG--NDVDSLFNQARQMGAVEGPIDHAR-SSGSSSFTGTGRVLSGETVRSA 105

Query: 63  PQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHV 122
           P QPE IVHNIVFW+NGFTVN+GPLRRLDDPEN+SFLESI+KSECP+ELEPAD+RSSVHV
Sbjct: 106 PDQPESIVHNIVFWSNGFTVNEGPLRRLDDPENSSFLESIRKSECPRELEPADRRSSVHV 165

Query: 123 NLIRRDVKCPEPEKHHVPFQGVGRTLGSS--STAASEPTVDSTPVNTASSSSEGLVVDEN 180
           NLIRR  +  EPEK  +PFQGVGRTLG S  S AA+EPT   T VN++ S S GL+VDE+
Sbjct: 166 NLIRRMEEYREPEKPRLPFQGVGRTLGGSAPSQAANEPTATPTDVNSSPSPSAGLIVDES 225

Query: 181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRT 240
           LPSTS+Q+RLADGTR+++HFN  HTISDI +FIDASRPG ARNYQLQ+MGFPPK+L+D T
Sbjct: 226 LPSTSIQLRLADGTRMVSHFNYQHTISDIRAFIDASRPGGARNYQLQLMGFPPKLLSDVT 285

Query: 241 QTIEQAGLANSVVIQKF 257
           QTIEQAGLANSVVIQKF
Sbjct: 286 QTIEQAGLANSVVIQKF 302

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	257
TAIR|locus:2132001	367	PUX3 "AT4G22150" [Arabidopsis	0.964	0.675	0.689	5.1e-90
TAIR|locus:2137291	303	PUX4 "plant UBX domain contain	0.968	0.821	0.675	6.5e-90
TAIR|locus:2130110	421	PUX5 "serine/threonine protein	0.968	0.591	0.584	2.5e-74
TAIR|locus:2089920	435	AT3G21660 "AT3G21660" [Arabido	0.420	0.248	0.508	7.4e-39
UNIPROTKB|Q9UNZ2	370	NSFL1C "NSFL1 cofactor p47" [H	0.976	0.678	0.353	1.8e-32
UNIPROTKB|Q3SZC4	370	NSFL1C "NSFL1 cofactor p47" [B	0.976	0.678	0.353	2.6e-31
MGI|MGI:3042273	370	Nsfl1c "NSFL1 (p97) cofactor (	0.976	0.678	0.349	8.8e-31
RGD|619952	370	Nsfl1c "NSFL1 (p97) cofactor (	0.976	0.678	0.349	8.8e-31
ASPGD|ASPL0000010843	373	AN11055 [Emericella nidulans (	0.817	0.563	0.368	3e-30
DICTYBASE|DDB_G0293498	415	DDB_G0293498 "UBX domain-conta	0.968	0.6	0.344	4.9e-30

TAIR|locus:2132001 PUX3 "AT4G22150" [Arabidopsis thaliana (taxid:3702)]

 Score = 898 (321.2 bits), Expect = 5.1e-90, P = 5.1e-90
 Identities = 178/258 (68%), Positives = 209/258 (81%)

Query:     4 GMLVQDPSKGDP--NDVDAIFNQAKELGAVEGPLEHLXXXXXXXXFTGTARLLSGETVPS 61
             GMLVQDP+K +P  +DVD IFNQA++LGAVEGPLEH         FTGT RLLSGE+VP+
Sbjct:   116 GMLVQDPTK-EPKHDDVDEIFNQARQLGAVEGPLEH---PSSSRSFTGTGRLLSGESVPT 171

Query:    62 APQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVH 121
             A QQPEP++HNI+FW+NGFTV+DGPLR+LDDPENASFL+SI+KSECPKELEP DKR+ VH
Sbjct:   172 ALQQPEPVIHNIIFWSNGFTVDDGPLRKLDDPENASFLDSIRKSECPKELEPVDKRAPVH 231

Query:   122 VNLIRRDVKCPEPEKHHVPFQGVGRTLG--SSSTAASEPTVDSTPVNTASSSSEGLVVDE 179
             VNL+RRD KCPE EK  V FQGVGRTLG  SSSTA+S+  +  T V    S  + LVVDE
Sbjct:   232 VNLMRRDEKCPEKEKLKVSFQGVGRTLGGASSSTASSQSNL--TDVAAVQSPLQSLVVDE 289

Query:   180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADR 239
              LPSTS+Q+RLADGTR++A FN HHT++DI  FI+ SRPG   NY LQ+MGFPPK L D 
Sbjct:   290 TLPSTSIQLRLADGTRMVAKFNNHHTVNDIRGFIEFSRPGNPNNYTLQVMGFPPKPLTDP 349

Query:   240 TQTIEQAGLANSVVIQKF 257
             +QTIEQAGLA+SVVIQKF
Sbjct:   350 SQTIEQAGLASSVVIQKF 367

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2137291 PUX4 "plant UBX domain containing protein 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 897 (320.8 bits), Expect = 6.5e-90, P = 6.5e-90
 Identities = 175/259 (67%), Positives = 208/259 (80%)

Query:     4 GMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLXXXXXXXXFTGTARLLSGETVPSAP 63
             GMLVQDPSK D  DVD IFNQA++LGAVEGPLE          FTGT RLLSGE VP+  
Sbjct:    50 GMLVQDPSKKD--DVDEIFNQARQLGAVEGPLEP---PPSSRSFTGTGRLLSGENVPTGN 104

Query:    64 QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVN 123
             QQPEP+VHNIVFW+NGFT++DGPLR+LDDPENASFLESI+KSECPKELEPAD+R+ VHVN
Sbjct:   105 QQPEPVVHNIVFWSNGFTIDDGPLRKLDDPENASFLESIRKSECPKELEPADRRAPVHVN 164

Query:   124 LIRRDVKCPEPEKHHVPFQGVGRTLGSSS--TAASEPTV-DSTPV--NTASSSSEGLVVD 178
             L+R++ KCPE +K  V FQGVGRTLG S+  + +S P   DS P+   T  + S+ LV+D
Sbjct:   165 LMRKEEKCPERQKRRVSFQGVGRTLGGSNEGSGSSSPVAPDSAPIPIQTEPAPSQSLVID 224

Query:   179 ENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLAD 238
             E +P+TS+Q+RLADGTRL+A FN HHT++DI  FID+SRPG + NYQLQ MGFPPK L D
Sbjct:   225 ETVPTTSIQLRLADGTRLVAKFNHHHTVNDIRGFIDSSRPGASLNYQLQTMGFPPKPLTD 284

Query:   239 RTQTIEQAGLANSVVIQKF 257
              TQTIE+AGLANSVV+QKF
Sbjct:   285 LTQTIEEAGLANSVVLQKF 303

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2130110 PUX5 "serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B prime gamma" [Arabidopsis thaliana (taxid:3702)]

 Score = 750 (269.1 bits), Expect = 2.5e-74, P = 2.5e-74
 Identities = 152/260 (58%), Positives = 185/260 (71%)

Query:     4 GMLVQDPSKGDPNDVDAIFNQAKELGAVEGPLEHLXXXXXXXXFTGTARLLSGETVPSAP 63
             GM+VQDP K    DVD +F+QA++  AV+ P+E          FTG ARLLSGE V S+P
Sbjct:   167 GMMVQDPKK--VKDVDELFDQARQ-SAVDRPVEP--SRSASTSFTGAARLLSGEAVSSSP 221

Query:    64 QQ-----PEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRS 118
             QQ     P+ I+H I FW NGFTVNDGPLR   DPENA+F+ SI +SECP ELEPADK+ 
Sbjct:   222 QQQQQEQPQRIMHTITFWLNGFTVNDGPLRGFSDPENAAFMNSISRSECPSELEPADKKI 281

Query:   119 SVHVNLIRRDVKCPEPEKHHVPFQGVGRTLGSS-STAASEPTVDSTPVNTASSSSEGLVV 177
              VHV+L+RR     EP K   PFQGVGRTLG+S S ++S P   S P+N A + S GLVV
Sbjct:   282 PVHVDLVRRGENFTEPPKPKNPFQGVGRTLGASGSGSSSAPQASSAPMNVAPAPSRGLVV 341

Query:   178 DENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA 237
             D   P+TS+Q+RLADGTRL++ FN HHT+ D+  FIDASRPG ++ YQL  MGFPPK L 
Sbjct:   342 DPAAPTTSIQLRLADGTRLVSRFNNHHTVRDVRGFIDASRPGGSKEYQLLTMGFPPKQLT 401

Query:   238 DRTQTIEQAGLANSVVIQKF 257
             +  QTIEQAG+AN+VVIQKF
Sbjct:   402 ELDQTIEQAGIANAVVIQKF 421

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2089920 AT3G21660 "AT3G21660" [Arabidopsis thaliana (taxid:3702)]

 Score = 278 (102.9 bits), Expect = 7.4e-39, Sum P(2) = 7.4e-39
 Identities = 57/112 (50%), Positives = 78/112 (69%)

Query:   146 RTLGSSSTAASEPTVDSTPVNTASSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHT 205
             +TL  S + ++EP + +T   + SS    LVVD   P+TS+Q+ LAD TR++  FN HHT
Sbjct:   328 QTLAGSESTSTEPPLTTTQPPSMSS----LVVDPAAPTTSIQLILADSTRIVTQFNTHHT 383

Query:   206 ISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF 257
             I DI  FID SRP  +++YQL +MG PP  L+D  QTIE+AG+ANSV++QKF
Sbjct:   384 IRDIRCFIDTSRPDGSKDYQLLIMGSPPTPLSDFDQTIEKAGIANSVLVQKF 435

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q9UNZ2 NSFL1C "NSFL1 cofactor p47" [Homo sapiens (taxid:9606)]

 Score = 355 (130.0 bits), Expect = 1.8e-32, P = 1.8e-32
 Identities = 93/263 (35%), Positives = 138/263 (52%)

Query:     6 LVQDPSKGDPND-VDAIFNQAKELGAV--EGPLEHLXXXXXXXXFTGTA-RLLSGETVPS 61
             +V  P K  PN+ VD +F  AKE GAV  E   +          F G   RL +     S
Sbjct:   106 IVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAAPEEES 165

Query:    62 A------PQQPEPIVHNIV-FWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPA 114
             A       Q     VH ++  W +GF++++G LR   DP NA FLESI++ E P EL   
Sbjct:   166 AYVAGEKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRL 225

Query:   115 DKRSSVHVNLI-RRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSE 173
                  V++++   RD    +P+     F G G+ LGS++      +  +      + +S 
Sbjct:   226 AHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLSTSSPAQQAENEAKASS 285

Query:   174 GLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP 233
              +++DE+ P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M  FP 
Sbjct:   286 SILIDESEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFILMTTFPN 345

Query:   234 KVLADRTQTIEQAGLANSVVIQK 256
             K LAD +QT+++A L N+V++Q+
Sbjct:   346 KELADESQTLKEANLLNAVIVQR 368

GO:0008289 "lipid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005795 "Golgi stack" evidence=IEA

UNIPROTKB|Q3SZC4 NSFL1C "NSFL1 cofactor p47" [Bos taurus (taxid:9913)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 93/263 (35%), Positives = 135/263 (51%)

Query:     6 LVQDPSKGDPND-VDAIFNQAKELGAV--EGPLEHLXXXXXXXXFTGTA-RLLSGETVPS 61
             +V  P K  PN+ VD +F  AKE GAV  E   +          F G   RL +     S
Sbjct:   106 IVGPPRKRSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAAPEEES 165

Query:    62 APQQPE------PIVHNIV-FWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPA 114
             A    E        VH ++  W  GF++++G LR   DP NA FLESI++ E P EL   
Sbjct:   166 AYVAGERRRHSGQDVHVVLKLWKTGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRL 225

Query:   115 DKRSSVHVNLI-RRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSE 173
                  V++++   RD    +P+     F G G+ LGS++      +  +      + +S 
Sbjct:   226 AHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQILNTSSPAQQAENEAKASS 285

Query:   174 GLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP 233
              + +DE+ P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M  FP 
Sbjct:   286 SISIDESQPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPN 345

Query:   234 KVLADRTQTIEQAGLANSVVIQK 256
             K LAD  QT+++A L N+V++Q+
Sbjct:   346 KELADENQTLKEANLLNAVIVQR 368

GO:0005795 "Golgi stack" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

MGI|MGI:3042273 Nsfl1c "NSFL1 (p97) cofactor (p47)" [Mus musculus (taxid:10090)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 92/263 (34%), Positives = 135/263 (51%)

Query:     6 LVQDPSKGDPND-VDAIFNQAKELGAV--EGPLEHLXXXXXXXXFTGTA-RLLSGETVPS 61
             +V  P K  PN+ VD +F  AKE GAV  E   +          F G   RL +     S
Sbjct:   106 IVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAAPEEES 165

Query:    62 APQQPE------PIVHNIV-FWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPA 114
             A    E        VH ++  W  GF++++G LR   DP NA FLESI++ E P EL   
Sbjct:   166 AYVAGERRRHSGQDVHVVLKLWKTGFSLDNGDLRSYQDPSNAQFLESIRRGEVPAELRRL 225

Query:   115 DKRSSVHVNLI-RRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSE 173
                  V++++   RD    +P+     F G G+ LGS++      +  +      + +S 
Sbjct:   226 AHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENEAKASS 285

Query:   174 GLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP 233
              ++++E  P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M  FP 
Sbjct:   286 SILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPN 345

Query:   234 KVLADRTQTIEQAGLANSVVIQK 256
             K LAD  QT+++A L N+V++Q+
Sbjct:   346 KELADENQTLKEANLLNAVIVQR 368

GO:0005515 "protein binding" evidence=IPI

GO:0005543 "phospholipid binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005829 "cytosol" evidence=ISO

GO:0007030 "Golgi organization" evidence=ISO

GO:0008289 "lipid binding" evidence=IEA

GO:0043130 "ubiquitin binding" evidence=ISO

GO:0051117 "ATPase binding" evidence=ISO

GO:0061025 "membrane fusion" evidence=ISO

RGD|619952 Nsfl1c "NSFL1 (p97) cofactor (p47)" [Rattus norvegicus (taxid:10116)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 92/263 (34%), Positives = 135/263 (51%)

Query:     6 LVQDPSKGDPND-VDAIFNQAKELGAV--EGPLEHLXXXXXXXXFTGTA-RLLSGETVPS 61
             +V  P K  PN+ VD +F  AKE GAV  E   +          F G   RL +     S
Sbjct:   106 IVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAAPEEES 165

Query:    62 APQQPE------PIVHNIV-FWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPA 114
             A    E        VH ++  W  GF++++G LR   DP NA FLESI++ E P EL   
Sbjct:   166 AYVAGERRRHSGQDVHVVLKLWKTGFSLDNGDLRSYQDPSNAQFLESIRRGEVPAELRRL 225

Query:   115 DKRSSVHVNLI-RRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSE 173
                  V++++   RD    +P+     F G G+ LGS++      +  +      + +S 
Sbjct:   226 AHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENEAKASS 285

Query:   174 GLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP 233
              ++++E  P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M  FP 
Sbjct:   286 SILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPN 345

Query:   234 KVLADRTQTIEQAGLANSVVIQK 256
             K LAD  QT+++A L N+V++Q+
Sbjct:   346 KELADENQTLKEANLLNAVIVQR 368

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005795 "Golgi stack" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

GO:0007030 "Golgi organization" evidence=IDA

GO:0008289 "lipid binding" evidence=IEA

GO:0043130 "ubiquitin binding" evidence=IDA

GO:0051117 "ATPase binding" evidence=IPI

GO:0061025 "membrane fusion" evidence=IDA

GO:0005543 "phospholipid binding" evidence=IDA

ASPGD|ASPL0000010843 AN11055 [Emericella nidulans (taxid:162425)]

 Score = 334 (122.6 bits), Expect = 3.0e-30, P = 3.0e-30
 Identities = 83/225 (36%), Positives = 115/225 (51%)

Query:    47 FTGTARLLSGETVPSA----------PQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENA 96
             FTG AR L GE  PS           PQ P  +   + FWA+GF+V+DG L R DDP+NA
Sbjct:   149 FTGPARTLGGEDTPSRVIDTPSGPAQPQIPRRVRRTLHFWADGFSVDDGELYRSDDPQNA 208

Query:    97 SFLESIKKSECPKELEPADKRSSVHVNLIRRDVKCPEPEKHHVPFQGVGRTLGSSSTAAS 156
               L SI++   P  +  A     V V + + D K   P+  + PF G G+ LGS +    
Sbjct:   209 EILNSIRQGRAPLSIMNAQHGQDVDVEIKQHDEKYVRPKPKYQPFAGKGQRLGSPTPGIR 268

Query:   157 EPTV-DSTPVNTASSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDA 215
              P   +  P   +SS      VDE+ P  ++QIRL DGTRL + FN  HTI D++ F+ A
Sbjct:   269 APAPSEPAPAPQSSSGPPKPNVDESQPVVTLQIRLGDGTRLTSRFNTTHTIGDVYDFVSA 328

Query:   216 SRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAG--LANSVVIQKF 257
             + P + AR + L +  FP K L D+   +          VV+QK+
Sbjct:   329 ASPQSQARPWVL-LTTFPSKELTDKAAVLGDLPEFKRGGVVVQKW 372

GO:0005977 "glycogen metabolic process" evidence=IEA

GO:0030437 "ascospore formation" evidence=IEA

GO:0030433 "ER-associated protein catabolic process" evidence=IEA

GO:0000045 "autophagic vacuole assembly" evidence=IEA

GO:0034727 "piecemeal microautophagy of nucleus" evidence=IEA

GO:0031134 "sister chromatid biorientation" evidence=IEA

GO:0008599 "protein phosphatase type 1 regulator activity" evidence=IEA

GO:0043130 "ubiquitin binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

DICTYBASE|DDB_G0293498 DDB_G0293498 "UBX domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 96/279 (34%), Positives = 155/279 (55%)

Query:     4 GMLVQD-PSKGD---PND-VDAIFNQAKELGAV---EGPLEHLXXXXXXXXFTGTARLLS 55
             G++V+  P KG      D V+ +F+ AK  GAV   E  +E            G      
Sbjct:   139 GLVVESAPKKGKNGGSGDIVNDVFDSAKRHGAVASNEKKVEKPDSFDSVGYQLGATD--Q 196

Query:    56 GETVPSAPQQPEP---IVH-NIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKEL 111
             G    S P++ +P   +V   + FW  GFT++DGPLR+ D+PEN   L+ I++   P+EL
Sbjct:   197 GNRNVSKPKEKDPNSQVVEVKVTFWNQGFTIDDGPLRKYDNPENKELLDDIQRGIVPREL 256

Query:   112 EP-ADKRSSVHVNLIRR-DVKCPEPEK-HHVPFQGVGRTLGSSSTAASEPTVDS------ 162
             +  A   + + V LI   +    EP K  +V F G G+TLGSSST+ +    ++      
Sbjct:   257 QKKATTPNGLSVTLINNHNQDYVEPAKPKYVAFSGGGQTLGSSSTSTNNNNNNNNNNNNR 316

Query:   163 -TPVNTASSSS---EGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRP 218
              T  +T ++S+     + VD++ P+T+VQIRLA+G+RL   FN  HT+ D+ ++I++S  
Sbjct:   317 ATTTSTTTTSTPNVSSINVDQSQPTTTVQIRLANGSRLSTTFNHSHTLQDVINYINSSS- 375

Query:   219 GTARNYQLQMMGFPPKVLADRTQT-IEQAGLANSVVIQK 256
             G+ +++ L + GFP K + + T T ++ AGL N+++IQK
Sbjct:   376 GSNQSFDL-LTGFPQKPVTNPTSTTLKDAGLLNALLIQK 413

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0008289 "lipid binding" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005795 "Golgi stack" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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: GSVIVG00011514001 SubName- Full=Putative uncharacterized protein (Chromosome chr10 scaffold_312, whole genome shotgun sequence); (299 aa) (Vitis vinifera)

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	257
smart00553	93	smart00553, SEP, Domain present in Saccharomyces c	4e-34
pfam08059	75	pfam08059, SEP, SEP domain	2e-32
cd01770	79	cd01770, p47_UBX, p47-like ubiquitin domain	2e-22
cd01767	77	cd01767, UBX, UBX (ubiquitin regulatory X) domain	1e-17
pfam00789	78	pfam00789, UBX, UBX domain	4e-14
cd01772	79	cd01772, SAKS1_UBX, SAKS1-like UBX domain	4e-06
smart00166	77	smart00166, UBX, Domain present in ubiquitin-regul	5e-05

>gnl|CDD|197786 smart00553, SEP, Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47

 Score =  117 bits (296), Expect = 4e-34
 Identities = 40/87 (45%), Positives = 53/87 (60%), Gaps = 1/87 (1%)

Query: 67  EPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLI- 125
           + ++H + FW+NGF+V+DGPLR  DDPENA FLESI++ E P EL    K   V+V++  
Sbjct: 1   QKVIHTLTFWSNGFSVDDGPLRTYDDPENAEFLESIRRGEAPLELLRVAKGQPVNVDVED 60

Query: 126 RRDVKCPEPEKHHVPFQGVGRTLGSSS 152
            RD     P     PF G G+ LGS  
Sbjct: 61  HRDEDYVAPPGAFKPFSGSGQKLGSPG 87

Length = 93

>gnl|CDD|219713 pfam08059, SEP, SEP domain

 Score =  113 bits (285), Expect = 2e-32
 Identities = 38/75 (50%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 73  IVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLI-RRDVKC 131
           +  W NGF+V+DGPLRR DDPENA FLESI K E P EL        V V +  RRD   
Sbjct: 1   LTLWKNGFSVDDGPLRRYDDPENAQFLESINKGEAPLELLNVYPGQGVDVKVEDRRDEDY 60

Query: 132 PEPEKHHVPFQGVGR 146
             P+K + PF G G+
Sbjct: 61  VPPKKKYKPFSGSGQ 75

The SEP domain is named after Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. In p47, the SEP domain has been shown to bind to and inhibit the cysteine protease cathepsin L. Most SEP domains are succeeded closely by a UBX domain. Length = 75

>gnl|CDD|176365 cd01770, p47_UBX, p47-like ubiquitin domain

 Score = 87.8 bits (218), Expect = 2e-22
 Identities = 36/76 (47%), Positives = 52/76 (68%), Gaps = 2/76 (2%)

Query: 182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG-TARNYQLQMMGFPPKVLADRT 240
           P+TS+QIRLADG RL+  FN  H +SD+  FI  +RP   AR + L M  FP K L+D +
Sbjct: 3   PTTSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTL-MTAFPVKELSDES 61

Query: 241 QTIEQAGLANSVVIQK 256
            T+++A L N+V++Q+
Sbjct: 62  LTLKEANLLNAVIVQR 77

p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Length = 79

>gnl|CDD|176362 cd01767, UBX, UBX (ubiquitin regulatory X) domain

 Score = 74.5 bits (184), Expect = 1e-17
 Identities = 33/76 (43%), Positives = 46/76 (60%), Gaps = 4/76 (5%)

Query: 182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADR-- 239
           P+T +QIRL DG RL   FN  H +SD+  F++++ P  A  + L M  FP +VL D   
Sbjct: 1   PTTKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGP-PAEPFTL-MTSFPRRVLTDLDY 58

Query: 240 TQTIEQAGLANSVVIQ 255
             T+++AGL N VV Q
Sbjct: 59  ELTLQEAGLVNEVVFQ 74

The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation. Length = 77

>gnl|CDD|216120 pfam00789, UBX, UBX domain

 Score = 65.4 bits (160), Expect = 4e-14
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 3/78 (3%)

Query: 182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQ 241
               +QIRL DG+RL+  FN    + D++ F+D++R      + L    FP + L D   
Sbjct: 2   DVCRLQIRLPDGSRLVRRFNSSDPLQDVYDFVDSNRYDDDEPFSLNTN-FPRRPLTDDDD 60

Query: 242 -TIEQAGL-ANSVVIQKF 257
            T+++AGL  NS ++ + 
Sbjct: 61  KTLKEAGLLPNSTLVLEP 78

This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module. Length = 78

>gnl|CDD|176367 cd01772, SAKS1_UBX, SAKS1-like UBX domain

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQ 241
           T +QIRL DGT L   F     ++ +  F++ +       + L M  FP KV    D  +
Sbjct: 5   TRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGNGGP-FTL-MTPFPRKVFTEDDMEK 62

Query: 242 TIEQAGLANSVVIQ 255
            +++ GL  S V+ 
Sbjct: 63  PLQELGLVPSAVLI 76

SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Length = 79

>gnl|CDD|197552 smart00166, UBX, Domain present in ubiquitin-regulatory proteins

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 4/76 (5%)

Query: 184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLAD---RT 240
             +QIRL DG+RL+  F    T+  ++ F+ A+       + L    FP +         
Sbjct: 2   CRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALGDGNDPFTLNSP-FPRRTFTKDDYSK 60

Query: 241 QTIEQAGLANSVVIQK 256
           + +E A L +S ++ +
Sbjct: 61  KLLELALLPSSTLVLE 76

Present in FAF1 and Shp1p. Length = 77

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	257
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	100.0
smart00553	93	SEP Domain present in Saccharomyces cerevisiae Shp	100.0
PF08059	75	SEP: SEP domain; InterPro: IPR012989 The SEP (afte	99.97
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	99.93
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	99.85
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	99.8
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	99.79
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	99.79
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	99.76
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	99.76
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	99.75
KOG2689	290	consensus Predicted ubiquitin regulatory protein [	99.33
KOG1364	356	consensus Predicted ubiquitin regulatory protein,	99.0
KOG2507	506	consensus Ubiquitin regulatory protein UBXD2, cont	98.82
KOG1363	460	consensus Predicted regulator of the ubiquitin pat	98.32
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	97.62
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	97.41
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	97.29
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	97.26
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	97.2
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	97.18
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	97.13
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	97.0
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	96.99
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	96.95
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	96.86
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	96.79
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	96.75
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	96.73
PTZ00044	76	ubiquitin; Provisional	96.72
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	96.64
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	96.59
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	96.59
PF12090	182	Spt20: Spt20 family; InterPro: IPR021950 This pres	96.59
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	96.53
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	96.47
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	96.38
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	95.97
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	95.94
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	95.74
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	95.33
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	94.91
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	94.86
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	94.54
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	94.46
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	94.36
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	93.7
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	92.82
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	92.47
PLN02560	308	enoyl-CoA reductase	90.71
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	90.6
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	89.15
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	87.96
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	86.83
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	86.74
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	84.3
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	83.15
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	82.82
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	82.18
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	81.89

>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]

Probab=100.00  E-value=2.5e-67  Score=486.81  Aligned_cols=252  Identities=49%  Similarity=0.803  Sum_probs=211.9

Q ss_pred             ccccccCCCCCC--CchHHHHHHHHHHcCCCCCCCCCCCCCCCCCceeeeeeecCCCCCCCCCC-------CCCCceEEE
Q 025134            3 CGMLVQDPSKGD--PNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSFTGTARLLSGETVPSAPQ-------QPEPIVHNI   73 (257)
Q Consensus         3 SG~~V~~p~~~~--~~~v~~if~~A~~~ga~~~~~~~~~~~~~~~~F~G~G~~Lg~~~~~~~~~-------~~~~~~~~l   73 (257)
                      |||+|.+|+++.  .+.|+++|++|+++||++.+...  .-.....|.|++.-|.|+.+|...+       .++.+.|+|
T Consensus       112 ~gq~~v~~~~k~~~~e~v~~~~~~a~q~~a~~~~~~~--~~~~~~~~~gs~~~lsg~~~~~~~q~~~~~~~~~~~v~~~l  189 (380)
T KOG2086|consen  112 SGQMVVEPPDKKSSEEDVDEIFGQARQMGAVEGPLAP--SESSSGEFLGSGGDLSGEVVPLGTQQQQREAQPPEPVTVTL  189 (380)
T ss_pred             ccccccCCCccccHHHHHHHHHhhhcccCccccCccC--ccccccccccccccccCccccCCcccCcccccCCCcceeEE
Confidence            676666665543  35899999999999997644211  1123467889988888888775443       257799999


Q ss_pred             EEeccceeecCCCCccCCChhhHHHHHHHhcCCCCCcccCCCCCCceEEEEe-cccccCCCCCCCCccccccccccccCC
Q 025134           74 VFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLI-RRDVKCPEPEKHHVPFQGVGRTLGSSS  152 (257)
Q Consensus        74 ~lw~nGF~VddGp~R~y~dP~n~~FL~~I~~G~~P~EL~~~~~~~~V~v~l~-~r~e~y~~p~~~~~~F~G~G~~LGs~~  152 (257)
                      +||||||+|||||||+|+||+|++||++|++|+||.||+.++++++|+|+|+ ||+|+|.+|++.+++|+|+||+||++.
T Consensus       190 ~lW~nGFsvdDGplr~ydDP~N~~fL~~I~~Ge~P~eL~~~~~~~~V~v~v~~~r~E~~~~~~~~~~pF~G~Gq~LGs~~  269 (380)
T KOG2086|consen  190 KLWKNGFSVDDGPLRSYDDPANAEFLESIRKGEAPSELLPVDPGQEVDVKVEDHRDEDYLEPKPVFKPFSGEGQRLGSTA  269 (380)
T ss_pred             EEeeccccccCCCcccccChhHHHHHHHHhccCCCHHHhccccCCccceeccccccccccCCCcccCCCCCcCeecCCcC
Confidence            9999999999999999999999999999999999999999999999999999 589999999888999999999999987


Q ss_pred             CCCCCCC-CCCCC---CC-CCCCCCCCcccCCCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC-CcCeEE
Q 025134          153 TAASEPT-VDSTP---VN-TASSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQL  226 (257)
Q Consensus       153 p~~~~~~-~~~~~---~~-~~~~~~~~~~vd~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~-~~~f~L  226 (257)
                      |....++ +....   ++ .+..+...+.+|+..|+|+|||||+||+|+|++||++|||.|||.||..++|.+ ..+|.|
T Consensus       270 p~~~~ss~~~~~~~~p~~~~~~~~~~sl~~d~~~PtTsIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L  349 (380)
T KOG2086|consen  270 PGVSGSSSPPLTATVPANTQERSASSSLVIDPAEPTTSIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPGDSSTYFIL  349 (380)
T ss_pred             CCccccCCCcccccCCccccccccccccccCCCCCcceEEEEecCCceeeeeccCcccHHHHHHHHHhcCCCCcCCceee
Confidence            7654322 11111   11 223356678899999999999999999999999999999999999999999987 568999


Q ss_pred             EecCCCCcccCCccCcHhhhCCCCeeEEeeC
Q 025134          227 QMMGFPPKVLADRTQTIEQAGLANSVVIQKF  257 (257)
Q Consensus       227 ~t~~fP~k~l~d~s~TL~eagL~navivqk~  257 (257)
                      ++ +||+|+|+|+++|||+|||+|+||||||
T Consensus       350 ~~-~FPpk~l~D~sqTle~AgL~Nsvlvqr~  379 (380)
T KOG2086|consen  350 MM-AFPPKPLSDDSQTLEEAGLLNSVLVQRL  379 (380)
T ss_pred             ee-cCCCcccCCcchhHHhccchhhhhhhhc
Confidence            98 9999999999999999999999999997

>smart00553 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47

Probab=100.00  E-value=4.8e-37  Score=236.77  Aligned_cols=89  Identities=46%  Similarity=0.814  Sum_probs=84.3

Q ss_pred             CceEEEEEeccceeecCCCCccCCChhhHHHHHHHhcCCCCCcccCCCCCCceEEEEe-cccccCCCCCCCCcccccccc
Q 025134           68 PIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLI-RRDVKCPEPEKHHVPFQGVGR  146 (257)
Q Consensus        68 ~~~~~l~lw~nGF~VddGp~R~y~dP~n~~FL~~I~~G~~P~EL~~~~~~~~V~v~l~-~r~e~y~~p~~~~~~F~G~G~  146 (257)
                      .+.|+||||+|||+|||||||+||||+|++||++|++|++|.||++.++++.|+|+|+ +|+|+|++|++++++|+|+||
T Consensus         2 ~v~~~ltlw~nGFtVdDGplr~yddP~N~~FL~~I~~G~~P~EL~~~~~~~~V~v~l~d~~~E~y~~p~~~~~~F~G~G~   81 (93)
T smart00553        2 KVIVVLTFWSNGFSVDDGPLRTYDDPENAEFLESIRRGEAPLELLRVDKGQPVNVDVEDHRDEDYVAPPKAFKPFSGSGQ   81 (93)
T ss_pred             CeEEEEEEecCCcEecCCCcccCCCHhHHHHHHHHHcCCCCHHHHhhcCCCcEEEEeEeccCccccCCCCCccCCccCCc
Confidence            5789999999999999999999999999999999999999999999999999999998 679999999888999999999


Q ss_pred             ccccCCCCCC
Q 025134          147 TLGSSSTAAS  156 (257)
Q Consensus       147 ~LGs~~p~~~  156 (257)
                      +||+++|...
T Consensus        82 ~LGs~~p~~~   91 (93)
T smart00553       82 KLGSPGPQSL   91 (93)
T ss_pred             cCCCCCCCcc
Confidence            9999988764

>PF08059 SEP: SEP domain; InterPro: IPR012989 The SEP (after shp1, eyc and p47) domain is an eukaryotic domain, which occurs frequently and mainly in single units

Probab=99.97  E-value=3.6e-32  Score=202.43  Aligned_cols=74  Identities=50%  Similarity=0.855  Sum_probs=65.5

Q ss_pred             EEEeccceeecCCCCccCCChhhHHHHHHHhcCCCCCcccCCCCCCceEEEEec-ccccCCCCCCCCcccccccc
Q 025134           73 IVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIR-RDVKCPEPEKHHVPFQGVGR  146 (257)
Q Consensus        73 l~lw~nGF~VddGp~R~y~dP~n~~FL~~I~~G~~P~EL~~~~~~~~V~v~l~~-r~e~y~~p~~~~~~F~G~G~  146 (257)
                      ||||+|||+|||||||+|+||+|++||++|++|++|.||+..+|++.|+|+|++ |+|+|++|++++++|+|+||
T Consensus         1 l~~w~nGf~VddGplR~y~dp~n~~Fl~~I~~G~~P~EL~~~~p~~~v~v~l~d~~~e~y~~~~~~~~~F~G~G~   75 (75)
T PF08059_consen    1 LTFWRNGFTVDDGPLRPYDDPENAQFLEDINRGYFPSELQQRYPGDGVDVNLEDRRDEDYVPPKKKFKPFSGQGH   75 (75)
T ss_dssp             EEEETTEEEETTS-EEETTSTTCHHHHHHHHHT--SCHHHCTTSSS-EEEEEEEECTTSS-SSSSSSTTS-SSSS
T ss_pred             CEEecCceEecCCCcccCCCHhHHHHHHHHHhcCCCHHHHhccCCCeEEEEEEeCCCCccCCCCccccCCCcCCC
Confidence            799999999999999999999999999999999999999999998899999995 59999999888999999997

Almost all proteins containing a SEP domain are succeeded closely by a UBX domain (see PDOC50033 from PROSITEDOC). The function of the SEP domain is as yet unknown but it has been proposed to act as a reversible competitive inhibitor of the lysosomal cysteine protease cathepsin L [, ]. The sructure of the SEP domain comprises a beta-sheet composed of four strands, and two alpha-helices. One side of the beta-sheet faces alpha1 and alpha2. The longer helix alpha1 packs against the four- stranded beta-sheet, where as the shorter helix alpha2 is located at one edge of the globular structure formed by alpha1 and the four stranded beta sheet. A number of highly conserved hydrophobic residues are present in the SEP domain, which are predominantly buried and form the hydrophobic core [, ]. Some proteins known to contain a SEP domain are listed below: - Eukaryotic NSFL1 cofactor p37 (or p97 cofactor p37), an adapter protein required for Golgi and endoplasmic reticulum biogenesis. It is involved in Golgi and endoplasmic reticulum maintenance during interphase and in their reassembly at the end of mitosis. - Eukaryotic NSFL1 cofactor p47 (or p97 cofactor p47), a major adaptor molecule of the cytosolic AAA-type ATPase (ATPases associated with various cellular activities) p97. p47 is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. - Vertebrate UBX domain-containing protein 4 (UBXD4). - Plant UBA and UBX domain-containing protein. - Saccharomyces cerevisiae (Baker's yeast) UBX domain-containing protein 1 or Suppressor of high-copy PP1 protein (shp1), the homologue of p47. - Drosophila melanogaster (Fruit fly) eyes closed (eyc). ; PDB: 1S3S_G 1VAZ_A 1SS6_A.

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=99.93  E-value=1.8e-25  Score=168.02  Aligned_cols=76  Identities=46%  Similarity=0.773  Sum_probs=71.9

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC-CcCeEEEecCCCCcccCCccCcHhhhCCCCeeEEeeC
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF  257 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~navivqk~  257 (257)
                      +|+|+||||||||+|++++||.+|||+|||+||.++.++. ..+|.|++ +||+|+|+|+++||+||||+||+|+|||
T Consensus         2 ~p~t~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t-~fP~k~l~~~~~Tl~eagL~~s~v~q~~   78 (79)
T cd01770           2 EPTTSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMT-AFPVKELSDESLTLKEANLLNAVIVQRL   78 (79)
T ss_pred             CCeeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEec-CCCCcccCCCCCcHHHCCCcCcEEEEEe
Confidence            6899999999999999999999999999999999987654 58999999 9999999988999999999999999998

p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=99.85  E-value=6.2e-21  Score=142.05  Aligned_cols=74  Identities=43%  Similarity=0.779  Sum_probs=68.5

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCC--ccCcHhhhCCCCeeEEeeC
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLAD--RTQTIEQAGLANSVVIQKF  257 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d--~s~TL~eagL~navivqk~  257 (257)
                      |+|+||||||||+|++++|+.++||+|||+||..+... ..+|.|++ +||+|.|++  .++||+||||.|++++++|
T Consensus         1 p~t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~-~~~f~L~t-~~Pr~~~~~~~~~~TL~e~gL~~s~~~~~~   76 (77)
T cd01767           1 PTTKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP-AEPFTLMT-SFPRRVLTDLDYELTLQEAGLVNEVVFQRL   76 (77)
T ss_pred             CcEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEe-CCCCccCCCCCccCcHHHcCCccceEEEEe
Confidence            68999999999999999999999999999999987543 57899999 999999986  7999999999999999987

The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=99.80  E-value=2.8e-19  Score=134.11  Aligned_cols=76  Identities=24%  Similarity=0.430  Sum_probs=67.2

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCc--cCcHhhhCCC-CeeEEeeC
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADR--TQTIEQAGLA-NSVVIQKF  257 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~--s~TL~eagL~-navivqk~  257 (257)
                      ++.|+||||||||+|++++|+.++||+|||+||.........+|.|++ +||+|.|++.  ++||+|+||+ +++|+++|
T Consensus         2 ~~~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t-~~Prk~l~~~d~~~tL~e~gL~p~~~l~v~~   80 (80)
T smart00166        2 SDQCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNS-PFPRRTFTKDDYSKTLLELALLPSSTLVLEP   80 (80)
T ss_pred             CCeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEe-CCCCcCCccccccCCHHHCCCCCceEEEEeC
Confidence            478999999999999999999999999999999665433457899999 9999999854  7999999999 58888876

Present in FAF1 and Shp1p.

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=99.79  E-value=6e-19  Score=133.27  Aligned_cols=73  Identities=22%  Similarity=0.373  Sum_probs=65.1

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC-eeEE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-aviv  254 (257)
                      ++|+|+||||||||+|++++|+.++||.+||.||.+. .....+|.|+| +||+|.|+  |.++||+||||++ ++|+
T Consensus         2 ~~~~t~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~~-g~~~~~f~L~t-~FPRr~~~~~d~~~TL~e~GL~P~~~Lf   77 (82)
T cd01773           2 NGPKARLMLRYPDGKREQIALPEQAKLLALVRHVQSK-GYPNERFELLT-NFPRRKLSHLDYDITLQEAGLCPQETVF   77 (82)
T ss_pred             CCCeeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-CCCCCCEEEec-CCCCcccCCcccCCCHHHcCCCCCcEEE
Confidence            7899999999999999999999999999999999883 34468899999 99999997  5579999999997 4443

Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=99.79  E-value=6e-19  Score=134.36  Aligned_cols=70  Identities=29%  Similarity=0.488  Sum_probs=61.9

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC-------CccCcHhhhCCCCee
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA-------DRTQTIEQAGLANSV  252 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~-------d~s~TL~eagL~nav  252 (257)
                      ...|+||||||||+|+++||+.+|||++||+||.. .+....+|.|++ +||+|.|+       |.++||+||||.+++
T Consensus         2 ~~~~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~~~~~~f~L~t-~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~   78 (85)
T cd01774           2 PDTVKIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVT-NFPRRVLPCLPSEGDPPPPTLLEAGLSNSE   78 (85)
T ss_pred             CceEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEec-CCCCccccccccccCcCCCCHHHcCCCCcc
Confidence            35799999999999999999999999999999964 545567899999 99999997       458899999999853

Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=99.76  E-value=3.9e-18  Score=128.46  Aligned_cols=73  Identities=19%  Similarity=0.293  Sum_probs=64.0

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC-eeEE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-aviv  254 (257)
                      .+|+++||||||||+|+++||+.++||++||+||.+.. ....+|.|++ +||+|.|+  |.+.||+|+||.+ ++|+
T Consensus         1 ~~~~~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~~-~~~~~f~L~t-~fPRk~~~~~d~~~TL~e~gL~p~~~L~   76 (80)
T cd01771           1 GEPISKLRVRTPSGDFLERRFLGDTPLQVLLNFVASKG-YPIDEYKLLS-SWPRRDLTQLDPNFTLLELKLYPQETLI   76 (80)
T ss_pred             CCCeEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhcC-CCCCCEEEec-CCCCCCCcCCCCCCcHHHcCCCCCcEEE
Confidence            36899999999999999999999999999999998753 2346899999 99999997  5678999999996 5554

Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast

Probab=99.76  E-value=2.4e-18  Score=129.00  Aligned_cols=78  Identities=29%  Similarity=0.531  Sum_probs=67.5

Q ss_pred             CCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCc-CeEEEecCCCCcccCCcc-CcHhhhCCCC-eeEEe
Q 025134          179 ENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTAR-NYQLQMMGFPPKVLADRT-QTIEQAGLAN-SVVIQ  255 (257)
Q Consensus       179 ~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~-~f~L~t~~fP~k~l~d~s-~TL~eagL~n-avivq  255 (257)
                      +..+.|+||||||||++++++|+.++||++||+||......... .|.|++ +||++.|++++ +||+|+||.+ ++|++
T Consensus         2 ~~~~~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~-~~Pr~~l~~~~~~tl~e~~l~p~~~l~v   80 (82)
T PF00789_consen    2 EESDVVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELIT-AFPRRELTDEDSKTLEEAGLLPSATLIV   80 (82)
T ss_dssp             STSSEEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEE-SSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred             CCCCEEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEe-CCCCcCCCccccccHHHhcCCCCeEEEE
Confidence            35678999999999999999999999999999999886544434 399999 99999999655 9999999995 88888


Q ss_pred             eC
Q 025134          256 KF  257 (257)
Q Consensus       256 k~  257 (257)
                      +|
T Consensus        81 ~~   82 (82)
T PF00789_consen   81 EK   82 (82)
T ss_dssp             E-
T ss_pred             EC
Confidence            76

The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=99.75  E-value=7.8e-18  Score=126.37  Aligned_cols=71  Identities=30%  Similarity=0.544  Sum_probs=62.3

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-aviv  254 (257)
                      ..|+||||||||+|++.+|+.++||.+||+||..+... ..+|.|++ +||+|.|+  |.++||+|+||.+ |+|+
T Consensus         3 ~~~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~-~~~f~L~t-~fPrk~~~~~d~~~TL~elgL~Psa~L~   76 (79)
T cd01772           3 TETRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGN-GGPFTLMT-PFPRKVFTEDDMEKPLQELGLVPSAVLI   76 (79)
T ss_pred             cEEEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCC-CCCEEEEe-CCCCeECCcccccCCHHHCCCCCceEEE
Confidence            46899999999999999999999999999999886533 47899999 99999998  4589999999997 4443

SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]

Probab=99.33  E-value=6.3e-12  Score=112.98  Aligned_cols=77  Identities=26%  Similarity=0.496  Sum_probs=67.9

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC-eeEEee
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVIQK  256 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-avivqk  256 (257)
                      ....|+|||||+||+.+..+||...|+.+||.||..++.+...+|.|++ +||++.|+  |...+|++++|++ |+|+.+
T Consensus       207 ~ys~crlQiRl~DG~Tl~~tF~a~E~L~~VR~wVd~n~~~~~~P~~f~t-~fPR~tf~edD~~KpLq~L~L~Psa~lil~  285 (290)
T KOG2689|consen  207 DYSQCRLQIRLPDGQTLTQTFNARETLAAVRLWVDLNRGDGLDPYSFHT-GFPRVTFTEDDELKPLQELDLVPSAVLILE  285 (290)
T ss_pred             cccceEEEEEcCCCCeeeeecCchhhHHHHHHHHHHhccCCCCCeeeec-CCCceecccccccccHHHhccccchheecc
Confidence            3568999999999999999999999999999999998866667999999 99999997  5578999999998 666654


Q ss_pred             C
Q 025134          257 F  257 (257)
Q Consensus       257 ~  257 (257)
                      |
T Consensus       286 ~  286 (290)
T KOG2689|consen  286 P  286 (290)
T ss_pred             c
Confidence            3

>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]

Probab=99.00  E-value=2.6e-10  Score=105.70  Aligned_cols=72  Identities=28%  Similarity=0.419  Sum_probs=62.9

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC-CcCeEEEecCCCCcccC--CccCcHhhhCCCCe--eEEe
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVLA--DRTQTIEQAGLANS--VVIQ  255 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~-~~~f~L~t~~fP~k~l~--d~s~TL~eagL~na--vivq  255 (257)
                      +|+|+||+|||+|.++||..++||.-||.|+..+..+. ...|.|++ +||++.+.  +.+.||+||||.|+  ++.+
T Consensus       277 vt~i~vR~pdG~R~qrkf~~sepv~ll~~~~~s~~dg~~k~~FkLv~-a~P~~k~l~~~~daT~~eaGL~nS~~~~~~  353 (356)
T KOG1364|consen  277 VTSIQVRFPDGRRKQRKFLKSEPVQLLWSFCYSHMDGSDKKRFKLVQ-AIPASKTLDYGADATFKEAGLANSETLLSV  353 (356)
T ss_pred             eeEEEEecCCccHHHHhhccccHHHHHHHHHHHhhcccccccceeee-cccchhhhhccccchHHHhccCcccccccc
Confidence            68899999999999999999999999999999877655 67899999 99987765  45789999999998  4444

>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]

Probab=98.82  E-value=3.3e-09  Score=100.52  Aligned_cols=69  Identities=17%  Similarity=0.339  Sum_probs=61.7

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN  250 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n  250 (257)
                      -..|+||||||||+.++-+|..++-+..|++||.+........|.|.+ .||+|+++  |.++||-|+.|.+
T Consensus       312 ~d~~rLqiRLPdGssfte~Fps~~vL~~vr~yvrq~~~i~~g~f~Lat-pyPRReft~eDy~KtllEl~L~p  382 (506)
T KOG2507|consen  312 ADDVRLQIRLPDGSSFTEKFPSTSVLRMVRDYVRQNQTIGLGAFDLAT-PYPRREFTDEDYDKTLLELRLFP  382 (506)
T ss_pred             cceeEEEEecCCccchhhcCCcchHHHHHHHHHHhcccccccceeecc-ccccccccchhhhhhHHHhccCC
Confidence            367999999999999999999999999999999875433468999999 99999998  4578999999996

>KOG1363 consensus Predicted regulator of the ubiquitin pathway (contains UAS and UBX domains) [Signal transduction mechanisms]

Probab=98.32  E-value=1.1e-06  Score=85.45  Aligned_cols=74  Identities=24%  Similarity=0.453  Sum_probs=63.9

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCC--ccCcHhhhCCCC--eeEEe
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLAD--RTQTIEQAGLAN--SVVIQ  255 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d--~s~TL~eagL~n--avivq  255 (257)
                      ..++.+|.||+|+|+|+.+||..++++++||+||..+. .....|.|.+ +||++.+.+  .+.||++.||.+  .+|++
T Consensus       380 ~~~~~~l~iR~P~G~r~~RrF~~s~~~q~l~~~v~~~~-~~~~e~~~~~-~fPr~~~~~~~~~~sl~~~~l~p~qe~lfl  457 (460)
T KOG1363|consen  380 EEEAITVAIRLPSGTRLERRFLKSDKLQILYDYVDSNG-FHPEEYSLNT-SFPRRPLGDYEHSSSLQDIGLTPRQETLFL  457 (460)
T ss_pred             cccceeeEEECCCCCeeeeeeecccchhHHHHHHHhcc-CCchhhcccc-CCCcccccccccccccccCCcccccceeee
Confidence            45689999999999999999999999999999998865 4467899999 999999984  478999999996  44443

>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain

Probab=97.62  E-value=0.00029  Score=51.44  Aligned_cols=68  Identities=15%  Similarity=0.226  Sum_probs=54.4

Q ss_pred             EEEEcC-CCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEEee
Q 025134          186 VQIRLA-DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQK  256 (257)
Q Consensus       186 iqIRl~-dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avivqk  256 (257)
                      |-||+. +|+...+.+..+.||++|...|.....-......|+.   =.+.|+|++.||+++|+.+ ++|+.|
T Consensus         1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~---~Gk~L~D~~~~L~~~gi~~~~~l~l~   70 (71)
T cd01796           1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIY---NGRELVDNKRLLALYGVKDGDLVVLR   70 (71)
T ss_pred             CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEE---CCeEccCCcccHHHcCCCCCCEEEEe
Confidence            458899 8998999999999999999999875422244566654   5889999889999999995 777654

DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=97.41  E-value=0.0007  Score=49.46  Aligned_cols=65  Identities=15%  Similarity=0.305  Sum_probs=50.8

Q ss_pred             EEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCeeEE
Q 025134          186 VQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVI  254 (257)
Q Consensus       186 iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~naviv  254 (257)
                      +.||+.+|+...+.+..++||++|++.|.....-......|.   |=.+.|+| +.||+++++.+..+|
T Consensus         1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li---~~G~~L~D-~~~l~~~~i~~~~tv   65 (70)
T cd01794           1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWF---FSGKLLTD-KTRLQETKIQKDYVV   65 (70)
T ss_pred             CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEE---ECCeECCC-CCCHHHcCCCCCCEE
Confidence            468999999999999999999999999977532123445554   56788888 589999999964443

DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.

>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2

Probab=97.29  E-value=0.0018  Score=48.14  Aligned_cols=68  Identities=19%  Similarity=0.222  Sum_probs=55.0

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ..|.||..+|+.+.+.+..+.||++|.+-|.....-....+.|.. -|-.+.|.|+ .||.+.|+.+ ++|
T Consensus         3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~-~~~G~~L~D~-~tL~~~gi~~gs~l   71 (80)
T cd01792           3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAH-LDSREVLQDG-VPLVSQGLGPGSTV   71 (80)
T ss_pred             eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEe-ccCCCCCCCC-CCHHHcCCCCCCEE
Confidence            478999999999999999999999999999876432345677765 5777888874 7999999985 444

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=97.26  E-value=0.0022  Score=46.36  Aligned_cols=65  Identities=14%  Similarity=0.243  Sum_probs=51.6

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +|.||..+|+.+.+++..+.||++|.+.|.....-......|.   |-.+.|+| +.||.+.++.+ ++|
T Consensus         2 ~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~---~~g~~L~d-~~tl~~~~i~~g~~i   67 (76)
T cd01806           2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI---YSGKQMND-DKTAADYKLEGGSVL   67 (76)
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEE---ECCeEccC-CCCHHHcCCCCCCEE
Confidence            5889999999999999999999999999987542223445555   46888877 58999999996 444

Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=97.20  E-value=0.0022  Score=46.88  Aligned_cols=66  Identities=12%  Similarity=0.212  Sum_probs=53.2

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +|.||..+|+.+.+.+..++||++|++-|.....-......|..   =.+.|+|+ .||.+.|+.+ ++|.
T Consensus         2 ~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~---~G~~L~d~-~~L~~~~i~~~~~l~   68 (74)
T cd01807           2 FLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLF---KGKALADD-KRLSDYSIGPNAKLN   68 (74)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEE---CCEECCCC-CCHHHCCCCCCCEEE
Confidence            68899999999999999999999999999875322245677764   58889874 8999999995 5553

GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=97.18  E-value=0.0028  Score=47.06  Aligned_cols=66  Identities=17%  Similarity=0.197  Sum_probs=51.5

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .+|.||...|+...+.+..+.||++|++-|+....-......|   .|..+.|.|.  ||+++|+.+ ++|.
T Consensus         2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL---~~~Gk~L~d~--~L~~~gi~~~~~i~   68 (78)
T cd01804           2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLAL---LHRETRLSSG--KLQDLGLGDGSKLT   68 (78)
T ss_pred             eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEE---EECCcCCCCC--cHHHcCCCCCCEEE
Confidence            4789999999999999999999999999997754212233444   4678889885  899999985 5554

midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=97.13  E-value=0.0037  Score=46.09  Aligned_cols=67  Identities=15%  Similarity=0.115  Sum_probs=52.1

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .+|.||-..|+.+...+..++||++|.+.|.....-....-.|   .|..+.|.| +.||++.||.+ ++|.
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrL---i~~Gk~L~D-~~tL~~ygi~~~stv~   69 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVL---KKWYTIFKD-HISLGDYEIHDGMNLE   69 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEE---EeCCcCCCC-CCCHHHcCCCCCCEEE
Confidence            5788999999999999999999999999998764222333344   456888887 47999999986 5554

UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.

>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade

Probab=97.00  E-value=0.0025  Score=45.41  Aligned_cols=62  Identities=16%  Similarity=0.235  Sum_probs=49.8

Q ss_pred             EcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          189 RLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       189 Rl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      |..+|+.+.+.++.++||.+|.+.|.....-......|+.   -.+.|. ++.||.+.|+.+ ++|+
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~---~G~~L~-d~~tL~~~~i~~~~~I~   63 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIY---NGKELD-DDKTLSDYGIKDGSTIH   63 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEE---TTEEES-TTSBTGGGTTSTTEEEE
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceeee---eeeccc-CcCcHHHcCCCCCCEEE
Confidence            5678999999999999999999999886543345666664   788894 479999999996 6554

There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=96.99  E-value=0.0057  Score=43.71  Aligned_cols=66  Identities=14%  Similarity=0.206  Sum_probs=51.5

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +|-||..+|+....++..++||++|.+.|.....-......|+   |..+.|.| +.||.+.|+.+ ++|.
T Consensus         2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~---~~g~~L~d-~~~L~~~~i~~~~~l~   68 (72)
T cd01809           2 EIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLI---YSGRVLKD-DETLSEYKVEDGHTIH   68 (72)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEE---ECCEECCC-cCcHHHCCCCCCCEEE
Confidence            6889999999999999999999999999987542223345555   35777877 58999999986 5543

Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=96.95  E-value=0.0064  Score=44.32  Aligned_cols=66  Identities=14%  Similarity=0.299  Sum_probs=51.6

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCC--CCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG--TARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~--~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .|.||..+|+...+.+..++||++|++.|.....-  ......|+   |..+.|.| +.||+++|+.+ ++|+
T Consensus         2 ~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~---~~G~~L~d-~~~L~~~~i~~~~~i~   70 (77)
T cd01805           2 KITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLI---YSGKILKD-DTTLEEYKIDEKDFVV   70 (77)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEE---ECCEEccC-CCCHHHcCCCCCCEEE
Confidence            57899999999999999999999999999875422  23344554   57889987 48999999995 4443

RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).

>cd01803 Ubiquitin Ubiquitin

Probab=96.86  E-value=0.0073  Score=43.64  Aligned_cols=65  Identities=17%  Similarity=0.265  Sum_probs=51.1

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|-||..+|+.+.+.+..++||++|.+.|.....-......|.   |..+.|.| +.||.+.|+.+ ++|
T Consensus         2 ~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~---~~g~~L~d-~~~L~~~~i~~~~~i   67 (76)
T cd01803           2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI---FAGKQLED-GRTLSDYNIQKESTL   67 (76)
T ss_pred             EEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEE---ECCEECCC-CCcHHHcCCCCCCEE
Confidence            5789999999999999999999999999987542223345554   46888887 47999999986 444

Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)

>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway

Probab=96.79  E-value=0.0017  Score=48.82  Aligned_cols=69  Identities=17%  Similarity=0.228  Sum_probs=40.8

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCC-cccC-CccCcHhhhCCCCeeEE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP-KVLA-DRTQTIEQAGLANSVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~-k~l~-d~s~TL~eagL~naviv  254 (257)
                      .-||||.+||.. .+.+..++|+++|++-|..........|.|.. .... .++. +.++||+++||.++-++
T Consensus         5 milRvrS~dG~~-Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~-~~~~~~~l~s~~~~tl~~lglkHGdml   75 (80)
T PF11543_consen    5 MILRVRSKDGMK-RIEVSPSSTLSDLKEKISEQLSIPDSSQSLSK-DRNNKEELKSSDSKTLSSLGLKHGDML   75 (80)
T ss_dssp             -EEEEE-SSEEE-EEEE-TTSBHHHHHHHHHHHS---TTT---BS-SGGGGGCSSS-TT-CCCCT---TT-EE
T ss_pred             EEEEEECCCCCE-EEEcCCcccHHHHHHHHHHHcCCCCcceEEEe-cCCCCcccccCCcCCHHHcCCCCccEE
Confidence            468999999964 33578999999999999987654456788876 5444 3453 66899999999975443

Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.

>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein

Probab=96.75  E-value=0.0065  Score=43.77  Aligned_cols=64  Identities=17%  Similarity=0.308  Sum_probs=51.2

Q ss_pred             EEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          186 VQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       186 iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      |-||..+|..+.+.+..++||++|.+.|.....-......|.   |=.+.|+|+ .||.++|+.+ ++|
T Consensus         1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li---~~G~~L~d~-~~l~~~~i~~~stl   65 (70)
T cd01798           1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVI---FAGKELRNT-TTIQECDLGQQSIL   65 (70)
T ss_pred             CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEE---ECCeECCCC-CcHHHcCCCCCCEE
Confidence            458999999999999999999999999987642224456665   468889874 9999999995 555

parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.

>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2

Probab=96.73  E-value=0.0072  Score=44.13  Aligned_cols=64  Identities=19%  Similarity=0.336  Sum_probs=51.5

Q ss_pred             EEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          186 VQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       186 iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      |-||.++|+...+.+..++||++|++-|.....-....+.|.   |=.+.|.|+ .||.+.|+.+ ++|
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~---~~G~~L~D~-~tL~~~~i~~~~tl   65 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLS---FEGRPMEDE-HPLGEYGLKPGCTV   65 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEE---ECCEECCCC-CCHHHcCCCCCCEE
Confidence            468999999999999999999999999977532224567776   468899875 8999999985 544

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>PTZ00044 ubiquitin; Provisional

Probab=96.72  E-value=0.01  Score=43.20  Aligned_cols=65  Identities=12%  Similarity=0.252  Sum_probs=51.9

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|-||..+|+.+++++..++||++|..-|.....-......|.   |-.+.|+| +.||.+.++.+ ++|
T Consensus         2 ~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~---~~g~~L~d-~~~l~~~~i~~~~~i   67 (76)
T PTZ00044          2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLI---YSGKQMSD-DLKLSDYKVVPGSTI   67 (76)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE---ECCEEccC-CCcHHHcCCCCCCEE
Confidence            4789999999999999999999999999988642224456665   46888886 57899999995 444

>smart00213 UBQ Ubiquitin homologues

Probab=96.64  E-value=0.01  Score=40.97  Aligned_cols=61  Identities=16%  Similarity=0.230  Sum_probs=47.6

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      .|.||..+ ....+++..+.||++|...|.....-......|+.   -.+.|.| +.||.++|+.+
T Consensus         2 ~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~---~g~~L~d-~~tL~~~~i~~   62 (64)
T smart00213        2 ELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIY---KGKVLED-DRTLADYNIQD   62 (64)
T ss_pred             EEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE---CCEECCC-CCCHHHcCCcC
Confidence            57899998 67889999999999999999875422233456654   4788887 48999999975

Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression

>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2

Probab=96.59  E-value=0.015  Score=41.97  Aligned_cols=66  Identities=15%  Similarity=0.214  Sum_probs=50.7

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEEe
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQ  255 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avivq  255 (257)
                      +|-||..+|. ..+.+..+.||++|++-|+....-....+.|.   |..+.|.|+ .||.++|+.+ ++|..
T Consensus         2 ~i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li---~~Gk~L~d~-~tL~~~~i~~~stl~l   68 (71)
T cd01808           2 KVTVKTPKDK-EEIEIAEDASVKDFKEAVSKKFKANQEQLVLI---FAGKILKDT-DTLTQHNIKDGLTVHL   68 (71)
T ss_pred             EEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhCCCHHHEEEE---ECCeEcCCC-CcHHHcCCCCCCEEEE
Confidence            5788999996 58899999999999999987542223456664   578889874 7999999985 66643

hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=96.59  E-value=0.014  Score=41.65  Aligned_cols=65  Identities=18%  Similarity=0.298  Sum_probs=49.6

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +|.||.. |....+++..+.||++|.+-|.....-......|..   -.+.|.| +.||.++|+.+ ++|+
T Consensus         2 ~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~---~g~~l~d-~~~L~~~~i~~g~~l~   67 (71)
T cd01812           2 RVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIF---KGKERDD-AETLDMSGVKDGSKVM   67 (71)
T ss_pred             EEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEee---CCcccCc-cCcHHHcCCCCCCEEE
Confidence            5788886 777889999999999999999875422345567764   4677876 58999999986 4544

BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).

>PF12090 Spt20: Spt20 family; InterPro: IPR021950 This presumed domain is found in the Spt20 proteins from both human and yeast

Probab=96.59  E-value=0.002  Score=55.64  Aligned_cols=59  Identities=20%  Similarity=0.249  Sum_probs=48.7

Q ss_pred             ceEEEEEeccceee----cCCCCccCCChhhHHHHHHHhcCCCCCcccCCC-------CCCceEEEEe-ccc
Q 025134           69 IVHNIVFWANGFTV----NDGPLRRLDDPENASFLESIKKSECPKELEPAD-------KRSSVHVNLI-RRD  128 (257)
Q Consensus        69 ~~~~l~lw~nGF~V----ddGp~R~y~dP~n~~FL~~I~~G~~P~EL~~~~-------~~~~V~v~l~-~r~  128 (257)
                      ....|+||-++|.+    .++-..+|++|. +.||+.|.+|.+|..|.+..       .+|-|-|+|. +|.
T Consensus        14 pSl~vhL~p~~f~f~~~~~~~~~~pY~~~~-k~~L~~I~~~~iP~~Lle~l~~~~v~FYdGClIveV~D~R~   84 (182)
T PF12090_consen   14 PSLIVHLYPNHFRFSLNDQQDGSFPYNSPM-KEFLEYIDAGEIPHDLLELLDDANVPFYDGCLIVEVRDHRS   84 (182)
T ss_pred             CeEEEEECCCCeeEeecCCCCceecCCchH-HHHHHHHHcCCCCHHHHHHHHhCCCeeEcCEEEEEEecccc
Confidence            46889999999999    577789999999 99999999999999887653       3555677776 354

The Spt20 protein is part of the SAGA complex which is a large cmplex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=96.53  E-value=0.0053  Score=49.10  Aligned_cols=62  Identities=16%  Similarity=0.302  Sum_probs=48.8

Q ss_pred             CceEEEEEcCCCCEE-EEEeCCCCCHHHHHHHHHhhCCCC-------CcCeEEEecCCCCcccCCccCcHhhhC
Q 025134          182 PSTSVQIRLADGTRL-IAHFNLHHTISDIHSFIDASRPGT-------ARNYQLQMMGFPPKVLADRTQTIEQAG  247 (257)
Q Consensus       182 p~t~iqIRl~dG~rl-v~~fn~s~TI~dl~~fi~~~~p~~-------~~~f~L~t~~fP~k~l~d~s~TL~eag  247 (257)
                      ...-|+|||+||+-+ -.+|..++||++|.+-|....+..       ...-.|+   |--|.|.| +.||.+++
T Consensus         3 ~~~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLI---ysGKiLeD-~~TL~d~~   72 (113)
T cd01814           3 EQIEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLI---SAGKILEN-SKTVGECR   72 (113)
T ss_pred             ccEEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEE---eCCeecCC-CCcHHHhC
Confidence            346799999999876 789999999999999998776531       1223444   47788887 59999999

NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.

>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A

Probab=96.47  E-value=0.016  Score=46.22  Aligned_cols=63  Identities=25%  Similarity=0.379  Sum_probs=46.2

Q ss_pred             ceEEEEEcCCCC-EEEEEeCCCCCHHHHHHHHHhhCCCC-------CcCeEEEecCCCCcccCCccCcHhhhCCC
Q 025134          183 STSVQIRLADGT-RLIAHFNLHHTISDIHSFIDASRPGT-------ARNYQLQMMGFPPKVLADRTQTIEQAGLA  249 (257)
Q Consensus       183 ~t~iqIRl~dG~-rlv~~fn~s~TI~dl~~fi~~~~p~~-------~~~f~L~t~~fP~k~l~d~s~TL~eagL~  249 (257)
                      ...|++||.||+ +...+|..+.||++|.++|...-|..       .....|+.   =-|.|+| +.||.++++.
T Consensus         2 ~i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~---~GriL~d-~~tL~~~~~~   72 (111)
T PF13881_consen    2 KIELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIY---AGRILED-NKTLSDCRLP   72 (111)
T ss_dssp             SEEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEE---TTEEE-S-SSBTGGGT--
T ss_pred             eEEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEe---CCeecCC-cCcHHHhCCC
Confidence            357999999999 88999999999999999999866553       12355554   4567775 6899999877

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=96.38  E-value=0.025  Score=44.46  Aligned_cols=69  Identities=12%  Similarity=0.102  Sum_probs=55.2

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .++..|-||..+|+.+.+.+..++||++|++.|.....-......|+.   =.+.|+|+ .||++.+|.+ ++|
T Consensus        25 ~~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~---~Gk~L~D~-~tL~dy~I~~~stL   94 (103)
T cd01802          25 YDTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIW---NNMELEDE-YCLNDYNISEGCTL   94 (103)
T ss_pred             CCCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEE---CCEECCCC-CcHHHcCCCCCCEE
Confidence            346889999999999999999999999999999875322245577764   57888885 8999999995 444

AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=95.97  E-value=0.052  Score=37.87  Aligned_cols=64  Identities=17%  Similarity=0.310  Sum_probs=47.8

Q ss_pred             EEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEEe
Q 025134          188 IRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQ  255 (257)
Q Consensus       188 IRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avivq  255 (257)
                      ||..+|..+...+..+.||++|+..|.....-......|+   |-.+.|.| +.||.++++.+ +.|+.
T Consensus         2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~---~~g~~l~d-~~~l~~~~v~~~~~i~v   66 (69)
T cd01769           2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLI---YAGKILKD-DKTLSDYGIQDGSTLHL   66 (69)
T ss_pred             eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEE---ECCcCCCC-cCCHHHCCCCCCCEEEE
Confidence            5777899999999999999999999988643233445554   34577755 68999999996 54543

UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.

>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF

Probab=95.94  E-value=0.052  Score=40.35  Aligned_cols=66  Identities=14%  Similarity=0.147  Sum_probs=50.3

Q ss_pred             EEEEEcCCCCE-EEE-EeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTR-LIA-HFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~r-lv~-~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .|-||..+|+. ... ....++||++|++.|.....-......|+.   =.|.|.| +.||.+.|+.+ ++|.
T Consensus         2 ~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~---~Gk~L~D-~~tL~~y~i~~~~~i~   70 (78)
T cd01797           2 WIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFY---RGKQMED-GHTLFDYNVGLNDIIQ   70 (78)
T ss_pred             EEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEe---CCEECCC-CCCHHHcCCCCCCEEE
Confidence            57899999987 356 478899999999999875322245567764   5888987 58999999995 5554

NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=95.74  E-value=0.11  Score=39.17  Aligned_cols=66  Identities=11%  Similarity=0.201  Sum_probs=53.2

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ....+|.|+..+|+.+.+++..++||..|.+.+.....-....+.|+   |=-+.|.+ +.|++++|+.+
T Consensus         9 ~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~---f~G~~L~~-~~T~~~l~m~d   74 (87)
T cd01763           9 SEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFL---FDGQRIRD-NQTPDDLGMED   74 (87)
T ss_pred             CCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEE---ECCeECCC-CCCHHHcCCCC
Confidence            35677888999999999999999999999999987643334556665   45788887 47999999996

Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=95.33  E-value=0.078  Score=50.87  Aligned_cols=66  Identities=14%  Similarity=0.316  Sum_probs=52.6

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCC--CC-CcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRP--GT-ARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p--~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +|.||..+|+.+.+.+..++||.+|++.|.....  .. .....|+   |-.|.|.|+ .||+++||.+ .+||
T Consensus         2 kItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLI---y~GkiL~Dd-~tL~dy~I~e~~~Iv   71 (378)
T TIGR00601         2 TLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLI---YSGKILSDD-KTVREYKIKEKDFVV   71 (378)
T ss_pred             EEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEE---ECCEECCCC-CcHHHcCCCCCCEEE
Confidence            6889999999999999999999999999987542  12 3445665   468899874 7999999984 5554

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=94.91  E-value=0.17  Score=36.72  Aligned_cols=63  Identities=17%  Similarity=0.211  Sum_probs=46.8

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|-||.  ++.....+..++||++|..-|.....-......|+   |=.+.|+|+ .||+++|+.+ ++|
T Consensus         2 qi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li---~~Gk~L~D~-~tL~~~~i~~~~tl   65 (74)
T cd01793           2 QLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLL---LAGVPLEDD-ATLGQCGVEELCTL   65 (74)
T ss_pred             EEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEE---ECCeECCCC-CCHHHcCCCCCCEE
Confidence            456676  46678899999999999999977532123455665   457889885 9999999986 554

Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.

>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins

Probab=94.86  E-value=0.15  Score=36.47  Aligned_cols=62  Identities=19%  Similarity=0.263  Sum_probs=48.3

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCC-cCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTA-RNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~-~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      +|.+|..+|+.+..+...++|++.|.+.++....-.. ..+.|.   |=.+.|+. +.|++++||-+
T Consensus         2 ~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~---fdG~~L~~-~~T~~~~~ied   64 (72)
T PF11976_consen    2 TIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLI---FDGKRLDP-NDTPEDLGIED   64 (72)
T ss_dssp             EEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEE---ETTEEE-T-TSCHHHHT-ST
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEE---ECCEEcCC-CCCHHHCCCCC
Confidence            6889999999999999999999999998877543333 567765   46777765 47999999996

SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....

>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein

Probab=94.54  E-value=0.14  Score=38.44  Aligned_cols=60  Identities=13%  Similarity=0.264  Sum_probs=46.2

Q ss_pred             eEEEEEcCCCCE--EEEEeCCCCCHHHHHHHHHhhCCC-C-CcCeEEEecCCCCcccCCccCcHhhhC
Q 025134          184 TSVQIRLADGTR--LIAHFNLHHTISDIHSFIDASRPG-T-ARNYQLQMMGFPPKVLADRTQTIEQAG  247 (257)
Q Consensus       184 t~iqIRl~dG~r--lv~~fn~s~TI~dl~~fi~~~~p~-~-~~~f~L~t~~fP~k~l~d~s~TL~eag  247 (257)
                      .+|.||.++|+.  +...+..+.||++|.+-|....+. . ...-.|+   |-.|.|.| +.||++.+
T Consensus         2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLI---y~GKiLkD-~~tL~~~~   65 (79)
T cd01790           2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLI---YSGKLLPD-HLKLRDVL   65 (79)
T ss_pred             eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEE---EcCeeccc-hhhHHHHh
Confidence            468999999998  455558999999999999886543 2 2345565   47889987 48999985

Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=94.46  E-value=0.27  Score=36.10  Aligned_cols=68  Identities=16%  Similarity=0.167  Sum_probs=48.3

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +|.|++ .|+...+.++.++||++|.+-|.....-....-.|+...|=.+.+.| +.||.++++.+ +.|+
T Consensus         2 ~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D-~~~L~~~~i~~g~~i~   70 (74)
T cd01813           2 PVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAED-DVKISALKLKPNTKIM   70 (74)
T ss_pred             EEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCC-CcCHHHcCCCCCCEEE
Confidence            466766 56678899999999999999998864323455667630123455666 69999999985 4444

The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.

>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120

Probab=94.36  E-value=0.18  Score=36.94  Aligned_cols=59  Identities=20%  Similarity=0.249  Sum_probs=44.8

Q ss_pred             CCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          192 DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       192 dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +|+.+.+.+..++||++|.+-|.....-......|+.   -.+.|+| +.||.+.++.+ ++|.
T Consensus         6 ~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~---~G~~L~d-~~tL~~~~i~~g~~l~   65 (76)
T cd01800           6 NGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQY---EGIFIKD-SNSLAYYNLANGTIIH   65 (76)
T ss_pred             CCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE---CCEEcCC-CCcHHHcCCCCCCEEE
Confidence            5777889999999999999999875422245567765   3577777 48999999985 5543

SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=93.70  E-value=0.19  Score=39.55  Aligned_cols=58  Identities=19%  Similarity=0.236  Sum_probs=44.1

Q ss_pred             EEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEEee
Q 025134          196 LIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQK  256 (257)
Q Consensus       196 lv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avivqk  256 (257)
                      +.+..+.++||++|...|.+.-......-.|+. .  -+.|.|++.||.+.||.. |+|..+
T Consensus        17 ~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~-d--G~~L~DDsrTLssyGv~sgSvl~Ll   75 (107)
T cd01795          17 KALLVSANQTLKELKIQIMHAFSVAPFDQNLSI-D--GKILSDDCATLGTLGVIPESVILLK   75 (107)
T ss_pred             ceEEeCccccHHHHHHHHHHHhcCCcccceeee-c--CceeccCCccHHhcCCCCCCEEEEE
Confidence            467799999999999999886432222236776 4  679999999999999996 666543

The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,

>cd00196 UBQ Ubiquitin-like proteins

Probab=92.82  E-value=0.24  Score=31.89  Aligned_cols=60  Identities=18%  Similarity=0.222  Sum_probs=42.9

Q ss_pred             EEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          187 QIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       187 qIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      +|++.+|+.....++.++||++|++.|..........|.|.. ..+..  .+ ..++.+.++.+
T Consensus         1 ~v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~-~~~~~--~~-~~~~~~~~~~~   60 (69)
T cd00196           1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLV-NGKIL--PD-SLTLEDYGLQD   60 (69)
T ss_pred             CeEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEE-CCeEC--CC-CCcHHHcCCCC
Confidence            367779999999999999999999999886543356788887 54432  22 23445566664

Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=92.47  E-value=0.5  Score=34.88  Aligned_cols=57  Identities=11%  Similarity=0.052  Sum_probs=42.6

Q ss_pred             cCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCC-C
Q 025134          190 LADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLA-N  250 (257)
Q Consensus       190 l~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~-n  250 (257)
                      +..|..+.+.+..+.||++|...|.....-......| .   -.+.+.|++.||.+.|+. |
T Consensus         9 ~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~---~G~~L~dD~~tL~~ygi~~~   66 (75)
T cd01799           9 QSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-V---IGQRLARDQETLYSHGIRTN   66 (75)
T ss_pred             ccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-E---cCCeeCCCcCCHHHcCCCCC
Confidence            4456778899999999999999998753222344556 3   456687778999999999 5

HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.

>PLN02560 enoyl-CoA reductase

Probab=90.71  E-value=1.4  Score=41.10  Aligned_cols=71  Identities=18%  Similarity=0.272  Sum_probs=46.9

Q ss_pred             EEEEEcCCCCEE---EEEeCCCCCHHHHHHHHHhhCCC-CCcCeEEEec---CCCCc-ccCCccCcHhhhCCCC-eeEEe
Q 025134          185 SVQIRLADGTRL---IAHFNLHHTISDIHSFIDASRPG-TARNYQLQMM---GFPPK-VLADRTQTIEQAGLAN-SVVIQ  255 (257)
Q Consensus       185 ~iqIRl~dG~rl---v~~fn~s~TI~dl~~fi~~~~p~-~~~~f~L~t~---~fP~k-~l~d~s~TL~eagL~n-avivq  255 (257)
                      +|.|+..+|+.+   .+.+..+.||+||..-|.+.... ....-.|...   +=|.. .|. ++.||++.|+.+ ++|..
T Consensus         2 ~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~-d~ktL~d~gv~~gstLy~   80 (308)
T PLN02560          2 KVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLD-DSKSLKDYGLGDGGTVVF   80 (308)
T ss_pred             EEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccC-CCCCHHhcCCCCCceEEE
Confidence            478888888876   57889999999999999886432 2223344320   11222 344 467999999985 66654


Q ss_pred             e
Q 025134          256 K  256 (257)
Q Consensus       256 k  256 (257)
                      |
T Consensus        81 k   81 (308)
T PLN02560         81 K   81 (308)
T ss_pred             E
Confidence            4

>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A

Probab=90.60  E-value=1.2  Score=33.42  Aligned_cols=71  Identities=15%  Similarity=0.207  Sum_probs=48.0

Q ss_pred             eEEEEEcCCCC--EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEec----CCCCcccCCccCcHhhhCCCCeeEE
Q 025134          184 TSVQIRLADGT--RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMM----GFPPKVLADRTQTIEQAGLANSVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~--rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~----~fP~k~l~d~s~TL~eagL~naviv  254 (257)
                      .+|.|.-..-+  ....||..+.||++|..-|.....-......|...    .-+...++|+++||..-|+.+...|
T Consensus         2 v~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i   78 (87)
T PF14560_consen    2 VKLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRI   78 (87)
T ss_dssp             EEEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEE
T ss_pred             EEEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEE
Confidence            45677666653  78999999999999999998865333444555441    1122345677899999999974443

>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A

Probab=89.15  E-value=1.7  Score=33.39  Aligned_cols=58  Identities=21%  Similarity=0.134  Sum_probs=34.0

Q ss_pred             EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCC--cccCCccCcHhhhCCCCeeE
Q 025134          195 RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP--KVLADRTQTIEQAGLANSVV  253 (257)
Q Consensus       195 rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~--k~l~d~s~TL~eagL~navi  253 (257)
                      -+...|...|||+.|...+...-.- ...-.|-.+..+.  -.|.+...||+||||..+.+
T Consensus        15 ~~t~~FSk~DTI~~v~~~~rklf~i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~   74 (88)
T PF14836_consen   15 VLTKQFSKTDTIGFVEKEMRKLFNI-QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQV   74 (88)
T ss_dssp             EEEEEE-TTSBHHHHHHHHHHHCT--TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEE
T ss_pred             HhHhhccccChHHHHHHHHHHHhCC-CccceehhccCCcchhhhCCCCccHHHccCcCCCE
Confidence            4688999999999999998874322 2233333311222  23457789999999997443

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=87.96  E-value=3.6  Score=30.03  Aligned_cols=54  Identities=22%  Similarity=0.319  Sum_probs=38.2

Q ss_pred             CCCCCHHHHHHHHHhhCCCC-CcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEEee
Q 025134          201 NLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQK  256 (257)
Q Consensus       201 n~s~TI~dl~~fi~~~~p~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avivqk  256 (257)
                      ..+.||+||+..|....... .....|.. .+..+.|.|+ .||.+.|+.+ ++|..|
T Consensus        20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~-~~~g~~L~d~-~tL~~~gv~~g~~lyvK   75 (77)
T cd01801          20 SGDATIADLKKLIAKSSPQLTVNRQSLRL-EPKGKSLKDD-DTLVDLGVGAGATLYVR   75 (77)
T ss_pred             CCCccHHHHHHHHHHHcCCCCcceeEEEe-CCCCcccCCc-ccHhhcCCCCCCEEEEe
Confidence            46789999999998764332 34455655 6777888764 6899999986 555543

Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.

>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]

Probab=86.83  E-value=1.9  Score=40.59  Aligned_cols=69  Identities=10%  Similarity=0.230  Sum_probs=53.3

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCC-CCCcCeEEEecCCCCcccCCccCcHhhhCCC-CeeEEee
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRP-GTARNYQLQMMGFPPKVLADRTQTIEQAGLA-NSVVIQK  256 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p-~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~-navivqk  256 (257)
                      +|-||.-.|+.....++.+|||.+|..=|..... ++...+....  |-.|.|.| +.||.|.++. +..||.+
T Consensus         2 ~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLI--y~GkiL~D-~~tv~Eykv~E~~fiVvM   72 (340)
T KOG0011|consen    2 KLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLI--YSGKILKD-ETTVGEYKVKEKKFIVVM   72 (340)
T ss_pred             eeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheee--ecceeccC-CcchhhhccccCceEEEE
Confidence            5789999999999999999999999999988542 2333344433  57888888 5999999999 4555543

>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly

Probab=86.74  E-value=2.4  Score=30.61  Aligned_cols=58  Identities=16%  Similarity=0.111  Sum_probs=37.3

Q ss_pred             cCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCe
Q 025134          190 LADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANS  251 (257)
Q Consensus       190 l~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~na  251 (257)
                      .++++|...+...++|+.+|.+-+...-.-....|.|..   =.|.| |.+.++.-+||.|.
T Consensus         3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h---~~k~l-dlslp~R~snL~n~   60 (65)
T PF11470_consen    3 CYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKH---NNKPL-DLSLPFRLSNLPNN   60 (65)
T ss_dssp             -TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEE---TTEEE-SSS-BHHHH---SS
T ss_pred             ccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEE---CCEEe-ccccceeecCCCCC
Confidence            468999999999999999999998776433456899987   45666 66899999999973

TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.

>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []

Probab=84.30  E-value=3.1  Score=30.64  Aligned_cols=68  Identities=13%  Similarity=0.130  Sum_probs=44.1

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCC---C-Cc--CeEEEecCCCCcccCCccCcHhhhCCCCeeE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG---T-AR--NYQLQMMGFPPKVLADRTQTIEQAGLANSVV  253 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~---~-~~--~f~L~t~~fP~k~l~d~s~TL~eagL~navi  253 (257)
                      .++|-|...+|+++-+.+..+.||.+|..-|......   . ..  .|.|.+  -..+.|++ +.||.++|+.++-+
T Consensus         2 ~~rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~--~~g~~L~~-~~tL~~~gV~dGd~   75 (79)
T PF08817_consen    2 LCRVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLAR--AGGRPLDP-DQTLADAGVRDGDV   75 (79)
T ss_dssp             EEEEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG---GGTEEEET-TSBCGGGT--TT-E
T ss_pred             EEEEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEe--cCCcccCC-cCcHhHcCCCCCCE
Confidence            4788899988889999999999999999888774322   1 11  466663  35555655 69999999997444

Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.

>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain

Probab=83.15  E-value=1.4  Score=31.96  Aligned_cols=62  Identities=16%  Similarity=0.097  Sum_probs=42.6

Q ss_pred             EEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC-CcCeEEEe-cCC-CCcccCCccCcHhhhCCC
Q 025134          188 IRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQM-MGF-PPKVLADRTQTIEQAGLA  249 (257)
Q Consensus       188 IRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~-~~~f~L~t-~~f-P~k~l~d~s~TL~eagL~  249 (257)
                      |+|+||+.+...++.+.|+.||.+.|.....-. ..-|-|.. ..- ....+-|.+.+|.+..-.
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~   65 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKK   65 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBT
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHcCC
Confidence            789999999999999999999999998854222 35577765 111 112233667777766544

The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....

>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B

Probab=82.82  E-value=7.6  Score=29.00  Aligned_cols=65  Identities=15%  Similarity=0.214  Sum_probs=44.8

Q ss_pred             eEEEEEcCC-CCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCc-----ccCCccCcHhhhCCCC
Q 025134          184 TSVQIRLAD-GTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPK-----VLADRTQTIEQAGLAN  250 (257)
Q Consensus       184 t~iqIRl~d-G~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k-----~l~d~s~TL~eagL~n  250 (257)
                      .+|.|.... ......||..+.||++|.+-+.....-....-.|..  |..+     .|+|+..+|..-|+.+
T Consensus         2 v~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l--~~~~~~~~~~l~~d~~~L~~y~~~d   72 (84)
T cd01789           2 VTVNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQL--FDGDDKLVSKLDDDDALLGSYPVDD   72 (84)
T ss_pred             EEEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEE--EcCCCCeEeecCCCccEeeeccCCC
Confidence            346666643 334688999999999999999775422234445532  3333     5778889999999996

Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=82.18  E-value=2.8  Score=31.25  Aligned_cols=48  Identities=23%  Similarity=0.283  Sum_probs=35.7

Q ss_pred             CCCCHHHHHHHHHhhCCC--C-CcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          202 LHHTISDIHSFIDASRPG--T-ARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       202 ~s~TI~dl~~fi~~~~p~--~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .++||++|.+-|....++  . ...+.|+   |=.|.|.| +.||++.|+.+ ++|
T Consensus        19 ~~~TV~~LK~kI~~~~~egi~~~dqQrLI---y~GKiL~D-~~TL~dygI~~gstl   70 (75)
T cd01815          19 GGYQVSTLKQLIAAQLPDSLPDPELIDLI---HCGRKLKD-DQTLDFYGIQSGSTI   70 (75)
T ss_pred             ccCcHHHHHHHHHHhhccCCCChHHeEEE---eCCcCCCC-CCcHHHcCCCCCCEE
Confidence            579999999999886422  1 2346665   57888877 48999999995 544

BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.

>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]

Probab=81.89  E-value=1.3  Score=32.24  Aligned_cols=25  Identities=28%  Similarity=0.470  Sum_probs=22.8

Q ss_pred             CCEEEEEeCCCCCHHHHHHHHHhhC
Q 025134          193 GTRLIAHFNLHHTISDIHSFIDASR  217 (257)
Q Consensus       193 G~rlv~~fn~s~TI~dl~~fi~~~~  217 (257)
                      |+.+..+.|.++||+|+...|++..
T Consensus        11 GKKVRvKCn~dDtiGD~KKliaaQt   35 (73)
T KOG3493|consen   11 GKKVRVKCNTDDTIGDLKKLIAAQT   35 (73)
T ss_pred             CceEEEEeCCcccccCHHHHHHHhh
Confidence            8889999999999999999998753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	257
1s3s_G	127	Crystal Structure Of Aaa Atpase P97VCP ND1 IN COMPL		3e-18
1i42_A	89	Nmr Structure Of The Ubx Domain From P47 Length = 8		5e-16
1ss6_A	102	Solution Structure Of Sep Domain From Human P47 Len		6e-09
1vaz_A	88	Solution Structures Of The P47 Sep Domain Length =		4e-06

>pdb|1S3S|G Chain G, Crystal Structure Of Aaa Atpase P97VCP ND1 IN COMPLEX WITH P47 C Length = 127

Iteration: 1
 Score = 88.6 bits (218), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 46/125 (36%), Positives = 72/125 (57%)
Query: 133 EPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLVVDENLPSTSVQIRLAD 192
           +P+     F G G+ LGS++      +  +      + +S  ++++E  P+T++QIRLAD
Sbjct: 2   KPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENEAKASSSILINEAEPTTNIQIRLAD 61
Query: 193 GTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSV 252
           G RL+  FN  H ISDI  FI  +RP  A    + M  FP K LAD  QT+++A L N+V
Sbjct: 62  GGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAV 121
Query: 253 VIQKF 257
           ++Q+ 
Sbjct: 122 IVQRL 126

>pdb|1I42|A Chain A, Nmr Structure Of The Ubx Domain From P47 Length = 89

Iteration: 1
 Score = 81.3 bits (199), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 39/87 (44%), Positives = 57/87 (65%)
Query: 171 SSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMG 230
           +S  ++++E  P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M  
Sbjct: 2   ASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTT 61
Query: 231 FPPKVLADRTQTIEQAGLANSVVIQKF 257
           FP K LAD  QT+++A L N+V++Q+ 
Sbjct: 62  FPNKELADENQTLKEANLLNAVIVQRL 88

>pdb|1SS6|A Chain A, Solution Structure Of Sep Domain From Human P47 Length = 102

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 31/85 (36%), Positives = 49/85 (57%), Gaps = 2/85 (2%)
Query: 70  VHNIV-FWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNL-IRR 127
           VH ++  W +GF++++G LR   DP NA FLESI++ E P EL        V++++   R
Sbjct: 12  VHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRLAHGGQVNLDMEDHR 71
Query: 128 DVKCPEPEKHHVPFQGVGRTLGSSS 152
           D    +P+     F G G+ LGS++
Sbjct: 72  DEDFVKPKGAFKAFTGEGQKLGSTA 96

>pdb|1VAZ|A Chain A, Solution Structures Of The P47 Sep Domain Length = 88

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 70  VHNIV-FWANGFTVNDGPLRRLDDPENASFLESIKKSECPKEL 111
           VH ++  W  GF++++G LR   DP NA FLESI++ E P EL
Sbjct: 22  VHVVLKLWKTGFSLDNGDLRSYQDPSNAQFLESIRRGEVPAEL 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	257
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	2e-39
1ss6_A	102	P47, NSFL1 cofactor P47, P47 protein, P97; , SEP,	5e-34
1vaz_A	88	NSFL1 cofactor P47; beta-BETA-beta-alpha-alpha-bet	1e-24
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	3e-17
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	2e-16
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	2e-15
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	3e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05

>1s3s_G P47 protein; AAA ATPase, protein-protein complex, UBX domain, protein binding; HET: ADP; 2.90A {Rattus norvegicus} SCOP: d.15.1.2 PDB: 1i42_A 1jru_A Length = 127

 Score =  132 bits (333), Expect = 2e-39
 Identities = 46/125 (36%), Positives = 72/125 (57%)

Query: 133 EPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLVVDENLPSTSVQIRLAD 192
           +P+     F G G+ LGS++      +  +      + +S  ++++E  P+T++QIRLAD
Sbjct: 2   KPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENEAKASSSILINEAEPTTNIQIRLAD 61

Query: 193 GTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSV 252
           G RL+  FN  H ISDI  FI  +RP  A    + M  FP K LAD  QT+++A L N+V
Sbjct: 62  GGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAV 121

Query: 253 VIQKF 257
           ++Q+ 
Sbjct: 122 IVQRL 126

>1ss6_A P47, NSFL1 cofactor P47, P47 protein, P97; , SEP, signaling protein; NMR {Homo sapiens} SCOP: d.245.1.1 Length = 102

 Score =  117 bits (295), Expect = 5e-34
 Identities = 33/104 (31%), Positives = 52/104 (50%), Gaps = 6/104 (5%)

Query: 61  SAPQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSV 120
                 + +   +  W +GF++++G LR   DP NA FLESI++ E P EL        V
Sbjct: 4   KRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRLAHGGQV 63

Query: 121 HVNLI-RRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDST 163
           ++++   RD    +P+     F G G+ LGS++     P V ST
Sbjct: 64  NLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTA-----PQVLST 102

>1vaz_A NSFL1 cofactor P47; beta-BETA-beta-alpha-alpha-beta, novel fold, lipid binding protein; NMR {Rattus norvegicus} SCOP: d.245.1.1 Length = 88

 Score = 93.0 bits (231), Expect = 1e-24
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 60  PSAPQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSS 119
                  + +   +  W  GF++++G LR   DP NA FLESI++ E P EL        
Sbjct: 13  ERRRHSGQDVHVVLKLWKTGFSLDNGDLRSYQDPSNAQFLESIRRGEVPAELRRLAHGGQ 72

Query: 120 VHVNLI-RRDVKCPEP 134
           V++++   RD    +P
Sbjct: 73  VNLDMEDHRDEDFVKP 88

>1wj4_A KIAA0794 protein; UBX domain, beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.2 Length = 124

 Score = 74.6 bits (183), Expect = 3e-17
 Identities = 25/116 (21%), Positives = 48/116 (41%), Gaps = 6/116 (5%)

Query: 143 GVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLV--VDENLPSTSVQIRLADGTRLIAHF 200
           G   + G+++     P VDS  +      ++G+V  +D N P   + +R  DG R     
Sbjct: 1   GSSGSSGTATNHQGLPAVDSEILEMPPEKADGVVEGIDVNGPKAQLMLRYPDGKREQITL 60

Query: 201 NLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVL--ADRTQTIEQAGLANSVVI 254
                +  +   +  S+      ++L +  FP + L   D   T+++AGL     +
Sbjct: 61  PEQAKLLALVKHVQ-SKGYPNERFEL-LTNFPRRKLSHLDYDITLQEAGLCPQETV 114

>2dzk_A UBX domain-containing protein 2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} PDB: 2kxj_A Length = 109

 Score = 71.8 bits (176), Expect = 2e-16
 Identities = 18/86 (20%), Positives = 29/86 (33%), Gaps = 3/86 (3%)

Query: 171 SSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMG 230
            S G    +      +Q RL DG+     F     + +   F   +   T  N+ L    
Sbjct: 1   GSSGSSGRDRSTIARIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSL-ATM 59

Query: 231 FPPKVL--ADRTQTIEQAGLANSVVI 254
           FP +     D  + +    LA S  +
Sbjct: 60  FPRREFTREDYKRRLLDLELAPSASV 85

>3qx1_A FAS-associated factor 1; UBX, protein binding, P97 binding; 1.60A {Homo sapiens} PDB: 3qwz_B* 3qc8_B 3qca_A 3qq8_B 3r3m_B 1h8c_A Length = 84

 Score = 68.4 bits (168), Expect = 2e-15
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 179 ENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVL-- 236
              P + ++IR   G  L   F   + +  +  F+ +        Y+L +  FP + +  
Sbjct: 3   HMEPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPW-DEYKL-LSTFPRRDVTQ 60

Query: 237 ADRTQTIEQAGLANSVVI 254
            D  +++ +  L     +
Sbjct: 61  LDPNKSLLEVKLFPQETL 78

>2cr5_A Reproduction 8; UBX domain, D0H8S2298E protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.2 Length = 109

 Score = 55.2 bits (133), Expect = 3e-10
 Identities = 13/74 (17%), Positives = 26/74 (35%), Gaps = 3/74 (4%)

Query: 182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVL-ADRT 240
              +V +R  +G  L   F        +  ++          Y+L    FP + L  +  
Sbjct: 22  EVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMM-KVGYHKSLYRL-STSFPRRALEVEGG 79

Query: 241 QTIEQAGLANSVVI 254
            ++E  G+    V+
Sbjct: 80  SSLEDIGITVDTVL 93

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

 Score = 43.7 bits (102), Expect = 4e-05
 Identities = 35/271 (12%), Positives = 76/271 (28%), Gaps = 85/271 (31%)

Query: 54  LSGETVPSAPQQPEPIVHNIVFWANGFTVNDGPLRRLDDPEN-----ASFLESIKKSECP 108
           ++ +   S   Q +      +FW N        L+  + PE         L  I  +   
Sbjct: 166 VALDVCLSYKVQCKM--DFKIFWLN--------LKNCNSPETVLEMLQKLLYQIDPNWTS 215

Query: 109 K------------ELEPADKR---SSVHVN--LIRRDVKCPEPEKHHV-PFQGVGRTL-- 148
           +             ++   +R   S  + N  L+  +V+  +        F    + L  
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK----AWNAFNLSCKILLT 271

Query: 149 --------GSSSTAASEPTVDSTPVNTASSSSEGL---VVD---ENLPSTSVQI------ 188
                     S+   +  ++D   +       + L    +D   ++LP   +        
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331

Query: 189 ----RLADGTRLIAHF------NLHHTISDIHSFIDASRPGTARNYQLQMMGF------P 232
                + DG     ++       L   I    S ++   P   R    ++  F      P
Sbjct: 332 IIAESIRDGLATWDNWKHVNCDKLTTIIE---SSLNVLEPAEYRKMFDRLSVFPPSAHIP 388

Query: 233 PKVLA-----DRTQTIEQ--AGLANSVVIQK 256
             +L+          +      L    +++K
Sbjct: 389 TILLSLIWFDVIKSDVMVVVNKLHKYSLVEK 419

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	257
1ss6_A	102	P47, NSFL1 cofactor P47, P47 protein, P97; , SEP,	100.0
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	99.98
1vaz_A	88	NSFL1 cofactor P47; beta-BETA-beta-alpha-alpha-bet	99.96
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	99.82
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	99.8
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	99.8
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	99.75
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	98.86
2pjh_A	80	Protein NPL4, nuclear protein localization protein	97.67
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	97.45
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	97.44
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	97.43
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	97.41
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	97.38
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	97.34
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	97.24
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	97.23
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	97.23
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	97.22
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	97.2
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	97.1
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	97.09
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	97.07
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	97.05
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	97.0
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	97.0
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	96.98
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	96.96
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	96.95
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	96.95
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	96.93
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	96.89
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	96.88
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	96.87
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	96.87
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	96.86
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	96.84
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	96.84
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	96.82
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	96.81
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	96.81
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	96.81
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	96.75
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	96.68
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	96.67
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	96.67
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	96.65
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	96.57
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	96.56
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	96.55
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	96.54
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	96.5
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	96.45
1we6_A	111	Splicing factor, putative; structural genomics, ub	96.42
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	96.41
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	96.41
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	96.28
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	96.25
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	96.24
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	96.21
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	96.17
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	96.17
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	96.1
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	96.06
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	96.06
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	96.01
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	95.97
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	95.95
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	95.93
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	95.91
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	95.91
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	95.8
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	95.79
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	95.78
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	95.74
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	94.71
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	95.59
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	95.58
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	95.5
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	95.43
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	95.39
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	95.35
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	94.58
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	94.48
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	94.03
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	93.86
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	93.61
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	93.53
2kj6_A	97	Tubulin folding cofactor B; methods development, N	93.37
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	93.23
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	93.08
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	92.97
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	92.8
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	92.55
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	92.47
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	92.43
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	92.33
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	92.3
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	91.52
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	90.86
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	89.92
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	89.04
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	88.79
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	87.45
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	85.25
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	84.91
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	82.38
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	81.18

>1ss6_A P47, NSFL1 cofactor P47, P47 protein, P97; , SEP, signaling protein; NMR {Homo sapiens} SCOP: d.245.1.1

Probab=100.00  E-value=1.9e-37  Score=242.04  Aligned_cols=92  Identities=32%  Similarity=0.612  Sum_probs=86.4

Q ss_pred             CCCCceEEEEEeccceeecCCCCccCCChhhHHHHHHHhcCCCCCcccCCCCCCceEEEEec-ccccCCCCCCCCccccc
Q 025134           65 QPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIR-RDVKCPEPEKHHVPFQG  143 (257)
Q Consensus        65 ~~~~~~~~l~lw~nGF~VddGp~R~y~dP~n~~FL~~I~~G~~P~EL~~~~~~~~V~v~l~~-r~e~y~~p~~~~~~F~G  143 (257)
                      .++.+.|+||||+|||+|||||||+|+||+|++||++|++|+||.||+.++++++|+|+|++ ++|+|++|++++++|+|
T Consensus         8 ~~~~~~~~ltlw~nGFtVdDGplR~ydDP~N~~FL~~I~~G~~P~EL~~~~~~~~V~v~v~d~~~e~y~~p~~~~~~F~G   87 (102)
T 1ss6_A            8 SSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTG   87 (102)
T ss_dssp             CCSCEEEEEEEESSEEEETTSCEEETTCTTTHHHHHHHHHTCCCHHHHTTSCSSCEEEEEEEEETTCCCSSSSSSTTSCS
T ss_pred             CCCCceEEEEEecCceEecCCCcccCCCHhHHHHHHHHHhCCCCHHHhcccCCCeEEEEeeeccCccccCCCCcccCCcc
Confidence            34678999999999999999999999999999999999999999999999999999999995 59999999888999999


Q ss_pred             cccccccCCCCCC
Q 025134          144 VGRTLGSSSTAAS  156 (257)
Q Consensus       144 ~G~~LGs~~p~~~  156 (257)
                      +||+||+++|...
T Consensus        88 ~G~~LGs~~p~~~  100 (102)
T 1ss6_A           88 EGQKLGSTAPQVL  100 (102)
T ss_dssp             SSSSGGGCCSSSS
T ss_pred             cCeECCCCCCCCc
Confidence            9999999988764

>1s3s_G P47 protein; AAA ATPase, protein-protein complex, UBX domain, protein binding; HET: ADP; 2.90A {Rattus norvegicus} SCOP: d.15.1.2 PDB: 1i42_A 1jru_A

Probab=99.98  E-value=1.3e-33  Score=228.83  Aligned_cols=124  Identities=37%  Similarity=0.637  Sum_probs=95.6

Q ss_pred             CCCCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHH
Q 025134          133 EPEKHHVPFQGVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSF  212 (257)
Q Consensus       133 ~p~~~~~~F~G~G~~LGs~~p~~~~~~~~~~~~~~~~~~~~~~~vd~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~f  212 (257)
                      +||+++++|+|+||+|||++|...+.++++..+.+++.+...+.+|+++++|+|||||+||+|++.+|+.+|||+|||+|
T Consensus         2 ~p~~~~~~F~G~G~~Lgs~~p~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~t~IqIRlpdG~rl~~rF~~~~tl~~v~~f   81 (127)
T 1s3s_G            2 KPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENEAKASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLF   81 (127)
T ss_dssp             --------CCSCCCCCCSSCCCCCCCSCTTHHHHHHHHHHHHSCCCTTSCCCCEEEEETTTTEEEEECCSSCBHHHHHHH
T ss_pred             CCCCCCCCceecCeECCCCCCCCCCCCCCccccccccccCCCccccCCCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHH
Confidence            46667899999999999998876422111110111111223477899999999999999999999999999999999999


Q ss_pred             HHhhCCCC-CcCeEEEecCCCCcccCCccCcHhhhCCCCeeEEeeC
Q 025134          213 IDASRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF  257 (257)
Q Consensus       213 i~~~~p~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~navivqk~  257 (257)
                      |..++++. ..+|.|++ +||+|.|+|+++||+||||.|++|||||
T Consensus        82 V~~~~~~~~~~~f~L~t-~fPrk~l~d~~~TL~eagL~psavl~k~  126 (127)
T 1s3s_G           82 IVDARPAMAATSFVLMT-TFPNKELADENQTLKEANLLNAVIVQRL  126 (127)
T ss_dssp             HHHHCSGGGTSCEEEEE-TTTTEECCSTTCBHHHHTCSSCEEEEEE
T ss_pred             HHHhCcCCCCCCeEEec-CCCCCCCCCCCCcHHHCCCcCceEEEEe
Confidence            99987754 67899999 9999999998999999999999999998

>1vaz_A NSFL1 cofactor P47; beta-BETA-beta-alpha-alpha-beta, novel fold, lipid binding protein; NMR {Rattus norvegicus} SCOP: d.245.1.1

Probab=99.96  E-value=9.6e-30  Score=192.70  Aligned_cols=70  Identities=33%  Similarity=0.644  Sum_probs=65.5

Q ss_pred             CCCCceEEEEEeccceeecCCCCccCCChhhHHHHHHHhcCCCCCcccCCCCCCceEEEEec-ccccCCCC
Q 025134           65 QPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIR-RDVKCPEP  134 (257)
Q Consensus        65 ~~~~~~~~l~lw~nGF~VddGp~R~y~dP~n~~FL~~I~~G~~P~EL~~~~~~~~V~v~l~~-r~e~y~~p  134 (257)
                      .++++.++||||+|||+|||||||+|+||+|++||++|++|+||.||++++++++|+|+|++ ++|+|++|
T Consensus        18 ~~~~v~~~LtlW~nGFtVdDGpLR~ydDP~N~~FL~~I~~G~~P~EL~~~~~~~~V~v~l~d~r~E~Y~~P   88 (88)
T 1vaz_A           18 SGQDVHVVLKLWKTGFSLDNGDLRSYQDPSNAQFLESIRRGEVPAELRRLAHGGQVNLDMEDHRDEDFVKP   88 (88)
T ss_dssp             CSSCCEEEEEEETTEEECTTSCEEETTSSTHHHHHHHHHHTCCSSHHHHTTSSSCCEEEEEECTTTSSCCC
T ss_pred             CCCCceEEEEEecCceEecCCCCcCCCCHhHHHHHHHHHcCCCCHHHHcccCCCceEEEeEECCCCccCCc
Confidence            34668999999999999999999999999999999999999999999999999999999995 59999875

>2dzk_A UBX domain-containing protein 2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} PDB: 2kxj_A

Probab=99.82  E-value=4e-20  Score=145.69  Aligned_cols=78  Identities=21%  Similarity=0.329  Sum_probs=69.0

Q ss_pred             CCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC-eeEEe
Q 025134          179 ENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVIQ  255 (257)
Q Consensus       179 ~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-avivq  255 (257)
                      ...++|+||||||||+|++.+|+.+|||++||+||..+......+|.|++ +||+|.|+  |.++||+||||.| ++|++
T Consensus         9 ~~~~~t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~f~L~t-~fPrk~l~~~d~~~TL~elgL~psa~L~v   87 (109)
T 2dzk_A            9 DRSTIARIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLAT-MFPRREFTREDYKRRLLDLELAPSASVVL   87 (109)
T ss_dssp             CCSCCEEEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHTTSSCSCEEEC-SSSCCBCCTTTTTSBTGGGTCSSEEEEEE
T ss_pred             CCCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccCCCCCceEEEc-CCCCcCCcccccCCCHHHCCCCCceEEEE
Confidence            35678999999999999999999999999999999987533357899999 99999998  6789999999998 77777


Q ss_pred             eC
Q 025134          256 KF  257 (257)
Q Consensus       256 k~  257 (257)
                      +|
T Consensus        88 ~~   89 (109)
T 2dzk_A           88 LP   89 (109)
T ss_dssp             EC
T ss_pred             EE
Confidence            65

>3qx1_A FAS-associated factor 1; UBX, protein binding, P97 binding; 1.60A {Homo sapiens} PDB: 3qwz_B* 3qc8_B 3qca_A 3qq8_B 3r3m_B 1h8c_A

Probab=99.80  E-value=1.3e-19  Score=135.98  Aligned_cols=75  Identities=17%  Similarity=0.284  Sum_probs=66.1

Q ss_pred             CCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC-eeEEe
Q 025134          179 ENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVIQ  255 (257)
Q Consensus       179 ~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-avivq  255 (257)
                      +++|+|+||||||||+|++.+|+.+|||++||+||.... ....+|.|++ +||+|.|+  |.++||+||||.| ++|+.
T Consensus         3 ~~~~~~~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~~~-~~~~~f~L~t-~fPrk~l~~~d~~~TL~e~gL~p~a~L~v   80 (84)
T 3qx1_A            3 HMEPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKG-FPWDEYKLLS-TFPRRDVTQLDPNKSLLEVKLFPQETLFL   80 (84)
T ss_dssp             -CCCEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHTT-CCTTTEEEEC-SSSCCBGGGSCTTSBTTTTTCCSEEEEEE
T ss_pred             CCCCeEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHcC-CCCCCeEEEe-CCCCCCCcCCCCCCCHHHCCCCCCCEEEE
Confidence            368999999999999999999999999999999999853 3468999999 99999997  7789999999997 55543

>1wj4_A KIAA0794 protein; UBX domain, beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.2

Probab=99.80  E-value=4.4e-19  Score=142.81  Aligned_cols=83  Identities=22%  Similarity=0.321  Sum_probs=72.6

Q ss_pred             CCcccCCCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCccc--CCccCcHhhhCCCC
Q 025134          173 EGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVL--ADRTQTIEQAGLAN  250 (257)
Q Consensus       173 ~~~~vd~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l--~d~s~TL~eagL~n  250 (257)
                      ..+.+|++.++|+||||||||+|++++|+.+|||++||+||... .....+|.|++ +||+|.|  +|.++||+||||.|
T Consensus        33 ~~~~~d~~~~~t~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~~~~~~F~L~t-~fPrk~l~~~d~~~TL~e~gL~p  110 (124)
T 1wj4_A           33 VVEGIDVNGPKAQLMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLT-NFPRRKLSHLDYDITLQEAGLCP  110 (124)
T ss_dssp             CCCCCCCSSCEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEEC-SSSCCEETSSCSSSCTTTTTCCS
T ss_pred             cccccCCCCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEec-CCCCcCCccCCCCCCHHHCCCCC
Confidence            34678999999999999999999999999999999999999886 22357899999 9999999  57799999999998


Q ss_pred             --eeEEeeC
Q 025134          251 --SVVIQKF  257 (257)
Q Consensus       251 --avivqk~  257 (257)
                        +++||++
T Consensus       111 sa~Liv~~~  119 (124)
T 1wj4_A          111 QETVFVQES  119 (124)
T ss_dssp             SBCCEEEEC
T ss_pred             ceEEEEEEc
Confidence              6666653

>2cr5_A Reproduction 8; UBX domain, D0H8S2298E protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.2

Probab=99.75  E-value=1.9e-18  Score=135.94  Aligned_cols=72  Identities=18%  Similarity=0.280  Sum_probs=64.2

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC-CccCcHhhhCCCC-eeEE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA-DRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~-d~s~TL~eagL~n-aviv  254 (257)
                      .++|+||||||||+|+++||+.+|||++||+||.+.. ....+|.|++ +||+|.|+ |.++||+||||.| ++|+
T Consensus        21 ~~~~~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~~-~~~~~f~L~t-~fPrk~l~~d~~~TL~e~gL~p~a~L~   94 (109)
T 2cr5_A           21 EEVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVG-YHKSLYRLST-SFPRRALEVEGGSSLEDIGITVDTVLN   94 (109)
T ss_dssp             SSEEEEEEECTTSCEEEEEEESSSBTHHHHHHHHHHT-CCTTTEEEEC-SSSCCBCCCCSSCBHHHHTCSSCEEEE
T ss_pred             CCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhcC-CCCCCeEEEe-CCCCcCCCCCCCCCHHHcCCCCCeEEE
Confidence            6799999999999999999999999999999999753 3357899999 99999998 7899999999998 4443

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=98.86  E-value=2.7e-09  Score=79.52  Aligned_cols=70  Identities=20%  Similarity=0.386  Sum_probs=57.3

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC-eeEEe
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVIQ  255 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-avivq  255 (257)
                      +|+||+.+|+.++..|+.++||+||+.+|.....-....+.|+. +||+|.|+  |++.||+++||.+ ++|+.
T Consensus         2 ~i~vr~~~G~~~v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~-~~p~k~l~l~~~~~tL~~~gl~~g~~l~v   74 (86)
T 2kzr_A            2 RVRCKAKGGTHLLQGLSSRTRLRELQGQIAAITGIAPGSQRILV-GYPPECLDLSDRDITLGDLPIQSGDMLIV   74 (86)
T ss_dssp             CEEEEETTEEEEECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEE-SSCCCCCCCCCSSCBTTTSSCCTTCEEEC
T ss_pred             EEEEEcCCCCEEeeecCCCCCHHHHHHHHHHHhCCCccceEEEe-CCCCcccccCCCCCCHHHcCCCCCCEEEE
Confidence            68999999977543399999999999999987543346788998 99999986  4689999999996 55553

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=97.67  E-value=3.3e-05  Score=56.86  Aligned_cols=68  Identities=4%  Similarity=0.102  Sum_probs=54.5

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCC-cccC-CccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP-KVLA-DRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~-k~l~-d~s~TL~eagL~n-avi  253 (257)
                      ..||||.++|... +.+..+.|+++|++.|....+.....|.|.. +||+ +.|. +.++||+++||.+ ..|
T Consensus         5 m~lRvrs~~G~~R-i~v~~~~t~~~L~~~I~~~~~i~~~~~~l~~-~~~p~~~l~~~~~~~l~~lgl~hGd~l   75 (80)
T 2pjh_A            5 IIIRVQSPDGVKR-ITATKRETAATFLKKVAKEFGFQNNGFSVYI-NRNKTGEITASSSKSLHLLKIKHGDLL   75 (80)
T ss_dssp             CCCEEECSSEEEE-CCCCSSCCHHHHHHHHHHHTCCCTTTCCCCC-SCCGGGGSSSCCCCTTTTTCCCTTCCE
T ss_pred             EEEEEECCCCCEE-EEcCCcChHHHHHHHHHHHcCCCCCcceEEe-cCCCCCcccCCCCCCHHHcCCCCCCEE
Confidence            4689999999653 3488999999999999987654456788887 9998 6774 4688999999986 444

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.45  E-value=0.00086  Score=47.86  Aligned_cols=68  Identities=13%  Similarity=0.211  Sum_probs=54.2

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...+|.||..+|+.+.+.+..++||++|.+.|.....-......|+.   ..+.|.| +.||.+.|+.+ ++|
T Consensus         6 ~~m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~---~gk~L~d-~~tL~~~~i~~g~~i   74 (81)
T 2dzi_A            6 SGMQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLF---KGKALAD-GKRLSDYSIGPNSKL   74 (81)
T ss_dssp             SSEEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEE---TTEECCT-TSBGGGGTCCSSBCC
T ss_pred             CcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEE---CCeECCC-CCcHHHcCCCCCCEE
Confidence            45788999999998899999999999999999886432344566654   6888876 68999999986 544

>1wju_A NEDD8 ultimate buster-1; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=97.44  E-value=0.00081  Score=51.66  Aligned_cols=70  Identities=17%  Similarity=0.184  Sum_probs=56.1

Q ss_pred             CCceEEEEEcCC----CCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          181 LPSTSVQIRLAD----GTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       181 ~p~t~iqIRl~d----G~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...++|+||+++    |+.+.+.+..++||.+|..-|.....-......|+.   --|.|.| +.||++.||.+ ++|+
T Consensus        13 tg~ati~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~---~GKiL~D-~~TL~~y~I~~gsti~   87 (100)
T 1wju_A           13 TGIATIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVI---NKKQLQL-GKTLEEQGVAHNVKAM   87 (100)
T ss_dssp             CCEEEEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEE---TTEECCT-TSBHHHHTCCSSEEEE
T ss_pred             cceEEEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEe---CCeECCC-CCcHHHcCCCCCCEEE
Confidence            467899999999    778999999999999999999886432244566664   5889977 58999999995 5543

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} SCOP: d.15.1.1

Probab=97.43  E-value=0.00086  Score=48.24  Aligned_cols=68  Identities=16%  Similarity=0.255  Sum_probs=54.4

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...|.||..+|+.+.+.+..++||.+|.+.|.....-......|+   |..+.|.| +.||.+.++.+ ++|.
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~---~~g~~L~d-~~tL~~~~i~~~~~l~   71 (85)
T 3mtn_B            3 HMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI---FAGKQLED-GRTLSDYNIQKWSTLF   71 (85)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEE---ETTEECCT-TSBTGGGTCCTTCEEE
T ss_pred             eEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHEEEE---ECCEECCC-CCCHHHcCCCCCCEEE
Confidence            467899999999999999999999999999988543233456665   46788987 58999999995 5553

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ...

Probab=97.41  E-value=0.00064  Score=47.71  Aligned_cols=65  Identities=15%  Similarity=0.235  Sum_probs=52.0

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|+.+...++.++||++|.+.|.....-......|+.   ..+.|.| +.||++.|+.+ ++|
T Consensus         2 ~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~---~g~~L~d-~~tL~~~~i~~g~~i   67 (76)
T 3a9j_A            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQRESTL   67 (76)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEE---TTEECCT-TCBTGGGTCCTTCEE
T ss_pred             EEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEE---CCeECCC-CCcHHHcCCCCCCEE
Confidence            58899999998999999999999999999875422234556654   6788877 68999999996 544

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A

Probab=97.38  E-value=0.00084  Score=47.07  Aligned_cols=65  Identities=12%  Similarity=0.230  Sum_probs=51.8

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|+.+.+.+..++||++|...|.....-......|+   |-.+.|.| +.||.+.|+.+ ++|
T Consensus         2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~---~~g~~L~d-~~tL~~~~i~~g~~i   67 (76)
T 1ndd_A            2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI---YSGKQMND-EKTAADYKILGGSVL   67 (76)
T ss_dssp             EEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEE---ETTEECCT-TSBGGGGTCCTTCEE
T ss_pred             EEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEE---ECCEECCC-CCcHHHcCCCCCCEE
Confidence            6889999999999999999999999999987542223455665   46788876 58999999996 544

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=97.34  E-value=0.00094  Score=49.73  Aligned_cols=68  Identities=16%  Similarity=0.248  Sum_probs=55.4

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .....|.||..+|+.+.+.+..++||.+|...|....   .....|+.   -.+.|.|++.||.+.|+.+ ++|.
T Consensus         5 ~~~m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~---~Gk~L~D~~~tL~~y~i~~g~~i~   73 (95)
T 1wia_A            5 SSGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIY---QGRLLQDPARTLSSLNITNNCVIH   73 (95)
T ss_dssp             CCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST---TTTCEEEE---TTEECCCSSCBTTTTTCCTTEEEE
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC---cCcEEEEE---CCEEccCCcCCHHHcCCCCCCEEE
Confidence            4567899999999999999999999999999998754   34566654   6789998779999999986 5553

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=97.24  E-value=0.0028  Score=45.99  Aligned_cols=68  Identities=18%  Similarity=0.224  Sum_probs=54.4

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +...|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|+| +.||.+.++.+ ++|
T Consensus         6 ~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~---~Gk~L~d-~~tL~~~~i~~g~~i   74 (87)
T 1wh3_A            6 SGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEF---QGQVLQD-WLGLGIYGIQDSDTL   74 (87)
T ss_dssp             SSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEE---TTEECCS-SSBHHHHTCCTTEEE
T ss_pred             CCEEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEE---CCEEccC-CCCHHHCCCCCCCEE
Confidence            46788999999998999999999999999999886432345566654   5788876 58999999986 554

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=97.23  E-value=0.0015  Score=48.85  Aligned_cols=65  Identities=15%  Similarity=0.238  Sum_probs=52.4

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +|.||..+|+.+.+.+..+.||++|...|.....-......|+.   -.+.|.| +.||.+.|+.+ ++|
T Consensus         2 ~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~---~Gk~L~D-~~tL~~~gi~~g~~i   67 (98)
T 1yx5_B            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTL   67 (98)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEE---TTEECCT-TSBTGGGTCCTTCEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEE---CCEECCC-CCCHHHcCCCCCCEE
Confidence            68899999998999999999999999999886432234566654   6788877 68999999996 554

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: d.15.1.1 PDB: 3dbr_I 3dbl_I

Probab=97.23  E-value=0.002  Score=46.67  Aligned_cols=70  Identities=13%  Similarity=0.158  Sum_probs=54.8

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .....|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|.
T Consensus        10 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~---~G~~L~d-~~tL~~~~i~~~~~i~   80 (88)
T 3dbh_I           10 GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIY---SGKQMND-EKTAADYKILGGSVLH   80 (88)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEE---TTEECCT-TSBGGGGTCCTTCEEE
T ss_pred             CCcEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcCHHHEEEEE---CCeECCC-CCcHHHcCCCCCCEEE
Confidence            345789999999999999999999999999999875422234455654   5578877 68999999995 5554

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=97.22  E-value=0.0026  Score=46.91  Aligned_cols=71  Identities=17%  Similarity=0.197  Sum_probs=55.1

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ......|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|.| +.||.+.|+.+ ++|.
T Consensus        14 ~~~~m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~---~Gk~L~D-~~tL~~~gi~~g~~i~   85 (91)
T 3v6c_B           14 PRGSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTLH   85 (91)
T ss_dssp             CCCSEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEE---TTEECCT-TCBTGGGTCCTTCEEE
T ss_pred             CCCeEEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhhEEEEE---CCeECCC-cCcHHHCCCCCCCEEE
Confidence            3456789999999999999999999999999999885422234456654   4678877 58999999996 5543

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=97.20  E-value=0.0021  Score=45.90  Aligned_cols=68  Identities=19%  Similarity=0.233  Sum_probs=53.9

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +...|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|
T Consensus         3 ~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~---~G~~L~d-~~tL~~~~i~~~~~l   71 (79)
T 3phx_B            3 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTF---EGKPLED-QLPLGEYGLKPLSTV   71 (79)
T ss_dssp             CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEE---TTEECCT-TSBGGGGTCCTTCEE
T ss_pred             CCEEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcCCCHHHEEEEE---CCEECCC-CCcHHHCCCCCCCEE
Confidence            45789999999999999999999999999999875322234456654   5688887 68999999996 554

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=97.10  E-value=0.0014  Score=47.16  Aligned_cols=68  Identities=18%  Similarity=0.242  Sum_probs=53.0

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...|.||..+|+.+.+.+..++||.+|.+.|.....-......|+.   -.+.|+| +.||.+.++.+ ++|.
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~---~g~~L~d-~~tL~~~~i~~~~~i~   71 (85)
T 3n3k_B            3 HMRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIHNHSALY   71 (85)
T ss_dssp             -CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEE---TBEECCT-TCBTTTTTCCTTCEEE
T ss_pred             eEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE---CCeECCC-CCCHHHCCCCCCCEEE
Confidence            3578999999999999999999999999999885422234566654   5688877 57999999995 5543

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=97.09  E-value=0.0044  Score=46.35  Aligned_cols=70  Identities=16%  Similarity=0.286  Sum_probs=54.5

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +.....|.||..+| ...+.+..++||++|...|.....-......|+   |..+.|.|++.||.+.|+.+ ++|
T Consensus        12 ~~~~~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi---~~Gk~L~D~~~tL~~ygI~~gstl   82 (94)
T 2kan_A           12 AVRKIHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIVENTPIKRMQLY---YSGIELADDYRNLNEYGITEFSEI   82 (94)
T ss_dssp             SSCCEEEEEECSSC-EEEEEECTTCBHHHHHHHHHHHSSSCTTTEEEE---ETTEEECCTTSBHHHHTCCTTEEE
T ss_pred             CCCCEEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEE---ECCEECCCCcccHHHCCCCCCCEE
Confidence            34567899999888 778899999999999999988642224455665   46789988559999999986 544

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=97.07  E-value=0.0056  Score=44.61  Aligned_cols=68  Identities=16%  Similarity=0.125  Sum_probs=53.2

Q ss_pred             CceEEEEEcCCC-CEEEE-EeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADG-TRLIA-HFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG-~rlv~-~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ....|.||..+| +.+.+ .+..++||.+|...|.....-......|+.   -.+.|.| +.||.+.|+.+ ++|
T Consensus         6 ~~m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~---~gk~L~d-~~tL~~~~i~~g~~i   76 (89)
T 1wy8_A            6 SGMWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFY---RGKQLEN-GYTLFDYDVGLNDII   76 (89)
T ss_dssp             SCEEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEE---TTEECCS-SSBHHHHTCCTTCEE
T ss_pred             CcEEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEE---CCeECCC-CCCHHHCCCCCCCEE
Confidence            457889999999 67888 599999999999999886432345566654   5788876 68999999986 544

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A

Probab=97.05  E-value=0.0036  Score=45.80  Aligned_cols=69  Identities=16%  Similarity=0.208  Sum_probs=53.6

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCeeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~naviv  254 (257)
                      +...|.||..+|+.+.+.+..++||.+|...|.....-......|+.   =.+.|.| +.||.+.|+-+++|.
T Consensus         4 ~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~---~Gk~L~d-~~tL~~~~i~g~~i~   72 (90)
T 4dwf_A            4 DSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIY---QGRVLQD-DKKLQEYNVGGKVIH   72 (90)
T ss_dssp             CEEEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEE---TTEECCT-TSBGGGGTCTTEEEE
T ss_pred             cEEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEE---CCeECCC-CCCHHHcCCCCcEEE
Confidence            45689999999999999999999999999999875422234456654   5688877 689999999445553

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=97.00  E-value=0.0029  Score=44.57  Aligned_cols=66  Identities=18%  Similarity=0.244  Sum_probs=51.1

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .+|.||. +|+...+.+..++||++|...|.....-......|+   |..+.|.| +.||++.|+.+ ++|.
T Consensus         5 m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~---~~gk~L~d-~~tL~~~~i~~g~~i~   71 (77)
T 2bwf_A            5 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLI---YSGKILKD-DQTVESYHIQDGHSVH   71 (77)
T ss_dssp             EEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEE---ETTEECCT-TSBTGGGTCCTTCEEE
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCCHHHEEEE---ECCeEcCC-CCCHHHcCCCCCCEEE
Confidence            5677888 898889999999999999999987542223455665   46788877 48999999985 5553

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A

Probab=97.00  E-value=0.005  Score=44.34  Aligned_cols=68  Identities=13%  Similarity=0.257  Sum_probs=53.3

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhC--CC-CCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASR--PG-TARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~--p~-~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...|.||..+|+.+.+.+..++||++|...|....  .. ......|+.   -.+.|+| +.||.+.|+.+ ++|.
T Consensus         5 ~m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~~~i~~g~~i~   76 (85)
T 2wyq_A            5 AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIY---AGKILSD-DVPIRDYRIDEKNFVV   76 (85)
T ss_dssp             CEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEE---TTEECCT-TSBGGGGCCCTTSEEE
T ss_pred             eEEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEE---CCEECcC-CCCHHHcCCCCCCEEE
Confidence            46789999999999999999999999999998851  22 234556654   5788876 58999999985 5553

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=96.98  E-value=0.0036  Score=46.96  Aligned_cols=69  Identities=16%  Similarity=0.216  Sum_probs=54.0

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ....|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|.
T Consensus        21 ~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~~~i~~g~~i~   90 (98)
T 4hcn_B           21 RPMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTLH   90 (98)
T ss_dssp             -CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEE---TTEECCT-TCBSGGGTCCTTEEEE
T ss_pred             CeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEE---CCEECCC-CCcHHHCCCCCCCEEE
Confidence            35789999999999999999999999999999885432234556654   6688876 68999999996 5543

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=96.96  E-value=0.0038  Score=45.81  Aligned_cols=67  Identities=21%  Similarity=0.266  Sum_probs=53.0

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...|.||..+|+.+.+.+..++||++|...|.....-......|+   |-.+.|+| +.||.+.|+.+ ++|
T Consensus         4 ~m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~---~~Gk~L~D-~~tL~~~~I~~g~~i   71 (88)
T 2hj8_A            4 PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLT---FEGKPLED-QLPLGEYGLKPLSTV   71 (88)
T ss_dssp             EEEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEE---SSSSCCCT-TSBHHHHHCSTTCEE
T ss_pred             cEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEE---ECCEECCC-CCcHHHcCCCCCCEE
Confidence            467889999999999999999999999999988643234455555   46788876 68999999986 554

>2uyz_B Small ubiquitin-related modifier 1; sumoylation, cell division, nuclear protein, ubiquitin-like modifier, UBL conjugation pathway; 1.4A {Homo sapiens} SCOP: d.15.1.1 PDB: 2vrr_B 2iy0_B 2iy1_B 2g4d_B 2las_A 2io2_B 1z5s_B 3uip_B* 1tgz_B* 2bf8_B

Probab=96.95  E-value=0.0038  Score=44.52  Aligned_cols=67  Identities=10%  Similarity=0.199  Sum_probs=53.1

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...|.||..+|+.+.+++..++||++|.+.|.....-......|.   |-.+.|.| +.||++.++.+ ++|
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~---~~G~~L~d-~~tl~~~~i~~~~~i   70 (79)
T 2uyz_B            3 YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFL---FEGQRIAD-NHTPKELGMEEEDVI   70 (79)
T ss_dssp             EEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TCCHHHHTCCTTEEE
T ss_pred             eEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCCCcccEEEE---ECCEEeCC-CCCHHHcCCCCCCEE
Confidence            357889999999999999999999999999987542223455554   57899987 48999999996 554

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A

Probab=96.95  E-value=0.0032  Score=46.56  Aligned_cols=67  Identities=16%  Similarity=0.244  Sum_probs=52.5

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ..|.||..+|+.+.+.+..++||.+|...|.....-......|+   |-.+.|.| +.||.+.|+.+ ++|.
T Consensus         2 m~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~---~~G~~L~d-~~tL~~~~i~~~~~i~   69 (96)
T 3k9o_B            2 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI---FAGKQLED-GRTLSDYNIQKESTLH   69 (96)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEE---ETTEECCT-TSBTGGGTCCTTCEEE
T ss_pred             cEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhHEEEE---ECCEECCC-CCcHHHcCCCCCCEEE
Confidence            46899999999999999999999999999988542223445565   46788876 57999999985 5543

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B

Probab=96.93  E-value=0.0039  Score=45.84  Aligned_cols=66  Identities=12%  Similarity=0.189  Sum_probs=52.1

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|.
T Consensus         2 ~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~~~i~~g~~l~   68 (88)
T 4fbj_B            2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIY---SGKQMND-EKTAADYKILGGSVLH   68 (88)
T ss_dssp             EEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEE---TTEECCT-TSBTTTTTCCTTCEEE
T ss_pred             EEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChhHEEEEE---CCeECCC-CCcHHHcCCCCCCEEE
Confidence            58899999999999999999999999999875422234456654   5688877 68999999996 5543

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=96.89  E-value=0.0065  Score=45.25  Aligned_cols=65  Identities=12%  Similarity=0.256  Sum_probs=51.7

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhC--CC-CCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASR--PG-TARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~--p~-~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +|.||..+|+.+.+.+..++||++|...|....  .. ......|+.   -.+.|+| +.||.+.|+.+ ++|
T Consensus         2 ~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~ygI~~g~~i   70 (95)
T 1uel_A            2 QVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIY---AGKILND-DTALKEYKIDEKNFV   70 (95)
T ss_dssp             EEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEE---TTEECCT-TSBGGGGTCCSSSEE
T ss_pred             EEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEE---CCEECCC-cCcHHHCCCCCCCEE
Confidence            688999999999999999999999999998862  12 234566654   5788876 58999999986 554

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=96.88  E-value=0.0059  Score=44.44  Aligned_cols=70  Identities=16%  Similarity=0.219  Sum_probs=54.0

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCeeEE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVI  254 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~naviv  254 (257)
                      .....|.||..+|+...+.+..++||.+|...|.....-......|+   |-.+.|.| +.||.+.|+-+++|.
T Consensus        15 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi---~~Gk~L~D-~~tL~~~~i~g~~i~   84 (88)
T 4eew_A           15 PDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLI---YQGRVLQD-DKKLQEYNVGGKVIH   84 (88)
T ss_dssp             CCEEEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TSBGGGGTCTTEEEE
T ss_pred             CCeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEE---ECCEECCC-CCcHHHcCCCCcEEE
Confidence            34578999999999999999999999999999987532223345555   45688887 689999999445553

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=96.87  E-value=0.0064  Score=45.12  Aligned_cols=68  Identities=16%  Similarity=0.154  Sum_probs=52.2

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ....+|.||.. |+.+.+.+..++||.+|.+.|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|
T Consensus        15 ~~~m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~---~Gk~L~D-~~tL~~~gi~~g~~i   83 (96)
T 1wx8_A           15 SRIIRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIF---TGKILRD-QDILSQRGILDGSTV   83 (96)
T ss_dssp             SCEEEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEE---TTEECCT-TSCHHHHTCCTTEEE
T ss_pred             CCcEEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEE---CCEECCC-cCCHHHCCCCCCCEE
Confidence            34577888888 888999999999999999999886422234455543   5788876 58999999986 444

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=96.87  E-value=0.0077  Score=45.53  Aligned_cols=69  Identities=13%  Similarity=0.200  Sum_probs=52.9

Q ss_pred             ceEEEEEcCCC----CEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          183 STSVQIRLADG----TRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       183 ~t~iqIRl~dG----~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...|.||..+|    +.+.+.+..++||++|...|.....-......|+.   -.+.|.|+..||.+.|+.+ ++|+
T Consensus         7 ~m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~---~gk~L~D~~~tL~~ygI~~g~~l~   80 (102)
T 1v5o_A            7 GMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVY---MEQLLTDDHCSLGSYGLKDGDMVV   80 (102)
T ss_dssp             CEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEE---TTEEECCSSSBHHHHTCCTTEEEE
T ss_pred             eEEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEE---CCEECCCCcccHHHCCCCCCCEEE
Confidence            36688888755    57789999999999999999886432334556664   4588988778999999985 5554

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=96.86  E-value=0.0025  Score=49.27  Aligned_cols=68  Identities=19%  Similarity=0.258  Sum_probs=55.3

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC---C------------cCeEEEecCCCCcccCCccCcHhhhC
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT---A------------RNYQLQMMGFPPKVLADRTQTIEQAG  247 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~---~------------~~f~L~t~~fP~k~l~d~s~TL~eag  247 (257)
                      ..+|.|+..+|+.+.+.+..++||.||..-|.....-.   .            ..|.|+   |..+.|.|++.||++.|
T Consensus         7 ~M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li---~~Gk~L~dD~~tL~dyg   83 (105)
T 1v2y_A            7 GMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLT---SAGEKLTEDRKKLRDYG   83 (105)
T ss_dssp             SEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEE---SSSCEECCSSSBHHHHT
T ss_pred             cEEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEE---eCCcCccCCcCCHHHcC
Confidence            47899999999999999999999999999998753110   0            246775   58899988889999999


Q ss_pred             CCC-eeE
Q 025134          248 LAN-SVV  253 (257)
Q Consensus       248 L~n-avi  253 (257)
                      +.+ ++|
T Consensus        84 I~~g~~l   90 (105)
T 1v2y_A           84 IRNRDEV   90 (105)
T ss_dssp             CCSSEEE
T ss_pred             CCCCCEE
Confidence            996 544

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=96.84  E-value=0.021  Score=44.98  Aligned_cols=67  Identities=15%  Similarity=0.178  Sum_probs=52.3

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...+|.||.. |+.+.+.+..++||.+|...|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|
T Consensus        31 ~~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~---~Gk~L~D-~~tL~dygI~~gstI   98 (125)
T 1j8c_A           31 KIIKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIF---AGKILKD-QDTLIQHGIHDGLTV   98 (125)
T ss_dssp             CCEEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEE---TTEEEST-TSCGGGTTCSSSEEE
T ss_pred             CcEEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHCcCcceEEEEE---CCEEcCC-CCCHHHcCCCCCCEE
Confidence            4578888888 888999999999999999999885422234556654   5788876 58999999986 444

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=96.84  E-value=0.0054  Score=47.13  Aligned_cols=68  Identities=15%  Similarity=0.218  Sum_probs=54.4

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ....|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|.| +.||.+.|+.+ ++|
T Consensus        34 ~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~~gI~~gs~I  102 (111)
T 2ojr_A           34 LAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTL  102 (111)
T ss_dssp             SCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEEE---TTEECCS-SCBTTTTTCCTTCEE
T ss_pred             CeEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCcccEEEEE---CCEECCC-CCcHHHcCCCCCCEE
Confidence            46789999999999999999999999999999885422345566664   5788876 68999999985 544

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=96.82  E-value=0.0047  Score=43.79  Aligned_cols=67  Identities=15%  Similarity=0.131  Sum_probs=51.9

Q ss_pred             ceEEEEEcCCCCEE-EEE-eCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          183 STSVQIRLADGTRL-IAH-FNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       183 ~t~iqIRl~dG~rl-v~~-fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...|.||..+|+.+ .+. +..++||++|..-|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|
T Consensus         2 ~m~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~---~g~~L~d-~~tL~~~~i~~g~~i   71 (78)
T 2faz_A            2 SMWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFY---RGKQMED-GHTLFDYEVRLNDTI   71 (78)
T ss_dssp             CEEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEE---TTEECCT-TCBTTTTTCCTTCEE
T ss_pred             cEEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEE---CCEECCC-CCCHHHcCCCCCCEE
Confidence            35789999999885 788 99999999999999885422234556654   5788876 58999999985 554

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=96.81  E-value=0.0078  Score=45.84  Aligned_cols=69  Identities=16%  Similarity=0.188  Sum_probs=54.2

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ....|.||..+|+.+.+.+..++||++|...|.....-......|+.   -.+.|.| +.||.+.|+.+ ++|.
T Consensus        22 ~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~ygI~~g~ti~   91 (106)
T 1ttn_A           22 YECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFF---SGRPLTD-KMKFEELKIPKDYVVQ   91 (106)
T ss_dssp             CSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEE---TTEECCT-TSHHHHCCCSSSCEEE
T ss_pred             CeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEE---CCEECCC-CCcHHHcCCCCCCEEE
Confidence            45788999999998999999999999999999875422244566664   5688876 68999999985 5543

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A

Probab=96.81  E-value=0.0048  Score=46.72  Aligned_cols=72  Identities=13%  Similarity=0.103  Sum_probs=54.7

Q ss_pred             CCCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          178 DENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       178 d~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ....+...|-|+...|+.+.+.+++++||++|.+-|+....-....-.|.   |=.+.|.| ..||++.++.+ ++|
T Consensus        16 ~~~~~mIqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLi---f~Gk~LkD-~~TL~dY~I~dgstL   88 (93)
T 3plu_A           16 PRGSHMIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQ---KGGSVLKD-HISLEDYEVHDQTNL   88 (93)
T ss_dssp             ----CEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TSBTGGGTCCTTCEE
T ss_pred             CCCCceEEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhCCCHHHEEEE---eCCEEccC-cCCHHHcCCCCCCEE
Confidence            34567889999999999999999999999999999987532123445565   46688888 58999999996 444

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=96.81  E-value=0.0043  Score=45.60  Aligned_cols=66  Identities=17%  Similarity=0.234  Sum_probs=52.9

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ..|.||..+|+.+.+.+..++||++|.+-|.....-......|+.   -.+.|.| +.||++.|+.+ ++|
T Consensus        10 ~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~---~Gk~L~D-~~tL~~~gi~~g~~i   76 (88)
T 1sif_A           10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTL   76 (88)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEE---TTEECCT-TSBSGGGTCCTTCEE
T ss_pred             eEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcChhhEEEEE---CCEECCC-CCcHHHcCCCCCCEE
Confidence            568899999999999999999999999999875422234566654   5788877 68999999986 544

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=96.75  E-value=0.013  Score=44.45  Aligned_cols=67  Identities=16%  Similarity=0.176  Sum_probs=51.7

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...+|.||..+|+ ..+.+..++||.+|+..|.....-......|+.   -.+.|.| +.||.+.|+.+ ++|
T Consensus        16 ~~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~~gi~~g~~i   83 (106)
T 1wx7_A           16 HLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIF---AGKILKD-PDSLAQCGVRDGLTV   83 (106)
T ss_dssp             SEEEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHHTCCTTTEEEEE---TTEECCT-TSCHHHHTCCTTEEE
T ss_pred             ceEEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEE---CCEECCC-cCcHHHcCCCCCCEE
Confidence            4578889988885 688999999999999999875422244566664   5688876 68999999986 444

>1wxv_A BAG-family molecular chaperone regulator-1; structural genomics, apoptosis, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=96.68  E-value=0.019  Score=42.16  Aligned_cols=69  Identities=12%  Similarity=0.176  Sum_probs=53.0

Q ss_pred             CceEEEEEcCCCCEEEEEeCCC-----CCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLH-----HTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s-----~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...+|.|+. .|+...+.+..+     .||.+|...|.....-....-.|+.   -.+.|.|++.||.+.|+.+ +.|+
T Consensus         6 ~~~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~---~Gk~L~D~~~~L~~~~i~~g~~i~   80 (92)
T 1wxv_A            6 SGLTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIF---KGKSLKEMETPLSALGIQDGCRVM   80 (92)
T ss_dssp             SSEEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEE---TTEEECCSSSBHHHHTCCSSEEEE
T ss_pred             CeEEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEE---CCeecCCCcccHHHCCCCCCCEEE
Confidence            357788887 477888899985     9999999999886432345566664   5788998889999999986 5443

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=96.67  E-value=0.0068  Score=44.37  Aligned_cols=67  Identities=16%  Similarity=0.175  Sum_probs=53.3

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcc-cCCccCcHhhhCCCC-eeE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKV-LADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~-l~d~s~TL~eagL~n-avi  253 (257)
                      -.+|.||..+|+...+.+..++||++|..-|.....-......|+   |-.+. |+| +.||++.|+.+ ++|
T Consensus        10 ~~~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi---~~Gk~lL~D-~~tL~~y~I~~gs~i   78 (84)
T 2kk8_A           10 HMKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLI---VDGIVILRE-DLTVEQCQIVPTSDI   78 (84)
T ss_dssp             CEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEE---ETTEECCCS-SSBHHHHTCCTTSCE
T ss_pred             ceEEEEEecCCcEEEEEECCCChHHHHHHHHHHHHCcChHHEEEE---ECCEEecCC-cCCHHHcCCCCCCEE
Confidence            468999999999999999999999999999988643223455665   46788 766 68999999986 544

>1wyw_B Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 1y8r_C* 2asq_A 2pe6_B 1a5r_A 2kqs_A 3kyc_D* 3rzw_C

Probab=96.67  E-value=0.0071  Score=45.31  Aligned_cols=68  Identities=10%  Similarity=0.194  Sum_probs=54.1

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ....|.||..+|+.+.+++..++||++|...|.....-......|+   |-.+.|.| +.||++.++.+ ++|
T Consensus        20 ~~m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~gip~~~qrLi---f~Gk~L~d-~~tl~dy~i~~g~~I   88 (97)
T 1wyw_B           20 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFL---FEGQRIAD-NHTPKELGMEEEDVI   88 (97)
T ss_dssp             CEEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TCCHHHHTCCTTCEE
T ss_pred             CcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEE---ECCeEcCC-CCCHHHCCCCCCCEE
Confidence            4578889999999999999999999999999987542223455565   47889987 58999999985 544

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=96.65  E-value=0.0061  Score=48.76  Aligned_cols=72  Identities=21%  Similarity=0.271  Sum_probs=55.0

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC-CcCeEEEecCCCCc---------------------------c
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPK---------------------------V  235 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~-~~~f~L~t~~fP~k---------------------------~  235 (257)
                      -.|+|||+||+...++.+.+.||..+-..|...-.-. ...|.|.. ..|..                           .
T Consensus        12 r~LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kigI~n~~ey~L~~-~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~k~k   90 (128)
T 2kc2_A           12 RPLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVR-ELMEEKKDEGTGTLRKDKTLLRDEKKMEKLKQK   90 (128)
T ss_dssp             EEEEEECTTSCEEEEEEEECSSHHHHHHHHHHHHTCCCCSSEEEEE-ECCCCCCCCCSSCCSSSSSCSCCSCCSCSSCCS
T ss_pred             ccEEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhCCCCcccccccc-cccccccccCchhhccccccccchhHHHHHHHH
Confidence            3699999999999999999999999999998854222 35688886 54422                           1


Q ss_pred             --------cCCccCcHhhhCCC-CeeEEee
Q 025134          236 --------LADRTQTIEQAGLA-NSVVIQK  256 (257)
Q Consensus       236 --------l~d~s~TL~eagL~-navivqk  256 (257)
                              .-|.+.||.|-|+. +.+|+.|
T Consensus        91 L~~dd~~~WLD~srtL~EQGI~e~~tllLR  120 (128)
T 2kc2_A           91 LHTDDELNWLDHGRTLREQGVEEHETLLLR  120 (128)
T ss_dssp             CCCSSSEEEECSSSCHHHHTCCTTSEEEEE
T ss_pred             hcccCCCCcccCCCcHHHcCCCCCCEEEEE
Confidence                    12558999999999 4777765

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.57  E-value=0.007  Score=46.20  Aligned_cols=67  Identities=19%  Similarity=0.281  Sum_probs=52.2

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ..|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|.| +.||.+.|+.+ ++|.
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~---~Gk~L~D-~~tL~~~~i~~g~~i~   69 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIY---SGKVLQD-SKTVSECGLKDGDQVV   69 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEE---TTEECCT-TSBTTTTTCCTTCEEE
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEE---CCEECCC-cCCHHHcCCCCCCEEE
Confidence            468899999999999999999999999999885422234456654   5788887 68999999995 5553

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=96.56  E-value=0.012  Score=44.46  Aligned_cols=68  Identities=16%  Similarity=0.162  Sum_probs=52.3

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .....|.||..+|+ ..+.+..++||.+|.+.|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|
T Consensus        20 ~~~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~---~Gk~L~D-~~tL~~ygI~~gstI   88 (100)
T 1yqb_A           20 PHLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIF---AGKILKD-PDSLAQCGVRDGLTV   88 (100)
T ss_dssp             TTEEEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEE---TTEECCT-TSBHHHHTCCTTCEE
T ss_pred             CCeEEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEE---CCEECCC-cCcHHHCCCCCCCEE
Confidence            45678999999885 688999999999999999875422234555654   5788876 58999999986 444

>3vdz_A Ubiquitin-40S ribosomal protein S27A; gadolinium, MRI contrast agent, peptide-based contrast agent lanthanide binding TAG; 2.40A {Synthetic construct} PDB: 2ojr_A

Probab=96.55  E-value=0.0094  Score=45.84  Aligned_cols=67  Identities=16%  Similarity=0.260  Sum_probs=53.4

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...|.||..+|+.+.+++..++||.+|...|.....-......|+   |-.+.|.| +.||.+.|+.+ ++|
T Consensus        35 ~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi---~~Gk~L~D-~~tL~~~gI~~gs~I  102 (111)
T 3vdz_A           35 AMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI---FAGKQLED-GRTLSDYNIQKESTL  102 (111)
T ss_dssp             CEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEE---ETTEECCT-TSBTTTTTCCTTCEE
T ss_pred             cEEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCCChHHEEEE---ECCEECCC-CCcHHHCCCCCCCEE
Confidence            578899999999999999999999999999988542223455665   46788887 57999999995 554

>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=96.54  E-value=0.012  Score=45.11  Aligned_cols=70  Identities=14%  Similarity=0.109  Sum_probs=55.0

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ..+...|-|+...|+.+.+.+..++||++|.+-|.....-....-.|+   |..|.|.| +.||.+.|+.+ ++|
T Consensus        25 ~~~mm~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi---~~Gk~L~D-~~TL~dygI~~gstl   95 (100)
T 1uh6_A           25 AATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLK---KWYTIFKD-HVSLGDYEIHDGMNL   95 (100)
T ss_dssp             CCCEEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEE---ETTEECCS-SCBHHHHTCCTTEEE
T ss_pred             CCCeEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEE---ECCEECCC-CCCHHHcCCCCCCEE
Confidence            345688999999999999999999999999999988632123344554   56899977 69999999996 554

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=96.50  E-value=0.013  Score=44.22  Aligned_cols=67  Identities=15%  Similarity=0.183  Sum_probs=51.8

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ....|.||.. |+.+.+.+..++||++|...|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|
T Consensus        24 ~~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~~gI~~g~~I   91 (101)
T 2klc_A           24 KIMKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIF---AGKILKD-QDTLSQHGIHDGLTV   91 (101)
T ss_dssp             CCEEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEE---TTEEECT-TCCTGGGTCCTTCEE
T ss_pred             CeEEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHCcChhhEEEEE---CCEECCC-cCcHHHcCCCCCCEE
Confidence            4578889988 888899999999999999999875422234555654   5788876 58999999986 444

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=96.45  E-value=0.032  Score=43.69  Aligned_cols=65  Identities=17%  Similarity=0.209  Sum_probs=51.4

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC--------CcCeEEEecCCCCcccCCccCcHhhhCCC
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT--------ARNYQLQMMGFPPKVLADRTQTIEQAGLA  249 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~--------~~~f~L~t~~fP~k~l~d~s~TL~eagL~  249 (257)
                      .....|.||+.+|....+.+..++||.+|.+.|....|..        .....|+   |=-|.|+| +.||.+.++.
T Consensus        14 ~~~m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLI---y~GK~LeD-~~TL~~y~I~   86 (116)
T 1wgh_A           14 ADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLI---YQGRFLHG-NVTLGALKLP   86 (116)
T ss_dssp             SSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEE---ETTEEECS-SCBTTTTTCC
T ss_pred             CCeEEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEE---ECCcCCCC-CCcHHHcCCC
Confidence            3457889999999999999999999999999999843221        2345555   46788987 5899999985

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=96.42  E-value=0.018  Score=44.03  Aligned_cols=69  Identities=10%  Similarity=0.173  Sum_probs=53.6

Q ss_pred             CceEEEEEcC---CCCEEEEEeCC-CCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLA---DGTRLIAHFNL-HHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~---dG~rlv~~fn~-s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +...|.||.+   +|+.+.+.+.. ++||.+|..-|.....-....-.|+.   -.+.|+| +.||.+.|+.+ ++|.
T Consensus        26 ~~i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~---~Gk~L~D-~~tL~~y~I~~g~~l~   99 (111)
T 1we6_A           26 GPATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSG---KAGFLKD-NMSLAHYNVGAGEILT   99 (111)
T ss_dssp             SCEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEEC---SSSBCCT-TSBTTTTTCSSSCEEE
T ss_pred             CcEEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEE---CCEECCC-CCcHHHCCCCCCCEEE
Confidence            4578999998   89889999997 99999999999886422234556654   5677777 68999999996 5543

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=96.41  E-value=0.012  Score=48.27  Aligned_cols=70  Identities=14%  Similarity=0.200  Sum_probs=54.0

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +.+...|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|+| +.||.+.||.+ ++|
T Consensus        17 ~~~~m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~---~g~~L~d-~~tL~~~~i~~~~~l   87 (172)
T 3u30_A           17 RGSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTL   87 (172)
T ss_dssp             --CCEEEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEE---TTEECCT-TCBTGGGTCCTTCEE
T ss_pred             CCCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEE---CCccccc-cCCHhHcCCccccee
Confidence            4456889999999999999999999999999999885422234456654   5688877 68999999995 444

>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; ENDPLASMIC reticulum stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=96.41  E-value=0.028  Score=41.42  Aligned_cols=68  Identities=12%  Similarity=0.197  Sum_probs=52.3

Q ss_pred             CceEEEEEcCCCC--EEEEEeCCCCCHHHHHHHHHhhCCC--CCcCeEEEecCCCCcccCCccCcHhhh--CCCC-eeE
Q 025134          182 PSTSVQIRLADGT--RLIAHFNLHHTISDIHSFIDASRPG--TARNYQLQMMGFPPKVLADRTQTIEQA--GLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~--rlv~~fn~s~TI~dl~~fi~~~~p~--~~~~f~L~t~~fP~k~l~d~s~TL~ea--gL~n-avi  253 (257)
                      ...+|.||..+|+  .+.+.+..++||.+|.+.|....+.  ......|+.   -.+.|.| +.||.+.  ++.+ ++|
T Consensus         6 ~~m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~---~Gk~L~D-~~tL~~~~~~i~~~~~i   80 (93)
T 1wgd_A            6 SGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIY---SGKLLLD-HQCLRDLLPKQEKRHVL   80 (93)
T ss_dssp             CCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEE---TTEECCS-SSCHHHHSCSSSCSEEE
T ss_pred             cEEEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEE---CCEECcC-cCCHHHHhcCCCCCCEE
Confidence            3478999999998  5666677999999999999987532  245566764   5889987 4899999  9986 444

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=96.28  E-value=0.016  Score=42.98  Aligned_cols=65  Identities=14%  Similarity=0.178  Sum_probs=49.2

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...|.||.  |+.+.+.+..++||.+|...|.....-......|+.   -.+.|+| +.||++.|+.+ ++|
T Consensus        19 ~m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~y~I~~gstI   84 (93)
T 2l7r_A           19 SMQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLL---AGAPLED-EATLGQCGVEALTTL   84 (93)
T ss_dssp             -CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEE---TTEECCT-TSBHHHHTCCSSCEE
T ss_pred             cEEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEE---CCEECCC-CCcHHHCCCCCCCEE
Confidence            35667776  888899999999999999999885422234566654   5788876 68999999986 544

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A

Probab=96.25  E-value=0.023  Score=43.80  Aligned_cols=69  Identities=19%  Similarity=0.286  Sum_probs=53.2

Q ss_pred             CCceEEEEEcCC----------CCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          181 LPSTSVQIRLAD----------GTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       181 ~p~t~iqIRl~d----------G~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ....+|.|++++          |+.+.+.+..++||.+|...|.....-......|+.   -.+.|.| +.||.+.++.+
T Consensus        23 ~~~i~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~---~Gk~L~D-~~tL~~y~i~~   98 (115)
T 1we7_A           23 KGPVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQY---EGIFIKD-SNSLAYYNMAS   98 (115)
T ss_dssp             CSCEEEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEE---TTEEECT-TSBHHHHTCCS
T ss_pred             CCCEEEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEE---CCEECCC-CCCHHHCCCCC
Confidence            346889999985          667889999999999999999886422244566654   5788876 58999999986


Q ss_pred             -eeE
Q 025134          251 -SVV  253 (257)
Q Consensus       251 -avi  253 (257)
                       ++|
T Consensus        99 g~~i  102 (115)
T 1we7_A           99 GAVI  102 (115)
T ss_dssp             SCEE
T ss_pred             CCEE
Confidence             444

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1

Probab=96.24  E-value=0.015  Score=43.45  Aligned_cols=68  Identities=12%  Similarity=0.109  Sum_probs=49.6

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ....+|.|++ .|+.+.+.+..++||.+|.+-|.....-....-.|+   |..+.| |+. ||.+.+|.+ +.|+
T Consensus        15 ~~~~~i~Vk~-~g~~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~---~~Gk~L-dd~-tL~~~~i~~g~~i~   83 (95)
T 1v86_A           15 KELVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVM---YKGLVP-EDK-TLREIKVTSGAKIM   83 (95)
T ss_dssp             CCCEEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCB---SSSBCC-SSS-BHHHHCCCTTEEEE
T ss_pred             CceEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEE---ECCeeC-CcC-cHHHCCCCCCCEEE
Confidence            3457788885 677888999999999999999988542222333443   678888 444 999999986 5543

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=96.21  E-value=0.016  Score=44.76  Aligned_cols=67  Identities=16%  Similarity=0.194  Sum_probs=53.1

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .-.|.|+..+|+.+.+.+..++||.+|..-|.....-......|+.   -.+.|.| +.||.+.|+.+ ++|
T Consensus         9 ~~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~---~Gk~L~D-~~tL~~ygI~~gstI   76 (114)
T 2kdi_A            9 EFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIW---AGKQLED-GRTLSDYNIQRESTL   76 (114)
T ss_dssp             CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEE---TTEECCT-TCBTTTTTCCSSCEE
T ss_pred             cEEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEE---CCEECCC-CCcHHHCCCCCCCEE
Confidence            4578999999999999999999999999999885422234556654   5788876 68999999986 544

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=96.17  E-value=0.029  Score=42.47  Aligned_cols=70  Identities=16%  Similarity=0.247  Sum_probs=51.9

Q ss_pred             CCceEEEEEcCCCCEEEE--EeCCCCCHHHHHHHHHhhCCCC-CcCeEEEecCCCCcccCCccCcHhhhCC-C-CeeEE
Q 025134          181 LPSTSVQIRLADGTRLIA--HFNLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAGL-A-NSVVI  254 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~--~fn~s~TI~dl~~fi~~~~p~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL-~-naviv  254 (257)
                      .+...|.||..+|+.+.+  .+..++||++|.+.|.....+. ...-.|+.   -.+.|.| +.||.+.++ . +++|+
T Consensus        17 ~~~m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~---~Gk~L~D-~~tL~dy~I~~~g~ti~   91 (98)
T 4a20_A           17 NAAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLL---KGKVLHD-NLFLSDLKVTPANSTIT   91 (98)
T ss_dssp             -CCEEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEE---TTEEECT-TCBGGGSCCBTTBCEEE
T ss_pred             CCCEEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcCCChhhEEEEE---CCEECcC-cCCHHHcCcCCCCCEEE
Confidence            456789999999987655  6679999999999994433332 34556654   5788987 589999999 6 45554

>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 2kx3_A

Probab=96.17  E-value=0.023  Score=41.82  Aligned_cols=70  Identities=10%  Similarity=0.136  Sum_probs=52.2

Q ss_pred             CceEEEEEcCCCCEEEE-EeCCCCCHHHHHHHHHhhCCCCCcCeEEEecC-CCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIA-HFNLHHTISDIHSFIDASRPGTARNYQLQMMG-FPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~-~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~-fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...+|.|+. .|+.+.+ .+..++||.+|..-|.....-....-.|+. . |-.+.|.| +.||.+.||.+ +.|+
T Consensus         6 ~~m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~-~k~~Gk~L~D-~~~L~~~~i~~g~~l~   78 (90)
T 1v5t_A            6 SGLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLG-LKVKGKPAEN-DVKLGALKLKPNTKIM   78 (90)
T ss_dssp             CSCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEES-CEETTEECCT-TSBHHHHTCCTTEEEE
T ss_pred             ceEEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEe-eccCCcCcCC-CCCHHHcCCCCCCEEE
Confidence            346788886 6777788 889999999999999886433345566763 3 45678876 58999999985 5554

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=96.10  E-value=0.018  Score=43.24  Aligned_cols=67  Identities=12%  Similarity=0.071  Sum_probs=50.2

Q ss_pred             CceEEEEEcCCCCEE-EEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRL-IAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rl-v~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...+|.||. .|+.+ .+.+..++||.+|..-|.....-....-.|+   |..+.|.|+  ||.+.||.+ +.|+
T Consensus         6 ~~m~i~Vk~-~g~~~~~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi---~~Gk~L~D~--tL~~~~I~~g~~i~   74 (96)
T 1wgg_A            6 SGYSVTVKW-GKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVM---VKGGTLKDD--DWGNIKMKNGMTVL   74 (96)
T ss_dssp             CEEEEEEEE-TTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCE---ETTEECCSS--CCCSCCCCSSCEEE
T ss_pred             cEEEEEEEE-CCEEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEE---ECCcCCCCC--CHHHCCCCCCCEEE
Confidence            456778885 67777 5899999999999999988642223444554   578899885  999999985 5554

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=96.06  E-value=0.034  Score=42.16  Aligned_cols=69  Identities=10%  Similarity=0.180  Sum_probs=52.1

Q ss_pred             CCCceEEEEEcCCCC--EEEEEeCCCCCHHHHHHHHHhhCCCC--CcCeEEEecCCCCcccCCccCcHhhh--CCCCee
Q 025134          180 NLPSTSVQIRLADGT--RLIAHFNLHHTISDIHSFIDASRPGT--ARNYQLQMMGFPPKVLADRTQTIEQA--GLANSV  252 (257)
Q Consensus       180 s~p~t~iqIRl~dG~--rlv~~fn~s~TI~dl~~fi~~~~p~~--~~~f~L~t~~fP~k~l~d~s~TL~ea--gL~nav  252 (257)
                      +.....|.||.++|+  .+.+.+..++||.+|.+-|....++.  .....|+.   -.|.|.| +.||.+.  ++.+..
T Consensus        20 ~~~~m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy---~Gk~L~D-~~tL~~y~~~I~~~~   94 (99)
T 2kdb_A           20 QGHPVTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVY---SGRLLPD-HLQLKDILRKQDEYH   94 (99)
T ss_dssp             ---CEEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEE---TTEEECT-TSBTHHHHTTTCSEE
T ss_pred             CCCeEEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEE---CCEECCC-CCCHHHHhcCCCCCC
Confidence            345688999999998  46778899999999999999754332  24566664   5788986 5899999  998743

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1

Probab=96.06  E-value=0.036  Score=42.18  Aligned_cols=68  Identities=22%  Similarity=0.274  Sum_probs=51.9

Q ss_pred             CceEEEEEcCCC---CEEEEEeCC---------CCCHHHHHHHHHhhCCC--CCcC-eEEEecCCCCcccCCccCcHhhh
Q 025134          182 PSTSVQIRLADG---TRLIAHFNL---------HHTISDIHSFIDASRPG--TARN-YQLQMMGFPPKVLADRTQTIEQA  246 (257)
Q Consensus       182 p~t~iqIRl~dG---~rlv~~fn~---------s~TI~dl~~fi~~~~p~--~~~~-f~L~t~~fP~k~l~d~s~TL~ea  246 (257)
                      ...+|.||..+|   ....+.|..         ++||.+|...|....+.  .... ..|+   |-.+.|.| +.||.+.
T Consensus        11 ~~~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi---~~Gk~L~D-~~tL~~y   86 (107)
T 1x1m_A           11 SDWHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLI---YCGRKLKD-DQTLDFY   86 (107)
T ss_dssp             CSCCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEE---ETTEECCT-TCBHHHH
T ss_pred             CceEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEE---ECCeECCC-CCcHHHc
Confidence            346789999999   778888665         59999999999987632  2345 5665   46788976 5899999


Q ss_pred             CCCC-eeE
Q 025134          247 GLAN-SVV  253 (257)
Q Consensus       247 gL~n-avi  253 (257)
                      |+.+ ++|
T Consensus        87 ~i~~g~~i   94 (107)
T 1x1m_A           87 GIQPGSTV   94 (107)
T ss_dssp             TCCTTCEE
T ss_pred             CCCCCCEE
Confidence            9986 444

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=96.01  E-value=0.034  Score=44.03  Aligned_cols=64  Identities=17%  Similarity=0.218  Sum_probs=51.0

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC--------CcCeEEEecCCCCcccCCccCcHhhhCCC
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT--------ARNYQLQMMGFPPKVLADRTQTIEQAGLA  249 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~--------~~~f~L~t~~fP~k~l~d~s~TL~eagL~  249 (257)
                      ....|.||+.+|+...+.+..++||++|.+.|....|..        .....|+   |=.|.|+| +.||.+.++.
T Consensus        16 ~~m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLI---y~GK~LeD-~~TL~~y~I~   87 (125)
T 2gow_A           16 DMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLI---YQGRFLHG-NVTLGALKLP   87 (125)
T ss_dssp             TCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEE---SSSSEEES-SCBTGGGCCC
T ss_pred             CeEEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEE---ECCcCCCC-CCcHHHcCCC
Confidence            357899999999999999999999999999998754321        1234454   57788887 5899999997

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=95.97  E-value=0.038  Score=41.17  Aligned_cols=74  Identities=11%  Similarity=0.167  Sum_probs=54.1

Q ss_pred             CceEEEEEcC---CCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEec--CCCCc--ccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLA---DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMM--GFPPK--VLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~---dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~--~fP~k--~l~d~s~TL~eagL~n-avi  253 (257)
                      ...+|.|+.+   +|..+..+|..+.||++|...|.....-......|...  .+|..  .|+|++.||..-|+.+ ..|
T Consensus         8 ~~v~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~gip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I   87 (97)
T 1wjn_A            8 QLLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCL   87 (97)
T ss_dssp             CEEEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEE
T ss_pred             ccEEEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHHCCChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEE
Confidence            4567888864   67789999999999999999998865333445566542  15533  3678899999999996 455


Q ss_pred             Ee
Q 025134          254 IQ  255 (257)
Q Consensus       254 vq  255 (257)
                      ..
T Consensus        88 ~V   89 (97)
T 1wjn_A           88 LV   89 (97)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B

Probab=95.95  E-value=0.025  Score=44.69  Aligned_cols=65  Identities=15%  Similarity=0.238  Sum_probs=51.2

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|+.+.+.+..++||++|...|.....-......|+.   ..+.|+| +.||.+.|+.+ ++|
T Consensus         2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~L~~---~g~~L~d-~~tL~~~~i~~~~~l   67 (152)
T 3b08_A            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTL   67 (152)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEE---TTEECCT-TSBTGGGTCCTTCEE
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHeEEEE---CCeECcC-cccHHHhccCCCCee
Confidence            58899999999999999999999999999875422234456654   5788876 68999999986 444

>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural genomics, protein structure initiative, CESG; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=95.93  E-value=0.033  Score=44.29  Aligned_cols=65  Identities=20%  Similarity=0.299  Sum_probs=51.7

Q ss_pred             CceEEEEEcCCCCEE-EEEeCCCCCHHHHHHHHHhhCCCC--C-----cCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          182 PSTSVQIRLADGTRL-IAHFNLHHTISDIHSFIDASRPGT--A-----RNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       182 p~t~iqIRl~dG~rl-v~~fn~s~TI~dl~~fi~~~~p~~--~-----~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ....|.||+.+|+.+ .+.|..++||.+|.+-|....|..  .     ..-.|+   |-.|.|+| +.||.+.++..
T Consensus        15 ~~~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLI---y~GK~LeD-~~TLsdy~I~~   87 (126)
T 1se9_A           15 NQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLI---SAGKVLEN-SKTVKDYRSPV   87 (126)
T ss_dssp             CCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEE---ETTEECCT-TSBGGGGSCCT
T ss_pred             ccEEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEE---ECCeECcC-CCcHHHcCCCc
Confidence            568899999999988 699999999999999998765432  1     223444   46788887 58999999985

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A

Probab=95.91  E-value=0.027  Score=45.33  Aligned_cols=67  Identities=16%  Similarity=0.241  Sum_probs=52.2

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCC-CCcccCCccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGF-PPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~f-P~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ..|.||..+|+.+.+.+..++||.+|..-|.....-....-.|+.  | ..+.|.| +.||.+.|+.+ ++|
T Consensus         3 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~--~~~g~~L~d-~~tL~~y~i~~~~~l   71 (159)
T 3rt3_B            3 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAV--HPSGVALQD-RVPLASQGLGPGSTV   71 (159)
T ss_dssp             CEEEEEETTSCEEEEECCTTCCHHHHHHHHHHHHCCCGGGEEEEE--ETTCCBCCT-TSCGGGGTCCTTCEE
T ss_pred             eEEEEEECCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEE--cCCCCCCCC-CCCHHHcCCCCCCEE
Confidence            468899899999999999999999999999885422233455552  6 5788865 68999999995 444

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=95.91  E-value=0.026  Score=41.85  Aligned_cols=67  Identities=18%  Similarity=0.284  Sum_probs=51.1

Q ss_pred             eEEEEEcCCCCEEEEE--eCCCCCHHHHHHHH-HhhCCCC-CcCeEEEecCCCCcccCCccCcHhhhCC--CCeeEEe
Q 025134          184 TSVQIRLADGTRLIAH--FNLHHTISDIHSFI-DASRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAGL--ANSVVIQ  255 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~--fn~s~TI~dl~~fi-~~~~p~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL--~navivq  255 (257)
                      ..|-||..+|+.+.+.  +..++||.+|.+.| .. ..+. .....|+.   -.|.|.| +.||.+.++  .+++|..
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~-~~gip~~~QrLi~---~Gk~L~D-~~tL~~y~I~~~~stl~v   74 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISE-EKASHISEIKLLL---KGKVLHD-NLFLSDLKVTPANSTITV   74 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHT-TSCSSSTTEEEEE---TTEECCT-TCBHHHHCCCGGGCEEEE
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHH-hcCCChHHEEEEE---CCEECcC-cCCHHHcCCCCCCCEEEE
Confidence            4688999999987776  55999999999999 55 3332 45566664   6789987 589999999  3577654

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=95.80  E-value=0.053  Score=40.70  Aligned_cols=72  Identities=7%  Similarity=0.064  Sum_probs=53.4

Q ss_pred             CCceEEEEEcCCCC--EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCc---ccCCccCcHhhhCCCC-eeE
Q 025134          181 LPSTSVQIRLADGT--RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPK---VLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       181 ~p~t~iqIRl~dG~--rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k---~l~d~s~TL~eagL~n-avi  253 (257)
                      ....+|.|+...++  .+.+++..++||++|..-|.....-....-.|+. ..+.+   .|.+++.||.+.|+.+ ++|
T Consensus        13 ~~~v~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~-~~~g~~~~~L~~D~~tL~~Y~i~~gsti   90 (95)
T 2kjr_A           13 SDFIKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQV-FKGDTCVSTMDNNDAQLGYYANSDGLRL   90 (95)
T ss_dssp             CCEEEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEE-EETTEEEEECCCTTSBHHHHCCSSSCEE
T ss_pred             CCeEEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEE-ecCCcccceeCCCCCCHhHCCcCCCCEE
Confidence            45678888887775  6899999999999999999885422244556665 43444   5656689999999986 554

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=95.79  E-value=0.034  Score=47.11  Aligned_cols=68  Identities=16%  Similarity=0.240  Sum_probs=54.1

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...|.||..+|+.+.+.+..++||.+|..-|.....-......|+   |-.+.|+| +.||.+.++.+ ++|.
T Consensus       105 eMqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi---~~Gk~L~D-~~tL~dygI~~gstI~  173 (189)
T 3q3f_A          105 GGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI---FAGKQLED-GRTLSDYNIQKESTLH  173 (189)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEE---ETTEECCT-TCBGGGGTCCTTCEEE
T ss_pred             ceeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccCCCHHHEEEE---ECCEECCC-CCCHHHCCCCCCCEEE
Confidence            368899999999999999999999999999987542223445565   46788987 68999999985 5553

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=95.78  E-value=0.035  Score=40.47  Aligned_cols=67  Identities=18%  Similarity=0.298  Sum_probs=48.9

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +..+.+. .+|+.+.+.+..+.||++|...|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|.
T Consensus        12 ~~~~~~~-~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~---~Gk~L~D-~~tL~~~gi~~g~~l~   79 (85)
T 2kd0_A           12 TIKLTVK-FGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIF---KGKVLVE-TSTLKQSDVGSGAKLM   79 (85)
T ss_dssp             CEEEEEE-ETTEEEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEE---TTEECCT-TCBTTTTTCCTTEEEE
T ss_pred             cEEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEE---CCeECCC-cCCHHHCCCCCCCEEE
Confidence            3444444 47888889999999999999999875422234556653   5788876 58999999986 5553

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=95.74  E-value=0.027  Score=42.97  Aligned_cols=70  Identities=26%  Similarity=0.321  Sum_probs=48.7

Q ss_pred             eEEEEEcCCCCEEEEEeC-CCCCHHHHHHHHHhhCCCCCcCeEEEecCC------CCc--cc---CCccCcHhhhCCCC-
Q 025134          184 TSVQIRLADGTRLIAHFN-LHHTISDIHSFIDASRPGTARNYQLQMMGF------PPK--VL---ADRTQTIEQAGLAN-  250 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn-~s~TI~dl~~fi~~~~p~~~~~f~L~t~~f------P~k--~l---~d~s~TL~eagL~n-  250 (257)
                      ..|+||..+|+. .+.+. .++||.+|.+-|.....-......|...+.      |+.  .|   .+++.||.+.||.+ 
T Consensus         8 M~irvrs~~G~~-~v~v~~~~~Tv~~LK~kI~~~~gip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~G   86 (107)
T 1wf9_A            8 TMLRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHG   86 (107)
T ss_dssp             EEEEEECSSCEE-EEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTT
T ss_pred             EEEEEECCCCCE-EEEECCCCCcHHHHHHHHHHHhCcCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCCC
Confidence            579999999965 56788 999999999999876543333444432122      111  44   46689999999996 


Q ss_pred             eeEE
Q 025134          251 SVVI  254 (257)
Q Consensus       251 aviv  254 (257)
                      ++|.
T Consensus        87 ~~L~   90 (107)
T 1wf9_A           87 SMVY   90 (107)
T ss_dssp             CEEE
T ss_pred             CEEE
Confidence            5554

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A

Probab=94.71  E-value=0.0017  Score=45.83  Aligned_cols=65  Identities=17%  Similarity=0.267  Sum_probs=49.1

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|+.+.+.+..++||++|...|.....-......|+   |-.+.|.| +.||.+.|+.+ ++|
T Consensus         2 ~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~---~~gk~L~d-~~tL~~~~i~~g~~i   67 (76)
T 3b1l_X            2 IVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVI---FAGKELPN-HLTVQNCDLEQQSIV   67 (76)
Confidence            4778889998888999999999999999987532122334443   56788876 58999999986 443

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B

Probab=95.59  E-value=0.04  Score=43.44  Aligned_cols=69  Identities=14%  Similarity=0.205  Sum_probs=54.2

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +...|.|+..+|+.+.+.+..++||.+|..-|.....-......|+.   ..+.|+| +.||++.|+.+ ++|.
T Consensus        75 ~~~~i~Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~qrL~~---~g~~L~d-~~tL~~~~i~~~~~i~  144 (152)
T 3b08_A           75 GGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTLH  144 (152)
T ss_dssp             TCEEEEEEESSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEE---TTEECCT-TSBTGGGTCCTTCEEE
T ss_pred             cccceeeeecCCCEEEEEeCCCCcHHHHHHHHHHHhCcChhhEEEEE---CCEECCC-CCCHHHcCCCCCCEEE
Confidence            34678899999999999999999999999999875422234566654   6788876 68999999985 5543

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.58  E-value=0.041  Score=40.66  Aligned_cols=71  Identities=17%  Similarity=0.242  Sum_probs=51.7

Q ss_pred             eEEEEEcCCCCEE--EE-EeCCCCCHHHHHHHHHhhCCC-CCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEEee
Q 025134          184 TSVQIRLADGTRL--IA-HFNLHHTISDIHSFIDASRPG-TARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQK  256 (257)
Q Consensus       184 t~iqIRl~dG~rl--v~-~fn~s~TI~dl~~fi~~~~p~-~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avivqk  256 (257)
                      ..|-|+...|+..  .+ .+..++||.+|.+-|....+. ....-.|.. .+=.+.|.| +.||++.|+.+ ++|+.|
T Consensus        11 M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~-~~~Gk~L~D-~~tL~~y~i~~~stl~~K   86 (88)
T 2dzj_A           11 YEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRL-DPKGKSLKD-EDVLQKLPVGTTATLYFR   86 (88)
T ss_dssp             EEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEES-STTSCCCCT-TCBTTTSSCCSEEEEEEC
T ss_pred             EEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEe-cCCCcCcCC-CCCHHHcCCCCCCEEEEE
Confidence            5677888888764  36 889999999999999885333 233345554 444678876 68999999996 666654

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A

Probab=95.50  E-value=0.061  Score=43.18  Aligned_cols=68  Identities=19%  Similarity=0.233  Sum_probs=54.3

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +...|.||..+|+.+.+.+..++||++|..-|.....-......|+.   -.+.|.| +.||.+.|+.+ ++|
T Consensus        80 ~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~q~L~~---~G~~L~d-~~tL~~y~i~~g~~l  148 (159)
T 3rt3_B           80 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTF---EGKPLED-QLPLGEYGLKPLSTV  148 (159)
T ss_dssp             CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEE---TTEECCT-TSBGGGGTCCTTCEE
T ss_pred             CcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCHHHEEEEE---CCeecCC-CCCHHHcCCCCCCEE
Confidence            45788999999999999999999999999999875322235567764   5688887 68999999996 554

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.43  E-value=0.11  Score=40.95  Aligned_cols=70  Identities=13%  Similarity=0.245  Sum_probs=53.2

Q ss_pred             CCCceEEEEE-cCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCeeE
Q 025134          180 NLPSTSVQIR-LADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVV  253 (257)
Q Consensus       180 s~p~t~iqIR-l~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~navi  253 (257)
                      .++..+|.|. .++|.+++..|..+.||++|.+.++....-....-.|   -|-.|.|.| +.||++.|+.+.-.
T Consensus        12 ~~~~itvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrL---Iy~GKiLKD-~eTL~~~gIk~g~T   82 (118)
T 2daf_A           12 EDSLATVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQI---RYSGKILKN-NETLVQHGVKPQEI   82 (118)
T ss_dssp             CSSCEEEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHTCCTTTEEE---EETTEEECS-SCCHHHHSCCSSCE
T ss_pred             cCccEEEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhCCChHHEEE---EECCeEcCC-cchHHHcCCCCCCE
Confidence            4456778887 6788899999999999999999998753222333444   457999987 57999999986433

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=95.39  E-value=0.063  Score=44.34  Aligned_cols=65  Identities=17%  Similarity=0.246  Sum_probs=51.9

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|+.+.+.+..++||.+|...|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|
T Consensus         2 qI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~---~Gk~L~D-~~tL~~y~I~~gstI   67 (169)
T 3l0w_B            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTL   67 (169)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEE---TTEECCT-TSBGGGGTCCTTCEE
T ss_pred             EEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEE---CCccccC-cCcHHHcCCCCCCEE
Confidence            58899999999999999999999999999875432234556664   5678877 68999999996 544

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=95.35  E-value=0.019  Score=43.40  Aligned_cols=66  Identities=18%  Similarity=0.217  Sum_probs=49.9

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .+|.||. +|+.+.+.+..++||++|.+.|.....-......|+.   -.+.|+| +.||.+.|+.+ ++|.
T Consensus        29 i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~---~Gk~L~D-~~tL~~~gI~~g~tI~   95 (101)
T 3m63_B           29 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIY---SGKILKD-DQTVESYHIQDGHSVH   95 (101)
T ss_dssp             CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEE---TTEECCT-TSBTTTTTCCTTEEEE
T ss_pred             EEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHCcChHHEEEEE---CCEECCC-cCcHHHCCCCCCCEEE
Confidence            4677876 8888888999999999999999875422233445554   5688877 68999999996 5543

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=94.58  E-value=0.13  Score=41.99  Aligned_cols=69  Identities=14%  Similarity=0.205  Sum_probs=54.5

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +...|.||..+|+.+.+++..++||.+|..-|.....-......|+.   -.+.|+| +.||.+.++.+ ++|.
T Consensus        95 gg~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~q~L~~---~g~~L~D-~~tL~~y~i~~g~tl~  164 (172)
T 3u30_A           95 GGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTLH  164 (172)
T ss_dssp             CCEEEEEEESSCCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEE---TTEECCT-TSBSGGGTCCTTCEEE
T ss_pred             ccccceeecccCcceeEEecCCCCHHHHHHHHHHHhCCCceeEEEEE---CCccCCC-CCcHHHhCCCCCCEEE
Confidence            45678899999999999999999999999999885422245566764   5788876 68999999996 5553

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=94.48  E-value=0.13  Score=46.65  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=55.1

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ......|.||..+|+.+.+.+..++||++|.+-|.....-....-.|+.   ..+.|+| +.||.+.|+.+ ++|
T Consensus       230 ~~~~MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~---~Gk~L~D-~~TLsdygI~~gstL  300 (307)
T 3ai5_A          230 ITGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTL  300 (307)
T ss_dssp             SCCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEE---TTEECCT-TSBTGGGTCCTTCEE
T ss_pred             CCCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEe---CCeecCC-CCCHHHcCCCCCCEE
Confidence            3456789999999999999999999999999999875422234556654   5788876 68999999985 544

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.03  E-value=0.3  Score=36.99  Aligned_cols=67  Identities=9%  Similarity=0.184  Sum_probs=47.5

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ..+.+++ .|+.+.+.+..++||++|..-|.....-....-.|+  .||...|.| +.||.+.+|.+ ++|+
T Consensus        10 ~~~~vk~-~Gk~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi--~~~~gkL~D-~~tLs~~~I~~gstL~   77 (100)
T 2dzm_A           10 LDFRVEY-RDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLK--GWKTGDVED-STVLKSLHLPKNNSLY   77 (100)
T ss_dssp             EEEEEEC-SSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEE--CCSSSCCCT-TSBHHHHCCCSEEEEE
T ss_pred             EEEEEEe-CCeEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEE--ccCCCCCCC-cCCHHHcCCCCCCEEE
Confidence            4566666 677788899999999999999987532222222343  567666765 68999999996 5554

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A

Probab=93.86  E-value=0.12  Score=47.98  Aligned_cols=68  Identities=13%  Similarity=0.259  Sum_probs=53.2

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhC--CCC-CcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASR--PGT-ARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~--p~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...+|.||..+|+.+.+.+..++||.+|...|....  ... .....|+   |-.|.|.| +.||.+.||.+ ++|
T Consensus         6 ~~M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLi---y~GK~L~D-~~tL~dygI~~gstI   77 (368)
T 1oqy_A            6 SAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLI---YAGKILSD-DVPIRDYRIDEKNFV   77 (368)
T ss_dssp             CCCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEE---SSSSEECS-SSBTTTTCCCTTSCE
T ss_pred             ceEEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEE---ECCeecCC-cCCHHHcCCCCCCEE
Confidence            356799999999999999999999999999998842  111 2344554   57899987 58999999995 444

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4b6a_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p

Probab=93.61  E-value=0.012  Score=46.24  Aligned_cols=65  Identities=18%  Similarity=0.273  Sum_probs=0.0

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.|+..+|+.+.+.+..++||++|..-|.....-......|+   |-.+.|+| +.||.+.|+.+ ++|
T Consensus         2 ~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi---~~Gk~L~D-~~tL~~~~I~~gsti   67 (128)
T 3u5e_m            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLI---FAGKQLED-GRTLSDYNIQKESTL   67 (128)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             EEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCcChHHEEEE---ECCEECCC-CCchhhhccCCCCEE
Confidence            4678889999999999999999999999977431112333443   57788876 68999999985 444

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=93.53  E-value=0.3  Score=36.61  Aligned_cols=65  Identities=17%  Similarity=0.195  Sum_probs=53.3

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|-|..++|.|...+...+.|+.+|.+-..+.-.-....|.|..   -+|.| |.++.+.=+||-| |.+
T Consensus        11 ~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~gl~~~~~~Lkh---~~k~l-DLSlpfRlsgLpnnAkL   76 (90)
T 2al3_A           11 AVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKF---QRTVL-DLSLQWRFANLPNNAKL   76 (90)
T ss_dssp             CEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEE---TTEEE-SSSCBHHHHCCCSSCEE
T ss_pred             EEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhCCChhhCeEEe---CCEec-cccceeEecCCCCCCEE
Confidence            68899999999999999999999998777665433467899987   46767 7789999999996 544

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=93.37  E-value=0.64  Score=34.84  Aligned_cols=74  Identities=12%  Similarity=0.079  Sum_probs=52.1

Q ss_pred             CCCceEEEEEcCCCC--EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCc---ccCCccCcHhhhCCCC-eeE
Q 025134          180 NLPSTSVQIRLADGT--RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPK---VLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       180 s~p~t~iqIRl~dG~--rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k---~l~d~s~TL~eagL~n-avi  253 (257)
                      .....+|.|.....+  .+.++|..++||++|..-|.....-....-.|+..+=..+   .|.+++.||.+.++.+ ++|
T Consensus        11 ~~~~v~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~~Gip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~I   90 (97)
T 2kj6_A           11 GDDSVHLHITHANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRL   90 (97)
T ss_dssp             CCCCEEEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEE
T ss_pred             CCceEEEEEEECCCCceEEEEEeCCCChHHHHHHHHHHHHCcCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEE
Confidence            456678888876664  6899999999999999999885422234556654121123   3556689999999986 554

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1

Probab=93.23  E-value=0.54  Score=34.87  Aligned_cols=65  Identities=14%  Similarity=0.208  Sum_probs=50.8

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ...+|.|+..+|+.+.+++..++++..|.+..+....-....+.|+   |--+.|.+ +.|.++++|-+
T Consensus         4 ~~i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~---FdG~~l~~-~~Tp~dl~med   68 (91)
T 2io0_B            4 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFR---FDGQPINE-TDTPAQLEMED   68 (91)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEE---ETTEECCT-TCCTTTTTCCT
T ss_pred             CeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEE---ECCEEcCC-CCCHHHcCCCC
Confidence            3467888888999999999999999999988877543234556655   46788876 48999999985

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B

Probab=93.08  E-value=0.48  Score=33.22  Aligned_cols=66  Identities=14%  Similarity=0.228  Sum_probs=50.6

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .+|.|+..+|+.+.+++..+++++.|.+..+....-....+.|+   |-.+.|.+ +.|.+++++-+ .+|
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~---fdG~~l~~-~~Tp~~l~medgD~I   68 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFR---FDGQPINE-TDTPAQLEMEDEDTI   68 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEE---ETTEECCT-TCCTTTTTCCTTEEE
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcceEEEE---ECCEEcCC-CCCHHHcCCCCCCEE
Confidence            46888889999999999999999999988776432223556655   46778876 48999999986 444

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=92.97  E-value=0.018  Score=47.12  Aligned_cols=65  Identities=18%  Similarity=0.260  Sum_probs=0.0

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|+.+.+.+..++||++|...|.....-......|   -|-.+.|+| +.||.+.||.+ ++|
T Consensus         2 qI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~gip~~~QrL---i~~Gk~L~D-~~tL~dygI~~gstL   67 (152)
T 3u5c_f            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRL---IFAGKQLED-GRTLSDYNIQKESTL   67 (152)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEE---EECCEEccc-cCcHHHcCCCCCCEE
Confidence            477889999988999999999999999997743211223334   357788877 58999999985 444

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=92.80  E-value=0.38  Score=35.87  Aligned_cols=65  Identities=14%  Similarity=0.208  Sum_probs=50.4

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ...+|.|+-.+|+.+.+++..++++..|.+.++....-....+.|+   |--+.|.+ +.|+++++|-+
T Consensus         6 ~~i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~---FdG~~l~~-~~Tp~dl~med   70 (94)
T 2io1_B            6 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFR---FDGQPINE-TDTPAQLEMED   70 (94)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TCCTTTTTCCT
T ss_pred             CeEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhCCCcccEEEE---ECCEEcCC-CCCHHHcCCCC
Confidence            3467788888999999999999999999988876543223455554   56888876 48999999985

>1v6e_A Cytoskeleton-associated protein 1; tubulin-specific chaperone B, tubulin folding cofactor B, microtubule, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=92.55  E-value=0.52  Score=34.72  Aligned_cols=70  Identities=13%  Similarity=0.090  Sum_probs=49.1

Q ss_pred             eEEEEEcCCCC-EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCC-CCcc---cCCccCcHhhhCCCC-eeEE
Q 025134          184 TSVQIRLADGT-RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGF-PPKV---LADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~-rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~f-P~k~---l~d~s~TL~eagL~n-aviv  254 (257)
                      .+|.|+..... ...+++..++||++|..-|.....-....-.|.. .- +.+.   |.+++.||.+.|+.+ ++|.
T Consensus         8 v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~-~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~   83 (95)
T 1v6e_A            8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELEL-YGADDKFYSKLDQEDALLGSYPVDDGCRIH   83 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEE-ECSSSCEEEECCCSSSBTTSSSCCTTCEEE
T ss_pred             EEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEE-eCCCCccccccCCCcCCHhHCCCCCCCEEE
Confidence            66777766553 5889999999999999999886422234455554 33 2343   555679999999986 5543

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=92.47  E-value=1.1  Score=32.12  Aligned_cols=65  Identities=9%  Similarity=0.114  Sum_probs=49.9

Q ss_pred             CceEEEEEcCCCC-EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          182 PSTSVQIRLADGT-RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       182 p~t~iqIRl~dG~-rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ...+|.|+..+|+ .+.+++..++++..|.+..+....-....+.|+   |=.+.|.+ +.|.++++|-+
T Consensus         6 ~~i~ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~gi~~~~~rf~---fdG~~l~~-~~Tp~~l~med   71 (79)
T 3a4r_A            6 QELRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMGLSGHKLSFF---FDGTKLSG-KELPADLGLES   71 (79)
T ss_dssp             CCEEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHTCTTCCCEEE---ETTEECCS-CCCHHHHTCCT
T ss_pred             CEEEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhCCCcccEEEE---ECCEEcCC-CCCHHHcCCCC
Confidence            3467888889996 899999999999999988876532223445554   46777876 58999999985

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=92.43  E-value=0.65  Score=34.39  Aligned_cols=65  Identities=14%  Similarity=0.208  Sum_probs=50.3

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ...+|.|+..+|+.+.+++..++++..|.+.++....-....+.|+   |=.+.|.+ +.|.++++|-+
T Consensus        16 ~~i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~---fdG~~l~~-~~Tp~dl~med   80 (93)
T 2d07_B           16 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFR---FDGQPINE-TDTPAQLEMED   80 (93)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TCCTTTTTCCT
T ss_pred             CeEEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHhCCCccceEEE---ECCEEcCC-CCCHHHcCCCC
Confidence            4567888888999999999999999999988876543233445554   56888876 48999999985

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=92.33  E-value=0.73  Score=35.06  Aligned_cols=65  Identities=14%  Similarity=0.208  Sum_probs=50.3

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ...+|.|+-.+|+.+.+++..++++..|.+.++....-....+.|+   |--+.|.+ +.|.++++|-+
T Consensus        23 ~~I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~---FdG~~l~~-~~Tp~dl~med   87 (104)
T 1wz0_A           23 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFR---FDGQPINE-TDTPAQLEMED   87 (104)
T ss_dssp             CCEEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHTCCTTTSCEE---SSSSBCCT-TSCTTTTTCCT
T ss_pred             CeEEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCcceEEEE---ECCEEcCC-CCCHHHcCCCC
Confidence            4577888888999999999999999999988776542223445554   56778876 48999999985

>2daj_A KIAA0977 protein, COBL-like 1; ubiquitin-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=92.30  E-value=0.64  Score=34.56  Aligned_cols=69  Identities=14%  Similarity=0.197  Sum_probs=57.3

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      +-+.+++|-++--+..+.|.+..-++++|.-.|.....-....|.|.- ..=..+--|.+.+|.|.||..
T Consensus         8 E~TvRLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kcefdp~~~~Ll~-d~~~~e~LdLskSLndlgirE   76 (91)
T 2daj_A            8 EKTVRVVINFKKTQKTIVRVSPHASLQELAPIICSKCEFDPLHTLLLK-DYQSQEPLDLTKSLNDLGLRE   76 (91)
T ss_dssp             CSCEEEEEEETTTEEEEEEECSSSCTTTHHHHHHHHTTCCTTSEEEES-CSSCCCBCCTTSCHHHHTCSE
T ss_pred             ccEEEEEEeecCcceeEEEeCCCCcHHHHHHHHhhcccCChhhEEEec-CCCCCcccchhcchhhhhhhh
Confidence            357899999998888999999999999999999987755567888887 554444447789999999986

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=91.52  E-value=1  Score=34.64  Aligned_cols=65  Identities=14%  Similarity=0.227  Sum_probs=50.5

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ...+|.|+..+|+.+.+++..++++..|.+.++....-....+.|+   |--+.|.+ +.|.++++|-+
T Consensus        25 ~~I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfi---FdG~~L~~-~~Tp~dl~mED   89 (110)
T 2k8h_A           25 ALVAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFL---FDGTPIDE-TKTPEELGMED   89 (110)
T ss_dssp             CCEEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEE---SSSCBCCS-SSHHHHHHCSS
T ss_pred             CeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEE---ECCEEcCC-CCCHHHcCCCC
Confidence            4577888888999999999999999999988776432223445554   57788876 48999999986

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A

Probab=90.86  E-value=0.58  Score=36.61  Aligned_cols=60  Identities=12%  Similarity=0.223  Sum_probs=44.7

Q ss_pred             EEEEcCCCC-EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCC
Q 025134          186 VQIRLADGT-RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLA  249 (257)
Q Consensus       186 iqIRl~dG~-rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~  249 (257)
                      ++||.--|+ .+.+.+..++||.+|..-|.....-......|+   |-.|.|+| +.||.+.|+.
T Consensus         3 mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~egIP~~qQrLi---~~Gk~LeD-~~TLsdy~I~   63 (118)
T 2fnj_B            3 VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLY---KDDQLLDD-GKTLGECGFT   63 (118)
T ss_dssp             EEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEE---ETTEECCT-TSBHHHHTCC
T ss_pred             EEEEEecCCEEEEEEeCCcChHHHHHHHHHHHhCCCHHHeEEE---ECCeECCC-CCCHHHcCcc
Confidence            455555565 478899999999999999987532223455665   46788876 6999999999

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1

Probab=89.92  E-value=2  Score=32.76  Aligned_cols=64  Identities=5%  Similarity=0.108  Sum_probs=48.9

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ...+|.|+- +|+.+.+++..++++..|.+.++....-....+.|+   |=-+.|.+ +.|.++++|-+
T Consensus        30 ~~I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~---FdG~rl~~-~~Tp~dl~med   93 (106)
T 2eke_C           30 THINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFL---YDGIRIQA-DQTPEDLDMED   93 (106)
T ss_dssp             SEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TCCTTTTTCCT
T ss_pred             CeEEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhCCCcccEEEE---ECCeEcCC-CCCHHHcCCCC
Confidence            456778888 899999999999999999988876442223445554   56778876 48999999985

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=89.04  E-value=0.68  Score=42.01  Aligned_cols=70  Identities=14%  Similarity=0.099  Sum_probs=51.9

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecC-CCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMG-FPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~-fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...+|.|+. .|+...+.+..++||++|..-|.....-....-.|+. . |..+.|.| +.||.+.||.+ +.|+
T Consensus         4 ~~i~i~Vk~-~g~~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~-~k~~Gk~l~D-~~~L~~~~ik~g~~l~   75 (320)
T 3shq_A            4 KEVVVIVKW-SGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLN-LKYKGKTAAD-NVKISALELKPNFKLM   75 (320)
T ss_dssp             CEEEEEEEE-TTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETT-CBSSSSBCCT-TSBTTSSCCC--CEEE
T ss_pred             ceEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEee-cccCCcccCc-cccHHHcCCCCCCEEE
Confidence            346788886 6888899999999999999999875422233445652 2 67788887 58999999995 5554

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1

Probab=88.79  E-value=1.7  Score=33.50  Aligned_cols=72  Identities=10%  Similarity=0.189  Sum_probs=49.0

Q ss_pred             ceEEEEEcCCCC-EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCc---ccCCccCcHhhhCCCC-eeEE
Q 025134          183 STSVQIRLADGT-RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPK---VLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       183 ~t~iqIRl~dG~-rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k---~l~d~s~TL~eagL~n-aviv  254 (257)
                      ..+|.|+...+. .+.+++..+.||++|..-|.....-....-.|...+=..+   .|.+++.||.+.||.+ ++|.
T Consensus         6 ~v~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ih   82 (122)
T 1t0y_A            6 VYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIH   82 (122)
T ss_dssp             EEEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEE
T ss_pred             EEEEEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEE
Confidence            466777766554 5889999999999999999886422234455554110123   3455689999999986 5553

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1

Probab=87.45  E-value=2.4  Score=32.96  Aligned_cols=66  Identities=9%  Similarity=0.142  Sum_probs=50.1

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ....+|+|+-.||..+.+++..+.++..|.+..+....-....+.++   |-.+.|.+ +.|.++++|-+
T Consensus        38 ~~~I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~Gl~~~~irFl---FDG~rI~~-~~TP~dL~MED  103 (115)
T 3kyd_D           38 GEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFL---FEGQRIAD-NHTPKELGMEE  103 (115)
T ss_dssp             -CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCTTSEEEE---ETTEECCT-TCCTTTTTCCT
T ss_pred             CCeEEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhCCChhhEEEE---ECCeECCC-CCCHHHcCCCC
Confidence            35667788888999999999999999999987766432223455554   46778876 58999999986

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=85.25  E-value=1.8  Score=31.46  Aligned_cols=69  Identities=17%  Similarity=0.184  Sum_probs=44.2

Q ss_pred             eEEEEEcC-CCCE-EEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecC----CCCcccCCccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLA-DGTR-LIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMG----FPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~-dG~r-lv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~----fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .+|.|.-. .+.+ ...||..++||++|..-|.....-....-.|....    |..+.++| +.||.+-|+.+ ++|
T Consensus         3 V~v~iths~~~~~~~E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d-~~tL~~Y~i~~g~~i   78 (86)
T 4b6w_A            3 VKVSLTHSASRMRVPEKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMAN-DKQLGYYQCRDEFVI   78 (86)
T ss_dssp             EEEEEEETTCSCCEEEEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCT-TSBGGGGTCCTTCEE
T ss_pred             EEEEEEEcCCCCeEEEEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCC-CCCHHHCCCCCCCEE
Confidence            34555432 2334 58999999999999999987532223344555311    33344444 69999999996 554

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=84.91  E-value=2.7  Score=32.10  Aligned_cols=64  Identities=11%  Similarity=0.111  Sum_probs=43.6

Q ss_pred             CceEEEEEcCC--C--CEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCC
Q 025134          182 PSTSVQIRLAD--G--TRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLA  249 (257)
Q Consensus       182 p~t~iqIRl~d--G--~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~  249 (257)
                      ...+++|.+.|  +  ..+.+.+..++||++|.+-|.....-....-.|..   -.+ +.+++.||.+.|+.
T Consensus        21 ~~i~l~v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~---ggk-ll~D~~TL~~ygI~   88 (105)
T 4dbg_A           21 QDIRLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVI---GQR-LARDQETLHSHGVR   88 (105)
T ss_dssp             CCEEEEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEE---TTE-EECTTCBTGGGTCC
T ss_pred             CcEEEEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhCCCHHHEEEec---cCe-EccCcCcHHHcCCC
Confidence            35677777766  3  35788999999999999999875321222223443   455 44447999999994

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=82.38  E-value=13  Score=27.83  Aligned_cols=68  Identities=9%  Similarity=0.144  Sum_probs=49.7

Q ss_pred             CCCceEEEEEcCCCC-EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCe
Q 025134          180 NLPSTSVQIRLADGT-RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANS  251 (257)
Q Consensus       180 s~p~t~iqIRl~dG~-rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~na  251 (257)
                      .....+|+|+-.||. .+.+++..+.++..|.+..+....-....+.++   |=...|.. +.|.++++|-+.
T Consensus        22 ~~~~I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~---FDG~rI~~-~~TP~dLdMEDg   90 (97)
T 2jxx_A           22 TSQQLQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMGLSGRKLSFF---FDGTKLSG-RELPADLGMESG   90 (97)
T ss_dssp             SCSEEEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTTCSSSCCEEE---ETTEECCS-CSCHHHHTCCTT
T ss_pred             CCCeEEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHCCCcccEEEE---ECCEEcCC-CCCHHHcCCCCC
Confidence            345567888889995 789999999999999887766543233455554   45666765 579999999863

>4ajy_B Transcription elongation factor B polypeptide 2; E3 ubiquitin ligase, transcription factor, hypoxic signaling transcription; 1.73A {Homo sapiens} PDB: 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A 3ztc_A* 3ztd_A* 3zun_A* 1lm8_B 4b95_A* 2fnj_B 4b9k_A* 4awj_A*

Probab=81.18  E-value=2.6  Score=32.90  Aligned_cols=59  Identities=10%  Similarity=0.224  Sum_probs=42.2

Q ss_pred             EEcCCCC-EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          188 IRLADGT-RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       188 IRl~dG~-rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      ||+--++ .+.+.+..++||.+|..-|.....-....-.|+   |=.+.|+| +.||.+.|+.+
T Consensus         5 l~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI---~~Gk~LeD-~kTL~dy~I~~   64 (118)
T 4ajy_B            5 LMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLY---KDDQLLDD-GKTLGECGFTS   64 (118)
T ss_dssp             EEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEE---ETTEECCT-TSBTTTTTCCG
T ss_pred             EEEecCCEEEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEE---eCCeECCC-cCCHHHcCCCc
Confidence            3444455 567789999999999999987432122344555   45688876 79999999986

---

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	257
d1ss6a_	102	d.245.1.1 (A:) NSFL1 (p97 ATPase) cofactor p47, SE	3e-33
d1i42a_	89	d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId:	8e-28
d1wj4a_	124	d.15.1.2 (A:) Hypothetical protein KIAA0794 {Human	9e-18
d1s3si_	50	d.15.1.2 (I:) p47 {Rat (Rattus norvegicus) [TaxId:	3e-17
d1h8ca_	82	d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human	8e-15
d2cr5a1	96	d.15.1.2 (A:8-103) UBX domain-containing protein 6	6e-14

>d1ss6a_ d.245.1.1 (A:) NSFL1 (p97 ATPase) cofactor p47, SEP domain {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: NSFL1 (p97 ATPase) cofactor p47, SEP domain
superfamily: NSFL1 (p97 ATPase) cofactor p47, SEP domain
family: NSFL1 (p97 ATPase) cofactor p47, SEP domain
domain: NSFL1 (p97 ATPase) cofactor p47, SEP domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  114 bits (287), Expect = 3e-33
 Identities = 33/102 (32%), Positives = 52/102 (50%), Gaps = 6/102 (5%)

Query: 63  PQQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHV 122
               + +   +  W +GF++++G LR   DP NA FLESI++ E P EL        V++
Sbjct: 6   QHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRLAHGGQVNL 65

Query: 123 NLI-RRDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTVDST 163
           ++   RD    +P+     F G G+ LGS++     P V ST
Sbjct: 66  DMEDHRDEDFVKPKGAFKAFTGEGQKLGSTA-----PQVLST 102

>d1i42a_ d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 89

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score =  100 bits (250), Expect = 8e-28
 Identities = 39/87 (44%), Positives = 57/87 (65%)

Query: 171 SSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMG 230
           +S  ++++E  P+T++QIRLADG RL+  FN  H ISDI  FI  +RP  A    + M  
Sbjct: 2   ASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTT 61

Query: 231 FPPKVLADRTQTIEQAGLANSVVIQKF 257
           FP K LAD  QT+++A L N+V++Q+ 
Sbjct: 62  FPNKELADENQTLKEANLLNAVIVQRL 88

>d1wj4a_ d.15.1.2 (A:) Hypothetical protein KIAA0794 {Human (Homo sapiens) [TaxId: 9606]} Length = 124

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Hypothetical protein KIAA0794
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.7 bits (183), Expect = 9e-18
 Identities = 22/114 (19%), Positives = 41/114 (35%), Gaps = 2/114 (1%)

Query: 143 GVGRTLGSSSTAASEPTVDSTPVNTASSSSEGLV--VDENLPSTSVQIRLADGTRLIAHF 200
           G   + G+++     P VDS  +      ++G+V  +D N P   + +R  DG R     
Sbjct: 1   GSSGSSGTATNHQGLPAVDSEILEMPPEKADGVVEGIDVNGPKAQLMLRYPDGKREQITL 60

Query: 201 NLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVI 254
                +  +   + +      R   L           D   T+++AGL     +
Sbjct: 61  PEQAKLLALVKHVQSKGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETV 114

>d1s3si_ d.15.1.2 (I:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 50

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 70.9 bits (174), Expect = 3e-17
 Identities = 22/45 (48%), Positives = 32/45 (71%)

Query: 169 SSSSEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFI 213
           + +S  ++++E  P+T++QIRLADG RL+  FN  H ISDI  FI
Sbjct: 5   AKASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFI 49

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Fas-associated factor 1, Faf1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.6 bits (160), Expect = 8e-15
 Identities = 10/73 (13%), Positives = 23/73 (31%)

Query: 182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQ 241
           P + ++IR   G  L   F   + +  +  F+ +          L           D  +
Sbjct: 4   PVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNK 63

Query: 242 TIEQAGLANSVVI 254
           ++ +  L     +
Sbjct: 64  SLLEVKLFPQETL 76

>d2cr5a1 d.15.1.2 (A:8-103) UBX domain-containing protein 6 (Reproduction 8) {Mouse (Mus musculus) [TaxId: 10090]} Length = 96

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: UBX domain-containing protein 6 (Reproduction 8)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.8 bits (155), Expect = 6e-14
 Identities = 11/78 (14%), Positives = 25/78 (32%), Gaps = 3/78 (3%)

Query: 178 DENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA 237
           +      +V +R  +G  L   F        +  ++       +         FP + L 
Sbjct: 11  ETAEEVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVGYHKSLYRLSTS--FPRRALE 68

Query: 238 -DRTQTIEQAGLANSVVI 254
            +   ++E  G+    V+
Sbjct: 69  VEGGSSLEDIGITVDTVL 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	257
d1ss6a_	102	NSFL1 (p97 ATPase) cofactor p47, SEP domain {Human	100.0
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	99.92
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	99.79
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	99.75
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	99.69
d1s3si_	50	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	99.63
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	97.77
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	97.37
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	97.29
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	97.26
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	97.24
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	97.23
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	97.14
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	97.14
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	97.13
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	97.12
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	97.09
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	97.04
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	97.0
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	96.96
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	96.95
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	96.93
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	96.85
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	96.84
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	96.69
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	96.66
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	96.6
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	96.59
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	96.55
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	96.54
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	96.47
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	96.33
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	96.27
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	96.26
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	96.05
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	96.02
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	95.95
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	95.45
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	95.27
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	95.2
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	94.39
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	91.94
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	89.79
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	89.37
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	88.95
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	88.42
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	86.28

>d1ss6a_ d.245.1.1 (A:) NSFL1 (p97 ATPase) cofactor p47, SEP domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: NSFL1 (p97 ATPase) cofactor p47, SEP domain
superfamily: NSFL1 (p97 ATPase) cofactor p47, SEP domain
family: NSFL1 (p97 ATPase) cofactor p47, SEP domain
domain: NSFL1 (p97 ATPase) cofactor p47, SEP domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.3e-38  Score=245.00  Aligned_cols=92  Identities=32%  Similarity=0.615  Sum_probs=86.8

Q ss_pred             CCCceEEEEEeccceeecCCCCccCCChhhHHHHHHHhcCCCCCcccCCCCCCceEEEEe-cccccCCCCCCCCcccccc
Q 025134           66 PEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLI-RRDVKCPEPEKHHVPFQGV  144 (257)
Q Consensus        66 ~~~~~~~l~lw~nGF~VddGp~R~y~dP~n~~FL~~I~~G~~P~EL~~~~~~~~V~v~l~-~r~e~y~~p~~~~~~F~G~  144 (257)
                      .++++|+||||+|||+|||||||+|+||+|++||++|++|+||.||++++++++|+|+|+ |++|+|.+|++++++|+|+
T Consensus         9 ~~~v~v~l~lw~nGFtVdDGplR~yddP~N~~FL~~I~~G~~P~EL~~~~~~~~V~v~v~D~~~e~y~~pk~~~~~F~G~   88 (102)
T d1ss6a_           9 SQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGEVPAELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTGE   88 (102)
T ss_dssp             CSCEEEEEEEESSEEEETTSCEEETTCTTTHHHHHHHHHTCCCHHHHTTSCSSCEEEEEEEEETTCCCSSSSSSTTSCSS
T ss_pred             CCcceEEEEEecCceEecCCCcccCCCHhHHHHHHHHHhccCCHHHhcccCCCeEeEEEEeccCCcccCCCCcccCcccc
Confidence            467899999999999999999999999999999999999999999999999999999999 5699999998889999999


Q ss_pred             ccccccCCCCCCC
Q 025134          145 GRTLGSSSTAASE  157 (257)
Q Consensus       145 G~~LGs~~p~~~~  157 (257)
                      |++|||++|..++
T Consensus        89 G~~LGSp~P~v~~  101 (102)
T d1ss6a_          89 GQKLGSTAPQVLS  101 (102)
T ss_dssp             SSSGGGCCSSSSC
T ss_pred             CccCCCCCCCccc
Confidence            9999999998753

>d1i42a_ d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.92  E-value=2.1e-25  Score=168.03  Aligned_cols=84  Identities=45%  Similarity=0.751  Sum_probs=78.7

Q ss_pred             CCcccCCCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC-CcCeEEEecCCCCcccCCccCcHhhhCCCCe
Q 025134          173 EGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAGLANS  251 (257)
Q Consensus       173 ~~~~vd~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~na  251 (257)
                      ..+.||+++|+|+||||||||++++++|+.++||+|||+||.++.++. ..+|.|++ +||+|.|+|.++||+||||+||
T Consensus         4 ~~~~vde~~p~t~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~~~~~~f~L~t-~~Prr~l~d~~~TL~e~gL~~s   82 (89)
T d1i42a_           4 SSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMT-TFPNKELADENQTLKEANLLNA   82 (89)
T ss_dssp             SCCCCCTTSCCEEEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTTTSSCCEEEEE-TTTTEECCCCSSCSGGGTTCCS
T ss_pred             cccccCCCCCcEEEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCccCCCCCEEEec-CCCCcccCCCcCcHHHCCCcCc
Confidence            457899999999999999999999999999999999999999887654 57899999 9999999999999999999999


Q ss_pred             eEEeeC
Q 025134          252 VVIQKF  257 (257)
Q Consensus       252 vivqk~  257 (257)
                      +|+|||
T Consensus        83 ~vl~k~   88 (89)
T d1i42a_          83 VIVQRL   88 (89)
T ss_dssp             EEEEEE
T ss_pred             eEEEEe
Confidence            999998

>d1wj4a_ d.15.1.2 (A:) Hypothetical protein KIAA0794 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Hypothetical protein KIAA0794
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=3.4e-19  Score=141.43  Aligned_cols=78  Identities=22%  Similarity=0.356  Sum_probs=68.3

Q ss_pred             cccCCCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC-e
Q 025134          175 LVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-S  251 (257)
Q Consensus       175 ~~vd~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-a  251 (257)
                      ..+|.+.|+|+||||||||+|++++|+.++||.+||+||.... ....+|.|++ +||++.|+  |.++||+||||++ +
T Consensus        35 ~~~d~~~p~~~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~~-~~~~~~~L~~-~fPr~~l~~~d~~~TL~e~gL~P~~  112 (124)
T d1wj4a_          35 EGIDVNGPKAQLMLRYPDGKREQITLPEQAKLLALVKHVQSKG-YPNERFELLT-NFPRRKLSHLDYDITLQEAGLCPQE  112 (124)
T ss_dssp             CCCCCSSCEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHH-CCTTTEEEEC-SSSCCEETSSCSSSCTTTTTCCSSB
T ss_pred             CCCCCCCCceEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhcc-cCCcceEEee-cccccccccccccCcHHHcCCCCCC
Confidence            3468899999999999999999999999999999999998753 2357899999 99999997  7789999999995 4


Q ss_pred             eEE
Q 025134          252 VVI  254 (257)
Q Consensus       252 viv  254 (257)
                      +|+
T Consensus       113 ~L~  115 (124)
T d1wj4a_         113 TVF  115 (124)
T ss_dssp             CCE
T ss_pred             EEE
Confidence            443

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Fas-associated factor 1, Faf1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.9e-18  Score=125.74  Aligned_cols=73  Identities=18%  Similarity=0.312  Sum_probs=64.6

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC--CccCcHhhhCCCC-eeEE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-aviv  254 (257)
                      ++|+|+|+||||||+|++++|+.++||++||+||.+... ...+|.|++ +||++.|+  |.++||+|+||.+ ++|+
T Consensus         2 ~e~~~~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~~~-~~~~~~l~~-~~Pr~~l~~~d~~~TL~e~gL~p~~~L~   77 (82)
T d1h8ca_           2 AEPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGF-PWDEYKLLS-TFPRRDVTQLDPNKSLLEVKLFPQETLF   77 (82)
T ss_dssp             CCCCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHTC-CSSSEEEEE-TTTTEETTTCCTTSBHHHHCCCSEEEEE
T ss_pred             CCCcEEEEEECCCCCEEEEEECCCCcHHHHHHHHHhcCC-CCCceEEEe-cCcccccccccccCCHHHCCCCCCCEEE
Confidence            578999999999999999999999999999999988642 357899999 99999997  6689999999995 5554

>d2cr5a1 d.15.1.2 (A:8-103) UBX domain-containing protein 6 (Reproduction 8) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: UBX domain-containing protein 6 (Reproduction 8)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=3.6e-17  Score=123.64  Aligned_cols=74  Identities=18%  Similarity=0.269  Sum_probs=64.9

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccC-CccCcHhhhCCCC-eeEEe
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA-DRTQTIEQAGLAN-SVVIQ  255 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~-d~s~TL~eagL~n-avivq  255 (257)
                      ..++|+||||||||+|++++|+.++||++||+||..... ....|.|++ +||++.|. |.++||+||||.+ ++|+.
T Consensus        13 ~~~~~~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~~~-~~~~f~l~~-~~Pr~~~~~d~~~TL~e~gl~p~~~L~v   88 (96)
T d2cr5a1          13 AEEVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVGY-HKSLYRLST-SFPRRALEVEGGSSLEDIGITVDTVLNV   88 (96)
T ss_dssp             CSSEEEEEEECTTSCEEEEEEESSSBTHHHHHHHHHHTC-CTTTEEEEC-SSSCCBCCCCSSCBHHHHTCSSCEEEEE
T ss_pred             CCCeEEEEEECCCCCEEEEEECCcccHHHHHHHHHHhcc-Ccccceeec-CCCceecCccCCCcHHHCCCCCCCEEEE
Confidence            557899999999999999999999999999999988653 357899999 99999997 6789999999996 55543

>d1s3si_ d.15.1.2 (I:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.63  E-value=8.5e-18  Score=111.89  Aligned_cols=42  Identities=52%  Similarity=0.856  Sum_probs=13.9

Q ss_pred             CCCcccCCCCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHH
Q 025134          172 SEGLVVDENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFI  213 (257)
Q Consensus       172 ~~~~~vd~s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi  213 (257)
                      ...+.+|+++|+|+|||||+||+|++.|||++|||+|||+||
T Consensus         8 ~~~~~vd~s~PtT~iQiRL~dG~R~v~rFN~~Htv~dir~fI   49 (50)
T d1s3si_           8 SSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFI   49 (50)
T ss_dssp             HTTC--------------------------CCCCHHHHHHHC
T ss_pred             cccccccCCCCceEEEEEeCCCCEEEEEccCccCHHHHHHhh
Confidence            345789999999999999999999999999999999999997

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.77  E-value=8.2e-05  Score=56.79  Aligned_cols=67  Identities=16%  Similarity=0.190  Sum_probs=54.5

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCC--------CCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG--------TARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~--------~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      +.+...|+||+.+|+...+.|..++||.+|...|....|.        ......|+   |=.|.|.| +.||++++|.+
T Consensus        13 ~~~~i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLi---y~Gk~L~D-~~tL~~~~i~~   87 (116)
T d1wgha_          13 PADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLI---YQGRFLHG-NVTLGALKLPF   87 (116)
T ss_dssp             CSSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEE---ETTEEECS-SCBTTTTTCCS
T ss_pred             CCCeEEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEE---ECCEEecC-CCCHHHcCCCC
Confidence            4577899999999999999999999999999999754432        13455665   47788877 69999999984

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.37  E-value=0.00039  Score=50.97  Aligned_cols=68  Identities=16%  Similarity=0.271  Sum_probs=55.6

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ....+|.||+.||+...+....++||++|..-|....+   ....|+   |=.|.|.|++.||.+.||.+ ++|.
T Consensus         5 ~s~m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~~~~~---~~qrLi---~~Gk~L~dd~~tL~~y~i~~g~~v~   73 (95)
T d1wiaa_           5 SSGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQE---SQMKLI---YQGRLLQDPARTLSSLNITNNCVIH   73 (95)
T ss_dssp             CCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSSSTT---TTCEEE---ETTEECCCSSCBTTTTTCCTTEEEE
T ss_pred             CCcEEEEEEcCCCCEEEEEECCcCcHHHHHHHHhcCCc---ceeEEE---ECCEEcccCCCCHHHcCCCCCCEEE
Confidence            45678999999999999999999999999998865422   345665   57899988889999999996 5553

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.29  E-value=0.00053  Score=47.32  Aligned_cols=65  Identities=18%  Similarity=0.271  Sum_probs=52.9

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|+.+.+.+..++||.+|.+-|.....-......|.   |-.+.|.| +.||++.|+.+ ++|
T Consensus         2 ~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~gi~~~~qrLi---~~Gk~L~d-~~tL~~y~I~~~sti   67 (73)
T d1bt0a_           2 LIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI---YAGKQLAD-DKTAKDYNIEGGSVL   67 (73)
T ss_dssp             EEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEE---ETTEECCT-TSBTGGGTCCTTCEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChHHEEEE---ECCeEcCC-CCcHHHcCCCCCCEE
Confidence            5889999999999999999999999999987542223456665   57899987 58999999996 554

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.26  E-value=0.0011  Score=47.26  Aligned_cols=69  Identities=19%  Similarity=0.240  Sum_probs=55.6

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ....|-||..+|+.+.+.+..++||.+|...|.....-......|+.   =.|.|+| +.||.+.||.+ ++|.
T Consensus         6 ~~mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~---~Gk~L~d-~~tL~~y~I~~~stl~   75 (87)
T d1wh3a_           6 SGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEF---QGQVLQD-WLGLGIYGIQDSDTLI   75 (87)
T ss_dssp             SSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEE---TTEECCS-SSBHHHHTCCTTEEEE
T ss_pred             CcEEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEe---eceEcCC-CCcHHHcCCCCCCEEE
Confidence            45678999999999999999999999999999876422345566664   6789987 68999999996 5553

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.24  E-value=0.00089  Score=46.41  Aligned_cols=67  Identities=21%  Similarity=0.266  Sum_probs=53.9

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...|-||..+|+.+.+.++.++||.+|..-|.....-......|.   |=.+.|.| +.||.+.|+.+ ++|
T Consensus         3 ~~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~---~~gk~L~d-~~tL~~y~I~~~sti   70 (76)
T d1z2ma2           3 PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLT---FEGKPLED-QLPLGEYGLKPLSTV   70 (76)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TSBGGGGTCCTTCEE
T ss_pred             CEEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhcCChhHeEEE---ECCeECCC-CCcHHHcCCCCCCEE
Confidence            467889999999999999999999999999988642223455555   46888987 68999999996 554

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.23  E-value=0.00073  Score=47.51  Aligned_cols=68  Identities=16%  Similarity=0.206  Sum_probs=54.9

Q ss_pred             ceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          183 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       183 ~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .+.|.||+.+|+.+.+.+..++||++|..-|.....-......|+.   =.+.|+| +.||.+.|+.+ ++|.
T Consensus         3 e~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~---~Gk~L~d-~~tL~~y~I~~~sti~   71 (80)
T d1ttna1           3 ECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFF---SGRPLTD-KMKFEELKIPKDYVVQ   71 (80)
T ss_dssp             SEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEE---TTEECCT-TSHHHHCCCSSSCEEE
T ss_pred             eEEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCcccEEEEE---CceEcCC-CCcHHHcCCCCCCEEE
Confidence            4679999999999999999999999999999875432345566654   6788976 68999999996 6653

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.14  E-value=0.00082  Score=46.87  Aligned_cols=68  Identities=16%  Similarity=0.243  Sum_probs=53.6

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .|.||..+|+.+.+.+..++||.+|..-|.....-....-.|+. ..-.+.|.| +.||.+.||.+ ++|.
T Consensus         2 ~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~-~~~Gk~L~D-~~tL~~y~i~~g~~i~   70 (76)
T d1z2ma1           2 DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAV-HPSGVALQD-RVPLASQGLGPGSTVL   70 (76)
T ss_dssp             EEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEE-ETTCCBCCS-SSCSGGGTCCTTCEEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhccCCccEEEEE-cCCCeeccC-CCcHHHcCCCCCCEEE
Confidence            47899999999999999999999999999886432334556664 334588887 58999999996 5543

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.14  E-value=0.00063  Score=47.46  Aligned_cols=68  Identities=13%  Similarity=0.258  Sum_probs=54.4

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC---CcCeEEEecCCCCcccCCccCcHhhhCCC-CeeEEe
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT---ARNYQLQMMGFPPKVLADRTQTIEQAGLA-NSVVIQ  255 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~---~~~f~L~t~~fP~k~l~d~s~TL~eagL~-navivq  255 (257)
                      .+|.||..+|+...+.+..++||++|..-|.......   .....|.   |=.|.|.| +.||.+.|+. +++|+.
T Consensus         3 ~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi---~~Gk~L~D-~~tL~~y~I~~~s~i~~   74 (77)
T d1oqya4           3 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLI---YAGKILSD-DVPIRDYRIDEKNFVVV   74 (77)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEE---SSSSEECS-SSBTTTTCCCTTSCEEE
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeE---ECCcCccC-CCcHHHcCCCCCCEEEE
Confidence            5789999999999999999999999999998764321   2344554   57899987 6999999999 476653

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.13  E-value=0.0016  Score=48.24  Aligned_cols=67  Identities=21%  Similarity=0.294  Sum_probs=53.0

Q ss_pred             CCceEEEEEcCCCCEE-EEEeCCCCCHHHHHHHHHhhCCCC-------CcCeEEEecCCCCcccCCccCcHhhhCCCCe
Q 025134          181 LPSTSVQIRLADGTRL-IAHFNLHHTISDIHSFIDASRPGT-------ARNYQLQMMGFPPKVLADRTQTIEQAGLANS  251 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rl-v~~fn~s~TI~dl~~fi~~~~p~~-------~~~f~L~t~~fP~k~l~d~s~TL~eagL~na  251 (257)
                      +....|.||+.||+.+ ..+|..++||.+|.+-|....+..       .....|+   |=.|.|.| +.||.++++.++
T Consensus         5 ~~~i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLI---f~Gk~L~D-~~tL~dy~i~~g   79 (101)
T d1se9a_           5 HNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLI---SAGKVLEN-SKTVKDYRSPVS   79 (101)
T ss_dssp             CCCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEE---ETTEECCT-TSBGGGGSCCTT
T ss_pred             cceEEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEE---ECCeEecC-CCCHHHcCCCCC
Confidence            4567899999999987 599999999999999998754322       1235565   47889977 599999999764

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.12  E-value=0.0015  Score=48.08  Aligned_cols=71  Identities=17%  Similarity=0.189  Sum_probs=56.1

Q ss_pred             CCCceEEEEEcC----CCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          180 NLPSTSVQIRLA----DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       180 s~p~t~iqIRl~----dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ....++|+|+++    .|+.+.+.+..++||.+|..-|.....-......|+.   =.|.|.| +.||.+.|+.+ +.|+
T Consensus        12 ~tg~ati~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~---~Gk~L~d-~~tL~~~gI~~~s~i~   87 (100)
T d1wjua_          12 TTGIATIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVI---NKKQLQL-GKTLEEQGVAHNVKAM   87 (100)
T ss_dssp             CCCEEEEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEE---TTEECCT-TSBHHHHTCCSSEEEE
T ss_pred             ccceEEEEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEE---cccCcCC-CcCHHHcCCCCCCEEE
Confidence            346678999996    4888999999999999999999886532345566664   7888888 69999999995 6553

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.09  E-value=0.0011  Score=46.05  Aligned_cols=65  Identities=15%  Similarity=0.238  Sum_probs=52.4

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|+.+.+..+.++||.+|.+-|.....-......|+.   =.+.|.| +.||.+.|+.+ ++|
T Consensus         2 qI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~---~Gk~L~d-~~tL~~y~i~~~s~I   67 (76)
T d1ogwa_           2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF---AGKQLED-GRTLSDYNIQKESTL   67 (76)
T ss_dssp             EEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEE---TTEECCT-TSBGGGGTCCTTCEE
T ss_pred             EEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcCCChHHEEeEE---CCeEcCC-CCCHHHcCCCCCCEE
Confidence            58899999999999999999999999999875422234455554   5788987 68999999996 555

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like modifier protein hub1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.04  E-value=0.0015  Score=45.10  Aligned_cols=66  Identities=14%  Similarity=0.160  Sum_probs=53.4

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ..|-||-..|+.+....+.++||.+|..-|+....-....+.|..   =.+.|.| +.||++.|+.+ ++|
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~---~Gk~L~d-~~tL~~y~I~~gstl   68 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQK---GGSVLKD-HISLEDYEVHDQTNL   68 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEES---SSCEECT-TSBHHHHTCCTTEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEE---EeEEecc-cCcHHHcCCCCCCEE
Confidence            357888899999999999999999999999885432345677764   6789977 58999999997 444

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.00  E-value=0.0013  Score=46.06  Aligned_cols=66  Identities=17%  Similarity=0.258  Sum_probs=52.5

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ..|-||+.+|+.+.+.++.++||.+|.+-|.....-......|+   |=.|.|+| +.||.++|+.+ ++|
T Consensus         3 M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi---~~Gk~L~d-~~tL~~y~I~~~sti   69 (78)
T d2zeqa1           3 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVI---FAGKELPN-HLTVQNCDLEQQSIV   69 (78)
T ss_dssp             EEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHTCCGGGEEEE---ETTEEECT-TCBGGGSSCCTTCEE
T ss_pred             eEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHCcChhHeEEE---EeeeEcCC-CCCHHHcCCCCCCEE
Confidence            46899999999999999999999999999987532123344554   57889987 68999999996 554

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.96  E-value=0.0023  Score=46.62  Aligned_cols=76  Identities=11%  Similarity=0.188  Sum_probs=55.7

Q ss_pred             CceEEEEEcCC---CCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEec--CCCCc--ccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLAD---GTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMM--GFPPK--VLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~d---G~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~--~fP~k--~l~d~s~TL~eagL~n-avi  253 (257)
                      -..+|.|+.++   ++.+..++..+.||++|..-|...-.-....-.|...  ..|..  +|+++++||.+.|+.+ ++|
T Consensus         8 ~~iti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I   87 (97)
T d1wjna_           8 QLLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCL   87 (97)
T ss_dssp             CEEEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEE
T ss_pred             CeEEEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEE
Confidence            45778888764   6778999999999999999998754222334455431  12332  4778899999999995 888


Q ss_pred             EeeC
Q 025134          254 IQKF  257 (257)
Q Consensus       254 vqk~  257 (257)
                      +.+|
T Consensus        88 ~V~~   91 (97)
T d1wjna_          88 LVRW   91 (97)
T ss_dssp             EEEC
T ss_pred             EEEe
Confidence            8876

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog B (Hhr23B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.95  E-value=0.0022  Score=46.29  Aligned_cols=66  Identities=12%  Similarity=0.255  Sum_probs=52.8

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCC---CCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG---TARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~---~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .|.||..+|+.+.+.+..++||++|.+.|......   ......|+.   =.+.|.| +.||++.|+.+ ++|+
T Consensus         2 ~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~---~Gk~L~d-~~tL~~y~I~~~s~i~   71 (95)
T d1uela_           2 QVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIY---AGKILND-DTALKEYKIDEKNFVV   71 (95)
T ss_dssp             EEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEE---TTEECCT-TSBGGGGTCCSSSEEE
T ss_pred             EEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEE---CCeEccC-CCcHHHcCCCCCCEEE
Confidence            58899999999999999999999999999864321   134566664   6889988 58999999995 5554

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.93  E-value=0.0078  Score=43.99  Aligned_cols=67  Identities=16%  Similarity=0.196  Sum_probs=52.0

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...+|.|+..+++ ..+.++.++||.+|..-|.....-......|+   |-.+.|.| +.||+++||.+ ++|
T Consensus        31 ~~i~V~Vk~~~~~-~~i~V~~~~tV~~LK~~I~~~~gi~~~~qrLi---~~Gk~L~D-~~tL~~~~I~~g~~I   98 (103)
T d1j8ca_          31 KIIKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLI---FAGKILKD-QDTLIQHGIHDGLTV   98 (103)
T ss_dssp             CCEEEEEECSSCE-EEEEECTTCCHHHHHHHHHHHHCSCSSSEEEE---ETTEEEST-TSCGGGTTCSSSEEE
T ss_pred             CeEEEEEECCCcc-EEEEECCCChHHHHHHHHHHHHCcCHHHeeee---eeeecccC-CCcHHHcCCCCCCEE
Confidence            4577888888775 57899999999999999988542234566666   47789987 68999999997 554

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.85  E-value=0.0047  Score=45.39  Aligned_cols=70  Identities=14%  Similarity=0.107  Sum_probs=53.7

Q ss_pred             CCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          181 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       181 ~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .....|.|+...|+.+.+++..++||++|.+-|.....-......|+.   =.+.|.| +.||++.|+.+ ++|.
T Consensus        26 ~~~i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~---~Gk~L~D-~~tL~dygI~~GstI~   96 (100)
T d1uh6a_          26 ATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKK---WYTIFKD-HVSLGDYEIHDGMNLE   96 (100)
T ss_dssp             CCEEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEE---TTEECCS-SCBHHHHTCCTTEEEE
T ss_pred             CceEEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHCCCcceEEEEE---EeecccC-cCCHHHcCCCCCCEEE
Confidence            345677788888999999999999999999999875422234555654   5688877 58999999997 4443

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.84  E-value=0.002  Score=44.36  Aligned_cols=65  Identities=15%  Similarity=0.258  Sum_probs=52.1

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCeeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~navi  253 (257)
                      .|.||..+|+...+.+..++||.+|..-|.....-......|+   |=.+.|.| +.||.+.++-+++|
T Consensus         2 ~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi---~~Gk~L~d-~~tL~dy~i~~~ti   66 (73)
T d1wx9a1           2 EVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLI---YQGRVLQD-DKKLQEYNVGGKVI   66 (73)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHCCCTTTCCCE---ETTEECCS-SSBHHHHTCTTEEE
T ss_pred             EEEEEcCCCCEEEEEECCCChHHHHHHHHHHHhCCChHHEEEE---ECCeEccC-CCCHHHhCCCCCEE
Confidence            5889999999999999999999999999988542223344554   46788987 58999999977765

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.69  E-value=0.0039  Score=45.87  Aligned_cols=63  Identities=16%  Similarity=0.243  Sum_probs=49.8

Q ss_pred             EcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          189 RLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       189 Rl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      |=.+|..+.+....+.||.+|...|+....-......|+   |-.|.|.|++.||+++||.+ ++|+
T Consensus        17 ~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li---~~Gk~L~dd~~tL~~~gI~~g~~i~   80 (102)
T d1v5oa_          17 RDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIV---YMEQLLTDDHCSLGSYGLKDGDMVV   80 (102)
T ss_dssp             CCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEE---ETTEEECCSSSBHHHHTCCTTEEEE
T ss_pred             cCCCCCEEEEEECCcccHHHHHHHHHHHhCCCcceEEEE---eCCeEeecccCCHHHcCCCCCCEEE
Confidence            445688899999999999999999988643234456665   47899988789999999996 5554

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.66  E-value=0.0072  Score=41.91  Aligned_cols=65  Identities=17%  Similarity=0.178  Sum_probs=50.1

Q ss_pred             EEEEEcCCCCE-EEE-EeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTR-LIA-HFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~r-lv~-~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|++ .+. ....++||.+|..-|.....-......|+   |=.+.|+| +.||.+.|+.+ ++|
T Consensus         2 ~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~gip~~~qrLi---~~Gk~L~d-~~tL~~y~I~~~s~i   69 (76)
T d1wy8a1           2 WIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLF---YRGKQLEN-GYTLFDYDVGLNDII   69 (76)
T ss_dssp             EEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEE---ETTEECCS-SSBHHHHTCCTTCEE
T ss_pred             EEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHCCCchhcEEE---EEeeEecC-CCCHHHcCCCCCCEE
Confidence            68999999964 554 68999999999999988642224455555   47788877 68999999997 444

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.60  E-value=0.0054  Score=43.11  Aligned_cols=70  Identities=17%  Similarity=0.187  Sum_probs=53.0

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      .....+|.|+.++++ ..+.+..++||++|..-|.....-......|+   |=.+.|.| +.||.++|+.+ ++|.
T Consensus         7 ~~~~i~v~Vk~~~~~-~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~---f~Gk~L~d-~~tL~~~gI~~gs~I~   77 (83)
T d1wx8a1           7 SSRIIRVSVKTPQDC-HEFFLAENSNVRRFKKQISKYLHCNADRLVLI---FTGKILRD-QDILSQRGILDGSTVH   77 (83)
T ss_dssp             CSCEEEEEEECSSSE-EEEEEETTCCHHHHHHHHHHHTCSCTTTBCCE---ETTEECCT-TSCHHHHTCCTTEEEE
T ss_pred             CCCeEEEEEEcCCCc-EEEEECCCChHHHHHHHHHHHhCCChhHEEEE---EEhhcccc-CCcHHHcCCCCCCEEE
Confidence            445688999988764 58899999999999999988643233445554   46789987 56999999996 5553

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.59  E-value=0.0043  Score=42.53  Aligned_cols=65  Identities=18%  Similarity=0.242  Sum_probs=49.8

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .+|+||..+ .+..+.++.++||.+|.+.|.....-......|+.   =.+.|.|+ .||.+.|+.+ ++|
T Consensus         2 i~I~Vk~~~-~~~~i~v~~~~tV~~lK~~I~~~~gip~~~qrLi~---~Gk~L~D~-~tL~~~~I~~g~~i   67 (73)
T d2bwfa1           2 LNIHIKSGQ-DKWEVNVAPESTVLQFKEAINKANGIPVANQRLIY---SGKILKDD-QTVESYHIQDGHSV   67 (73)
T ss_dssp             EEEEEEETT-EEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEE---TTEECCTT-SBTGGGTCCTTCEE
T ss_pred             EEEEEEeCC-eEEEEEECCCChHHHHHHHHHHHHCcChHHeEEEE---CCeEccCC-CcHHHCCCCCCCEE
Confidence            467888754 46788999999999999999886422235566664   68899874 7999999996 544

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.55  E-value=0.0027  Score=46.16  Aligned_cols=68  Identities=12%  Similarity=0.025  Sum_probs=53.2

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...+|.|+..+++...+.++.++||.+|.+-|.....-....-.|+   |-.+.|.|+  ||.++|+.+ ++|+
T Consensus         6 ~~~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi---~~Gk~L~d~--tL~~~gi~~g~~i~   74 (96)
T d1wgga_           6 SGYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVM---VKGGTLKDD--DWGNIKMKNGMTVL   74 (96)
T ss_dssp             CEEEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCE---ETTEECCSS--CCCSCCCCSSCEEE
T ss_pred             CceEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcCccceeeEEe---ecCcccCCC--cHHHCCCCCCCEEE
Confidence            4567899998887778999999999999999988643223445555   578999874  799999996 5554

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.54  E-value=0.0049  Score=43.47  Aligned_cols=67  Identities=18%  Similarity=0.215  Sum_probs=51.7

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      -+.+|.|+.+++ +..+.+..++||++|..-|.....-......|+   |-.+.|.| +.||+++||.+ ++|
T Consensus         6 ~~i~I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~---~~Gk~L~D-~~tL~~y~i~~gsti   73 (84)
T d1yqba1           6 HLIKVTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLI---FAGKILKD-PDSLAQCGVRDGLTV   73 (84)
T ss_dssp             TEEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TSBHHHHTCCTTCEE
T ss_pred             CEEEEEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHCcCchhEEEE---Eeeeeccc-cCcHHHcCCCCCCEE
Confidence            357888999866 568899999999999999987542223456665   46889976 57999999996 555

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.47  E-value=0.011  Score=41.93  Aligned_cols=58  Identities=22%  Similarity=0.323  Sum_probs=46.2

Q ss_pred             CCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          192 DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       192 dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +|+.+.+.++.++||++|...|.....-......|.   |=.+.|.| +.||.+.||.+ ++|
T Consensus        20 ~G~~~~l~v~~~~tV~~lK~~I~~~~~ip~~~q~Li---~~Gk~L~D-~~tL~dY~I~~gsti   78 (86)
T d1zkha1          20 NGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQ---YEGIFIKD-SNSLAYYNMANGAVI   78 (86)
T ss_dssp             SSCEEEEEECTTSBHHHHHHHHHHHTCCCTTTEEEE---ETTEEECT-TSBHHHHTCCTTEEE
T ss_pred             CCeEEEEEECCCChHHHHHHHHHhhhcCChHHEEEE---eCCcCcCC-CCCHHHcCCCCCCEE
Confidence            788899999999999999999988643234556665   46788887 68999999997 444

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.33  E-value=0.014  Score=40.80  Aligned_cols=66  Identities=14%  Similarity=0.212  Sum_probs=49.8

Q ss_pred             EEEEEcCCCCEEEEEe-----CCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          185 SVQIRLADGTRLIAHF-----NLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~f-----n~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      +|.|.. .+.+....+     +.+.||+||.+-|.....-......|+   |-.+.|.|++.||.++|+.+ +.|+
T Consensus         3 ~i~V~~-~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~tgvp~~~QkL~---~~G~~L~~d~~tL~~~gi~~g~~i~   74 (81)
T d1wxva1           3 TVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLI---FKGKSLKEMETPLSALGIQDGCRVM   74 (81)
T ss_dssp             EEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEE---ETTEEECCSSSBHHHHTCCSSEEEE
T ss_pred             EEEEEE-CCeeEEEEEecCCCCCccHHHHHHHHHHHHHCcCHHHEEee---ecCeEeCcCCCChHHCCCCCCCEEE
Confidence            566633 566777777     578999999999988653335566776   47899988889999999996 5554

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=96.27  E-value=0.0091  Score=44.54  Aligned_cols=68  Identities=10%  Similarity=0.171  Sum_probs=52.5

Q ss_pred             CceEEEEEcC---CCCEEEEEeCC-CCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLA---DGTRLIAHFNL-HHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~---dG~rlv~~fn~-s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      ...+|+|+++   ||+.+.+.+.. ++||.+|..-|.....-......|+   |-.|.|.| +.||.+.+|.+ ++|
T Consensus        26 g~~ti~V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi---~~Gk~L~D-~~tL~~ynI~~gsti   98 (111)
T d1we6a_          26 GPATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLS---GKAGFLKD-NMSLAHYNVGAGEIL   98 (111)
T ss_dssp             SCEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEE---CSSSBCCT-TSBTTTTTCSSSCEE
T ss_pred             CCEEEEEEcccCCCCeEEEEEecCCccHHHHHHHHHHHHHCCCccceEEE---EeeEEccc-cCCHHHcCCCCCCEE
Confidence            3467888874   69999999986 9999999999988642224456665   47899987 58999999996 444

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.26  E-value=0.0066  Score=44.77  Aligned_cols=69  Identities=19%  Similarity=0.238  Sum_probs=54.4

Q ss_pred             CceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCC--C-------------CcCeEEEecCCCCcccCCccCcHhhh
Q 025134          182 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG--T-------------ARNYQLQMMGFPPKVLADRTQTIEQA  246 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~--~-------------~~~f~L~t~~fP~k~l~d~s~TL~ea  246 (257)
                      ...+|.||..||+.+.+....+.||.||...|.....-  .             ...|.|+   |=.+.|.|+..||.+.
T Consensus         6 s~M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li---~~G~~L~d~~~tL~~~   82 (105)
T d1v2ya_           6 SGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLT---SAGEKLTEDRKKLRDY   82 (105)
T ss_dssp             CSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEE---SSSCEECCSSSBHHHH
T ss_pred             CcEEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEE---ECCEECcccCCCHHHc
Confidence            34689999999999999999999999999998764200  0             1245665   5779999888899999


Q ss_pred             CCCC-eeE
Q 025134          247 GLAN-SVV  253 (257)
Q Consensus       247 gL~n-avi  253 (257)
                      ||.+ ++|
T Consensus        83 gI~~g~~l   90 (105)
T d1v2ya_          83 GIRNRDEV   90 (105)
T ss_dssp             TCCSSEEE
T ss_pred             CCCCCCEE
Confidence            9996 554

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.05  E-value=0.0099  Score=42.89  Aligned_cols=69  Identities=10%  Similarity=0.122  Sum_probs=50.8

Q ss_pred             CCCceEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          180 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       180 s~p~t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ..+...|+|++ +|+...+.+..++||.+|.+-|.....-......|+   |..+ |.| +.||.+.+|.+ +.|+
T Consensus        14 ~~~~i~v~V~~-~~k~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li---~~g~-l~D-~~tL~~~~I~~gs~i~   83 (95)
T d1v86a_          14 GKELVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVM---YKGL-VPE-DKTLREIKVTSGAKIM   83 (95)
T ss_dssp             CCCCEEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCB---SSSB-CCS-SSBHHHHCCCTTEEEE
T ss_pred             CccEEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEE---eccc-ccC-CCcHHHCCCCCCCEEE
Confidence            45677888874 788899999999999999999987532223334444   4444 655 68999999996 5554

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.02  E-value=0.014  Score=40.29  Aligned_cols=65  Identities=14%  Similarity=0.139  Sum_probs=49.9

Q ss_pred             EEEEEcCCCC-EEEE-EeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGT-RLIA-HFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~-rlv~-~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      .|.||..+|+ ...+ ....++||++|...|.....-......|.   |-.+.|+| +.||.+.|+.+ ++|
T Consensus         2 ~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi---~~Gk~L~D-~~tL~~y~I~~~sti   69 (76)
T d2faza1           2 WIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLF---YRGKQMED-GHTLFDYEVRLNDTI   69 (76)
T ss_dssp             EEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEE---ETTEECCT-TCBTTTTTCCTTCEE
T ss_pred             EEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHCcChHHeEEE---EeeEeccC-CCcHHHcCCCCCCEE
Confidence            6889999996 4555 58999999999999987542223445554   58899988 58999999996 554

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.95  E-value=0.009  Score=42.50  Aligned_cols=71  Identities=10%  Similarity=0.163  Sum_probs=51.5

Q ss_pred             CceEEEEEcCCCCEEEE-EeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC-eeEE
Q 025134          182 PSTSVQIRLADGTRLIA-HFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI  254 (257)
Q Consensus       182 p~t~iqIRl~dG~rlv~-~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-aviv  254 (257)
                      ...+|.|+. .|.+... .++.++||.+|.+-|.....-......|+...|=.+.|.| +.||.++|+.+ ++|+
T Consensus         6 ~~~~i~Vk~-~~~~~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D-~~tL~~~~i~~g~~i~   78 (90)
T d1v5ta_           6 SGLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAEN-DVKLGALKLKPNTKIM   78 (90)
T ss_dssp             CSCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCT-TSBHHHHTCCTTEEEE
T ss_pred             CcEEEEEEE-CCeEEEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCC-cCcHHHcCCCCCCEEE
Confidence            446688997 5556555 7999999999999998864323455677641245688887 58999999996 5554

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.45  E-value=0.028  Score=38.61  Aligned_cols=64  Identities=9%  Similarity=0.183  Sum_probs=51.6

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCe
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANS  251 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~na  251 (257)
                      .+|.|+..||+.+..+...++|++.|.+..+....-....+.|+   |-.+.|.+ +.|+++++|-+.
T Consensus         3 I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~---fdG~~l~~-~~T~~~l~~edg   66 (77)
T d2uyzb1           3 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFL---FEGQRIAD-NHTPKELGMEEE   66 (77)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEE---ETTEECCT-TCCHHHHTCCTT
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCChhHEEEE---ECCEECCC-CCCHHHcCCCCC
Confidence            57899999999999999999999999998876543333455554   68888887 479999999963

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

Probab=95.27  E-value=0.032  Score=38.46  Aligned_cols=65  Identities=6%  Similarity=0.174  Sum_probs=47.3

Q ss_pred             ceEEEEEcC-CCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCe
Q 025134          183 STSVQIRLA-DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANS  251 (257)
Q Consensus       183 ~t~iqIRl~-dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~na  251 (257)
                      .+.|.||.- +|+.+..++..++||+.|.+.++....-....+.|+   |=.+.|.+ +.|++++||.+.
T Consensus         2 ~~~I~ikv~~~~~~~~f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~---f~G~~l~~-~~T~~~~~i~dg   67 (79)
T d1euvb_           2 ETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFL---YDGIRIQA-DQTPEDLDMEDN   67 (79)
T ss_dssp             CSEEEEEEESSSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGEEEE---ETTEECCT-TCCTTTTTCCTT
T ss_pred             CcEEEEEECCCCeEEEEEECCCCcHHHHHHHHHHHhCCChHhEEEE---ECCEEeCC-CCCHHHCCCCCC
Confidence            344444433 677889999999999999999987643333455554   57788876 479999999963

>d1wf9a1 d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NPL4-like protein 1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=95.20  E-value=0.028  Score=40.60  Aligned_cols=70  Identities=24%  Similarity=0.330  Sum_probs=45.3

Q ss_pred             eEEEEEcCCCC-EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEe-----cCC-CC-----cccCCccCcHhhhCCCCe
Q 025134          184 TSVQIRLADGT-RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQM-----MGF-PP-----KVLADRTQTIEQAGLANS  251 (257)
Q Consensus       184 t~iqIRl~dG~-rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t-----~~f-P~-----k~l~d~s~TL~eagL~na  251 (257)
                      |-|+||.-||. |+.+ =+..-||++|+..|+.........-.|.+     ++= |.     ..+.|+..+|+++|+.|+
T Consensus         1 ~iiRiRsrdG~eRv~v-~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hG   79 (94)
T d1wf9a1           1 TMLRVRSRDGLERVSV-DGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHG   79 (94)
T ss_dssp             EEEEEECSSCEEEEEE-CCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTT
T ss_pred             CeEEEEecCCceEEEe-cCCCCcHHHHHHHHHHHhCCCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCc
Confidence            46899999997 4444 14467999999999986533222222211     011 22     125677899999999986


Q ss_pred             eEE
Q 025134          252 VVI  254 (257)
Q Consensus       252 viv  254 (257)
                      .||
T Consensus        80 siv   82 (94)
T d1wf9a1          80 SMV   82 (94)
T ss_dssp             CEE
T ss_pred             eEE
Confidence            665

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.39  E-value=0.12  Score=36.74  Aligned_cols=63  Identities=11%  Similarity=0.161  Sum_probs=49.6

Q ss_pred             ceEEEEEcCCCCE--EEEEeCCCCCHHHHHHHHHhhCCCC--CcCeEEEecCCCCcccCCccCcHhhhCCC
Q 025134          183 STSVQIRLADGTR--LIAHFNLHHTISDIHSFIDASRPGT--ARNYQLQMMGFPPKVLADRTQTIEQAGLA  249 (257)
Q Consensus       183 ~t~iqIRl~dG~r--lv~~fn~s~TI~dl~~fi~~~~p~~--~~~f~L~t~~fP~k~l~d~s~TL~eagL~  249 (257)
                      ..+|.|+.++++.  +.+.+..+.||.+|.+.|....+..  .....|+.   =.|.|.| +.||.+..+.
T Consensus         7 ~i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy---~Gk~L~D-~~~L~d~~~~   73 (93)
T d1wgda_           7 GVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIY---SGKLLLD-HQCLRDLLPK   73 (93)
T ss_dssp             CCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEE---TTEECCS-SSCHHHHSCS
T ss_pred             cEEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEE---CCeEccC-CCCHHHhCcc
Confidence            3689999999875  6777789999999999998865432  35677775   5788877 6899998765

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.94  E-value=0.25  Score=35.42  Aligned_cols=64  Identities=19%  Similarity=0.121  Sum_probs=42.7

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCC---CcCeEEEecCCCCcccCCccCcHhhhCCCC-eeE
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT---ARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~---~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-avi  253 (257)
                      +.-|++++.+.-. .-..+.||.+|.+.|....+..   .....|+   |=.|.|.| +.||.+.|+.+ ++|
T Consensus        20 k~~i~~p~~~~~~-~~~~~~tV~~lK~~i~~~~~~~~P~p~~~rLI---y~Gk~L~D-~~tL~~y~I~~gsti   87 (94)
T d1x1ma1          20 KSILQLPETELGE-YSLGGYSISFLKQLIAGKLQESVPDPELIDLI---YCGRKLKD-DQTLDFYGIQPGSTV   87 (94)
T ss_dssp             CEEECCCCCSSCS-SCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEE---ETTEECCT-TCBHHHHTCCTTCEE
T ss_pred             cceEECCCCccCc-cCCCccCHHHHHHHHHHHcccCCCChhheEEE---ECCeEECC-CccHHHcCCCCCCEE
Confidence            3455566543211 1124789999999998766543   2456666   47899987 68999999996 444

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.79  E-value=0.28  Score=35.65  Aligned_cols=51  Identities=12%  Similarity=0.242  Sum_probs=39.3

Q ss_pred             EEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCC
Q 025134          195 RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLA  249 (257)
Q Consensus       195 rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~  249 (257)
                      .+.+.+..++||.+|...|.....-......|+   |=.+.|+| +.||.+.||.
T Consensus        12 Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi---~~Gk~L~D-~~TL~dYgI~   62 (103)
T d2c9wb1          12 TIFTDAKESSTVFELKRIVEGILKRPPDEQRLY---KDDQLLDD-GKTLGECGFT   62 (103)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEE---ETTEECCT-TSBHHHHTCC
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEE---ECCEEcCC-CCCHHHcCCC
Confidence            467899999999999999987532223445555   47899976 5899999995

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.37  E-value=0.91  Score=30.24  Aligned_cols=67  Identities=15%  Similarity=0.213  Sum_probs=50.5

Q ss_pred             eEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCCeeEE
Q 025134          184 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVI  254 (257)
Q Consensus       184 t~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~naviv  254 (257)
                      .+|+|+-.||+.+..++..+++++.|.+..+...........++   |-.+.|.. +.|.++++|-+.-+|
T Consensus         2 I~lkv~~~~g~~v~f~vk~~t~l~kl~~~y~~~~~~~~~~~~f~---fdG~~i~~-~~Tp~~l~med~D~I   68 (72)
T d1wm3a_           2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFR---FDGQPINE-TDTPAQLEMEDEDTI   68 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEE---ETTEECCT-TCCTTTTTCCTTEEE
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCccceEEE---ECCEEcCC-CCCHHHcCCCCCCEE
Confidence            46889999999999999999999999987666433333445444   57777865 479999999875444

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.95  E-value=1  Score=31.67  Aligned_cols=72  Identities=14%  Similarity=0.166  Sum_probs=49.3

Q ss_pred             CceEEEEEcC-CCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCc---ccCCccCcHhhhCCCC-eeE
Q 025134          182 PSTSVQIRLA-DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPK---VLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       182 p~t~iqIRl~-dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k---~l~d~s~TL~eagL~n-avi  253 (257)
                      ....|.|.-. ++....+||+.+.||.+|..-|.....-....-.|...+=+.+   .+.+++.||.+-++.+ ++|
T Consensus         6 s~v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tGip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~i   82 (95)
T d1v6ea_           6 SGVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRI   82 (95)
T ss_dssp             CCEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEE
T ss_pred             CcEEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhCcCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEE
Confidence            3466788874 5556899999999999999999886533333334443222222   3567789999999996 444

>d2al3a1 d.15.1.2 (A:10-85) Tether containing UBX domain for GLUT4 (Tug) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Tether containing UBX domain for GLUT4 (Tug)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.42  E-value=1  Score=30.84  Aligned_cols=62  Identities=18%  Similarity=0.194  Sum_probs=51.0

Q ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCCcccCCccCcHhhhCCCC
Q 025134          185 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN  250 (257)
Q Consensus       185 ~iqIRl~dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n  250 (257)
                      .|.|=.++|.|..++..++.|+.+|.+-+.+...-....|.|.. .  +|.| |.++.+.=+||.|
T Consensus         2 ~V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh-~--~k~l-dLsl~~R~sgLpn   63 (76)
T d2al3a1           2 AVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKF-Q--RTVL-DLSLQWRFANLPN   63 (76)
T ss_dssp             CEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEE-T--TEEE-SSSCBHHHHCCCS
T ss_pred             cEEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhCCChhHceeee-C--CEEc-CccceeeecCCCC
Confidence            35666899999999999999999999998876544467899987 3  5555 5579999999996

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=86.28  E-value=1.8  Score=29.88  Aligned_cols=70  Identities=10%  Similarity=0.194  Sum_probs=47.1

Q ss_pred             eEEEEEcC-CCCEEEEEeCCCCCHHHHHHHHHhhCCCCCcCeEEEecCCCC---cccCCccCcHhhhCCCC-eeE
Q 025134          184 TSVQIRLA-DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP---KVLADRTQTIEQAGLAN-SVV  253 (257)
Q Consensus       184 t~iqIRl~-dG~rlv~~fn~s~TI~dl~~fi~~~~p~~~~~f~L~t~~fP~---k~l~d~s~TL~eagL~n-avi  253 (257)
                      ..|.|... .+..+..||..+.||++|..-|.....-....=.|...+=..   ..|.|++.||.+-|+.+ +.|
T Consensus         5 ~~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~I   79 (90)
T d1t0ya_           5 YDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRI   79 (90)
T ss_dssp             EEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEE
T ss_pred             EEEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEE
Confidence            45666642 244579999999999999999988643333344454321111   24677889999999996 444