Citrus Sinensis ID: 025774

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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-------25
Protein Sequence
MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQALAASMETIKDASGVSSSDTDVASTDKDEASATEKPAYPILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTWE
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHccEEEEEEEcccHHHHHHHHHHccccccEEEEEccccccEEEEEcccccHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcHHHHHcccccccccccccccccccHHccccccccccccccccccccEEEEEEEcccccEEEEEEccccHHHHHHHHHHHHccccccccEEEEcccccccccccccccccHHHccccccEEEEEEc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHcEEEEEEEcccHccHEEEEEEccccccEEEEEccccccEEEEEcccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccHHccccccccccccccccccccccEEEEEEEcccccEEEEEEccccHHHHHHHHHHHHccccccccEEEEEccccccccccccccccHHHccccccEEEEEEc
Coil and Loop (DISEMBL)
MLNRDTWANEAVSQTISTNFIFWQvyddtsegkkvctyykldsipvvlvvdpitgqkmrswcgmvqpeslledlvpfmdggpreqhakvshkrprgssttpqqknkdkpdiENEELLQALAASMETIkdasgvsssdtdvastdkdeasatekpaypilpeepkvdrsllcrvgvrlpdgrrmqrnflrtdPIQLLWSYCYsqlegsemkpfrlthaipgatksldydskltfedsgLANAMISVTWE
Flexible Loop (DISEMBL)
MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTyykldsipvvLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGGPREQhakvshkrprgssttpqqknkdkpdIENEELLQALAASMETIkdasgvsssdtdvastdkdeasatekpaypilpeepkvdrslLCRVGvrlpdgrrmqrnflrtdpiqLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTWE
Low Complexity Region (SEG)
MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQALAASMETIKdasgvsssdtdvastdkdEASATEKPAYPILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTWE
Disordered region (IsUnstruct)
******WANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF*****************************************************************************************RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFE***L**********
Disordered Region (DISOPRED)
MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQ*********QPESLLEDLVPFMDGGPREQHA********************************************************************************SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLD*DSKLTFEDSGLANAMISVTWE
Disordered Region (DISEMBL)
*********EAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGGP***************************DIENEELLQALAASMETI*************************KPAYPILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTWE
Disordered Region (DISPRO)
**NRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG******************************************************************************PEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTWE
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQALAASMETIKDASGVSSSDTDVASTDKDEASATEKPAYPILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTWE
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	248	2.2.26 [Sep-21-2011]
O14048	427	UBX domain-containing pro	yes	no	0.915	0.531	0.273	1e-20
Q6P5G6	467	UBX domain-containing pro	yes	no	0.504	0.267	0.335	6e-15
Q5REY7	489	UBX domain-containing pro	yes	no	0.455	0.231	0.351	8e-15
O94888	489	UBX domain-containing pro	yes	no	0.455	0.231	0.351	8e-15
Q55BU7	503	UBX domain-containing pro	yes	no	0.524	0.258	0.323	8e-13
Q06682	500	UBX domain-containing pro	yes	no	0.923	0.458	0.227	9e-11

>sp|O14048|UBX2_SCHPO UBX domain-containing protein 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ubx2 PE=1 SV=1

 Score =  100 bits (249), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 71/260 (27%), Positives = 125/260 (48%), Gaps = 33/260 (12%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           +LNRD W +E+V + I  +F+F Q+ DD   G +   +Y + S P + ++DP TG++++ 
Sbjct: 189 VLNRDLWKDESVKEVIRAHFLFLQLLDDEEPGMEFKRFYPVRSTPHIAILDPRTGERVKE 248

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQAL 120
           W     P   +  L  F++G   ++ +    K P G+ +   QK  +    E+E++ +A+
Sbjct: 249 WSKSFTPADFVIALNDFLEGCTLDETS--GRKNPLGAKS---QKPVEAMS-EDEQMHKAI 302

Query: 121 AASM---ETIKDASGVSSS---------DTDVASTDKDEASATEKPAYPILPEEPKVDRS 168
           AAS+    +  ++ G SSS         D  V   D  E  A E    P           
Sbjct: 303 AASLGNGNSTTESQGESSSQQAESHGVADDTVHKIDSAECDAEEPSPGPN---------- 352

Query: 169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYD 228
            + R+ +R+P+G R  R F  TDP+  +++Y     EG++ +PF LT        SLD  
Sbjct: 353 -VTRIQIRMPNGARFIRRFSLTDPVSKVYAYVKGVAEGADKQPFSLTFQRKSLWTSLDS- 410

Query: 229 SKLTFEDSGLANAMISVTWE 248
              T +++G+ N  +   ++
Sbjct: 411 ---TIKEAGIQNTALQFEFQ 427

Involved in CDC48-dependent protein degradation through the ubiquitin/proteasome pathway.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q6P5G6|UBXN7_MOUSE UBX domain-containing protein 7 OS=Mus musculus GN=Ubxn7 PE=1 SV=2

 Score = 81.3 bits (199), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 47/140 (33%), Positives = 71/140 (50%), Gaps = 15/140 (10%)

Query: 2   LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
           LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  W
Sbjct: 161 LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEW 220

Query: 62  CGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDI----ENEELL 117
              +   S L+ +  F+            H +  G S++P +K      +    E+ +L 
Sbjct: 221 -HQLDVSSFLDQVTGFLG----------EHGQLDGLSSSPPKKCARSESLIDASEDSQLE 269

Query: 118 QALAASMETIKDASGVSSSD 137
            A+ AS++     S  +  D
Sbjct: 270 AAIRASLQETHFDSAQAKQD 289

Mus musculus (taxid: 10090)

>sp|Q5REY7|UBXN7_PONAB UBX domain-containing protein 7 OS=Pongo abelii GN=UBXN7 PE=2 SV=2

 Score = 80.9 bits (198), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 45/128 (35%), Positives = 68/128 (53%), Gaps = 15/128 (11%)

Query: 2   LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
           LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  W
Sbjct: 183 LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEW 242

Query: 62  CGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDI----ENEELL 117
              +   S L+ +  F+            H +  G S++P +K      +    E+ +L 
Sbjct: 243 -HQLDVSSFLDQVTGFLG----------EHGQLDGLSSSPPKKCARSESLIDASEDSQLE 291

Query: 118 QALAASME 125
            A+ AS++
Sbjct: 292 AAIRASLQ 299

Pongo abelii (taxid: 9601)

>sp|O94888|UBXN7_HUMAN UBX domain-containing protein 7 OS=Homo sapiens GN=UBXN7 PE=1 SV=2

 Score = 80.9 bits (198), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 45/128 (35%), Positives = 68/128 (53%), Gaps = 15/128 (11%)

Query: 2   LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
           LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  W
Sbjct: 183 LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEW 242

Query: 62  CGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDI----ENEELL 117
              +   S L+ +  F+            H +  G S++P +K      +    E+ +L 
Sbjct: 243 -HQLDVSSFLDQVTGFLG----------EHGQLDGLSSSPPKKCARSESLIDASEDSQLE 291

Query: 118 QALAASME 125
            A+ AS++
Sbjct: 292 AAIRASLQ 299

Homo sapiens (taxid: 9606)

>sp|Q55BU7|UBXN7_DICDI UBX domain-containing protein 7 homolog OS=Dictyostelium discoideum GN=ubxd7 PE=4 SV=1

 Score = 74.3 bits (181), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 44/136 (32%), Positives = 69/136 (50%), Gaps = 6/136 (4%)

Query: 2   LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
           LNRDTW+N+ + + I  NF+FWQV     EGK     Y +   P + ++DP TGQK++  
Sbjct: 179 LNRDTWSNKDLKELIGENFVFWQVNSANPEGKWFTQIYPVFKFPYIAIIDPRTGQKLQDM 238

Query: 62  CGMVQPESLLEDLVPFMDGGPRE-QHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQAL 120
            G +  E + + LV F+       Q          G+S     K + K + E+EEL  A+
Sbjct: 239 TGFIDAEEMAQYLVTFLSTNSFSGQIDPPPSSSSSGAS-----KKQKKYNTEDEELELAI 293

Query: 121 AASMETIKDASGVSSS 136
           A S++  ++ +  S S
Sbjct: 294 ALSLKQEQERNSKSGS 309

Dictyostelium discoideum (taxid: 44689)

>sp|Q06682|UBX5_YEAST UBX domain-containing protein 5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=UBX5 PE=1 SV=1

 Score = 67.4 bits (163), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 57/251 (22%), Positives = 112/251 (44%), Gaps = 22/251 (8%)

Query: 2   LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKL---DSIPVVLVVDPITGQKM 58
           LNRD W++  V   I  NF+F Q   ++   +    +Y L   D +P + ++DPITG+++
Sbjct: 253 LNRDLWSSRPVKTIIKENFVFLQYQYESRNAQPYLQFYHLNNKDDLPHIAILDPITGERV 312

Query: 59  RSWCGMVQ-PESLLEDLVPFMDG---GPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENE 114
           + W  +V  PE  + ++  F+      P+  +  V+   P+   TT  ++ + +  I+  
Sbjct: 313 KQWNRVVPIPEQFISEINEFLASFSLDPKVPNPTVNEPLPKVDPTTLTEEQQMELAIKES 372

Query: 115 ELLQALAASMETIKDASGVSSSDTDVASTDKDEASATEKPAYPILPEEPKVDRSLLCRVG 174
               +  ++ E +      S+ +      + D  S  E   +P  P +P     +  R+ 
Sbjct: 373 LNNNSSKSNQEEVP-----STGEEQKRVQEPDPFSTIEARVHPEPPNKP----GITTRIQ 423

Query: 175 VRLPDGRRMQRNF-LRTDPIQLLWSYCYSQLEGSEMKPFRLT-HAIPGATKSLDYDSKLT 232
           +R  DG R+ R F    D ++ ++    ++++G     F L  H        L+    +T
Sbjct: 424 IRTGDGSRLVRRFNALEDTVRTIYEVIKTEMDGFADSRFTLNDHQREDLIDKLN----MT 479

Query: 233 FEDSGLANAMI 243
             D+GL N+ +
Sbjct: 480 IADAGLKNSSL 490

Involved in CDC48-dependent protein degradation through the ubiquitin/proteasome pathway.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	248
359473684	456	PREDICTED: UBX domain-containing protein	1.0	0.543	0.742	1e-101
359473686	447	PREDICTED: UBX domain-containing protein	1.0	0.554	0.742	1e-101
224111366	444	predicted protein [Populus trichocarpa]	0.975	0.545	0.703	1e-100
255561727	452	UBX domain-containing protein, putative	0.991	0.544	0.714	4e-99
449445306	450	PREDICTED: UBX domain-containing protein	0.983	0.542	0.705	9e-98
449498388	288	PREDICTED: UBX domain-containing protein	0.983	0.847	0.705	1e-97
356526695	468	PREDICTED: UBX domain-containing protein	0.995	0.527	0.681	2e-97
357517375	461	UBX domain-containing protein [Medicago	1.0	0.537	0.666	2e-96
356559122	467	PREDICTED: UBX domain-containing protein	0.995	0.528	0.673	8e-96
356526697	476	PREDICTED: UBX domain-containing protein	0.995	0.518	0.660	4e-95

>gi|359473684|ref|XP_003631347.1| PREDICTED: UBX domain-containing protein 2-like isoform 2 [Vitis vinifera] gi|297738308|emb|CBI27509.3| unnamed protein product [Vitis vinifera]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 187/252 (74%), Positives = 218/252 (86%), Gaps = 4/252 (1%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAV+QTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLV+DPITGQKMRS
Sbjct: 205 MLNRDTWANEAVAQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVIDPITGQKMRS 264

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNK---DKPDIENEELL 117
           WCGM+QPE LLEDL+PFMDGGP++ H  +SHKRPR SS TP QK +   D+ + E+EE+ 
Sbjct: 265 WCGMIQPERLLEDLLPFMDGGPKDHHVTLSHKRPRESSLTPPQKIQVAADETNEEDEEVQ 324

Query: 118 QALAASMETIKDASGVSSSDTDVASTD-KDEASATEKPAYPILPEEPKVDRSLLCRVGVR 176
            ALAASM ++KD SG++S + DV +TD K+E  + +KP YP LPEEPK DR+LLCRVGVR
Sbjct: 325 LALAASMASMKDPSGLTSKEKDVTTTDKKEEMCSAKKPEYPPLPEEPKGDRNLLCRVGVR 384

Query: 177 LPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDS 236
           LPDGRR+QRNFLRTDPIQLLWS+CYSQLE    +PF LT AIPGA+++LDYD +LTFE+S
Sbjct: 385 LPDGRRIQRNFLRTDPIQLLWSFCYSQLEEVVSRPFHLTQAIPGASQNLDYDRELTFEES 444

Query: 237 GLANAMISVTWE 248
           GLAN+MISVTWE
Sbjct: 445 GLANSMISVTWE 456

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473686|ref|XP_002274120.2| PREDICTED: UBX domain-containing protein 2-like isoform 1 [Vitis vinifera]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 187/252 (74%), Positives = 218/252 (86%), Gaps = 4/252 (1%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAV+QTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLV+DPITGQKMRS
Sbjct: 196 MLNRDTWANEAVAQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVIDPITGQKMRS 255

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNK---DKPDIENEELL 117
           WCGM+QPE LLEDL+PFMDGGP++ H  +SHKRPR SS TP QK +   D+ + E+EE+ 
Sbjct: 256 WCGMIQPERLLEDLLPFMDGGPKDHHVTLSHKRPRESSLTPPQKIQVAADETNEEDEEVQ 315

Query: 118 QALAASMETIKDASGVSSSDTDVASTD-KDEASATEKPAYPILPEEPKVDRSLLCRVGVR 176
            ALAASM ++KD SG++S + DV +TD K+E  + +KP YP LPEEPK DR+LLCRVGVR
Sbjct: 316 LALAASMASMKDPSGLTSKEKDVTTTDKKEEMCSAKKPEYPPLPEEPKGDRNLLCRVGVR 375

Query: 177 LPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDS 236
           LPDGRR+QRNFLRTDPIQLLWS+CYSQLE    +PF LT AIPGA+++LDYD +LTFE+S
Sbjct: 376 LPDGRRIQRNFLRTDPIQLLWSFCYSQLEEVVSRPFHLTQAIPGASQNLDYDRELTFEES 435

Query: 237 GLANAMISVTWE 248
           GLAN+MISVTWE
Sbjct: 436 GLANSMISVTWE 447

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111366|ref|XP_002315828.1| predicted protein [Populus trichocarpa] gi|222864868|gb|EEF01999.1| predicted protein [Populus trichocarpa]

 Score =  370 bits (949), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 180/256 (70%), Positives = 211/256 (82%), Gaps = 14/256 (5%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAV+QTISTNFIFWQVYDDTSEG+KVCTYYKLDSIPVVL++DPITGQKM S
Sbjct: 195 MLNRDTWANEAVAQTISTNFIFWQVYDDTSEGQKVCTYYKLDSIPVVLIIDPITGQKMHS 254

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQAL 120
           W GMVQPESLLEDLVPFMDGGPR+ H  +SHKR RGSS TP +  +     E+EE+L+AL
Sbjct: 255 WVGMVQPESLLEDLVPFMDGGPRDHHKTLSHKRQRGSSLTPPKSKE-----EDEEVLRAL 309

Query: 121 AASMETIKDASGVSSSDTDVASTDKDEAS--------ATEKPAYPILPEEPKVDRSLLCR 172
           AASME++KD+S ++S+  D+AS DKD+AS        +T+   YP LPEEP  D+SLLCR
Sbjct: 310 AASMESMKDSSVIASNKKDIASNDKDDASTAKGEEKCSTKTLTYPPLPEEPSGDKSLLCR 369

Query: 173 VGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLT 232
           VG+RLPDGRR+QRNFL+TDPI+LLWS+CYSQLE +  K F L  AIPGA K LDYDS +T
Sbjct: 370 VGIRLPDGRRVQRNFLKTDPIRLLWSFCYSQLEEAGTKLFCLKEAIPGA-KRLDYDSTMT 428

Query: 233 FEDSGLANAMISVTWE 248
           F +SGLAN+MISV WE
Sbjct: 429 FGESGLANSMISVAWE 444

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255561727|ref|XP_002521873.1| UBX domain-containing protein, putative [Ricinus communis] gi|223538911|gb|EEF40509.1| UBX domain-containing protein, putative [Ricinus communis]

 Score =  366 bits (940), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 185/259 (71%), Positives = 213/259 (82%), Gaps = 13/259 (5%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAV+QTISTNFIFWQVYDDTS GKKVCTYYKLDSIPVVLV+DPITGQKMR+
Sbjct: 196 MLNRDTWANEAVAQTISTNFIFWQVYDDTSGGKKVCTYYKLDSIPVVLVIDPITGQKMRA 255

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDI--------- 111
           W GMVQPE LLEDLVP+MDGGPR+ H  +SHKRPRGSS    QKNK K  +         
Sbjct: 256 WSGMVQPECLLEDLVPYMDGGPRDHHVTLSHKRPRGSSQA-LQKNKGKLGLLPAFTNETN 314

Query: 112 -ENEELLQALAASMETIKDASGVSSSDTDVASTDKDEASATEKP-AYPILPEEPKVDRSL 169
            E+EE+L+ALAASME +KD++ + S   + AS D+DE S + K  AYP LPEEPK +RS+
Sbjct: 315 EEDEEMLRALAASMEGMKDSNRMPSDGKEAASADEDEKSCSTKILAYPPLPEEPKGERSI 374

Query: 170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDS 229
           LCRVG+RLPDGRR+QRNFL+TDPIQLLWS+C SQLE +  +PFRLT AIPGA KSLDYDS
Sbjct: 375 LCRVGLRLPDGRRIQRNFLKTDPIQLLWSFCTSQLEEAGTRPFRLTQAIPGA-KSLDYDS 433

Query: 230 KLTFEDSGLANAMISVTWE 248
           K+TF +SGLAN+MISV WE
Sbjct: 434 KVTFGESGLANSMISVAWE 452

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449445306|ref|XP_004140414.1| PREDICTED: UBX domain-containing protein 7-like [Cucumis sativus]

 Score =  362 bits (928), Expect = 9e-98,   Method: Compositional matrix adjust.
 Identities = 175/248 (70%), Positives = 206/248 (83%), Gaps = 4/248 (1%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAVSQTISTNFIFWQVYDD++EG+KVCTYYKL+SIP VLV+DPITGQKM S
Sbjct: 207 MLNRDTWANEAVSQTISTNFIFWQVYDDSTEGQKVCTYYKLESIPAVLVIDPITGQKMHS 266

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQAL 120
           W GMVQPE LLEDL+PFMDGGP++ H  +SHKRPR SS TP  K ++    E+EE+ +AL
Sbjct: 267 WFGMVQPERLLEDLLPFMDGGPKDHHVTLSHKRPRESSLTP-PKVREVEYEEDEEVQRAL 325

Query: 121 AASMETIKDASGVSSSDTDVASTDKDEASATEKPAYPILPEEPKVDRSLLCRVGVRLPDG 180
           A S+E +K+A  +SS D D    +K+E      P YP LPEEPK DR LLCR+GVRLP+G
Sbjct: 326 AVSLEGMKEAVKLSSEDKDTKVAEKEEEKC---PTYPPLPEEPKGDRKLLCRIGVRLPNG 382

Query: 181 RRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN 240
           RR QRNFLRTDPIQLLWS+C SQLE  E KPF+LTHAIPGATK+LDYD+++TFE+SGLAN
Sbjct: 383 RRCQRNFLRTDPIQLLWSFCSSQLEDGETKPFKLTHAIPGATKTLDYDTQMTFEESGLAN 442

Query: 241 AMISVTWE 248
           +MISVTW+
Sbjct: 443 SMISVTWD 450

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449498388|ref|XP_004160525.1| PREDICTED: UBX domain-containing protein 2-like [Cucumis sativus]

 Score =  361 bits (927), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 175/248 (70%), Positives = 206/248 (83%), Gaps = 4/248 (1%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAVSQTISTNFIFWQVYDD++EG+KVCTYYKL+SIP VLV+DPITGQKM S
Sbjct: 45  MLNRDTWANEAVSQTISTNFIFWQVYDDSTEGQKVCTYYKLESIPAVLVIDPITGQKMHS 104

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQAL 120
           W GMVQPE LLEDL+PFMDGGP++ H  +SHKRPR SS TP  K ++    E+EE+ +AL
Sbjct: 105 WFGMVQPERLLEDLLPFMDGGPKDHHVTLSHKRPRESSLTP-PKVREVEYEEDEEVQRAL 163

Query: 121 AASMETIKDASGVSSSDTDVASTDKDEASATEKPAYPILPEEPKVDRSLLCRVGVRLPDG 180
           A S+E +K+A  +SS D D    +K+E      P YP LPEEPK DR LLCR+GVRLP+G
Sbjct: 164 AVSLEGMKEAVKLSSEDKDTKVAEKEEEKC---PTYPPLPEEPKGDRKLLCRIGVRLPNG 220

Query: 181 RRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN 240
           RR QRNFLRTDPIQLLWS+C SQLE  E KPF+LTHAIPGATK+LDYD+++TFE+SGLAN
Sbjct: 221 RRCQRNFLRTDPIQLLWSFCSSQLEDGETKPFKLTHAIPGATKTLDYDTQMTFEESGLAN 280

Query: 241 AMISVTWE 248
           +MISVTW+
Sbjct: 281 SMISVTWD 288

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526695|ref|XP_003531952.1| PREDICTED: UBX domain-containing protein 7-like isoform 1 [Glycine max]

 Score =  360 bits (925), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 173/254 (68%), Positives = 210/254 (82%), Gaps = 7/254 (2%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAVSQTISTN IFWQVYDDT+EG+KVCTYY+LDSIPVVLV+DPITGQKMRS
Sbjct: 216 MLNRDTWANEAVSQTISTNCIFWQVYDDTTEGRKVCTYYRLDSIPVVLVIDPITGQKMRS 275

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQK---NKDKPDIENEELL 117
           W GMVQPESLLE L+ F+D GP++ H  +SHKRPRGSS+ P+ K     D+   E+EE+ 
Sbjct: 276 WIGMVQPESLLEGLLAFLDAGPKDHHITLSHKRPRGSSSPPKSKALVESDENKEEDEEVQ 335

Query: 118 QALAASMETIKDA---SGVSSSDTDVASTDKDEASATEKPAYPILPEEPKVDRSLLCRVG 174
           +ALAASME++K++   +G  + DTDVA   + + +  ++P YP LPEEPKV+R+LLCRVG
Sbjct: 336 RALAASMESMKESTVMTGRDNIDTDVAVYGQ-QTTLAKRPIYPALPEEPKVERNLLCRVG 394

Query: 175 VRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFE 234
           VRLPDG R+QRNFLRTDPIQLLWS+  +QL   E KPFRLTHAIPGA+K LDY+S  TF+
Sbjct: 395 VRLPDGHRIQRNFLRTDPIQLLWSFISAQLGEDERKPFRLTHAIPGASKILDYESNSTFQ 454

Query: 235 DSGLANAMISVTWE 248
           +SGLAN+MISVTW+
Sbjct: 455 ESGLANSMISVTWD 468

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357517375|ref|XP_003628976.1| UBX domain-containing protein [Medicago truncatula] gi|358345084|ref|XP_003636613.1| UBX domain-containing protein [Medicago truncatula] gi|355502548|gb|AES83751.1| UBX domain-containing protein [Medicago truncatula] gi|355522998|gb|AET03452.1| UBX domain-containing protein [Medicago truncatula]

 Score =  358 bits (918), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 168/252 (66%), Positives = 208/252 (82%), Gaps = 4/252 (1%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAVSQTI TNFIFWQVYDDT+EGKKVCTYY+LDSIPVVL++DPITGQKMR+
Sbjct: 210 MLNRDTWANEAVSQTIKTNFIFWQVYDDTTEGKKVCTYYRLDSIPVVLIIDPITGQKMRA 269

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQK---NKDKPDIENEELL 117
           W GMVQP+SLLE L+PF D GP++ H  +SHKRPRGSS+ P+ K   + D    E+EE+ 
Sbjct: 270 WGGMVQPDSLLEGLLPFFDAGPKDHHNTLSHKRPRGSSSPPKPKATLDSDANKEEDEEVQ 329

Query: 118 QALAASMETIKDASGVSSSDTDVASTDKD-EASATEKPAYPILPEEPKVDRSLLCRVGVR 176
           +ALAAS+E++K++S ++  D   A+   + + +A  +PAYP LPEEPK +R+LLCRVGVR
Sbjct: 330 RALAASLESVKESSEMAEGDDKEANVAGNVQETALPRPAYPTLPEEPKAERNLLCRVGVR 389

Query: 177 LPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDS 236
           LPDGRR+QRNFLR++PIQLLWS+   QL   E KPF+LTHAIPGATK+LDY+S  TFE+S
Sbjct: 390 LPDGRRVQRNFLRSEPIQLLWSFIAVQLGEDETKPFKLTHAIPGATKNLDYESNSTFEES 449

Query: 237 GLANAMISVTWE 248
           GLA +MISVTW+
Sbjct: 450 GLAYSMISVTWD 461

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559122|ref|XP_003547850.1| PREDICTED: UBX domain-containing protein 7-like isoform 1 [Glycine max]

 Score =  355 bits (912), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 171/254 (67%), Positives = 205/254 (80%), Gaps = 7/254 (2%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAVSQTISTN IFWQVYDDT+EG+KVCTYY+LDSIPVVLV+DPITGQKMRS
Sbjct: 215 MLNRDTWANEAVSQTISTNCIFWQVYDDTTEGRKVCTYYRLDSIPVVLVIDPITGQKMRS 274

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQK---NKDKPDIENEELL 117
           W GMVQPESLLE L+ F+D GP++ H  +SHKRPRGSS+ P+ K     D+   E EE+ 
Sbjct: 275 WIGMVQPESLLEGLLAFLDAGPKDHHITMSHKRPRGSSSPPKSKALVESDENKEEYEEVQ 334

Query: 118 QALAASMETIKDA---SGVSSSDTDVASTDKDEASATEKPAYPILPEEPKVDRSLLCRVG 174
           +ALAASME++K++   +G  + D DVA  +  E    ++P YP LPEEPKV+R+LLCRVG
Sbjct: 335 RALAASMESMKESTAMAGRDNKDADVA-VNGQETPMAKRPTYPTLPEEPKVERNLLCRVG 393

Query: 175 VRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFE 234
           VRLPDGRR+QRNFLRTDPIQLLWS+  +QL   E   FRLTHAIPGA+K LDY+   TF+
Sbjct: 394 VRLPDGRRVQRNFLRTDPIQLLWSFISAQLGEDETNSFRLTHAIPGASKILDYEINSTFQ 453

Query: 235 DSGLANAMISVTWE 248
           +SGLAN+MISVTW+
Sbjct: 454 ESGLANSMISVTWD 467

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526697|ref|XP_003531953.1| PREDICTED: UBX domain-containing protein 7-like isoform 2 [Glycine max]

 Score =  353 bits (905), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 173/262 (66%), Positives = 209/262 (79%), Gaps = 15/262 (5%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           MLNRDTWANEAVSQTISTN IFWQVYDDT+EG+KVCTYY+LDSIPVVLV+DPITGQKMRS
Sbjct: 216 MLNRDTWANEAVSQTISTNCIFWQVYDDTTEGRKVCTYYRLDSIPVVLVIDPITGQKMRS 275

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTT-PQQKN----------KDKP 109
           W GMVQPESLLE L+ F+D GP++ H  +SHKRPRGSS   P+ K            D+ 
Sbjct: 276 WIGMVQPESLLEGLLAFLDAGPKDHHITLSHKRPRGSSICLPKNKGGLGIKDLSLFTDEN 335

Query: 110 DIENEELLQALAASMETIKDA---SGVSSSDTDVASTDKDEASATEKPAYPILPEEPKVD 166
             E+EE+ +ALAASME++K++   +G  + DTDVA   + + +  ++P YP LPEEPKV+
Sbjct: 336 KEEDEEVQRALAASMESMKESTVMTGRDNIDTDVAVYGQ-QTTLAKRPIYPALPEEPKVE 394

Query: 167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLD 226
           R+LLCRVGVRLPDG R+QRNFLRTDPIQLLWS+  +QL   E KPFRLTHAIPGA+K LD
Sbjct: 395 RNLLCRVGVRLPDGHRIQRNFLRTDPIQLLWSFISAQLGEDERKPFRLTHAIPGASKILD 454

Query: 227 YDSKLTFEDSGLANAMISVTWE 248
           Y+S  TF++SGLAN+MISVTW+
Sbjct: 455 YESNSTFQESGLANSMISVTWD 476

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	248
TAIR|locus:2204497	468	AT1G14570 "AT1G14570" [Arabido	1.0	0.529	0.645	5.8e-82
TAIR|locus:2202872	307	AT1G59550 "AT1G59550" [Arabido	0.709	0.573	0.338	4.8e-31
TAIR|locus:505006365	152	AT3G23605 "AT3G23605" [Arabido	0.370	0.605	0.567	9.6e-29
POMBASE|SPAC2C4.15c	427	ubx2 "UBX domain protein Ubx2"	0.955	0.555	0.26	1e-20
UNIPROTKB|E1BTX4	492	UBXN7 "Uncharacterized protein	0.455	0.229	0.367	5.5e-19
ZFIN|ZDB-GENE-040704-8	505	ubxn7 "UBX domain protein 7" [	0.387	0.190	0.393	1.1e-18
MGI|MGI:2146388	467	Ubxn7 "UBX domain protein 7" [	0.455	0.241	0.351	1.6e-18
UNIPROTKB|I3LQY9	476	UBXN7 "Uncharacterized protein	0.455	0.237	0.351	1.7e-18
UNIPROTKB|E2R9U7	489	UBXN7 "Uncharacterized protein	0.455	0.231	0.351	2e-18
UNIPROTKB|O94888	489	UBXN7 "UBX domain-containing p	0.455	0.231	0.351	2e-18

TAIR|locus:2204497 AT1G14570 "AT1G14570" [Arabidopsis thaliana (taxid:3702)]

 Score = 822 (294.4 bits), Expect = 5.8e-82, P = 5.8e-82
 Identities = 164/254 (64%), Positives = 191/254 (75%)

Query:     1 MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
             MLNRDTWAN+AVSQTI  NFIFWQVYDDT+EG+KVCTYYKL+SIPVVLV+DP TGQ+MR 
Sbjct:   215 MLNRDTWANDAVSQTIKANFIFWQVYDDTTEGRKVCTYYKLESIPVVLVIDPTTGQRMRM 274

Query:    61 WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGS-STTPQQKNKDK--PDIENEELL 117
             W GMV PE+LLEDLVPFMDGGPRE  A +S KRPRGS S TP  K K+    D E EEL 
Sbjct:   275 WTGMVDPENLLEDLVPFMDGGPREHFASLSKKRPRGSFSLTPHSKPKEDVAKDEEEEELQ 334

Query:   118 QALAASMETIKXXXXXXXXXXXXXXXXXXEA-SATEKPAYPILPEEPKV-DRSLLCRVGV 175
             +ALAAS+E                     EA ++   P +P LPEEPK  DRSL CRVG+
Sbjct:   335 RALAASLEDNNMKESSDDQSTIIPEEVAVEAVTSAVLPTFPPLPEEPKGGDRSLQCRVGI 394

Query:   176 RLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMK-PFRLTHAIPGATKSLDYDSKLTFE 234
             RLP+G+R+QRNFL+TD IQLLWS+CYSQLE SE K P +LT AIPG +K+L+Y+S LT E
Sbjct:   395 RLPNGQRLQRNFLKTDTIQLLWSFCYSQLEESERKKPLKLTQAIPGESKTLEYESNLTLE 454

Query:   235 DSGLANAMISVTWE 248
              SG+AN+MIS TWE
Sbjct:   455 QSGVANSMISATWE 468

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR|locus:2202872 AT1G59550 "AT1G59550" [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 4.8e-31, Sum P(2) = 4.8e-31
 Identities = 64/189 (33%), Positives = 106/189 (56%)

Query:    63 GMVQPESLLEDLVPFMDGGPREQHAKVSHK-RPRGSSTTPQQKNKDKPDIENEELLQALA 121
             G ++ +  L+DL  ++D  P E  A  +   R +         + D+ D+ N      L+
Sbjct:   129 GEIKAKGFLKDLKKYIDASPHEHIASTARNMRVKAEKIC----HSDQQDMGN------LS 178

Query:   122 ASMETIKXXXXXXXXXXXXXXXXXXEASATEKPAYPILPEEPK--VDRSLLCRVGVRLPD 179
             +    +                      +++   +P+L +EPK   DRS++C + VR P+
Sbjct:   179 SDSVVVSSCGREFDDVVTLSEDEEETCLSSDLFEFPVLTKEPKGDCDRSVVCSISVRFPN 238

Query:   180 GRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA 239
             GRR QR FL+++P+QLLWS+CYS ++ S+ K F+L  AIPGA+K+LDY ++ +F+  G+A
Sbjct:   239 GRRKQRKFLKSEPVQLLWSFCYSHMDESDNKAFKLVQAIPGASKTLDYGAEASFDQYGIA 298

Query:   240 NAMISVTWE 248
             N++ISVTWE
Sbjct:   299 NSIISVTWE 307

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:505006365 AT3G23605 "AT3G23605" [Arabidopsis thaliana (taxid:3702)]

 Score = 282 (104.3 bits), Expect = 9.6e-29, Sum P(2) = 9.6e-29
 Identities = 55/97 (56%), Positives = 74/97 (76%)

Query:   156 YPILPEEPK--VDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQL--EGSEMKP 211
             +P LPEEP   +D+S+LCR+ VRLPDGRR+QR+FL+++ +QLLWS+CYSQ+  E SE K 
Sbjct:    55 FPNLPEEPNRDMDQSVLCRICVRLPDGRRIQRSFLKSESVQLLWSFCYSQIGDESSERKR 114

Query:   212 -FRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTW 247
              F+L    PG  K+L + S  TFE SGLAN+++SVTW
Sbjct:   115 RFKLIQGFPGDYKNLYFGSNTTFEQSGLANSLVSVTW 151

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

POMBASE|SPAC2C4.15c ubx2 "UBX domain protein Ubx2" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 248 (92.4 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 65/250 (26%), Positives = 119/250 (47%)

Query:     1 MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
             +LNRD W +E+V + I  +F+F Q+ DD   G +   +Y + S P + ++DP TG++++ 
Sbjct:   189 VLNRDLWKDESVKEVIRAHFLFLQLLDDEEPGMEFKRFYPVRSTPHIAILDPRTGERVKE 248

Query:    61 WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQAL 120
             W     P   +  L  F++G   ++ +    K P G+ +   QK  +    E+E++ +A+
Sbjct:   249 WSKSFTPADFVIALNDFLEGCTLDETS--GRKNPLGAKS---QKPVEAMS-EDEQMHKAI 302

Query:   121 AASMETIKXXXXXXXXXXXXXXXXXXEASAT--EKPAYPILPEEPKVDRSLLCRVGVRLP 178
             AAS+                       A  T  +  +     EEP    ++  R+ +R+P
Sbjct:   303 AASLGNGNSTTESQGESSSQQAESHGVADDTVHKIDSAECDAEEPSPGPNVT-RIQIRMP 361

Query:   179 DGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGL 238
             +G R  R F  TDP+  +++Y     EG++ +PF LT        SLD     T +++G+
Sbjct:   362 NGARFIRRFSLTDPVSKVYAYVKGVAEGADKQPFSLTFQRKSLWTSLDS----TIKEAGI 417

Query:   239 ANAMISVTWE 248
              N  +   ++
Sbjct:   418 QNTALQFEFQ 427

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0033554 "cellular response to stress" evidence=IEP

GO:0043130 "ubiquitin binding" evidence=IPI

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IGI

UNIPROTKB|E1BTX4 UBXN7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 202 (76.2 bits), Expect = 5.5e-19, Sum P(2) = 5.5e-19
 Identities = 47/128 (36%), Positives = 69/128 (53%)

Query:     2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
             LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  W
Sbjct:   186 LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLADFPYVSILDPRTGQKLVEW 245

Query:    62 CGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDI----ENEELL 117
                +   S L+ +  F+      +H ++      G ST P QK      +    E+ +L 
Sbjct:   246 -HQLDVTSFLDQVTGFLS-----EHGQLD-----GHSTNPPQKCSRSESLIDASEDSQLE 294

Query:   118 QALAASME 125
              A+ AS++
Sbjct:   295 AAIRASLQ 302

GO:0008134 "transcription factor binding" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0034098 "Cdc48p-Npl4p-Ufd1p AAA ATPase complex" evidence=IEA

GO:0043130 "ubiquitin binding" evidence=IEA

ZFIN|ZDB-GENE-040704-8 ubxn7 "UBX domain protein 7" [Danio rerio (taxid:7955)]

 Score = 196 (74.1 bits), Expect = 1.1e-18, Sum P(2) = 1.1e-18
 Identities = 39/99 (39%), Positives = 59/99 (59%)

Query:     2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
             LNRD W+N+AV   I  +FIFWQVY D+ EG++   +YKL+  P + ++DP TGQKM  W
Sbjct:   185 LNRDVWSNDAVKTIIREHFIFWQVYHDSEEGQRYIQFYKLNKFPYISILDPRTGQKMVEW 244

Query:    62 CGMVQPESLLEDLVPFM-DGGPRE-QHAKVSHKRPRGSS 98
                +   S ++ +  F+ + G  + Q ++   KR R  S
Sbjct:   245 -NQLDVSSFMDQVTGFLSEHGQLDGQSSQPPAKRARSES 282

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

MGI|MGI:2146388 Ubxn7 "UBX domain protein 7" [Mus musculus (taxid:10090)]

 Score = 194 (73.4 bits), Expect = 1.6e-18, Sum P(2) = 1.6e-18
 Identities = 45/128 (35%), Positives = 70/128 (54%)

Query:     2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
             LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  W
Sbjct:   161 LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEW 220

Query:    62 CGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDI----ENEELL 117
                +   S L+ +  F+      +H ++      G S++P +K      +    E+ +L 
Sbjct:   221 -HQLDVSSFLDQVTGFLG-----EHGQLD-----GLSSSPPKKCARSESLIDASEDSQLE 269

Query:   118 QALAASME 125
              A+ AS++
Sbjct:   270 AAIRASLQ 277

GO:0008134 "transcription factor binding" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0031625 "ubiquitin protein ligase binding" evidence=ISO

GO:0034098 "Cdc48p-Npl4p-Ufd1p AAA ATPase complex" evidence=ISO

GO:0043130 "ubiquitin binding" evidence=ISO

UNIPROTKB|I3LQY9 UBXN7 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 194 (73.4 bits), Expect = 1.7e-18, Sum P(2) = 1.7e-18
 Identities = 45/128 (35%), Positives = 70/128 (54%)

Query:     2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
             LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  W
Sbjct:   170 LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEW 229

Query:    62 CGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDI----ENEELL 117
                +   S L+ +  F+      +H ++      G S++P +K      +    E+ +L 
Sbjct:   230 -HQLDVSSFLDQVTGFLG-----EHGQLD-----GLSSSPPKKCARSESLIDASEDSQLE 278

Query:   118 QALAASME 125
              A+ AS++
Sbjct:   279 AAIRASLQ 286

GO:0043130 "ubiquitin binding" evidence=IEA

GO:0034098 "Cdc48p-Npl4p-Ufd1p AAA ATPase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

UNIPROTKB|E2R9U7 UBXN7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 194 (73.4 bits), Expect = 2.0e-18, Sum P(2) = 2.0e-18
 Identities = 45/128 (35%), Positives = 70/128 (54%)

Query:     2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
             LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  W
Sbjct:   183 LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEW 242

Query:    62 CGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDI----ENEELL 117
                +   S L+ +  F+      +H ++      G S++P +K      +    E+ +L 
Sbjct:   243 -HQLDVSSFLDQVTGFLG-----EHGQLD-----GLSSSPPKKCARSESLIDASEDSQLE 291

Query:   118 QALAASME 125
              A+ AS++
Sbjct:   292 AAIRASLQ 299

GO:0043130 "ubiquitin binding" evidence=IEA

GO:0034098 "Cdc48p-Npl4p-Ufd1p AAA ATPase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

UNIPROTKB|O94888 UBXN7 "UBX domain-containing protein 7" [Homo sapiens (taxid:9606)]

 Score = 194 (73.4 bits), Expect = 2.0e-18, Sum P(2) = 2.0e-18
 Identities = 45/128 (35%), Positives = 70/128 (54%)

Query:     2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
             LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  W
Sbjct:   183 LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEW 242

Query:    62 CGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDI----ENEELL 117
                +   S L+ +  F+      +H ++      G S++P +K      +    E+ +L 
Sbjct:   243 -HQLDVSSFLDQVTGFLG-----EHGQLD-----GLSSSPPKKCARSESLIDASEDSQLE 291

Query:   118 QALAASME 125
              A+ AS++
Sbjct:   292 AAIRASLQ 299

GO:0005515 "protein binding" evidence=IPI

GO:0008134 "transcription factor binding" evidence=IPI

GO:0043130 "ubiquitin binding" evidence=IDA

GO:0034098 "Cdc48p-Npl4p-Ufd1p AAA ATPase complex" evidence=IDA

GO:0031625 "ubiquitin protein ligase binding" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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: GSVIVG00035143001 SubName- Full=Chromosome chr1 scaffold_75, whole genome shotgun sequence; (453 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	248
cd02958	114	cd02958, UAS, UAS family; UAS is a domain of unkno	1e-35
smart00594	122	smart00594, UAS, UAS domain	1e-32
pfam00789	78	pfam00789, UBX, UBX domain	3e-16
cd01767	77	cd01767, UBX, UBX (ubiquitin regulatory X) domain	2e-06
smart00166	77	smart00166, UBX, Domain present in ubiquitin-regul	5e-04

>gnl|CDD|239256 cd02958, UAS, UAS family; UAS is a domain of unknown function

 Score =  122 bits (309), Expect = 1e-35
 Identities = 35/80 (43%), Positives = 53/80 (66%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           +LNRD W+NE+V + I  NFIFWQ   D+SEG++    YK+D  P + ++DP TG+ ++ 
Sbjct: 34  VLNRDLWSNESVKEFIRENFIFWQCDIDSSEGQRFLQSYKVDKYPHIAIIDPRTGEVLKV 93

Query: 61  WCGMVQPESLLEDLVPFMDG 80
           W G + PE LL  L+ F++ 
Sbjct: 94  WSGNITPEDLLSQLIEFLEE 113

Most members of this family are uncharacterized proteins with similarity to FAS-associated factor 1 (FAF1) and ETEA because of the presence of a UAS domain N-terminal to a ubiquitin-associated UBX domain. FAF1 is a longer protein, compared to the other members of this family, having additional N-terminal domains, a ubiquitin-associated UBA domain and a nuclear targeting domain. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. ETEA is the protein product of a highly expressed gene in T-cells and eosinophils of atopic dermatitis patients. The presence of the ubiquitin-associated UBX domain in the proteins of this family suggests the possibility of their involvement in ubiquitination. Recently, FAF1 has been shown to interact with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. Some members of this family are uncharacterized proteins containing only a UAS domain. Length = 114

>gnl|CDD|214737 smart00594, UAS, UAS domain

 Score =  115 bits (289), Expect = 1e-32
 Identities = 41/79 (51%), Positives = 54/79 (68%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
           + NRD   NEAV   I  NFIFWQV  DTSEG++V  +YKLDS P V +VDP TGQ++  
Sbjct: 44  VFNRDVLCNEAVKSLIRENFIFWQVDVDTSEGQRVSQFYKLDSFPYVAIVDPRTGQRVIE 103

Query: 61  WCGMVQPESLLEDLVPFMD 79
           W G+V+ E   E+L+ F++
Sbjct: 104 WVGVVEGEISPEELMTFLE 122

Length = 122

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

 Score = 70.8 bits (174), Expect = 3e-16
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSK 230
           CR+ +RLPDG R+ R F  +DP+Q ++ +  S     +  PF L    P    + D D  
Sbjct: 4   CRLQIRLPDGSRLVRRFNSSDPLQDVYDFVDSNRYDDDE-PFSLNTNFPRRPLTDDDDKT 62

Query: 231 LTFEDSGLANAMISVTW 247
           L  E   L N+ + +  
Sbjct: 63  LK-EAGLLPNSTLVLEP 78

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

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSL-DYDS 229
            ++ +RLPDG+R+++ F  T  +  +    + +  G   +PF L  + P   + L D D 
Sbjct: 3   TKIQIRLPDGKRLEQRFNSTHKLSDV--RDFVESNGPPAEPFTLMTSFP--RRVLTDLDY 58

Query: 230 KLTFEDSGLANAMISVTW 247
           +LT +++GL N ++    
Sbjct: 59  ELTLQEAGLVNEVVFQRL 76

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSK 230
           CR+ +RLPDG R+ R F  +D ++ ++ +  S   G    PF L    P  T + D  SK
Sbjct: 2   CRLQIRLPDGSRLVRRFPSSDTLRTVYEFV-SAALGDGNDPFTLNSPFPRRTFTKDDYSK 60

Query: 231 LTFEDSGLANAMISVTW 247
              E + L ++ + +  
Sbjct: 61  KLLELALLPSSTLVLEP 77

Present in FAF1 and Shp1p. Length = 77

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	248
KOG1363	460	consensus Predicted regulator of the ubiquitin pat	99.97
KOG1364	356	consensus Predicted ubiquitin regulatory protein,	99.95
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	99.89
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	99.87
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	99.87
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	99.87
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	99.86
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	99.82
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	99.82
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	99.82
cd02991	116	UAS_ETEA UAS family, ETEA subfamily; composed of p	99.79
KOG2507	506	consensus Ubiquitin regulatory protein UBXD2, cont	99.78
cd02990	136	UAS_FAF1 UAS family, FAS-associated factor 1 (FAF1	99.77
smart00594	122	UAS UAS domain.	99.64
cd02958	114	UAS UAS family; UAS is a domain of unknown functio	99.62
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	99.5
KOG2689	290	consensus Predicted ubiquitin regulatory protein [	99.36
COG2143	182	Thioredoxin-related protein [Posttranslational mod	97.69
cd02951	125	SoxW SoxW family; SoxW is a bacterial periplasmic	97.66
cd02953	104	DsbDgamma DsbD gamma family; DsbD gamma is the C-t	97.57
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	97.4
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	97.34
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	97.3
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	97.3
PF13899	82	Thioredoxin_7: Thioredoxin-like; PDB: 2LST_A 3PH9_	97.26
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	97.26
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	97.12
PF13098	112	Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_	97.06
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	97.05
cd02955	124	SSP411 TRX domain, SSP411 protein family; members	97.03
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	97.03
PTZ00044	76	ubiquitin; Provisional	96.96
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	96.88
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	96.8
cd02950	142	TxlA TRX-like protein A (TxlA) family; TxlA was or	96.78
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	96.67
cd03065	120	PDI_b_Calsequestrin_N PDIb family, Calsequestrin s	96.61
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	96.59
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	96.59
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	96.58
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	96.5
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	96.49
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	96.47
PRK11509	132	hydrogenase-1 operon protein HyaE; Provisional	96.41
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	96.4
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	96.34
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	96.29
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	95.9
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	95.79
KOG0910	150	consensus Thioredoxin-like protein [Posttranslatio	95.75
PF00085	103	Thioredoxin: Thioredoxin; InterPro: IPR013766 Thio	95.55
cd02956	96	ybbN ybbN protein family; ybbN is a hypothetical p	95.54
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	95.54
cd02965	111	HyaE HyaE family; HyaE is also called HupG and Hox	95.4
cd02997	104	PDI_a_PDIR PDIa family, PDIR subfamily; composed o	95.39
PRK00293	571	dipZ thiol:disulfide interchange protein precursor	95.37
PRK10996	139	thioredoxin 2; Provisional	95.32
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	95.29
cd02949	97	TRX_NTR TRX domain, novel NADPH thioredoxin reduct	95.25
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	95.17
TIGR01068	101	thioredoxin thioredoxin. Several proteins, such as	94.95
cd02985	103	TRX_CDSP32 TRX family, chloroplastic drought-induc	94.86
cd02960	130	AGR Anterior Gradient (AGR) family; members of thi	94.85
PRK09381	109	trxA thioredoxin; Provisional	94.35
cd03011	123	TlpA_like_ScsD_MtbDsbE TlpA-like family, suppresso	94.31
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	94.24
PF03190	163	Thioredox_DsbH: Protein of unknown function, DUF25	94.24
cd03002	109	PDI_a_MPD1_like PDI family, MPD1-like subfamily; c	94.19
TIGR00385	173	dsbE periplasmic protein thiol:disulfide oxidoredu	94.18
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	94.14
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	94.01
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	94.0
cd03003	101	PDI_a_ERdj5_N PDIa family, N-terminal ERdj5 subfam	93.7
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	93.69
PHA02278	103	thioredoxin-like protein	93.2
TIGR02740	271	TraF-like TraF-like protein. This protein is relat	93.17
PRK03147	173	thiol-disulfide oxidoreductase; Provisional	93.16
cd03005	102	PDI_a_ERp46 PDIa family, endoplasmic reticulum pro	93.02
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	92.64
cd02947	93	TRX_family TRX family; composed of two groups: Gro	92.5
cd02994	101	PDI_a_TMX PDIa family, TMX subfamily; composed of	92.41
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	92.34
cd02961	101	PDI_a_family Protein Disulfide Isomerase (PDIa) fa	92.32
cd02963	111	TRX_DnaJ TRX domain, DnaJ domain containing protei	92.24
TIGR02738	153	TrbB type-F conjugative transfer system pilin asse	92.07
cd02982	103	PDI_b'_family Protein Disulfide Isomerase (PDIb')	91.62
TIGR02739	256	TraF type-F conjugative transfer system pilin asse	91.53
TIGR01126	102	pdi_dom protein disulfide-isomerase domain. This m	91.52
cd03004	104	PDI_a_ERdj5_C PDIa family, C-terminal ERdj5 subfam	91.41
cd03006	113	PDI_a_EFP1_N PDIa family, N-terminal EFP1 subfamil	91.39
PRK15412	185	thiol:disulfide interchange protein DsbE; Provisio	91.28
cd03010	127	TlpA_like_DsbE TlpA-like family, DsbE (also known	91.26
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	91.22
cd02948	102	TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fus	91.11
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	91.1
PF13728	215	TraF: F plasmid transfer operon protein	91.1
PLN00410	142	U5 snRNP protein, DIM1 family; Provisional	91.01
cd02984	97	TRX_PICOT TRX domain, PICOT (for PKC-interacting c	90.62
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	89.84
TIGR00411	82	redox_disulf_1 small redox-active disulfide protei	89.83
PRK14018	521	trifunctional thioredoxin/methionine sulfoxide red	89.31
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	89.08
PRK13703	248	conjugal pilus assembly protein TraF; Provisional	88.71
cd02998	105	PDI_a_ERp38 PDIa family, endoplasmic reticulum pro	88.66
cd03000	104	PDI_a_TMX3 PDIa family, TMX3 subfamily; composed o	88.66
PRK13728	181	conjugal transfer protein TrbB; Provisional	88.55
cd02954	114	DIM1 Dim1 family; Dim1 is also referred to as U5 s	88.53
cd02999	100	PDI_a_ERp44_like PDIa family, endoplasmic reticulu	87.71
cd02966	116	TlpA_like_family TlpA-like family; composed of Tlp	87.24
cd02993	109	PDI_a_APS_reductase PDIa family, 5'-Adenylylsulfat	86.85
cd02957	113	Phd_like Phosducin (Phd)-like family; composed of	86.8
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	86.41
cd02996	108	PDI_a_ERp44 PDIa family, endoplasmic reticulum pro	86.0
PTZ00443	224	Thioredoxin domain-containing protein; Provisional	85.91
COG5100	571	NPL4 Nuclear pore protein [Nuclear structure]	84.83
TIGR02187	215	GlrX_arch Glutaredoxin-like domain protein. This f	84.75
PLN02560	308	enoyl-CoA reductase	84.57
cd03017	140	PRX_BCP Peroxiredoxin (PRX) family, Bacterioferrit	84.18
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	84.07
cd03001	103	PDI_a_P5 PDIa family, P5 subfamily; composed of eu	83.71
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	83.2
KOG0907	106	consensus Thioredoxin [Posttranslational modificat	82.9
PTZ00051	98	thioredoxin; Provisional	82.87
cd02975	113	PfPDO_like_N Pyrococcus furiosus protein disulfide	82.41
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	82.38
cd03008	146	TryX_like_RdCVF Tryparedoxin (TryX)-like family, R	81.25
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	80.98
cd02987	175	Phd_like_Phd Phosducin (Phd)-like family, Phd subf	80.95
cd02995	104	PDI_a_PDI_a'_C PDIa family, C-terminal TRX domain	80.81
cd02989	113	Phd_like_TxnDC9 Phosducin (Phd)-like family, Thior	80.59
cd02983	130	P5_C P5 family, C-terminal redox inactive TRX-like	80.46
PF02809	18	UIM: Ubiquitin interaction motif; InterPro: IPR003	80.38
TIGR01295	122	PedC_BrcD bacteriocin transport accessory protein,	80.23

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

Probab=99.97  E-value=3.3e-31  Score=243.56  Aligned_cols=234  Identities=21%  Similarity=0.285  Sum_probs=167.3

Q ss_pred             CcccccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCC----------------CCceEEEEeCCC-Cc-eEEeee
Q 025774            1 MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLD----------------SIPVVLVVDPIT-GQ-KMRSWC   62 (248)
Q Consensus         1 ~~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~----------------~~P~l~ii~~~~-g~-~l~~~~   62 (248)
                      .||+.+|||+.|++||+++||+|+||+++++++.+++.+.+.                .||++.++.... .. ++..++
T Consensus       199 ~F~~~iL~~e~v~~~l~~~~llw~~dvt~~e~~~~~~~~~~r~~~~~~~~~~~~~~~~~fP~~~iv~~~~~~~Ell~~l~  278 (460)
T KOG1363|consen  199 VFCGQILCNEAVVDYLRENFLLWGWDVTESENLLVFNSLLNRSISSPAAVTNKASKSERFPLVRIVIGSRSPEELLRYLQ  278 (460)
T ss_pred             HHHHhhhhhHHHHHHHhhceeeecccccCchhhHHHHHHhhcccchhhhhhcchhhcccCchhhhhhcCCCHHHHHHHHH
Confidence            389999999999999999999999999999999999999887                688887765321 11 566788


Q ss_pred             CCCChHHHHHHHhhhhhcCCCCccccccCCCCCCCCCCcccCCCCCCcchHHHHHHHHHHhhHhhhcc--CCC--CCCCc
Q 025774           63 GMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTTPQQKNKDKPDIENEELLQALAASMETIKDA--SGV--SSSDT  138 (248)
Q Consensus        63 G~~~~e~l~~~L~~~~~~~~~~~~~~l~~~r~~~~~~~~~~~~~~~~~~eeee~~~A~~~sl~~~~~~--~~~--~~ee~  138 (248)
                      |.++.++.+..+..+++.+....    ...+.  ++     ..+..|..-++|++.+|++||++|+.+  +..  .++.+
T Consensus       279 g~~~~~e~~~~~~~~~~~~~~~~----q~~~~--~~-----~er~~r~~~~~eQd~eyq~sle~Dr~r~~e~e~~~e~~r  347 (460)
T KOG1363|consen  279 GVTGVDEEMTLLLVAFEEEERRL----QMRRS--EQ-----DEREARLALEQEQDDEYQASLEADRVREAEAEQAAEEFR  347 (460)
T ss_pred             hcCCchHHHHHHHhhhhhhhHHH----hhccc--ch-----hHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhhHHHH
Confidence            88888888888877777652111    10010  00     011122333345678999999999876  111  11111


Q ss_pred             c----cCCcchhhhcccCCCCCCCCCCCCCCCCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEE
Q 025774          139 D----VASTDKDEASATEKPAYPILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRL  214 (248)
Q Consensus       139 ~----~~~~~~~e~~~~~~~~~~~l~~eP~~~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L  214 (248)
                      .    +++++++|.........+.||+||++...++++|+||+|+|.+..|||..+++++.||+||.++  +..+..|.+
T Consensus       348 ~e~er~~~~ee~e~~R~~l~~es~lp~EP~a~~~~~~~l~iR~P~G~r~~RrF~~s~~~q~l~~~v~~~--~~~~~e~~~  425 (460)
T KOG1363|consen  348 LEKERKEEEEERETARQLLALESSLPPEPSASEEEAITVAIRLPSGTRLERRFLKSDKLQILYDYVDSN--GFHPEEYSL  425 (460)
T ss_pred             HhhhhhhHHHHHHHHHHHHhhhccCCCCCCcCcccceeeEEECCCCCeeeeeeecccchhHHHHHHHhc--cCCchhhcc
Confidence            0    1111111111112234578999998788899999999999999999999999999999999997  456899999


Q ss_pred             EccCCCCccccCCCcCCCccccCCcC--ceEEEEeC
Q 025774          215 THAIPGATKSLDYDSKLTFEDSGLAN--AMISVTWE  248 (248)
Q Consensus       215 ~~~~Pr~~~~l~~d~~~tl~d~gl~~--~~v~v~~~  248 (248)
                      .++|||+.++- .....|+++.|+.+  .+|.++|.
T Consensus       426 ~~~fPr~~~~~-~~~~~sl~~~~l~p~qe~lflE~~  460 (460)
T KOG1363|consen  426 NTSFPRRPLGD-YEHSSSLQDIGLTPRQETLFLEEI  460 (460)
T ss_pred             ccCCCcccccc-cccccccccCCcccccceeeeecC
Confidence            99999997332 34589999999986  56777763

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

Probab=99.95  E-value=3.5e-28  Score=211.97  Aligned_cols=224  Identities=37%  Similarity=0.711  Sum_probs=162.8

Q ss_pred             HHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcCCCCccccccCC
Q 025774           13 SQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGGPREQHAKVSHK   92 (248)
Q Consensus        13 ~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~~~~~~~~l~~~   92 (248)
                      +.....++.-|..+.++.||.++..+|++.+.|+|+||+|+||+.|++|.|.+.+++|+..|+.||+.++.++-+.+...
T Consensus       124 k~~a~sk~~wllV~~Dtseg~~~~~Fy~~~~~P~i~iiDp~Tge~v~~ws~vi~~~~fl~~l~~Fi~~~~~d~vas~t~n  203 (356)
T KOG1364|consen  124 KSTASSKQRWLLVLDDTSEGQPFSAFYHISSLPHIAIIDPITGERVKRWSGVIEPEQFLSDLNEFIDSCPHDEVASLTRN  203 (356)
T ss_pred             hhcccccceEEEEeeccCCCCchhhheeccCCceEEEECCchhhhhhhhccccCHHHHHHHHHHHHhcCCcccccccccc
Confidence            44566789999999999999999999999999999999999999999999999999999999999999988765555443


Q ss_pred             CCCCCCCCcccCCCCCCcc-hHHHHHHHHHHhhHhhhccCCCCCCCcccCCcc-h--hhhcccCCCCCCCCCCCCCC--C
Q 025774           93 RPRGSSTTPQQKNKDKPDI-ENEELLQALAASMETIKDASGVSSSDTDVASTD-K--DEASATEKPAYPILPEEPKV--D  166 (248)
Q Consensus        93 r~~~~~~~~~~~~~~~~~~-eeee~~~A~~~sl~~~~~~~~~~~ee~~~~~~~-~--~e~~~~~~~~~~~l~~eP~~--~  166 (248)
                      |....      ....-... |+++++.|+..|+-.-.-. ..-++.-...+++ +  .++..   -.++.+..||..  +
T Consensus       204 ~~~p~------~e~~~~ss~e~~~~elai~~sv~~~~~~-~e~e~~~~s~~ee~e~~~e~~~---~~~~~a~~ep~~~~~  273 (356)
T KOG1364|consen  204 RKRPK------TEPTCLSSEEDMQMELAIKNSVVNPSSG-TEFEGQGASDEEELETVLEEDL---FVFPVATVEPKGDCD  273 (356)
T ss_pred             ccCCC------CCccccccccchhhhcccccccccCCCc-ccccCCCCcccchhhccccccc---cccceeeecCCCCCC
Confidence            32111      11112222 4445567777776543221 1001100000000 0  01110   112333344432  3


Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCce--EE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAM--IS  244 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~--v~  244 (248)
                      .+-+|+|+||||||+|.+|+|.++++++.||.|+.++.++++...|+|+++||++ +++.++.+.||+++||.|++  +.
T Consensus       274 ~svvt~i~vR~pdG~R~qrkf~~sepv~ll~~~~~s~~dg~~k~~FkLv~a~P~~-k~l~~~~daT~~eaGL~nS~~~~~  352 (356)
T KOG1364|consen  274 RSVVTSIQVRFPDGRRKQRKFLKSEPVQLLWSFCYSHMDGSDKKRFKLVQAIPAS-KTLDYGADATFKEAGLANSETLLS  352 (356)
T ss_pred             ccceeEEEEecCCccHHHHhhccccHHHHHHHHHHHhhcccccccceeeecccch-hhhhccccchHHHhccCccccccc
Confidence            3557889999999999999999999999999999999999899999999999976 68878899999999999984  45


Q ss_pred             EEe
Q 025774          245 VTW  247 (248)
Q Consensus       245 v~~  247 (248)
                      +.|
T Consensus       353 ~e~  355 (356)
T KOG1364|consen  353 VEW  355 (356)
T ss_pred             ccc
Confidence            666

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=99.89  E-value=4.5e-23  Score=147.44  Aligned_cols=78  Identities=24%  Similarity=0.416  Sum_probs=69.9

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEEe
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTW  247 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~~  247 (248)
                      .++|+|+||||||+|++++|+.+++|++||+||.++..+....+|.|.++||++.  +. +.++||+|+||.|++|+++|
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 EPTTSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPVKE--LS-DESLTLKEANLLNAVIVQRL   78 (79)
T ss_pred             CCeeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCCcc--cC-CCCCcHHHCCCcCcEEEEEe
Confidence            3579999999999999999999999999999999875444468999999999986  65 44999999999999999999


Q ss_pred             C
Q 025774          248 E  248 (248)
Q Consensus       248 ~  248 (248)
                      .
T Consensus        79 ~   79 (79)
T cd01770          79 K   79 (79)
T ss_pred             C
Confidence            5

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.

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=99.87  E-value=3.8e-22  Score=142.35  Aligned_cols=77  Identities=23%  Similarity=0.307  Sum_probs=68.6

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVT  246 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~  246 (248)
                      +.++|+|+||||||++++|+|+.+++|++||+||.++  ++++.+|+|+++||||+++- .|.++||+|+||+|+++++.
T Consensus         2 ~~~~t~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~~--g~~~~~f~L~t~FPRr~~~~-~d~~~TL~e~GL~P~~~LfV   78 (82)
T cd01773           2 NGPKARLMLRYPDGKREQIALPEQAKLLALVRHVQSK--GYPNERFELLTNFPRRKLSH-LDYDITLQEAGLCPQETVFV   78 (82)
T ss_pred             CCCeeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc--CCCCCCEEEecCCCCcccCC-cccCCCHHHcCCCCCcEEEE
Confidence            4578999999999999999999999999999999995  66789999999999998554 47789999999998776653

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.

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=99.87  E-value=5.8e-22  Score=141.37  Aligned_cols=76  Identities=26%  Similarity=0.493  Sum_probs=68.7

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCC-CcCCCccccCCcCceEEEEe
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDY-DSKLTFEDSGLANAMISVTW  247 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~-d~~~tl~d~gl~~~~v~v~~  247 (248)
                      ++|+|+||||||++++|+|+.+++|++||+||.++.  +...+|.|+++||++.  +.+ +.++||+|+||.|++++|+|
T Consensus         1 p~t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~--~~~~~f~L~t~~Pr~~--~~~~~~~~TL~e~gL~~s~~~~~~   76 (77)
T cd01767           1 PTTKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNG--PPAEPFTLMTSFPRRV--LTDLDYELTLQEAGLVNEVVFQRL   76 (77)
T ss_pred             CcEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcC--CCCCCEEEEeCCCCcc--CCCCCccCcHHHcCCccceEEEEe
Confidence            379999999999999999999999999999999873  3478999999999987  543 58999999999999999999


Q ss_pred             C
Q 025774          248 E  248 (248)
Q Consensus       248 ~  248 (248)
                      +
T Consensus        77 ~   77 (77)
T cd01767          77 K   77 (77)
T ss_pred             C
Confidence            5

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.

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=99.87  E-value=7.2e-22  Score=143.02  Aligned_cols=79  Identities=19%  Similarity=0.381  Sum_probs=68.4

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCcccc----CCCcCCCccccCCcCceE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSL----DYDSKLTFEDSGLANAMI  243 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l----~~d~~~tl~d~gl~~~~v  243 (248)
                      +++|+|+||||||+|++|||+.+++|++||+||.+.  ++.+.+|+|+++|||+.+.-    ..+.++||+|+||.|+++
T Consensus         2 ~~~~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~~--~~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~   79 (85)
T cd01774           2 PDTVKIVFKLPNGTRVERRFLFTQSLRVIHDFLFSL--KETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEV   79 (85)
T ss_pred             CceEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhC--CCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccE
Confidence            468999999999999999999999999999999875  44578999999999997321    136789999999999998


Q ss_pred             EEEeC
Q 025774          244 SVTWE  248 (248)
Q Consensus       244 ~v~~~  248 (248)
                      |++++
T Consensus        80 L~V~d   84 (85)
T cd01774          80 LFVQD   84 (85)
T ss_pred             EEEec
Confidence            88764

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=99.86  E-value=1.4e-21  Score=139.99  Aligned_cols=75  Identities=23%  Similarity=0.427  Sum_probs=66.3

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISV  245 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v  245 (248)
                      +++++|+||||||++++|||+.+++|++||+||.++  ++++.+|+|+++|||+.++. .|.+.||+|+||.++++|+
T Consensus         2 ~~~~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~--~~~~~~f~L~t~fPRk~~~~-~d~~~TL~e~gL~p~~~L~   76 (80)
T cd01771           2 EPISKLRVRTPSGDFLERRFLGDTPLQVLLNFVASK--GYPIDEYKLLSSWPRRDLTQ-LDPNFTLLELKLYPQETLI   76 (80)
T ss_pred             CCeEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc--CCCCCCEEEecCCCCCCCcC-CCCCCcHHHcCCCCCcEEE
Confidence            468999999999999999999999999999999986  67788999999999998443 4778999999999766554

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=99.82  E-value=6.3e-20  Score=132.29  Aligned_cols=79  Identities=38%  Similarity=0.555  Sum_probs=65.4

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +++.|+|+||||||++++|+|+.++||++||+||.++........|.|+++||++.  +..+.++||+|+||.+ ++|+|
T Consensus         3 ~~~~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~--l~~~~~~tl~e~~l~p~~~l~v   80 (82)
T PF00789_consen    3 ESDVVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRE--LTDEDSKTLEEAGLLPSATLIV   80 (82)
T ss_dssp             TSSEEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEE--CCSTTTSBTCCCTTSSCEEEEE
T ss_pred             CCCEEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcC--CCccccccHHHhcCCCCeEEEE
Confidence            46789999999999999999999999999999999986542233499999999986  5433369999999985 66778


Q ss_pred             Ee
Q 025774          246 TW  247 (248)
Q Consensus       246 ~~  247 (248)
                      +|
T Consensus        81 ~~   82 (82)
T PF00789_consen   81 EK   82 (82)
T ss_dssp             E-
T ss_pred             EC
Confidence            88

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 ....

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=99.82  E-value=8.1e-20  Score=131.20  Aligned_cols=76  Identities=26%  Similarity=0.486  Sum_probs=64.2

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCC-CcCCCccccCCcC-ceEEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDY-DSKLTFEDSGLAN-AMISVT  246 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~-d~~~tl~d~gl~~-~~v~v~  246 (248)
                      +.|+|+||||||++++|+|+.+++|++||+||.... +....+|.|+++||++.  +.. |.++||+|+||.| ++|+|+
T Consensus         3 ~~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~-~~~~~~f~L~t~~Prk~--l~~~d~~~tL~e~gL~p~~~l~v~   79 (80)
T smart00166        3 DQCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAAL-TDGNDPFTLNSPFPRRT--FTKDDYSKTLLELALLPSSTLVLE   79 (80)
T ss_pred             CeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcc-cCCCCCEEEEeCCCCcC--CccccccCCHHHCCCCCceEEEEe
Confidence            589999999999999999999999999999996643 33567899999999986  432 4589999999985 556677


Q ss_pred             e
Q 025774          247 W  247 (248)
Q Consensus       247 ~  247 (248)
                      |
T Consensus        80 ~   80 (80)
T smart00166       80 P   80 (80)
T ss_pred             C
Confidence            6

Present in FAF1 and Shp1p.

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=99.82  E-value=8.1e-20  Score=130.83  Aligned_cols=75  Identities=17%  Similarity=0.313  Sum_probs=65.2

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVT  246 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~  246 (248)
                      +.|+|+||||||++++++|+.+++|++||+||.++.  ....+|.|+++|||+.++. ++.++||+|+||.|+++|+.
T Consensus         3 ~~~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~--~~~~~f~L~t~fPrk~~~~-~d~~~TL~elgL~Psa~L~v   77 (79)
T cd01772           3 TETRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNT--GNGGPFTLMTPFPRKVFTE-DDMEKPLQELGLVPSAVLIV   77 (79)
T ss_pred             cEEEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcC--CCCCCEEEEeCCCCeECCc-ccccCCHHHCCCCCceEEEE
Confidence            579999999999999999999999999999999873  3358899999999997433 36789999999998887654

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.

>cd02991 UAS_ETEA UAS family, ETEA subfamily; composed of proteins similar to human ETEA protein, the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals

Probab=99.79  E-value=5.3e-19  Score=135.65  Aligned_cols=80  Identities=24%  Similarity=0.412  Sum_probs=75.8

Q ss_pred             cccccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCc--eEEeeeCCCChHHHHHHHhhhhh
Q 025774            2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQ--KMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus         2 ~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~--~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      |||+||||++|++||++|||+|++|++++||+++++.+++.+||++++|+|+++.  ++.+++|.++|++|+..|+.+++
T Consensus        35 fc~~~l~~~~v~~~ln~~fv~w~~dv~~~eg~~la~~l~~~~~P~~~~l~~~~~~~~vv~~i~G~~~~~~ll~~L~~~~~  114 (116)
T cd02991          35 FCRNTLCAPEVIEYINTRMLFWACSVAKPEGYRVSQALRERTYPFLAMIMLKDNRMTIVGRLEGLIQPEDLINRLTFIMD  114 (116)
T ss_pred             HHHHHcCCHHHHHHHHcCEEEEEEecCChHHHHHHHHhCCCCCCEEEEEEecCCceEEEEEEeCCCCHHHHHHHHHHHHh
Confidence            8999999999999999999999999999999999999999999999999988665  68999999999999999999987


Q ss_pred             cC
Q 025774           80 GG   81 (248)
Q Consensus        80 ~~   81 (248)
                      ++
T Consensus       115 ~~  116 (116)
T cd02991         115 AN  116 (116)
T ss_pred             cC
Confidence            53

ETEA shows homology to Fas-associated factor 1 (FAF1); both containing UAS and UBX (ubiquitin-associated) domains. Compared to FAF1, however, ETEA lacks the ubiquitin-associated UBA domain and a nuclear targeting domain. The function of ETEA is still unknown. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that ETEA could be involved in modulating Fas-mediated apoptosis of T-cells and eosinophils of atopic dermatitis patients, making them more resistant to apoptosis.

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

Probab=99.78  E-value=7.8e-19  Score=156.41  Aligned_cols=77  Identities=21%  Similarity=0.440  Sum_probs=71.8

Q ss_pred             CcccccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774            1 MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus         1 ~~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      +|+|-+|.+..|.+.+...||...++..+..+.+|+.+|++.+.|++++|+ .+|..|+++.|++++|+|...|.+++
T Consensus        35 kl~r~~w~d~~vs~~ls~~fVaIkiqags~aa~qFs~IYp~v~vPs~ffIg-~sGtpLevitg~v~adeL~~~i~Kv~  111 (506)
T KOG2507|consen   35 KLNRLTWTDASVSDSLSKYFVAIKIQAGSVAATQFSAIYPYVSVPSIFFIG-FSGTPLEVITGFVTADELASSIEKVW  111 (506)
T ss_pred             HHhhccchhhhhhhhhhcceEEEEeccCchhhhhhhhhcccccccceeeec-CCCceeEEeeccccHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999999999999999998 67999999999999999988776654

>cd02990 UAS_FAF1 UAS family, FAS-associated factor 1 (FAF1) subfamily; FAF1 contains a UAS domain of unknown function N-terminal to a ubiquitin-associated UBX domain

Probab=99.77  E-value=9.6e-19  Score=136.88  Aligned_cols=80  Identities=20%  Similarity=0.256  Sum_probs=73.5

Q ss_pred             cccccCCCHHHHHHhhcceEEEEEecCChH----------------HHHHHHhcCCCCCceEEEEeCCCCc--eEEeeeC
Q 025774            2 LNRDTWANEAVSQTISTNFIFWQVYDDTSE----------------GKKVCTYYKLDSIPVVLVVDPITGQ--KMRSWCG   63 (248)
Q Consensus         2 ~~r~vl~~~~v~~~l~~~fV~w~~d~~~~e----------------g~~~~~~~~~~~~P~l~ii~~~~g~--~l~~~~G   63 (248)
                      |||++|||+.|++||++|||+|+||++.++                ++++++.+++++||+++||++..+.  ++.+++|
T Consensus        39 Fc~~~L~se~Vi~fl~~nfv~Wg~dvt~~~~~~~fl~~~~~~~g~~a~~~~~~~~~~~fP~~avI~~~~~~~~vl~~i~G  118 (136)
T cd02990          39 FCSQLLCAESIVQYLSQNFITWGWDMTKESNKARFLSSCTRHFGSVAAQTIRNIKTDQLPAILIIMGKRSSNEVLNVIQG  118 (136)
T ss_pred             HHHHHhcCHHHHHHHHcCEEEEeeeccchhhhhHHHHhhhhhhhHHHHHHHHhcCcCCCCeEEEEEecCCceEEEEEEEC
Confidence            899999999999999999999999999887                6678888999999999999987554  7899999


Q ss_pred             CCChHHHHHHHhhhhhcC
Q 025774           64 MVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        64 ~~~~e~l~~~L~~~~~~~   81 (248)
                      .++|++++.+|+.+++.|
T Consensus       119 ~~~~~ell~~L~~~ve~~  136 (136)
T cd02990         119 NTGVDELLMRLIEAMEMF  136 (136)
T ss_pred             CCCHHHHHHHHHHHHhcC
Confidence            999999999999998864

FAF1 also contains ubiquitin-associated UBA and nuclear targeting domains, N-terminal to the UAS domain. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. It is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kB (NF-kB) by interfering with the nuclear

>smart00594 UAS UAS domain

Probab=99.64  E-value=4.2e-16  Score=120.66  Aligned_cols=74  Identities=53%  Similarity=0.798  Sum_probs=69.4

Q ss_pred             CcccccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCc----eEEeeeCCCChHHHHHHH
Q 025774            1 MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQ----KMRSWCGMVQPESLLEDL   74 (248)
Q Consensus         1 ~~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~----~l~~~~G~~~~e~l~~~L   74 (248)
                      +|||+||+|+.|+++|+++||+|++|+++++|..+++.|++++||+++||+|.+|+    ++.++.|.+++++|+..|
T Consensus        44 ~~~r~vl~~~~V~~~i~~~fv~~~~dv~~~eg~~l~~~~~~~~~P~~~~l~~~~g~~~~~~~~~~~G~~~~~~l~~~l  121 (122)
T smart00594       44 VFNRDVLCNEAVKSLIRENFIFWQVDVDTSEGQRVSQFYKLDSFPYVAIVDPRTGQRVIEWVGVVEGEISPEELMTFL  121 (122)
T ss_pred             HHHHHHccCHHHHHHHHcCEEEEEecCCChhHHHHHHhcCcCCCCEEEEEecCCCceeEEEeccccCCCCHHHHHHhh
Confidence            38999999999999999999999999999999999999999999999999999765    477899999999998876

>cd02958 UAS UAS family; UAS is a domain of unknown function

Probab=99.62  E-value=1.6e-15  Score=115.76  Aligned_cols=80  Identities=44%  Similarity=0.894  Sum_probs=76.5

Q ss_pred             CcccccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774            1 MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus         1 ~~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .|||+||+|+.|+++|+++||+|++|+++++|..++..|++..||++++|+|++|+++.++.|.+++++|+..|..+++.
T Consensus        34 ~~~~~vl~~~~v~~~l~~~~v~~~~d~~~~e~~~~~~~~~~~~~P~~~~i~~~~g~~l~~~~G~~~~~~f~~~L~~~~~~  113 (114)
T cd02958          34 VLNRDLWSNESVKEFIRENFIFWQCDIDSSEGQRFLQSYKVDKYPHIAIIDPRTGEVLKVWSGNITPEDLLSQLIEFLEE  113 (114)
T ss_pred             HHHHHHcCCHHHHHHHHhCEEEEEecCCCccHHHHHHHhCccCCCeEEEEeCccCcEeEEEcCCCCHHHHHHHHHHHHhc
Confidence            37899999999999999999999999999999999999999999999999998899999999999999999999998764

Most members of this family are uncharacterized proteins with similarity to FAS-associated factor 1 (FAF1) and ETEA because of the presence of a UAS domain N-terminal to a ubiquitin-associated UBX domain. FAF1 is a longer protein, compared to the other members of this family, having additional N-terminal domains, a ubiquitin-associated UBA domain and a nuclear targeting domain. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. ETEA is the protein product of a highly expressed gene in T-cells and eosinophils of atopic dermatitis patients. The presence of the ubiquitin-associated UBX domain in the proteins of this family suggests the possibility of their involvement in ubiquitination. Recently, FAF1 has been shown to interact with valosin-containing protein (VCP),

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

Probab=99.50  E-value=2.8e-14  Score=126.94  Aligned_cols=79  Identities=22%  Similarity=0.355  Sum_probs=71.3

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVT  246 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~  246 (248)
                      .+++|.|||||+||+|++-+|+.++||.+||.||...-.+.....|.|+++||.+.  |. |.+.||++|||.|++|+++
T Consensus       302 ~~PtTsIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L~~~FPpk~--l~-D~sqTle~AgL~Nsvlvqr  378 (380)
T KOG2086|consen  302 AEPTTSIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPGDSSTYFILMMAFPPKP--LS-DDSQTLEEAGLLNSVLVQR  378 (380)
T ss_pred             CCCcceEEEEecCCceeeeeccCcccHHHHHHHHHhcCCCCcCCceeeeecCCCcc--cC-CcchhHHhccchhhhhhhh
Confidence            36789999999999999999999999999999999875565567899999999986  74 7899999999999999998


Q ss_pred             eC
Q 025774          247 WE  248 (248)
Q Consensus       247 ~~  248 (248)
                      |.
T Consensus       379 ~~  380 (380)
T KOG2086|consen  379 LA  380 (380)
T ss_pred             cC
Confidence            84

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

Probab=99.36  E-value=1.7e-12  Score=110.42  Aligned_cols=78  Identities=18%  Similarity=0.365  Sum_probs=67.3

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceE-EEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMI-SVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v-~v~  246 (248)
                      -+.|+||||||||+.+...|+...+|..|..||+.+- +....+|.|.++|||+.|+- +|..++|+++||.|+++ +..
T Consensus       208 ys~crlQiRl~DG~Tl~~tF~a~E~L~~VR~wVd~n~-~~~~~P~~f~t~fPR~tf~e-dD~~KpLq~L~L~Psa~lil~  285 (290)
T KOG2689|consen  208 YSQCRLQIRLPDGQTLTQTFNARETLAAVRLWVDLNR-GDGLDPYSFHTGFPRVTFTE-DDELKPLQELDLVPSAVLILE  285 (290)
T ss_pred             ccceEEEEEcCCCCeeeeecCchhhHHHHHHHHHHhc-cCCCCCeeeecCCCceeccc-ccccccHHHhccccchheecc
Confidence            3789999999999999999999999999999999864 32456999999999998665 58899999999998664 455


Q ss_pred             e
Q 025774          247 W  247 (248)
Q Consensus       247 ~  247 (248)
                      |
T Consensus       286 ~  286 (290)
T KOG2689|consen  286 P  286 (290)
T ss_pred             c
Confidence            4

>COG2143 Thioredoxin-related protein [Posttranslational modification, protein turnover, chaperones]

Probab=97.69  E-value=0.00021  Score=56.87  Aligned_cols=77  Identities=18%  Similarity=0.293  Sum_probs=65.8

Q ss_pred             cccccCCCHHHHHHhhcceEEEEEecCChH--------------HHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCCh
Q 025774            2 LNRDTWANEAVSQTISTNFIFWQVYDDTSE--------------GKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQP   67 (248)
Q Consensus         2 ~~r~vl~~~~v~~~l~~~fV~w~~d~~~~e--------------g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~   67 (248)
                      |-+++...+.+++++..||+++-.+++..+              -..+|+.|+++++|++++.+ .+|..+..+-|.++|
T Consensus        60 ~KKd~~~~krlrEylk~hf~~~~l~i~~skpv~f~~g~kee~~s~~ELa~kf~vrstPtfvFfd-k~Gk~Il~lPGY~pp  138 (182)
T COG2143          60 FKKDLKNVKRLREYLKEHFSAYYLNISYSKPVLFKVGDKEEKMSTEELAQKFAVRSTPTFVFFD-KTGKTILELPGYMPP  138 (182)
T ss_pred             HHHhhcchHHHHHHHhhCeEEEEEEeccCcceEeecCceeeeecHHHHHHHhccccCceEEEEc-CCCCEEEecCCCCCH
Confidence            457899999999999999999999986443              23789999999999999999 469999999999999


Q ss_pred             HHHHHHHhhhhh
Q 025774           68 ESLLEDLVPFMD   79 (248)
Q Consensus        68 e~l~~~L~~~~~   79 (248)
                      ++|+..|.=.-+
T Consensus       139 e~Fl~vlkYVa~  150 (182)
T COG2143         139 EQFLAVLKYVAD  150 (182)
T ss_pred             HHHHHHHHHHHH
Confidence            999877765533

>cd02951 SoxW SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation

Probab=97.66  E-value=0.00031  Score=53.90  Aligned_cols=74  Identities=22%  Similarity=0.376  Sum_probs=61.3

Q ss_pred             CCCHHHHHHhhcceEEEEEecCCh-----------HHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774            7 WANEAVSQTISTNFIFWQVYDDTS-----------EGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus         7 l~~~~v~~~l~~~fV~w~~d~~~~-----------eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      +.++.+...++.+|++...|++..           ....++..|++..+|+++++++..|+.+.++.|..+.+.|...|.
T Consensus        37 ~~~~~~~~~~~~~~~~~~i~~d~~~~~~~~~~~~~~~~~l~~~~~v~~~Pt~~~~~~~gg~~~~~~~G~~~~~~~~~~l~  116 (125)
T cd02951          37 LNDPAVQAYIRAHFVVVYINIDGDKEVTDFDGEALSEKELARKYRVRFTPTVIFLDPEGGKEIARLPGYLPPDEFLAYLE  116 (125)
T ss_pred             cCcHHHHHHHHhheEEEEEEccCCceeeccCCCCccHHHHHHHcCCccccEEEEEcCCCCceeEEecCCCCHHHHHHHHH
Confidence            345678888888999999998754           356889999999999999999754788999999999999888888


Q ss_pred             hhhhc
Q 025774           76 PFMDG   80 (248)
Q Consensus        76 ~~~~~   80 (248)
                      .+++.
T Consensus       117 ~~~~~  121 (125)
T cd02951         117 YVQEK  121 (125)
T ss_pred             HHHhh
Confidence            77664

Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide fixation during autotrophic growth and the respiratory electron transport chain. It is unclear what the role of SoxW is, since it has been found to be dispensable in the oxidation of thiosulfate to sulfate. SoxW is specifically kept in the reduced state by SoxV, which is essential in thiosulfate oxidation.

>cd02953 DsbDgamma DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD

Probab=97.57  E-value=0.0003  Score=52.08  Aligned_cols=69  Identities=13%  Similarity=0.199  Sum_probs=56.7

Q ss_pred             cCCCHHHHHHhhcceEEEEEecCCh--HHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774            6 TWANEAVSQTISTNFIFWQVYDDTS--EGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus         6 vl~~~~v~~~l~~~fV~w~~d~~~~--eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      ++.++.+.+.++.++++...|++..  ....+++.|++..+|++.++.+-+|..+.++.|..+.++|...|
T Consensus        33 ~~~~~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~~~i~~~Pti~~~~~~~g~~~~~~~G~~~~~~l~~~l  103 (104)
T cd02953          33 VFSDPEVQAALKKDVVLLRADWTKNDPEITALLKRFGVFGPPTYLFYGPGGEPEPLRLPGFLTADEFLEAL  103 (104)
T ss_pred             hcCCHHHHHHHhCCeEEEEEecCCCCHHHHHHHHHcCCCCCCEEEEECCCCCCCCcccccccCHHHHHHHh
Confidence            3456788888888999999998643  36789999999999999999863578889999999999887655

It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD alpha). DsbD beta, a transmembrane domain comprising of eight helices, acquires its reducing potential from the cytoplasmic thioredoxin. DsbD alpha transfers the acquired reducing potential from DsbD gamma to target proteins such as the periplasmic protein disulphide isomerases, DsbC and DsbG. This flow of reducing potential from the cytoplasm through DsbD allows DsbC and DsbG to act as isomerases in the oxidizing environment of the bacterial periplasm. DsbD also transfers reducing potential from the cytoplasm to specific reductases in the periplasm which are involved in the maturation of cytochromes.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=97.40  E-value=0.0013  Score=45.87  Aligned_cols=69  Identities=16%  Similarity=0.232  Sum_probs=55.6

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      +|.||..+|+.+..++..+++|..|.+.+.... +.++...+|+  |..+.  +  +.+.||.+.|+. +++|.+.+
T Consensus         2 ~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~-g~~~~~qrL~--~~g~~--L--~d~~tl~~~~i~~g~~i~l~~   71 (76)
T cd01806           2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKE-GIPPQQQRLI--YSGKQ--M--NDDKTAADYKLEGGSVLHLVL   71 (76)
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhh-CCChhhEEEE--ECCeE--c--cCCCCHHHcCCCCCCEEEEEE
Confidence            688999999999999999999999999998764 6678888887  44553  5  457899999998 45565543

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.

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

Probab=97.34  E-value=0.0017  Score=46.09  Aligned_cols=72  Identities=14%  Similarity=0.179  Sum_probs=57.2

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      ..|-|+..+|+.+...+..++||.+|.+-+.... +.+...++|...|..+.  +  +++.||.+.|+. +++|.+.+
T Consensus         3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~-~i~~~~qrL~~~~~G~~--L--~D~~tL~~~gi~~gs~l~l~~   75 (80)
T cd01792           3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKI-GVPAFQQRLAHLDSREV--L--QDGVPLVSQGLGPGSTVLLVV   75 (80)
T ss_pred             eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHh-CCCHHHEEEEeccCCCC--C--CCCCCHHHcCCCCCCEEEEEE
Confidence            5788999999999999999999999999998764 66788889965565553  5  456899999998 56665543

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.

>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=97.30  E-value=0.00072  Score=48.26  Aligned_cols=72  Identities=17%  Similarity=0.094  Sum_probs=41.9

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMIS  244 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~  244 (248)
                      ..-||||-|||..- -....++++.+|++-|...+. .+...|.|....+... .+..+.++||.++||..+.++
T Consensus         4 ~milRvrS~dG~~R-ie~~~~~t~~~L~~kI~~~l~-~~~~~~~L~~~~~~~~-~l~s~~~~tl~~lglkHGdml   75 (80)
T PF11543_consen    4 SMILRVRSKDGMKR-IEVSPSSTLSDLKEKISEQLS-IPDSSQSLSKDRNNKE-ELKSSDSKTLSSLGLKHGDML   75 (80)
T ss_dssp             --EEEEE-SSEEEE-EEE-TTSBHHHHHHHHHHHS----TTT---BSSGGGGG-CSSS-TT-CCCCT---TT-EE
T ss_pred             cEEEEEECCCCCEE-EEcCCcccHHHHHHHHHHHcC-CCCcceEEEecCCCCc-ccccCCcCCHHHcCCCCccEE
Confidence            35699999999732 247799999999999999863 4566899987654442 343467899999999854443

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.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=97.30  E-value=0.0025  Score=44.64  Aligned_cols=70  Identities=13%  Similarity=0.110  Sum_probs=56.3

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      .+|.|+-..|+.+.-.+..++||.+|.+-+.... ++++..-+|+.  ..+.  +  ++++||++.|+. +++|++-|
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~-~~~~~~qrLi~--~Gk~--L--~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQT-GTRPEKIVLKK--WYTI--F--KDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHh-CCChHHEEEEe--CCcC--C--CCCCCHHHcCCCCCCEEEEEe
Confidence            5788999999999999999999999999998764 67788888874  4553  5  457899999998 56666543

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.

>PF13899 Thioredoxin_7: Thioredoxin-like; PDB: 2LST_A 3PH9_A 1UC7_A 2JU5_A 1VRS_D 2FWG_A 2FWF_A 2FWH_A 2FWE_A 3FK8_A

Probab=97.26  E-value=0.00075  Score=47.99  Aligned_cols=48  Identities=21%  Similarity=0.471  Sum_probs=39.7

Q ss_pred             cccccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeC
Q 025774            2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDP   52 (248)
Q Consensus         2 ~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~   52 (248)
                      |.+.+|.++.|.++++.+||++..|+++.++......   ..+|+++|++|
T Consensus        35 l~~~~~~~~~v~~~~~~~fv~v~vd~~~~~~~~~~~~---~~~P~~~~ldp   82 (82)
T PF13899_consen   35 LEREVFSDPEVQEALNKNFVLVKVDVDDEDPNAQFDR---QGYPTFFFLDP   82 (82)
T ss_dssp             HHHHTTTSHHHHHHHHHCSEEEEEETTTHHHHHHHHH---CSSSEEEEEET
T ss_pred             HHHHHcCCHHHHHHHHCCEEEEEEEcCCCChhHHhCC---ccCCEEEEeCC
Confidence            6788999999999999999999999987776442222   44999999986

...

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=97.26  E-value=0.0017  Score=44.73  Aligned_cols=70  Identities=14%  Similarity=0.116  Sum_probs=55.7

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      .+|.||.++|+.+...+..+++|.+|..-+.... +.++...+|..+  .+.  +  +.+.||.+.|+. ++.|.+.|
T Consensus         1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~-gi~~~~q~L~~~--g~~--L--~d~~~L~~~~i~~~~~l~l~~   71 (72)
T cd01809           1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEV-GIPVEQQRLIYS--GRV--L--KDDETLSEYKVEDGHTIHLVK   71 (72)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHH-CcCHHHeEEEEC--CEE--C--CCcCcHHHCCCCCCCEEEEEe
Confidence            3688999999999999999999999999997764 556677788753  432  4  457899999998 56676765

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.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=97.12  E-value=0.0029  Score=44.15  Aligned_cols=68  Identities=18%  Similarity=0.232  Sum_probs=55.4

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +|-||.++|+.+.-....++||.+|.+-+... .+.++..++|+.+  .+.  +  +.+.||.+.|+. +++|.+.
T Consensus         2 ~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~-~gi~~~~q~L~~~--G~~--L--~d~~~L~~~~i~~~~~l~l~   70 (74)
T cd01807           2 FLTVKLLQGRECSLQVSEKESVSTLKKLVSEH-LNVPEEQQRLLFK--GKA--L--ADDKRLSDYSIGPNAKLNLV   70 (74)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHH-HCCCHHHeEEEEC--CEE--C--CCCCCHHHCCCCCCCEEEEE
Confidence            68899999999999999999999999999875 4667888999754  443  5  457999999998 5666554

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

>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A

Probab=97.06  E-value=0.00038  Score=52.06  Aligned_cols=64  Identities=25%  Similarity=0.416  Sum_probs=47.4

Q ss_pred             HHHHHHhhcceEEEEEecCChH------------------HHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHH
Q 025774           10 EAVSQTISTNFIFWQVYDDTSE------------------GKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLL   71 (248)
Q Consensus        10 ~~v~~~l~~~fV~w~~d~~~~e------------------g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~   71 (248)
                      ..+..+++.++.+...++....                  ...++..|++..+|++++++ ..|..+.++.|.+++++|.
T Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~gtPt~~~~d-~~G~~v~~~~G~~~~~~l~  109 (112)
T PF13098_consen   31 NDVARYLKDDFQVIFVNIDDSRDESEAVLDFDGQKNVRLSNKELAQRYGVNGTPTIVFLD-KDGKIVYRIPGYLSPEELL  109 (112)
T ss_dssp             HHHHCEEHCECEEEECESHSHHHHHHHHHSHTCHSSCHHHHHHHHHHTT--SSSEEEECT-TTSCEEEEEESS--HHHHH
T ss_pred             HHHHHHhhcCeEEEEEecCCcccccccccccccchhhhHHHHHHHHHcCCCccCEEEEEc-CCCCEEEEecCCCCHHHHH
Confidence            3455566667888888887543                  24688999999999999998 4589899999999999998


Q ss_pred             HHH
Q 025774           72 EDL   74 (248)
Q Consensus        72 ~~L   74 (248)
                      ..|
T Consensus       110 ~~L  112 (112)
T PF13098_consen  110 KML  112 (112)
T ss_dssp             HHH
T ss_pred             hhC
Confidence            765

...

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=97.05  E-value=0.008  Score=43.45  Aligned_cols=73  Identities=22%  Similarity=0.324  Sum_probs=58.4

Q ss_pred             CCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEE
Q 025774          166 DRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMIS  244 (248)
Q Consensus       166 ~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~  244 (248)
                      +.+..+.|.|+.++|+.+.-+...+++|+.|++-+... .+.+...++|+..  .+.  +  +.+.|+.++|+.. ++|-
T Consensus         7 ~~~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~-~gi~~~~~rf~f~--G~~--L--~~~~T~~~l~m~d~d~I~   79 (87)
T cd01763           7 EISEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQR-QGLSMNSVRFLFD--GQR--I--RDNQTPDDLGMEDGDEIE   79 (87)
T ss_pred             CCCCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHH-hCCCccceEEEEC--CeE--C--CCCCCHHHcCCCCCCEEE
Confidence            34568899999999999999999999999999988775 4666788888775  333  5  5678999999984 5554


Q ss_pred             E
Q 025774          245 V  245 (248)
Q Consensus       245 v  245 (248)
                      |
T Consensus        80 v   80 (87)
T cd01763          80 V   80 (87)
T ss_pred             E
Confidence            4

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.

>cd02955 SSP411 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif

Probab=97.03  E-value=0.0018  Score=50.19  Aligned_cols=62  Identities=13%  Similarity=0.166  Sum_probs=48.1

Q ss_pred             cccccCCCHHHHHHhhcceEEEEEecCChH-H-HHHH----HhcCCCCCceEEEEeCCCCceEEeeeCC
Q 025774            2 LNRDTWANEAVSQTISTNFIFWQVYDDTSE-G-KKVC----TYYKLDSIPVVLVVDPITGQKMRSWCGM   64 (248)
Q Consensus         2 ~~r~vl~~~~v~~~l~~~fV~w~~d~~~~e-g-~~~~----~~~~~~~~P~l~ii~~~~g~~l~~~~G~   64 (248)
                      |.+.||.++.|.++|+.+||+...|++... - ..+.    ..|++..+|++++++|. |..+....|+
T Consensus        33 me~~~f~~~~V~~~l~~~fv~VkvD~~~~~~~~~~~~~~~~~~~~~~G~Pt~vfl~~~-G~~~~~~~~~  100 (124)
T cd02955          33 MEHESFEDEEVAAILNENFVPIKVDREERPDVDKIYMNAAQAMTGQGGWPLNVFLTPD-LKPFFGGTYF  100 (124)
T ss_pred             HHHHccCCHHHHHHHhCCEEEEEEeCCcCcHHHHHHHHHHHHhcCCCCCCEEEEECCC-CCEEeeeeec
Confidence            556789999999999999999999997532 1 1122    24688999999999974 8888776654

The human/rat protein, called SSP411, is specifically expressed in the testis in an age-dependent manner. The SSP411 mRNA is increased during spermiogenesis and is localized in round and elongated spermatids, suggesting a function in fertility regulation.

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=97.03  E-value=0.0027  Score=44.07  Aligned_cols=66  Identities=20%  Similarity=0.286  Sum_probs=53.2

Q ss_pred             EEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          173 VGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       173 i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +.||+++|+.+.-.+..++||.+|-..+... .+.++...+|+..  .+.  +  +++.||.++|+. +++|.|
T Consensus         1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~-~gi~~~~q~Li~~--G~~--L--~D~~~l~~~~i~~~~tv~~   67 (70)
T cd01794           1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAA-EGVDPCCQRWFFS--GKL--L--TDKTRLQETKIQKDYVVQV   67 (70)
T ss_pred             CeEEcCCCCEEEEEECCcChHHHHHHHHHHH-hCCCHHHeEEEEC--CeE--C--CCCCCHHHcCCCCCCEEEE
Confidence            3579999999999999999999999999775 5677888888753  443  5  568999999998 455544

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.

>PTZ00044 ubiquitin; Provisional

Probab=96.96  E-value=0.005  Score=42.99  Aligned_cols=69  Identities=17%  Similarity=0.290  Sum_probs=55.8

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      .|-||.++|+.+.-++..++||.+|-.-+.... +.++...+|+.  -.+.  +  +++.||++.|+. +++|.+.+
T Consensus         2 ~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~-gi~~~~q~L~~--~g~~--L--~d~~~l~~~~i~~~~~i~l~~   71 (76)
T PTZ00044          2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKE-GIDVKQIRLIY--SGKQ--M--SDDLKLSDYKVVPGSTIHMVL   71 (76)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHH-CCCHHHeEEEE--CCEE--c--cCCCcHHHcCCCCCCEEEEEE
Confidence            578999999999999999999999999998864 66788899984  4543  5  457899999998 56665543

>cd01803 Ubiquitin Ubiquitin

Probab=96.88  E-value=0.0065  Score=42.19  Aligned_cols=69  Identities=16%  Similarity=0.219  Sum_probs=54.8

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      .|-||.++|+.+.-.+..+++|.+|..-+.... +.++...+|..  ..+.  +  +++.||.++|+. +++|.+.+
T Consensus         2 ~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~-g~~~~~q~L~~--~g~~--L--~d~~~L~~~~i~~~~~i~l~~   71 (76)
T cd01803           2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIF--AGKQ--L--EDGRTLSDYNIQKESTLHLVL   71 (76)
T ss_pred             EEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHh-CCCHHHeEEEE--CCEE--C--CCCCcHHHcCCCCCCEEEEEE
Confidence            578999999999999999999999999998864 55677888874  4543  5  457899999998 56665543

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

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=96.80  E-value=0.0094  Score=42.13  Aligned_cols=67  Identities=13%  Similarity=0.209  Sum_probs=52.9

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      .+|-|+..+|+.+.-.+..++||.+|..-+.... +.+....+|+  |..+.  +. | + ||++.|+. +++|.+
T Consensus         2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~-~~~~~~qrL~--~~Gk~--L~-d-~-~L~~~gi~~~~~i~l   69 (78)
T cd01804           2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRL-KVPKERLALL--HRETR--LS-S-G-KLQDLGLGDGSKLTL   69 (78)
T ss_pred             eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHh-CCChHHEEEE--ECCcC--CC-C-C-cHHHcCCCCCCEEEE
Confidence            3688999999999999999999999999998764 5667777886  44553  53 3 4 89999998 566654

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.

>cd02950 TxlA TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus

Probab=96.78  E-value=0.013  Score=46.24  Aligned_cols=63  Identities=19%  Similarity=0.293  Sum_probs=52.6

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ..+-|..++++..+...++..|++..+|+++++++ +|.++.++.|..+.++|...|...+...
T Consensus        51 ~~~~~v~v~vd~~~~~~~~~~~~V~~iPt~v~~~~-~G~~v~~~~G~~~~~~l~~~l~~l~~~~  113 (142)
T cd02950          51 DQVNFVMLNVDNPKWLPEIDRYRVDGIPHFVFLDR-EGNEEGQSIGLQPKQVLAQNLDALVAGE  113 (142)
T ss_pred             cCeeEEEEEcCCcccHHHHHHcCCCCCCEEEEECC-CCCEEEEEeCCCCHHHHHHHHHHHHcCC
Confidence            34567777877666667889999999999999974 5899999999999999988888888765

It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport.

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

Probab=96.67  E-value=0.0091  Score=41.09  Aligned_cols=67  Identities=19%  Similarity=0.254  Sum_probs=53.9

Q ss_pred             EEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          173 VGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       173 i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      |-||.++|..+.-....+++|.+|-..+.... +.+...++|+.+  .+.  +  +.+.||.++|+. +++|.+.
T Consensus         1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~-gi~~~~q~Li~~--G~~--L--~d~~~l~~~~i~~~stl~l~   68 (70)
T cd01798           1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQ-GVPPDQLRVIFA--GKE--L--RNTTTIQECDLGQQSILHAV   68 (70)
T ss_pred             CEEEcCCCCEEEEEECCCChHHHHHHHHHHHH-CCCHHHeEEEEC--CeE--C--CCCCcHHHcCCCCCCEEEEE
Confidence            45899999999999999999999999998863 567788899754  443  5  457999999998 5666553

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.

>cd03065 PDI_b_Calsequestrin_N PDIb family, Calsequestrin subfamily, N-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle

Probab=96.61  E-value=0.015  Score=44.77  Aligned_cols=61  Identities=20%  Similarity=0.285  Sum_probs=49.7

Q ss_pred             HHh-hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           14 QTI-STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        14 ~~l-~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +++ ...+.|...|++..  ..++..|++.++|++.++-  +|+.+. +.|..+.+.++..|...++
T Consensus        59 ~~l~~~~v~~~kVD~d~~--~~La~~~~I~~iPTl~lfk--~G~~v~-~~G~~~~~~l~~~l~~~~~  120 (120)
T cd03065          59 QVLEDKGIGFGLVDSKKD--AKVAKKLGLDEEDSIYVFK--DDEVIE-YDGEFAADTLVEFLLDLIE  120 (120)
T ss_pred             HHhhcCCCEEEEEeCCCC--HHHHHHcCCccccEEEEEE--CCEEEE-eeCCCCHHHHHHHHHHHhC
Confidence            344 34789999999754  6899999999999998884  688877 9999999999888776653

It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=96.59  E-value=0.016  Score=40.52  Aligned_cols=67  Identities=13%  Similarity=0.169  Sum_probs=52.4

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCC--CCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGS--EMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~--~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +|-||.++|+.+.-....++||.+|...+.... +.  ++....|..  ..+.  +  +.+.||.++|+. +++|++
T Consensus         2 ~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~-~i~~~~~~q~L~~--~G~~--L--~d~~~L~~~~i~~~~~i~~   71 (77)
T cd01805           2 KITFKTLKQQTFPIEVDPDDTVAELKEKIEEEK-GCDYPPEQQKLIY--SGKI--L--KDDTTLEEYKIDEKDFVVV   71 (77)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhh-CCCCChhHeEEEE--CCEE--c--cCCCCHHHcCCCCCCEEEE
Confidence            578999999999899999999999999998753 44  567777764  4553  5  456899999998 455544

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).

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=96.59  E-value=0.0062  Score=45.96  Aligned_cols=64  Identities=19%  Similarity=0.242  Sum_probs=49.2

Q ss_pred             CceEEEEEcCCCce-EEEeeCCCCchHHHHHHHHhhcC-C-----CCCcCeEEEccCCCCccccCCCcCCCccccCC
Q 025774          169 LLCRVGVRLPDGRR-MQRNFLRTDPIQLLWSYCYSQLE-G-----SEMKPFRLTHAIPGATKSLDYDSKLTFEDSGL  238 (248)
Q Consensus       169 ~~~~i~iRlp~G~r-~~r~F~~~~~l~~l~~fv~~~~~-~-----~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl  238 (248)
                      ..+.|+|||+||+- =-.+|..++||.+|-.-|..... +     +....-+|+.+  .+.  |  +.++||+++++
T Consensus         3 ~~~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIys--GKi--L--eD~~TL~d~~~   73 (113)
T cd01814           3 EQIEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISA--GKI--L--ENSKTVGECRS   73 (113)
T ss_pred             ccEEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeC--Cee--c--CCCCcHHHhCC
Confidence            46789999999963 45789999999999999987653 2     34666777765  443  5  56899999993

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

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=96.58  E-value=0.014  Score=40.05  Aligned_cols=68  Identities=19%  Similarity=0.189  Sum_probs=53.1

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ++|.||.. |+....++..++||.+|.+-+... .+.++...+|...  .+.  +  +.+.||.++|+. +++|++.
T Consensus         1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~-~gi~~~~q~L~~~--g~~--l--~d~~~L~~~~i~~g~~l~v~   69 (71)
T cd01812           1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPV-TGVEPRDQKLIFK--GKE--R--DDAETLDMSGVKDGSKVMLL   69 (71)
T ss_pred             CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHh-hCCChHHeEEeeC--Ccc--c--CccCcHHHcCCCCCCEEEEe
Confidence            46888986 888889999999999999999875 4667888888754  332  5  347899999998 4556553

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).

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

Probab=96.50  E-value=0.018  Score=43.66  Aligned_cols=64  Identities=22%  Similarity=0.259  Sum_probs=47.5

Q ss_pred             ceEEEEEcCCCc-eEEEeeCCCCchHHHHHHHHhhcCCC------CCcCeEEEccCCCCccccCCCcCCCccccCCc
Q 025774          170 LCRVGVRLPDGR-RMQRNFLRTDPIQLLWSYCYSQLEGS------EMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA  239 (248)
Q Consensus       170 ~~~i~iRlp~G~-r~~r~F~~~~~l~~l~~fv~~~~~~~------~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~  239 (248)
                      .+.|+|||.||+ +..-+|..+.||.+|-++|...++..      .+...+|+..  .|.  |  +.+.||.++++.
T Consensus         2 ~i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~--Gri--L--~d~~tL~~~~~~   72 (111)
T PF13881_consen    2 KIELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYA--GRI--L--EDNKTLSDCRLP   72 (111)
T ss_dssp             SEEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEET--TEE--E---SSSBTGGGT--
T ss_pred             eEEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeC--Cee--c--CCcCcHHHhCCC
Confidence            478999999999 89999999999999999999876421      2445778774  342  5  568999999887

>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=96.49  E-value=0.014  Score=39.72  Aligned_cols=63  Identities=21%  Similarity=0.257  Sum_probs=51.4

Q ss_pred             EcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          176 RLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       176 Rlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      |.++|+.+.-.+..+++|.+|-.-|.... +.++....|+..  .+.  +  +++.||.+.|+.+ ++|.+
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~-~~~~~~~~L~~~--G~~--L--~d~~tL~~~~i~~~~~I~l   64 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEET-GIPPEQQRLIYN--GKE--L--DDDKTLSDYGIKDGSTIHL   64 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHH-TSTGGGEEEEET--TEE--E--STTSBTGGGTTSTTEEEEE
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhccccc-ccccccceeeee--eec--c--cCcCcHHHcCCCCCCEEEE
Confidence            56899999999999999999999998875 567888999774  443  5  6789999999995 44444

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 ....

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

Probab=96.47  E-value=0.015  Score=40.50  Aligned_cols=67  Identities=18%  Similarity=0.254  Sum_probs=53.4

Q ss_pred             EEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          173 VGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       173 i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      |-||.++|+.+.-....+++|.+|.+-+... .+.+...+.|...  .+.  +  +++.||.+.|+. +++|.+.
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~-~gi~~~~q~L~~~--G~~--L--~D~~tL~~~~i~~~~tl~l~   68 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQR-ERVQADQFWLSFE--GRP--M--EDEHPLGEYGLKPGCTVFMN   68 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHH-hCCCHHHeEEEEC--CEE--C--CCCCCHHHcCCCCCCEEEEE
Confidence            4589999999999999999999999999775 4667888999754  443  6  346999999998 5666544

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.

>PRK11509 hydrogenase-1 operon protein HyaE; Provisional

Probab=96.41  E-value=0.028  Score=43.96  Aligned_cols=59  Identities=12%  Similarity=0.106  Sum_probs=50.7

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      .+.+...|++..  ..++..|++.++|+++++  ++|+.+.++.|..+.++++..|..++++-
T Consensus        69 ~v~~akVDiD~~--~~LA~~fgV~siPTLl~F--kdGk~v~~i~G~~~k~~l~~~I~~~L~~~  127 (132)
T PRK11509         69 TWQVAIADLEQS--EAIGDRFGVFRFPATLVF--TGGNYRGVLNGIHPWAELINLMRGLVEPQ  127 (132)
T ss_pred             ceEEEEEECCCC--HHHHHHcCCccCCEEEEE--ECCEEEEEEeCcCCHHHHHHHHHHHhcCc
Confidence            367777887644  678999999999999998  56999999999999999999999998863

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=96.40  E-value=0.026  Score=42.17  Aligned_cols=72  Identities=8%  Similarity=0.080  Sum_probs=58.8

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      +.-.|-||..+|+.+.-....++||.+|..-|... .+.+...++|+.+  .+.  +  +++.||++.|+. +++|.+.+
T Consensus        26 ~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~-~gip~~~QrLi~~--Gk~--L--~D~~tL~dy~I~~~stL~l~~   98 (103)
T cd01802          26 DTMELFIETLTGTCFELRVSPFETVISVKAKIQRL-EGIPVAQQHLIWN--NME--L--EDEYCLNDYNISEGCTLKLVL   98 (103)
T ss_pred             CCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHH-hCCChHHEEEEEC--CEE--C--CCCCcHHHcCCCCCCEEEEEE
Confidence            45789999999999999999999999999999875 4667888999864  443  5  457899999998 56776654

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.

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

Probab=96.34  E-value=0.026  Score=38.92  Aligned_cols=68  Identities=10%  Similarity=0.191  Sum_probs=52.6

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      +|-|+.++|+ ..-.+..++||.+|..-+.... +.+...++|+.  ..+.  +  +++.||.++|+. +++|.+.+
T Consensus         2 ~i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~-~i~~~~~~Li~--~Gk~--L--~d~~tL~~~~i~~~stl~l~~   70 (71)
T cd01808           2 KVTVKTPKDK-EEIEIAEDASVKDFKEAVSKKF-KANQEQLVLIF--AGKI--L--KDTDTLTQHNIKDGLTVHLVI   70 (71)
T ss_pred             EEEEEcCCCC-EEEEECCCChHHHHHHHHHHHh-CCCHHHEEEEE--CCeE--c--CCCCcHHHcCCCCCCEEEEEE
Confidence            5888999996 4677889999999999998764 55677888864  4553  5  456899999998 56776654

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.

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

Probab=96.29  E-value=0.017  Score=40.05  Aligned_cols=67  Identities=13%  Similarity=0.188  Sum_probs=53.0

Q ss_pred             EEEEcC-CCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          173 VGVRLP-DGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       173 i~iRlp-~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      |-|+++ +|+.+.-....+.+|.+|-..+... .|.+....+|+.+  .+.  + .|...+|+++|+.+ +.|++
T Consensus         1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~-~gip~~~q~Li~~--Gk~--L-~D~~~~L~~~gi~~~~~l~l   69 (71)
T cd01796           1 ITVYTARSETTFSLDVDPDLELENFKALCEAE-SGIPASQQQLIYN--GRE--L-VDNKRLLALYGVKDGDLVVL   69 (71)
T ss_pred             CEEEECCCCCEEEEEECCcCCHHHHHHHHHHH-hCCCHHHeEEEEC--CeE--c-cCCcccHHHcCCCCCCEEEE
Confidence            457899 9998999999999999999999875 4677888899765  443  6 35568999999985 55544

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.

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

Probab=95.90  E-value=0.053  Score=37.29  Aligned_cols=68  Identities=26%  Similarity=0.344  Sum_probs=51.5

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCC-cCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEM-KPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~-~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      ++|.++..+|+.+.-+-..+++++.|++...... +.+. ..+.|...  ...  +  +.+.|++++|+.. +.|-|
T Consensus         1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~-~i~~~~~~~l~fd--G~~--L--~~~~T~~~~~ied~d~Idv   70 (72)
T PF11976_consen    1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKK-GIPPEESIRLIFD--GKR--L--DPNDTPEDLGIEDGDTIDV   70 (72)
T ss_dssp             EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHH-TTTT-TTEEEEET--TEE--E---TTSCHHHHT-STTEEEEE
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhh-CCCccceEEEEEC--CEE--c--CCCCCHHHCCCCCCCEEEE
Confidence            4788999999999999999999999999877654 4455 78888764  332  5  6789999999984 44433

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 ....

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

Probab=95.79  E-value=0.042  Score=39.80  Aligned_cols=62  Identities=19%  Similarity=0.251  Sum_probs=40.5

Q ss_pred             eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCce-EEE
Q 025774          182 RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAM-ISV  245 (248)
Q Consensus       182 r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~-v~v  245 (248)
                      .+++.|.++|||..|-..+...+.-  ...-+|..-|=...+.+-.+...|++|+||..+. |++
T Consensus        15 ~~t~~FSk~DTI~~v~~~~rklf~i--~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vli   77 (88)
T PF14836_consen   15 VLTKQFSKTDTIGFVEKEMRKLFNI--QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLI   77 (88)
T ss_dssp             EEEEEE-TTSBHHHHHHHHHHHCT---TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEE
T ss_pred             HhHhhccccChHHHHHHHHHHHhCC--CccceehhccCCcchhhhCCCCccHHHccCcCCCEEEE
Confidence            6899999999999999999886532  6677887644222233334788999999999555 444

>KOG0910 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]

Probab=95.75  E-value=0.031  Score=44.46  Aligned_cols=59  Identities=27%  Similarity=0.532  Sum_probs=49.3

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .+.|-|+..|++  +--.++..|.+.++|.++++.  +|+.+.++-|..+.+.+...+..++.
T Consensus        91 ~g~~k~~kvdtD--~~~ela~~Y~I~avPtvlvfk--nGe~~d~~vG~~~~~~l~~~i~k~l~  149 (150)
T KOG0910|consen   91 AGKFKLYKVDTD--EHPELAEDYEISAVPTVLVFK--NGEKVDRFVGAVPKEQLRSLIKKFLK  149 (150)
T ss_pred             cCeEEEEEEccc--cccchHhhcceeeeeEEEEEE--CCEEeeeecccCCHHHHHHHHHHHhc
Confidence            346889888875  445789999999999999995  69999999999999988877777653

>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms

Probab=95.55  E-value=0.15  Score=36.76  Aligned_cols=58  Identities=28%  Similarity=0.505  Sum_probs=47.4

Q ss_pred             HhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           15 TISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        15 ~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      -+..++.|...|.+  +...++..|++..+|++.++.  +|..+.++.|..+.+++...|.+
T Consensus        45 ~~~~~v~~~~vd~~--~~~~l~~~~~v~~~Pt~~~~~--~g~~~~~~~g~~~~~~l~~~i~~  102 (103)
T PF00085_consen   45 EYKDNVKFAKVDCD--ENKELCKKYGVKSVPTIIFFK--NGKEVKRYNGPRNAESLIEFIEK  102 (103)
T ss_dssp             HTTTTSEEEEEETT--TSHHHHHHTTCSSSSEEEEEE--TTEEEEEEESSSSHHHHHHHHHH
T ss_pred             ccccccccchhhhh--ccchhhhccCCCCCCEEEEEE--CCcEEEEEECCCCHHHHHHHHHc
Confidence            33447889999986  447789999999999999985  58888899999999998776653

Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....

>cd02956 ybbN ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain

Probab=95.54  E-value=0.1  Score=37.60  Aligned_cols=55  Identities=20%  Similarity=0.379  Sum_probs=43.8

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      +...+.+...|++.  ...++..|++.++|++.++.  +|..+.++.|..+.+++...|
T Consensus        41 ~~~~~~~~~vd~~~--~~~l~~~~~i~~~Pt~~~~~--~g~~~~~~~g~~~~~~l~~~l   95 (96)
T cd02956          41 YQGQFVLAKVNCDA--QPQIAQQFGVQALPTVYLFA--AGQPVDGFQGAQPEEQLRQML   95 (96)
T ss_pred             hCCcEEEEEEeccC--CHHHHHHcCCCCCCEEEEEe--CCEEeeeecCCCCHHHHHHHh
Confidence            34467788888865  34688899999999999995  688888999999888876543

Its gene has been sequenced from several gammaproteobacteria and actinobacteria.

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

Probab=95.54  E-value=0.089  Score=37.17  Aligned_cols=69  Identities=20%  Similarity=0.180  Sum_probs=52.3

Q ss_pred             EEEEEcCCCce-EEE-eeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          172 RVGVRLPDGRR-MQR-NFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       172 ~i~iRlp~G~r-~~r-~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      +|-||.++|+. +.- ....++||..|..-+... .+.+....+|+..  .+.  +  +.+.||.+.|+. +++|.+.+
T Consensus         2 ~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~-~gi~~~~QrLi~~--Gk~--L--~D~~tL~~y~i~~~~~i~l~~   73 (78)
T cd01797           2 WIQVRTMDGKETRTVDSLSRLTKVEELREKIQEL-FNVEPECQRLFYR--GKQ--M--EDGHTLFDYNVGLNDIIQLLV   73 (78)
T ss_pred             EEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHH-hCCCHHHeEEEeC--CEE--C--CCCCCHHHcCCCCCCEEEEEE
Confidence            57889999986 343 356789999999999775 4677888999864  443  5  558999999998 56666554

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.

>cd02965 HyaE HyaE family; HyaE is also called HupG and HoxO

Probab=95.40  E-value=0.083  Score=40.05  Aligned_cols=50  Identities=12%  Similarity=0.178  Sum_probs=41.8

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      .+.|...|++...  .++..|++.+.|+++++.  +|..+..+.|..+-+++..
T Consensus        61 ~v~f~kVdid~~~--~la~~f~V~sIPTli~fk--dGk~v~~~~G~~~~~e~~~  110 (111)
T cd02965          61 RFRAAVVGRADEQ--ALAARFGVLRTPALLFFR--DGRYVGVLAGIRDWDEYVA  110 (111)
T ss_pred             cEEEEEEECCCCH--HHHHHcCCCcCCEEEEEE--CCEEEEEEeCccCHHHHhh
Confidence            4567788887654  899999999999998884  6999999999998888753

They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the sole energy source. The E. coli HyaE protein is a chaperone that specifically interacts with the twin-arginine translocation (Tat) signal peptide of the [NiFe] hydrogenase-1 beta subunit precursor. Tat signal peptides target precursor proteins to the Tat protein export system, which facilitates the transport of fully folded proteins across the inner membrane. HyaE may be involved in regulating the traffic of [NiFe] hydrogenase-1 on the Tat transport pathway.

>cd02997 PDI_a_PDIR PDIa family, PDIR subfamily; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related)

Probab=95.39  E-value=0.091  Score=38.15  Aligned_cols=53  Identities=15%  Similarity=0.231  Sum_probs=43.4

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      ..+++...|.+..+...++..|++..||++.+..  +|..+.++.|..+.+.++.
T Consensus        50 ~~~~~~~id~~~~~~~~~~~~~~i~~~Pt~~~~~--~g~~~~~~~g~~~~~~l~~  102 (104)
T cd02997          50 GKGVLAAVDCTKPEHDALKEEYNVKGFPTFKYFE--NGKFVEKYEGERTAEDIIE  102 (104)
T ss_pred             CceEEEEEECCCCccHHHHHhCCCccccEEEEEe--CCCeeEEeCCCCCHHHHHh
Confidence            4588888898876677788999999999987663  5788889999999888754

PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity.

>PRK00293 dipZ thiol:disulfide interchange protein precursor; Provisional

Probab=95.37  E-value=0.051  Score=52.68  Aligned_cols=72  Identities=18%  Similarity=0.338  Sum_probs=58.8

Q ss_pred             cccCCCHHHHHHhhcceEEEEEecCC--hHHHHHHHhcCCCCCceEEEEeCCCCce--EEeeeCCCChHHHHHHHhhh
Q 025774            4 RDTWANEAVSQTISTNFIFWQVYDDT--SEGKKVCTYYKLDSIPVVLVVDPITGQK--MRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus         4 r~vl~~~~v~~~l~~~fV~w~~d~~~--~eg~~~~~~~~~~~~P~l~ii~~~~g~~--l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +.++.++.|.+.++ ++++...|++.  ++...+++.|++..+|++.++++ +|+.  ..++.|..++++|.+.|.+.
T Consensus       494 ~~~~~~~~v~~~l~-~~~~v~vDvt~~~~~~~~l~~~~~v~g~Pt~~~~~~-~G~~i~~~r~~G~~~~~~f~~~L~~~  569 (571)
T PRK00293        494 KYTFSDPQVQQALA-DTVLLQADVTANNAEDVALLKHYNVLGLPTILFFDA-QGQEIPDARVTGFMDAAAFAAHLRQL  569 (571)
T ss_pred             HHhcCCHHHHHHhc-CCEEEEEECCCCChhhHHHHHHcCCCCCCEEEEECC-CCCCcccccccCCCCHHHHHHHHHHh
Confidence            34688899999886 68999999975  35678999999999999999985 4775  46789999999998777653

>PRK10996 thioredoxin 2; Provisional

Probab=95.32  E-value=0.15  Score=39.97  Aligned_cols=58  Identities=19%  Similarity=0.308  Sum_probs=45.8

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +..++.+...|++..  ..++..|++..+|++.++.  +|+.+.++.|..+.+.+...|...
T Consensus        81 ~~~~v~~~~vd~~~~--~~l~~~~~V~~~Ptlii~~--~G~~v~~~~G~~~~e~l~~~l~~~  138 (139)
T PRK10996         81 RSGKVRFVKVNTEAE--RELSARFRIRSIPTIMIFK--NGQVVDMLNGAVPKAPFDSWLNEA  138 (139)
T ss_pred             hCCCeEEEEEeCCCC--HHHHHhcCCCccCEEEEEE--CCEEEEEEcCCCCHHHHHHHHHHh
Confidence            344788888888654  3678999999999998874  699999999999888887666543

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=95.29  E-value=0.13  Score=34.51  Aligned_cols=66  Identities=20%  Similarity=0.270  Sum_probs=50.4

Q ss_pred             EEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEEEe
Q 025774          175 VRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISVTW  247 (248)
Q Consensus       175 iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v~~  247 (248)
                      ||..+|..+...+..+.++.+|...+.... +.++....|..+  .+.  +  +.+.||.++|+.+ +.|.+.+
T Consensus         2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~-~~~~~~~~l~~~--g~~--l--~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769           2 VKTLTGKTFELEVSPDDTVAELKAKIAAKE-GVPPEQQRLIYA--GKI--L--KDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             eEccCCCEEEEEECCCChHHHHHHHHHHHH-CcChHHEEEEEC--CcC--C--CCcCCHHHCCCCCCCEEEEEE
Confidence            567789999999999999999999998764 455667777443  332  4  5578999999984 5566665

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.

>cd02949 TRX_NTR TRX domain, novel NADPH thioredoxin reductase (NTR) family; composed of fusion proteins found only in oxygenic photosynthetic organisms containing both TRX and NTR domains

Probab=95.25  E-value=0.13  Score=37.31  Aligned_cols=55  Identities=11%  Similarity=0.138  Sum_probs=43.7

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      +..++.+...|++..  ..++..|++..+|++.++.  +|..+.++.|..+.+++...|
T Consensus        42 ~~~~v~~~~id~d~~--~~l~~~~~v~~vPt~~i~~--~g~~v~~~~g~~~~~~~~~~l   96 (97)
T cd02949          42 FDGAVHFVEIDIDED--QEIAEAAGIMGTPTVQFFK--DKELVKEISGVKMKSEYREFI   96 (97)
T ss_pred             hCCceEEEEEECCCC--HHHHHHCCCeeccEEEEEE--CCeEEEEEeCCccHHHHHHhh
Confidence            334688888888644  3568899999999999994  588999999999888876554

The TRX domain functions as a protein disulfide reductase via the reversible oxidation of an active center dithiol present in a CXXC motif, while the NTR domain functions as a reductant to oxidized TRX. The fusion protein is bifunctional, showing both TRX and NTR activities, but it is not an independent NTR/TRX system. In plants, the protein is found exclusively in shoots and mature leaves and is localized in the chloroplast. It is involved in plant protection against oxidative stress.

>smart00213 UBQ Ubiquitin homologues

Probab=95.17  E-value=0.088  Score=34.78  Aligned_cols=62  Identities=18%  Similarity=0.213  Sum_probs=48.4

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCc
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANA  241 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~  241 (248)
                      +|.||.++ +...-.+..+.||..|..-+.... +.++....|..+  .+.  +  +.+.||.++|+.+.
T Consensus         2 ~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~-~~~~~~~~L~~~--g~~--L--~d~~tL~~~~i~~~   63 (64)
T smart00213        2 ELTVKTLD-GTITLEVKPSDTVSELKEKIAELT-GIPVEQQRLIYK--GKV--L--EDDRTLADYNIQDG   63 (64)
T ss_pred             EEEEEECC-ceEEEEECCCCcHHHHHHHHHHHH-CCCHHHEEEEEC--CEE--C--CCCCCHHHcCCcCC
Confidence            68899999 578889999999999999998764 555667888754  432  5  34689999999753

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

>TIGR01068 thioredoxin thioredoxin

Probab=94.95  E-value=0.23  Score=35.47  Aligned_cols=57  Identities=18%  Similarity=0.307  Sum_probs=44.9

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +.++.|+..|.+...  .++..|++.++|++.++.  +|..+....|..+.+++...|...
T Consensus        44 ~~~~~~~~vd~~~~~--~~~~~~~v~~~P~~~~~~--~g~~~~~~~g~~~~~~l~~~l~~~  100 (101)
T TIGR01068        44 EGKVKFVKLNVDENP--DIAAKYGIRSIPTLLLFK--NGKEVDRSVGALPKAALKQLINKN  100 (101)
T ss_pred             cCCeEEEEEECCCCH--HHHHHcCCCcCCEEEEEe--CCcEeeeecCCCCHHHHHHHHHhh
Confidence            446889999987554  467899999999999993  578888889998888887666543

Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model.

>cd02985 TRX_CDSP32 TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif

Probab=94.86  E-value=0.27  Score=36.20  Aligned_cols=54  Identities=24%  Similarity=0.484  Sum_probs=42.7

Q ss_pred             ceEEEEEecCCh-HHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           19 NFIFWQVYDDTS-EGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        19 ~fV~w~~d~~~~-eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ++.|...|.+.. +...++..|++..+|++.++  ++|..+.++.| ..+.++...+.
T Consensus        46 ~v~~~~vd~d~~~~~~~l~~~~~V~~~Pt~~~~--~~G~~v~~~~G-~~~~~l~~~~~  100 (103)
T cd02985          46 DVVFLLVNGDENDSTMELCRREKIIEVPHFLFY--KDGEKIHEEEG-IGPDELIGDVL  100 (103)
T ss_pred             CCEEEEEECCCChHHHHHHHHcCCCcCCEEEEE--eCCeEEEEEeC-CCHHHHHHHHH
Confidence            678888988754 35689999999999997777  57999999999 55677766554

CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form.

>cd02960 AGR Anterior Gradient (AGR) family; members of this family are similar to secreted proteins encoded by the cement gland-specific genes XAG-1 and XAG-2, expressed in the anterior region of dorsal ectoderm of Xenopus

Probab=94.85  E-value=0.038  Score=43.11  Aligned_cols=59  Identities=17%  Similarity=0.302  Sum_probs=42.7

Q ss_pred             cccccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCC
Q 025774            2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGM   64 (248)
Q Consensus         2 ~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~   64 (248)
                      |.+.+|.++.|.++++++||....+.+..+ ...+ . ....+|.++++++. |.++..+.|.
T Consensus        41 l~k~~f~~~eV~~~l~~~Fv~V~l~~d~td-~~~~-~-~g~~vPtivFld~~-g~vi~~i~Gy   99 (130)
T cd02960          41 LKKAFAEHKEIQKLAQEDFIMLNLVHETTD-KNLS-P-DGQYVPRIMFVDPS-LTVRADITGR   99 (130)
T ss_pred             HHHHhhCCHHHHHHHHhCeEEEEEEeccCC-CCcC-c-cCcccCeEEEECCC-CCCccccccc
Confidence            567899999999999999997777664221 0000 0 12469999999975 8888888874

They are implicated in the formation of the cement gland and the induction of forebrain fate. The human homologs, hAG-2 and hAG-3, are secreted proteins associated with estrogen-positive breast tumors. Yeast two-hybrid studies identified the metastasis-associated C4.4a protein and dystroglycan as binding partners, indicating possible roles in the development and progression of breast cancer. hAG-2 has also been implicated in prostate cancer. Its gene was cloned as an androgen-inducible gene and it was shown to be overexpressed in prostate cancer cells at the mRNA and protein levels. AGR proteins contain one conserved cysteine corresponding to the first cysteine in the CXXC motif of TRX. They show high sequence similarity to ERp19.

>PRK09381 trxA thioredoxin; Provisional

Probab=94.35  E-value=0.35  Score=35.64  Aligned_cols=57  Identities=18%  Similarity=0.222  Sum_probs=43.2

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ..++.+...|.+...  .++..|++.++|+++++.  +|..+.+..|..+.+++...|...
T Consensus        51 ~~~~~~~~vd~~~~~--~~~~~~~v~~~Pt~~~~~--~G~~~~~~~G~~~~~~l~~~i~~~  107 (109)
T PRK09381         51 QGKLTVAKLNIDQNP--GTAPKYGIRGIPTLLLFK--NGEVAATKVGALSKGQLKEFLDAN  107 (109)
T ss_pred             CCCcEEEEEECCCCh--hHHHhCCCCcCCEEEEEe--CCeEEEEecCCCCHHHHHHHHHHh
Confidence            345677777876543  457889999999998884  688899999999888776555544

>cd03011 TlpA_like_ScsD_MtbDsbE TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif

Probab=94.31  E-value=0.12  Score=38.82  Aligned_cols=61  Identities=20%  Similarity=0.266  Sum_probs=43.4

Q ss_pred             HHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774           10 EAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        10 ~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      +.+.++++++-+-|....+  ....++..|++.++|++.||++ +| +..+..|..+.+.+..++
T Consensus        62 ~~~~~~~~~~~~~~~~~~d--~~~~~~~~~~i~~~P~~~vid~-~g-i~~~~~g~~~~~~~~~~~  122 (123)
T cd03011          62 GAVARFMQKKGYGFPVIND--PDGVISARWGVSVTPAIVIVDP-GG-IVFVTTGVTSEWGLRLRL  122 (123)
T ss_pred             HHHHHHHHHcCCCccEEEC--CCcHHHHhCCCCcccEEEEEcC-CC-eEEEEeccCCHHHHHhhc
Confidence            4455555554444443332  2246888999999999999996 46 888999999999987653

The Salmonella typhimurium ScsD is a thioredoxin-like protein which confers copper tolerance to copper-sensitive mutants of E. coli. MtbDsbE has been characterized as an oxidase in vitro, catalyzing the disulfide bond formation of substrates like hirudin. The reduced form of MtbDsbE is more stable than its oxidized form, consistent with an oxidase function. This is in contrast to the function of DsbE from gram-negative bacteria which is a specific reductase of apocytochrome c.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=94.24  E-value=0.36  Score=33.43  Aligned_cols=66  Identities=17%  Similarity=0.195  Sum_probs=49.6

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +|-||.  ++.+.-....++||.+|-.-|... .+.++...+|+.+  .+.  +  +++.||+++|+. +++|.+.
T Consensus         2 qi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~-~gip~~~q~Li~~--Gk~--L--~D~~tL~~~~i~~~~tl~l~   68 (74)
T cd01793           2 QLFVRA--QNTHTLEVTGQETVSDIKAHVAGL-EGIDVEDQVLLLA--GVP--L--EDDATLGQCGVEELCTLEVA   68 (74)
T ss_pred             EEEEEC--CCEEEEEECCcCcHHHHHHHHHhh-hCCCHHHEEEEEC--CeE--C--CCCCCHHHcCCCCCCEEEEE
Confidence            355665  466778889999999999999875 4667788888764  443  5  457999999998 4666554

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.

>PF03190 Thioredox_DsbH: Protein of unknown function, DUF255; InterPro: IPR004879 This is a group of uncharacterised proteins

Probab=94.24  E-value=0.12  Score=41.79  Aligned_cols=58  Identities=16%  Similarity=0.301  Sum_probs=37.1

Q ss_pred             cccccCCCHHHHHHhhcceEEEEEecCChHHH--H---HH-HhcCCCCCceEEEEeCCCCceEEe
Q 025774            2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGK--K---VC-TYYKLDSIPVVLVVDPITGQKMRS   60 (248)
Q Consensus         2 ~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~--~---~~-~~~~~~~~P~l~ii~~~~g~~l~~   60 (248)
                      |.+.++.|+.|.++||++||-...|.+.....  .   ++ ...+...+|..+++.|. |..+..
T Consensus        55 M~~esf~d~eVa~~lN~~FI~VkvDree~Pdid~~y~~~~~~~~~~gGwPl~vfltPd-g~p~~~  118 (163)
T PF03190_consen   55 MERESFSDPEVAEYLNRNFIPVKVDREERPDIDKIYMNAVQAMSGSGGWPLTVFLTPD-GKPFFG  118 (163)
T ss_dssp             HHHHTTT-HHHHHHHHHH-EEEEEETTT-HHHHHHHHHHHHHHHS---SSEEEEE-TT-S-EEEE
T ss_pred             hcccCcCCHHHHHHHhCCEEEEEeccccCccHHHHHHHHHHHhcCCCCCCceEEECCC-CCeeee
Confidence            56789999999999999999999998753321  1   11 12367899999999985 675543

; PDB: 3IRA_A.

>cd03002 PDI_a_MPD1_like PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces cerevisiae MPD1 protein, which contains a single redox active TRX domain located at the N-terminus, and an ER retention signal at the C-terminus indicative of an ER-resident protein

Probab=94.19  E-value=0.25  Score=36.27  Aligned_cols=58  Identities=16%  Similarity=0.287  Sum_probs=42.9

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCC---CceEEeeeCCCChHHHHHH
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPIT---GQKMRSWCGMVQPESLLED   73 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~---g~~l~~~~G~~~~e~l~~~   73 (248)
                      ++..+.+...|.+..+...++..|++..||++.++.+..   +.......|..+.++|+.-
T Consensus        47 ~~~~~~~~~v~~~~~~~~~~~~~~~i~~~Pt~~~~~~~~~~~~~~~~~~~G~~~~~~l~~f  107 (109)
T cd03002          47 LDGLVQVAAVDCDEDKNKPLCGKYGVQGFPTLKVFRPPKKASKHAVEDYNGERSAKAIVDF  107 (109)
T ss_pred             hcCCceEEEEecCccccHHHHHHcCCCcCCEEEEEeCCCcccccccccccCccCHHHHHHH
Confidence            344567777888776667889999999999999997542   1345668888888877543

MPD1 has been shown to suppress the maturation defect of carboxypeptidase Y caused by deletion of the yeast PDI1 gene. Other characterized members of this subfamily include the Aspergillus niger prpA protein and Giardia PDI-1. PrpA is non-essential to strain viability, however, its transcript level is induced by heterologous protein expression suggesting a possible role in oxidative protein folding during high protein production. Giardia PDI-1 has the ability to refold scrambled RNase and exhibits transglutaminase activity.

>TIGR00385 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily

Probab=94.18  E-value=0.17  Score=41.00  Aligned_cols=45  Identities=22%  Similarity=0.317  Sum_probs=38.1

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .++..|++..+|+.++|++ +|.++.++.|.++.+++...|.+++.
T Consensus       128 ~~~~~~~v~~~P~~~~id~-~G~i~~~~~G~~~~~~l~~~l~~~~~  172 (173)
T TIGR00385       128 KLGLDLGVYGAPETFLVDG-NGVILYRHAGPLNNEVWTEGFLPAME  172 (173)
T ss_pred             chHHhcCCeeCCeEEEEcC-CceEEEEEeccCCHHHHHHHHHHHhh
Confidence            3456778888999999995 59999999999999999888888764

Involved in the biogenesis of c-type cytochromes as well as in disulfide bond formation in some periplasmic proteins.

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=94.14  E-value=0.21  Score=45.95  Aligned_cols=68  Identities=9%  Similarity=0.137  Sum_probs=54.0

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcC--CCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLE--GSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~--~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +|-||..+|+.+.-.+..++||.+|...|.....  +++....+|+..  .+.  |  ++++||+++|+. ++.|++
T Consensus         2 kItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~--Gki--L--~Dd~tL~dy~I~e~~~Ivv   72 (378)
T TIGR00601         2 TLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYS--GKI--L--SDDKTVREYKIKEKDFVVV   72 (378)
T ss_pred             EEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEEC--CEE--C--CCCCcHHHcCCCCCCEEEE
Confidence            6889999999999999999999999999987532  266788888764  443  5  456899999998 455544

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).

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

Probab=94.01  E-value=0.38  Score=34.19  Aligned_cols=71  Identities=13%  Similarity=0.073  Sum_probs=52.3

Q ss_pred             eEEEEEcCCCce--EEEeeCCCCchHHHHHHHHhhcC-CCCCcCeEEEccCCCCccccCCCcCCCccccC--Cc-CceEE
Q 025774          171 CRVGVRLPDGRR--MQRNFLRTDPIQLLWSYCYSQLE-GSEMKPFRLTHAIPGATKSLDYDSKLTFEDSG--LA-NAMIS  244 (248)
Q Consensus       171 ~~i~iRlp~G~r--~~r~F~~~~~l~~l~~fv~~~~~-~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~g--l~-~~~v~  244 (248)
                      ++|.||.|+|++  +.-.+..++||.+|-.-+....+ .+++..-+|+..  ++.  |  +++.||++.+  .. .-+|.
T Consensus         2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~--GKi--L--kD~~tL~~~~~~~~~~~tiH   75 (79)
T cd01790           2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYS--GKL--L--PDHLKLRDVLRKQDEYHMVH   75 (79)
T ss_pred             eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEc--Cee--c--cchhhHHHHhhcccCCceEE
Confidence            578999999998  55555899999999999987653 234577888764  443  5  4579999996  55 45666


Q ss_pred             EEe
Q 025774          245 VTW  247 (248)
Q Consensus       245 v~~  247 (248)
                      +++
T Consensus        76 LV~   78 (79)
T cd01790          76 LVC   78 (79)
T ss_pred             EEe
Confidence            654

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=94.00  E-value=0.41  Score=33.38  Aligned_cols=69  Identities=17%  Similarity=0.145  Sum_probs=52.0

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +|.|++ +|+.+.-.+..++|+.+|-+-+.+. .+.++...+|...-.+. ..+  +++.||.++|+. ++.|++
T Consensus         2 ~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~-tgvp~~~QKLi~~~~~G-k~l--~D~~~L~~~~i~~g~~i~l   71 (74)
T cd01813           2 PVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTL-TGVLPERQKLLGLKVKG-KPA--EDDVKISALKLKPNTKIMM   71 (74)
T ss_pred             EEEEEE-CCEEEEEEECCCCCHHHHHHHHHHH-HCCCHHHEEEEeecccC-CcC--CCCcCHHHcCCCCCCEEEE
Confidence            567777 7788888999999999999999885 46788889998620122 123  458999999998 455554

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.

>cd03003 PDI_a_ERdj5_N PDIa family, N-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains

Probab=93.70  E-value=0.33  Score=35.29  Aligned_cols=55  Identities=18%  Similarity=0.268  Sum_probs=42.2

Q ss_pred             HHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           14 QTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        14 ~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      +-+..++.|...|++..  ..++..|++..||++.++  .+|..+..+.|..+.+.|..
T Consensus        45 ~~~~~~~~~~~vd~~~~--~~~~~~~~v~~~Pt~~~~--~~g~~~~~~~G~~~~~~l~~   99 (101)
T cd03003          45 KEMDGVIRIGAVNCGDD--RMLCRSQGVNSYPSLYVF--PSGMNPEKYYGDRSKESLVK   99 (101)
T ss_pred             HHhcCceEEEEEeCCcc--HHHHHHcCCCccCEEEEE--cCCCCcccCCCCCCHHHHHh
Confidence            33445778888888753  457899999999999888  35777888999888887643

This subfamily is comprised of the first TRX domain of ERdj5 located after the DnaJ domain at the N-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation.

>cd00196 UBQ Ubiquitin-like proteins

Probab=93.69  E-value=0.34  Score=30.44  Aligned_cols=64  Identities=23%  Similarity=0.201  Sum_probs=47.1

Q ss_pred             EEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          175 VRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       175 iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +++++|......+..+.++.+|...+.... +..+..|.|....+..      ....++.+.++. +..+.+
T Consensus         2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~-~~~~~~~~l~~~~~~~------~~~~~~~~~~~~~~~~i~~   66 (69)
T cd00196           2 VKLNDGKTVELLVPSGTTVADLKEKLAKKL-GLPPEQQRLLVNGKIL------PDSLTLEDYGLQDGDELVL   66 (69)
T ss_pred             eEecCCCEEEEEcCCCCcHHHHHHHHHHHH-CcChHHeEEEECCeEC------CCCCcHHHcCCCCCCEEEE
Confidence            677899999999999999999999998865 3567889998876543      223344566665 444443

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.

>PHA02278 thioredoxin-like protein

Probab=93.20  E-value=0.51  Score=35.10  Aligned_cols=49  Identities=20%  Similarity=0.328  Sum_probs=39.2

Q ss_pred             EEEEEecCChH--HHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHH
Q 025774           21 IFWQVYDDTSE--GKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLL   71 (248)
Q Consensus        21 V~w~~d~~~~e--g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~   71 (248)
                      -|...|++..+  ...++..|++.+.|+++++-  +|+.+.++.|..+.+.+.
T Consensus        48 ~~~~vdvd~~~~d~~~l~~~~~I~~iPT~i~fk--~G~~v~~~~G~~~~~~l~   98 (103)
T PHA02278         48 PILTLNLDAEDVDREKAVKLFDIMSTPVLIGYK--DGQLVKKYEDQVTPMQLQ   98 (103)
T ss_pred             eEEEEECCccccccHHHHHHCCCccccEEEEEE--CCEEEEEEeCCCCHHHHH
Confidence            46777776432  45589999999999998884  599999999988887764

>TIGR02740 TraF-like TraF-like protein

Probab=93.17  E-value=0.67  Score=40.66  Aligned_cols=71  Identities=14%  Similarity=0.181  Sum_probs=51.3

Q ss_pred             CHHHHHHhhc-ceEEEEEecCChH---------HHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774            9 NEAVSQTIST-NFIFWQVYDDTSE---------GKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus         9 ~~~v~~~l~~-~fV~w~~d~~~~e---------g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      .+.+.++-++ ++.+.+++++...         ...++..|++..+|.++|+++.+|.+.....|.++.++|..++....
T Consensus       185 ~P~L~~la~~yg~~Vi~VsvD~~~~~~fp~~~~d~~la~~~gV~~vPtl~Lv~~~~~~v~~v~~G~~s~~eL~~~i~~~a  264 (271)
T TIGR02740       185 APILQAFEDRYGIEVLPVSVDGGPLPGFPNARPDAGQAQQLKIRTVPAVFLADPDPNQFTPIGFGVMSADELVDRILLAA  264 (271)
T ss_pred             hHHHHHHHHHcCcEEEEEeCCCCccccCCcccCCHHHHHHcCCCcCCeEEEEECCCCEEEEEEeCCCCHHHHHHHHHHHh
Confidence            3455556554 5667777765421         12368899999999999999766766666779999999988877664


Q ss_pred             h
Q 025774           79 D   79 (248)
Q Consensus        79 ~   79 (248)
                      .
T Consensus       265 ~  265 (271)
T TIGR02740       265 H  265 (271)
T ss_pred             c
Confidence            3

This protein is related to the F-type conjugation system pilus assembly proteins TraF (TIGR02739)and TrbB (TIGR02738) both of which exhibit a thioredoxin fold. The protein represented by this model has the same length and architecture as TraF, but lacks the CXXC-motif found in TrbB and believed to be responsible for the disulfide isomerase activity of that protein.

>PRK03147 thiol-disulfide oxidoreductase; Provisional

Probab=93.16  E-value=0.78  Score=36.59  Aligned_cols=43  Identities=23%  Similarity=0.428  Sum_probs=35.8

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      ..++..|++..+|++.+|++ +|+++..+.|..+.+++.+.|..
T Consensus       128 ~~~~~~~~v~~~P~~~lid~-~g~i~~~~~g~~~~~~l~~~l~~  170 (173)
T PRK03147        128 RQVIDAYGVGPLPTTFLIDK-DGKVVKVITGEMTEEQLEEYLEK  170 (173)
T ss_pred             chHHHHcCCCCcCeEEEECC-CCcEEEEEeCCCCHHHHHHHHHH
Confidence            36678899999999999985 58999999999999888766553

>cd03005 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains

Probab=93.02  E-value=0.64  Score=33.46  Aligned_cols=50  Identities=20%  Similarity=0.398  Sum_probs=39.2

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      ++.+...|.+...  .++..|++..+|++.++.  .|..+.+..|..+.+++..
T Consensus        51 ~~~~~~vd~~~~~--~~~~~~~v~~~Pt~~~~~--~g~~~~~~~G~~~~~~l~~  100 (102)
T cd03005          51 SVKIAKVDCTQHR--ELCSEFQVRGYPTLLLFK--DGEKVDKYKGTRDLDSLKE  100 (102)
T ss_pred             cEEEEEEECCCCh--hhHhhcCCCcCCEEEEEe--CCCeeeEeeCCCCHHHHHh
Confidence            5788888876543  678899999999999983  4777888999988777643

Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.

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

Probab=92.64  E-value=0.53  Score=32.81  Aligned_cols=62  Identities=16%  Similarity=0.244  Sum_probs=48.3

Q ss_pred             CCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          179 DGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       179 ~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      +|+.+.-.+..++||.+|-+-|... .+.++...+|+..  .+.  +  +.+.||.++|+. +++|.+.+
T Consensus         6 ~g~~~~l~v~~~~TV~~lK~~i~~~-~gip~~~q~L~~~--G~~--L--~d~~tL~~~~i~~g~~l~v~~   68 (76)
T cd01800           6 NGQMLNFTLQLSDPVSVLKVKIHEE-TGMPAGKQKLQYE--GIF--I--KDSNSLAYYNLANGTIIHLQL   68 (76)
T ss_pred             CCeEEEEEECCCCcHHHHHHHHHHH-HCCCHHHEEEEEC--CEE--c--CCCCcHHHcCCCCCCEEEEEE
Confidence            6888889999999999999999875 4677888899754  332  4  457899999998 56666543

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.

>cd02947 TRX_family TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains

Probab=92.50  E-value=1.1  Score=30.74  Aligned_cols=53  Identities=26%  Similarity=0.335  Sum_probs=42.1

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      .++.+...|.+.  ...++..|++..+|++.++.  .|..+..+.|..+.+++...|
T Consensus        40 ~~~~~~~i~~~~--~~~~~~~~~v~~~P~~~~~~--~g~~~~~~~g~~~~~~l~~~i   92 (93)
T cd02947          40 PKVKFVKVDVDE--NPELAEEYGVRSIPTFLFFK--NGKEVDRVVGADPKEELEEFL   92 (93)
T ss_pred             CCceEEEEECCC--ChhHHHhcCcccccEEEEEE--CCEEEEEEecCCCHHHHHHHh
Confidence            578888888865  44678889999999999985  478889999988887776544

Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functio

>cd02994 PDI_a_TMX PDIa family, TMX subfamily; composed of proteins similar to the TRX-related human transmembrane protein, TMX

Probab=92.41  E-value=1.1  Score=32.43  Aligned_cols=52  Identities=13%  Similarity=0.188  Sum_probs=39.8

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ++.+...|.+...  .++..|++..||++.++  .+|. +....|..+.+++...+.
T Consensus        49 ~v~~~~vd~~~~~--~~~~~~~i~~~Pt~~~~--~~g~-~~~~~G~~~~~~l~~~i~  100 (101)
T cd02994          49 GINVAKVDVTQEP--GLSGRFFVTALPTIYHA--KDGV-FRRYQGPRDKEDLISFIE  100 (101)
T ss_pred             CeEEEEEEccCCH--hHHHHcCCcccCEEEEe--CCCC-EEEecCCCCHHHHHHHHh
Confidence            5788888886544  47889999999999887  4576 477899888888765543

TMX is a type I integral membrane protein; the N-terminal redox active TRX domain is present in the endoplasmic reticulum (ER) lumen while the C-terminus is oriented towards the cytoplasm. It is expressed in many cell types and its active site motif (CPAC) is unique. In vitro, TMX reduces interchain disulfides of insulin and renatures inactive RNase containing incorrect disulfide bonds. The C. elegans homolog, DPY-11, is expressed only in the hypodermis and resides in the cytoplasm. It is required for body and sensory organ morphogeneis. Another uncharacterized TRX-related transmembrane protein, human TMX4, is included in the alignment. The active site sequence of TMX4 is CPSC.

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

Probab=92.34  E-value=1.3  Score=31.69  Aligned_cols=73  Identities=18%  Similarity=0.239  Sum_probs=51.0

Q ss_pred             eEEEEEcCCC--ceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccC-CCCc--cccCCCcCCCccccCCcCce-EE
Q 025774          171 CRVGVRLPDG--RRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAI-PGAT--KSLDYDSKLTFEDSGLANAM-IS  244 (248)
Q Consensus       171 ~~i~iRlp~G--~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~-Pr~~--~~l~~d~~~tl~d~gl~~~~-v~  244 (248)
                      ++|.|.-++-  ...++||..+.||++|-.-+.... |.++...+|.--. +...  ..+ .+.+++|...|+.+.. |.
T Consensus         2 v~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~-Gi~~~~m~L~l~~~~~~~~~~~~-~dd~~~L~~y~~~dg~~i~   79 (87)
T PF14560_consen    2 VKLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLT-GIPPSDMRLQLKSDKDDSKIEEL-DDDDATLGSYGIKDGMRIH   79 (87)
T ss_dssp             EEEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHH-TS-TTTEEEEEE-TSSSSEEEES-SGSSSBCCHHT-STTEEEE
T ss_pred             EEEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHh-CCCcccEEEEEEecCCCcccccc-CCCccEeecCCCCCCCEEE
Confidence            5677887766  489999999999999999998754 6677777775421 1111  122 4679999999999555 44


Q ss_pred             E
Q 025774          245 V  245 (248)
Q Consensus       245 v  245 (248)
                      |
T Consensus        80 V   80 (87)
T PF14560_consen   80 V   80 (87)
T ss_dssp             E
T ss_pred             E
Confidence            4

>cd02961 PDI_a_family Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants

Probab=92.32  E-value=0.6  Score=32.92  Aligned_cols=53  Identities=17%  Similarity=0.256  Sum_probs=40.9

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      +.++.|...|...  ...++..|++..+|++.++.+. |..+.+..|..++++++.
T Consensus        47 ~~~~~~~~v~~~~--~~~~~~~~~i~~~Pt~~~~~~~-~~~~~~~~g~~~~~~i~~   99 (101)
T cd02961          47 DGKVVVAKVDCTA--NNDLCSEYGVRGYPTIKLFPNG-SKEPVKYEGPRTLESLVE   99 (101)
T ss_pred             CCceEEEEeeccc--hHHHHHhCCCCCCCEEEEEcCC-CcccccCCCCcCHHHHHh
Confidence            3567777777754  5677899999999999999753 366777888888887754

Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies

>cd02963 TRX_DnaJ TRX domain, DnaJ domain containing protein family; composed of uncharacterized proteins of about 500-800 amino acids, containing an N-terminal DnaJ domain followed by one redox active TRX domain

Probab=92.24  E-value=1.2  Score=33.21  Aligned_cols=53  Identities=9%  Similarity=0.081  Sum_probs=41.3

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ++.+...|++..  ..++..|++.++|.+.++.  .|..+....|..+.+.+...|.
T Consensus        57 ~v~~~~vd~d~~--~~l~~~~~V~~~Pt~~i~~--~g~~~~~~~G~~~~~~l~~~i~  109 (111)
T cd02963          57 GVGIATVNAGHE--RRLARKLGAHSVPAIVGII--NGQVTFYHDSSFTKQHVVDFVR  109 (111)
T ss_pred             CceEEEEecccc--HHHHHHcCCccCCEEEEEE--CCEEEEEecCCCCHHHHHHHHh
Confidence            577778887643  3578999999999998884  6888888999888887755443

DnaJ is a member of the 40 kDa heat-shock protein (Hsp40) family of molecular chaperones, which regulate the activity of Hsp70s. TRX is involved in the redox regulation of many protein substrates through the reduction of disulfide bonds. TRX has been implicated to catalyse the reduction of Hsp33, a chaperone holdase that binds to unfolded protein intermediates. The presence of DnaJ and TRX domains in members of this family suggests that they could be involved in a redox-regulated chaperone network.

>TIGR02738 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB

Probab=92.07  E-value=1.1  Score=35.96  Aligned_cols=38  Identities=16%  Similarity=0.173  Sum_probs=30.8

Q ss_pred             CCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           40 KLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        40 ~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++..+|+..+|++..+.+..+..|.++.+++...+...
T Consensus       115 ~v~~iPTt~LID~~G~~i~~~~~G~~s~~~l~~~I~~l  152 (153)
T TIGR02738       115 RPVVTPATFLVNVNTRKAYPVLQGAVDEAELANRMDEI  152 (153)
T ss_pred             CCCCCCeEEEEeCCCCEEEEEeecccCHHHHHHHHHHh
Confidence            78999999999976555667899999999887766553

This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. The protein is closely related to TraF (TIGR02739) which is somewhat longer, lacks the cysteine motif and is apparently not functional as a disulfide bond isomerase.

>cd02982 PDI_b'_family Protein Disulfide Isomerase (PDIb') family, redox inactive TRX-like domain b'; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants

Probab=91.62  E-value=0.81  Score=33.07  Aligned_cols=56  Identities=23%  Similarity=0.280  Sum_probs=38.9

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCC--CCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLD--SIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~--~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ..+.|...|++.  ...++..|++.  .+|+++++...+|.......|..+.+.+..-+.
T Consensus        43 ~~v~f~~vd~~~--~~~~~~~~~i~~~~~P~~~~~~~~~~~k~~~~~~~~~~~~l~~fi~  100 (103)
T cd02982          43 GKLLFVVVDADD--FGRHLEYFGLKEEDLPVIAIINLSDGKKYLMPEEELTAESLEEFVE  100 (103)
T ss_pred             CeEEEEEEchHh--hHHHHHHcCCChhhCCEEEEEecccccccCCCccccCHHHHHHHHH
Confidence            356666666643  55689999998  999999998755665555556667776644443

Members of this family include PDI, calsequestrin and other PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5 and PDIR. PDI, ERp57, ERp72, P5 and PDIR are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and one or more redox inactive TRX-like (b) domains. The molecular structure of PDI is abb'a'. Also included in this family is the PDI-related protein ERp27, w

>TIGR02739 TraF type-F conjugative transfer system pilin assembly protein TraF

Probab=91.53  E-value=1.2  Score=38.79  Aligned_cols=69  Identities=10%  Similarity=0.138  Sum_probs=52.2

Q ss_pred             HHHhhc-ceEEEEEecCCh--H-------HHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           13 SQTIST-NFIFWQVYDDTS--E-------GKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        13 ~~~l~~-~fV~w~~d~~~~--e-------g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ..|-+. +|=+.+++++..  .       ....+..+++..+|.+++|.|.++...-+-.|.++.++|+.++......+
T Consensus       173 ~~fa~~ygi~v~~VS~DG~~~p~fp~~~~d~gqa~~l~v~~~Pal~Lv~~~t~~~~pv~~G~iS~deL~~Ri~~v~~~f  251 (256)
T TIGR02739       173 QAFAKEYGISVIPISVDGTLIPGLPNSRSDSGQAQHLGVKYFPALYLVNPKSQKMSPLAYGFISQDELKERILNVLTQF  251 (256)
T ss_pred             HHHHHHhCCeEEEEecCCCCCCCCCCccCChHHHHhcCCccCceEEEEECCCCcEEEEeeccCCHHHHHHHHHHHHhcc
Confidence            334443 566666666532  1       13456778899999999999998888888899999999999999887766

This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se.

>TIGR01126 pdi_dom protein disulfide-isomerase domain

Probab=91.52  E-value=1.6  Score=31.18  Aligned_cols=54  Identities=15%  Similarity=0.272  Sum_probs=39.3

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      ++.+...|.  .+...++..|++..+|.++++.+  |..+....|..+.++|...|.+
T Consensus        47 ~~~~~~~d~--~~~~~~~~~~~i~~~P~~~~~~~--~~~~~~~~g~~~~~~l~~~i~~  100 (102)
T TIGR01126        47 DIVLAKVDA--TAEKDLASRFGVSGFPTIKFFPK--GKKPVDYEGGRDLEAIVEFVNE  100 (102)
T ss_pred             ceEEEEEEc--cchHHHHHhCCCCcCCEEEEecC--CCcceeecCCCCHHHHHHHHHh
Confidence            466655565  34567889999999999999974  3336778998888887555543

This model describes a domain of eukaryotic protein disulfide isomerases, generally found in two copies. The high cutoff for total score reflects the expectation of finding both copies. The domain is similar to thioredoxin but the redox-active disulfide region motif is APWCGHCK.

>cd03004 PDI_a_ERdj5_C PDIa family, C-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains

Probab=91.41  E-value=1.1  Score=32.51  Aligned_cols=52  Identities=17%  Similarity=0.269  Sum_probs=39.6

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCC-hHHHHH
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQ-PESLLE   72 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~-~e~l~~   72 (248)
                      ..+.|...|.+..  ..+++.|++..||++.++.. +|..+..+.|..+ .++|..
T Consensus        50 ~~~~~~~vd~~~~--~~~~~~~~i~~~Pt~~~~~~-g~~~~~~~~G~~~~~~~l~~  102 (104)
T cd03004          50 GKVKVGSVDCQKY--ESLCQQANIRAYPTIRLYPG-NASKYHSYNGWHRDADSILE  102 (104)
T ss_pred             CCcEEEEEECCch--HHHHHHcCCCcccEEEEEcC-CCCCceEccCCCCCHHHHHh
Confidence            4567778887653  45789999999999998853 3477888999886 877643

This subfamily is composed of the three TRX domains located at the C-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation. Also included in the alignment is the single complete TRX domain of an uncharacterized protein from Tetraodon nigroviridis, which also contains a DnaJ domain at its N-terminus.

>cd03006 PDI_a_EFP1_N PDIa family, N-terminal EFP1 subfamily; EFP1 is a binding partner protein of thyroid oxidase (ThOX), also called Duox

Probab=91.39  E-value=1.1  Score=33.88  Aligned_cols=57  Identities=14%  Similarity=0.178  Sum_probs=42.5

Q ss_pred             HHHHhhcceEEEEEecCChHHHHHH-HhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           12 VSQTISTNFIFWQVYDDTSEGKKVC-TYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        12 v~~~l~~~fV~w~~d~~~~eg~~~~-~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      +.+-+.+...|...|.+...  .++ ..|++.+||++.+.  .+|....+..|..+.+.++.
T Consensus        54 la~~~~~~v~~~~Vd~d~~~--~l~~~~~~I~~~PTl~lf--~~g~~~~~y~G~~~~~~i~~  111 (113)
T cd03006          54 VAQKLSDQVLFVAINCWWPQ--GKCRKQKHFFYFPVIHLY--YRSRGPIEYKGPMRAPYMEK  111 (113)
T ss_pred             HHHHhcCCeEEEEEECCCCh--HHHHHhcCCcccCEEEEE--ECCccceEEeCCCCHHHHHh
Confidence            33344556788888887554  356 58999999999888  35777788999988888754

ThOX proteins are responsible for the generation of hydrogen peroxide, a crucial substrate of thyroperoxidase, which functions to iodinate thyroglobulin and synthesize thyroid hormones. EFP1 was isolated through a yeast two-hybrid method using the EF-hand fragment of dog Duox1 as a bait. It could be one of the partners in the assembly of a multiprotein complex constituting the thyroid hydrogen peroxide generating system. EFP1 contains two TRX domains related to the redox active TRX domains of protein disulfide isomerase (PDI). This subfamily is composed of the N-terminal TRX domain of EFP1, which contains a CXXS sequence in place of the typical CXXC motif, similar to ERp44. The CXXS motif allows the formation of stable mixed disulfides, crucial for the ER-retention function of ERp44.

>PRK15412 thiol:disulfide interchange protein DsbE; Provisional

Probab=91.28  E-value=0.53  Score=38.59  Aligned_cols=45  Identities=13%  Similarity=0.213  Sum_probs=37.3

Q ss_pred             HHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           35 VCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        35 ~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ++..|++..+|+.+||++. |.++.+..|.++.+++...+...+..
T Consensus       134 ~~~~~gv~~~P~t~vid~~-G~i~~~~~G~~~~~~l~~~i~~~~~~  178 (185)
T PRK15412        134 LGLDLGVYGAPETFLIDGN-GIIRYRHAGDLNPRVWESEIKPLWEK  178 (185)
T ss_pred             HHHhcCCCcCCeEEEECCC-ceEEEEEecCCCHHHHHHHHHHHHHH
Confidence            4557889999999999964 99999999999998887777777654

>cd03010 TlpA_like_DsbE TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c maturation (Ccm) factor with a redox active CXXC motif

Probab=91.26  E-value=0.38  Score=36.45  Aligned_cols=37  Identities=19%  Similarity=0.277  Sum_probs=31.1

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHH
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESL   70 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l   70 (248)
                      ..++..|++..+|...+|++ +|.++.++.|.++.+.+
T Consensus        90 ~~~~~~~~v~~~P~~~~ld~-~G~v~~~~~G~~~~~~~  126 (127)
T cd03010          90 GRVGIDLGVYGVPETFLIDG-DGIIRYKHVGPLTPEVW  126 (127)
T ss_pred             chHHHhcCCCCCCeEEEECC-CceEEEEEeccCChHhc
Confidence            45778899999999999985 59999999998887653

Assembly of cytochrome c requires the ligation of heme to reduced thiols of the apocytochrome. In bacteria, this assembly occurs in the periplasm. The reductase activity of DsbE in the oxidizing environment of the periplasm is crucial in the maturation of cytochrome c.

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

Probab=91.22  E-value=0.61  Score=32.82  Aligned_cols=70  Identities=26%  Similarity=0.365  Sum_probs=45.4

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCC--CCC---cCeEEEccCCCCccccCCCcCCCccccCCcCceEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEG--SEM---KPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMIS  244 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~--~~~---~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~  244 (248)
                      .|+|-|..++|+++.-....+-++..|..-+...+..  .+.   ..|.|.+. +.+.  +  +.+.||.++|+.++.++
T Consensus         2 ~~rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~-~g~~--L--~~~~tL~~~gV~dGd~L   76 (79)
T PF08817_consen    2 LCRVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARA-GGRP--L--DPDQTLADAGVRDGDVL   76 (79)
T ss_dssp             EEEEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-G-GTEE--E--ETTSBCGGGT--TT-EE
T ss_pred             EEEEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEec-CCcc--c--CCcCcHhHcCCCCCCEE
Confidence            5899999999899999999999999999988776432  112   24777632 2222  4  67999999999966554

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.

>cd02948 TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein

Probab=91.11  E-value=1.8  Score=31.59  Aligned_cols=50  Identities=18%  Similarity=0.203  Sum_probs=38.5

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ..|...|++.+   ..+..|++..+|++.++.  +|+.+.++.|. +++.+...|.
T Consensus        51 ~~~~~vd~d~~---~~~~~~~v~~~Pt~~~~~--~g~~~~~~~G~-~~~~~~~~i~  100 (102)
T cd02948          51 LHFATAEADTI---DTLKRYRGKCEPTFLFYK--NGELVAVIRGA-NAPLLNKTIT  100 (102)
T ss_pred             EEEEEEeCCCH---HHHHHcCCCcCcEEEEEE--CCEEEEEEecC-ChHHHHHHHh
Confidence            45667777733   578999999999988874  69999999994 7777766554

Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which

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

Probab=91.10  E-value=1.2  Score=30.96  Aligned_cols=64  Identities=19%  Similarity=0.059  Sum_probs=47.6

Q ss_pred             EEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEc-cCCCCccccCCCcCCCccccCCc
Q 025774          175 VRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTH-AIPGATKSLDYDSKLTFEDSGLA  239 (248)
Q Consensus       175 iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~-~~Pr~~~~l~~d~~~tl~d~gl~  239 (248)
                      |+||||+..+-....+.+.++|++-|..++.-....-|.|.. .-+...... .+.+++|.+.+-.
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~w-L~~~k~l~~q~~~   65 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHW-LDLDKKLKKQLKK   65 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEE-E-SSSBGGGSTBT
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCccee-ccCcccHHHHcCC
Confidence            689999999999999999999999999987544567788876 112221122 3778899888765

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 ....

>PF13728 TraF: F plasmid transfer operon protein

Probab=91.10  E-value=1.1  Score=37.88  Aligned_cols=63  Identities=16%  Similarity=0.182  Sum_probs=47.4

Q ss_pred             HHHHhhc-ceEEEEEecCCh---------HHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774           12 VSQTIST-NFIFWQVYDDTS---------EGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        12 v~~~l~~-~fV~w~~d~~~~---------eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      |..|-+. +|-+..++++..         .-...+..+++..+|.+++|.|.++...-+-.|.++.++|++++
T Consensus       142 l~~~~~~yg~~v~~vs~DG~~~~~fp~~~~~~g~~~~l~v~~~Pal~Lv~~~~~~~~pv~~G~~s~~~L~~ri  214 (215)
T PF13728_consen  142 LQQFADKYGFSVIPVSLDGRPIPSFPNPRPDPGQAKRLGVKVTPALFLVNPNTKKWYPVSQGFMSLDELEDRI  214 (215)
T ss_pred             HHHHHHHhCCEEEEEecCCCCCcCCCCCCCCHHHHHHcCCCcCCEEEEEECCCCeEEEEeeecCCHHHHHHhh
Confidence            3444443 677777777521         12346678899999999999998888888899999999998876

>PLN00410 U5 snRNP protein, DIM1 family; Provisional

Probab=91.01  E-value=1.8  Score=34.31  Aligned_cols=58  Identities=12%  Similarity=0.115  Sum_probs=44.8

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCc-eEEeeeC--------CCChHHHHHHHhhhhhc
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQ-KMRSWCG--------MVQPESLLEDLVPFMDG   80 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~-~l~~~~G--------~~~~e~l~~~L~~~~~~   80 (248)
                      ..|+.+|++..  ..++..|++...|.++++. ++|. .+++..|        ..+.++|+..+..++..
T Consensus        56 ~~~~kVDVDe~--~dla~~y~I~~~~t~~~ff-k~g~~~vd~~tG~~~k~~~~~~~k~~l~~~i~~~~~~  122 (142)
T PLN00410         56 AVIYLVDITEV--PDFNTMYELYDPCTVMFFF-RNKHIMIDLGTGNNNKINWALKDKQEFIDIVETVYRG  122 (142)
T ss_pred             eEEEEEECCCC--HHHHHHcCccCCCcEEEEE-ECCeEEEEEecccccccccccCCHHHHHHHHHHHHHH
Confidence            56699999744  4899999999777666554 4678 7888999        57888898888877664

>cd02984 TRX_PICOT TRX domain, PICOT (for PKC-interacting cousin of TRX) subfamily; PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes

Probab=90.62  E-value=1.7  Score=30.87  Aligned_cols=51  Identities=12%  Similarity=0.384  Sum_probs=38.9

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      ++.+...|.+.  ...++..|++..+|++.++.  .|..+.++.|. .++++...+
T Consensus        46 ~i~~~~vd~~~--~~~~~~~~~i~~~Pt~~~~~--~g~~~~~~~g~-~~~~l~~~~   96 (97)
T cd02984          46 SVLFLSIEAEE--LPEISEKFEITAVPTFVFFR--NGTIVDRVSGA-DPKELAKKV   96 (97)
T ss_pred             ceEEEEEcccc--CHHHHHhcCCccccEEEEEE--CCEEEEEEeCC-CHHHHHHhh
Confidence            78888888753  34578899999999988884  58889999995 456555443

PICOT contains an N-terminal TRX-like domain, which does not contain the catalytic CXXC motif, followed by one to three glutaredoxin domains. The TRX-like domain is required for interaction with PKC theta. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli.

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=89.84  E-value=1.4  Score=30.74  Aligned_cols=63  Identities=13%  Similarity=0.043  Sum_probs=47.2

Q ss_pred             EcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-C-ceEEE
Q 025774          176 RLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-N-AMISV  245 (248)
Q Consensus       176 Rlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~-~~v~v  245 (248)
                      +...|+.+.-.|..++||..|-..+... .|.++...+|   |-.+.  + .+.+.||+++|+. + .+|++
T Consensus         8 ~~~~~~t~~l~v~~~~TV~~lK~kI~~~-~gip~~~QrL---~~G~~--L-~dD~~tL~~ygi~~~g~~~~l   72 (75)
T cd01799           8 AQSHTVTIWLTVRPDMTVAQLKDKVFLD-YGFPPAVQRW---VIGQR--L-ARDQETLYSHGIRTNGDSAFL   72 (75)
T ss_pred             cccCCCeEEEEECCCCcHHHHHHHHHHH-HCcCHHHEEE---EcCCe--e-CCCcCCHHHcCCCCCCCEEEE
Confidence            3456778888999999999999999875 4667778888   33332  4 3567999999997 5 55543

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.

>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1

Probab=89.83  E-value=2.9  Score=28.67  Aligned_cols=51  Identities=14%  Similarity=0.218  Sum_probs=37.6

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++-+...|++..  ...+..|++..+|.+.+    .|.  .++.|..+++++...|..+
T Consensus        31 ~~~~~~vd~~~~--~~~~~~~~v~~vPt~~~----~g~--~~~~G~~~~~~l~~~l~~~   81 (82)
T TIGR00411        31 AVEVEYINVMEN--PQKAMEYGIMAVPAIVI----NGD--VEFIGAPTKEELVEAIKKR   81 (82)
T ss_pred             ceEEEEEeCccC--HHHHHHcCCccCCEEEE----CCE--EEEecCCCHHHHHHHHHhh
Confidence            466777787533  35667899999999875    354  3788999999887777654

This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.

>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional

Probab=89.31  E-value=1.3  Score=42.40  Aligned_cols=43  Identities=14%  Similarity=0.211  Sum_probs=36.6

Q ss_pred             HHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           32 GKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        32 g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ...++..|++..+|.++||++ +|.++..+.|.++.++|...|.
T Consensus       128 ~~~lak~fgV~giPTt~IIDk-dGkIV~~~~G~~~~eeL~a~Ie  170 (521)
T PRK14018        128 GGTLAQSLNISVYPSWAIIGK-DGDVQRIVKGSISEAQALALIR  170 (521)
T ss_pred             cHHHHHHcCCCCcCeEEEEcC-CCeEEEEEeCCCCHHHHHHHHH
Confidence            346788999999999999996 5999999999999888866655

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=89.08  E-value=1.2  Score=31.24  Aligned_cols=52  Identities=19%  Similarity=0.248  Sum_probs=38.7

Q ss_pred             CCCCchHHHHHHHHhhc-CCC-CCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          188 LRTDPIQLLWSYCYSQL-EGS-EMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       188 ~~~~~l~~l~~fv~~~~-~~~-~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ..++||.+|..-|.... ++. ++..++|+..  .+.  +  +++.||++.|+. +++|.+
T Consensus        18 ~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~--GKi--L--~D~~TL~dygI~~gstlhL   72 (75)
T cd01815          18 PGGYQVSTLKQLIAAQLPDSLPDPELIDLIHC--GRK--L--KDDQTLDFYGIQSGSTIHI   72 (75)
T ss_pred             CccCcHHHHHHHHHHhhccCCCChHHeEEEeC--CcC--C--CCCCcHHHcCCCCCCEEEE
Confidence            46899999999998874 233 4778999864  443  5  567999999998 566644

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.

>PRK13703 conjugal pilus assembly protein TraF; Provisional

Probab=88.71  E-value=1.1  Score=38.80  Aligned_cols=70  Identities=14%  Similarity=0.193  Sum_probs=51.3

Q ss_pred             HHHHhhc-ceEEEEEecCC---hH------HHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           12 VSQTIST-NFIFWQVYDDT---SE------GKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        12 v~~~l~~-~fV~w~~d~~~---~e------g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      |..|-+. +|-+.+++++.   ++      ..-.+..+++..+|.+++|.|.++...-.-.|.++.++|+.++......+
T Consensus       165 l~~fa~~yg~~v~~VS~DG~~~p~fp~~~~d~gqa~~l~v~~~PAl~Lv~~~t~~~~pv~~G~iS~deL~~Ri~~v~t~~  244 (248)
T PRK13703        165 INDFRDTYGLSVIPVSVDGVINPLLPDSRTDQGQAQRLGVKYFPALMLVDPKSGSVRPLSYGFITQDDLAKRFLNVSTDF  244 (248)
T ss_pred             HHHHHHHhCCeEEEEecCCCCCCCCCCCccChhHHHhcCCcccceEEEEECCCCcEEEEeeccCCHHHHHHHHHHHHhcc
Confidence            3444443 56666666642   10      11234678899999999999998898888999999999999998876655

>cd02998 PDI_a_ERp38 PDIa family, endoplasmic reticulum protein 38 (ERp38) subfamily; composed of proteins similar to the P5-like protein first isolated from alfalfa, which contains two redox active TRX (a) domains at the N-terminus, like human P5, and a C-terminal domain with homology to the C-terminal domain of ERp29, unlike human P5

Probab=88.66  E-value=1.9  Score=30.89  Aligned_cols=52  Identities=15%  Similarity=0.254  Sum_probs=39.6

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      ++.+...|...+ ...++..|++..+|++.++.+ +|.....+.|..+.+++..
T Consensus        52 ~~~~~~id~~~~-~~~~~~~~~i~~~P~~~~~~~-~~~~~~~~~g~~~~~~l~~  103 (105)
T cd02998          52 DVVIAKVDADEA-NKDLAKKYGVSGFPTLKFFPK-GSTEPVKYEGGRDLEDLVK  103 (105)
T ss_pred             CEEEEEEECCCc-chhhHHhCCCCCcCEEEEEeC-CCCCccccCCccCHHHHHh
Confidence            588888887653 457788899999999999974 3455666888888777643

The cDNA clone of this protein (named G1) was isolated from an alfalfa cDNA library by screening with human protein disulfide isomerase (PDI) cDNA. The G1 protein is constitutively expressed in all major organs of the plant and its expression is induced by treatment with tunicamycin, indicating that it may be a glucose-regulated protein. The G1 homolog in the eukaryotic social amoeba Dictyostelium discoideum is also described as a P5-like protein, which is located in the endoplasmic reticulum (ER) despite the absence of an ER-retrieval signal. G1 homologs from Aspergillus niger and Neurospora crassa have also been characterized, and are named TIGA and ER

>cd03000 PDI_a_TMX3 PDIa family, TMX3 subfamily; composed of eukaryotic proteins similar to human TMX3, a TRX related transmembrane protein containing one redox active TRX domain at the N-terminus and a classical ER retrieval sequence for type I transmembrane proteins at the C-terminus

Probab=88.66  E-value=3.5  Score=30.00  Aligned_cols=52  Identities=6%  Similarity=0.096  Sum_probs=37.6

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      +.+...|....  ..+++.|++.++|++.++.  +| .+....|..+.+++..-+..
T Consensus        51 ~~~~~vd~~~~--~~~~~~~~I~~~Pt~~l~~--~~-~~~~~~G~~~~~~l~~~~~~  102 (104)
T cd03000          51 VRVGKLDATAY--SSIASEFGVRGYPTIKLLK--GD-LAYNYRGPRTKDDIVEFANR  102 (104)
T ss_pred             EEEEEEECccC--HhHHhhcCCccccEEEEEc--CC-CceeecCCCCHHHHHHHHHh
Confidence            66667777542  3578899999999999984  34 45668898888877655543

The TMX3 transcript is found in a variety of tissues with the highest levels detected in skeletal muscle and the heart. In vitro, TMX3 showed oxidase activity albeit slightly lower than that of protein disulfide isomerase.

>PRK13728 conjugal transfer protein TrbB; Provisional

Probab=88.55  E-value=4.1  Score=33.61  Aligned_cols=69  Identities=10%  Similarity=0.136  Sum_probs=50.2

Q ss_pred             HHHHHhhc-ceEEEEEecCCh-----------HHHHHHHhcCC--CCCceEEEEeCCCCceE-EeeeCCCChHHHHHHHh
Q 025774           11 AVSQTIST-NFIFWQVYDDTS-----------EGKKVCTYYKL--DSIPVVLVVDPITGQKM-RSWCGMVQPESLLEDLV   75 (248)
Q Consensus        11 ~v~~~l~~-~fV~w~~d~~~~-----------eg~~~~~~~~~--~~~P~l~ii~~~~g~~l-~~~~G~~~~e~l~~~L~   75 (248)
                      .+.++-++ .|.+++++++..           .+..+...|++  ..+|..+||++. |.++ ....|.++.+++..++.
T Consensus        90 ~L~~l~~~~g~~Vi~Vs~D~~~~~~fPv~~dd~~~~~~~~~g~~~~~iPttfLId~~-G~i~~~~~~G~~~~~~L~~~I~  168 (181)
T PRK13728         90 VLKQLAQQYGFSVFPYTLDGQGDTAFPEALPAPPDVMQTFFPNIPVATPTTFLVNVN-TLEALPLLQGATDAAGFMARMD  168 (181)
T ss_pred             HHHHHHHHcCCEEEEEEeCCCCCCCCceEecCchhHHHHHhCCCCCCCCeEEEEeCC-CcEEEEEEECCCCHHHHHHHHH
Confidence            44555554 688888877632           23456778884  699999999964 6664 67999999999988877


Q ss_pred             hhhhc
Q 025774           76 PFMDG   80 (248)
Q Consensus        76 ~~~~~   80 (248)
                      ..+..
T Consensus       169 ~ll~~  173 (181)
T PRK13728        169 TVLQM  173 (181)
T ss_pred             HHHhh
Confidence            77654

>cd02954 DIM1 Dim1 family; Dim1 is also referred to as U5 small nuclear ribonucleoprotein particle (snRNP)-specific 15kD protein

Probab=88.53  E-value=1.5  Score=33.39  Aligned_cols=42  Identities=19%  Similarity=0.192  Sum_probs=34.6

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV   65 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~   65 (248)
                      ..|+.+|++..  ..++..|++.+.|+++++-  +|..+.+..|..
T Consensus        47 v~f~kVDvD~~--~~la~~~~V~~iPTf~~fk--~G~~v~~~~G~~   88 (114)
T cd02954          47 AVIYLVDIDEV--PDFNKMYELYDPPTVMFFF--RNKHMKIDLGTG   88 (114)
T ss_pred             eEEEEEECCCC--HHHHHHcCCCCCCEEEEEE--CCEEEEEEcCCC
Confidence            46888998754  4789999999999999984  699888888843

It is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 interacts with multiple splicing-associated proteins, suggesting that it functions at multiple control points in the splicing of pre-mRNA as part of a large spliceosomal complex involving many protein-protein interactions. U5 snRNP contains seven core proteins (common to all snRNPs) and nine U5-specific proteins, one of which is Dim1. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif. It is essential for G2/M phase transition, as a consequence to its role in pre-mRNA splicing.

>cd02999 PDI_a_ERp44_like PDIa family, endoplasmic reticulum protein 44 (ERp44)-like subfamily; composed of uncharacterized PDI-like eukaryotic proteins containing only one redox active TRX (a) domain with a CXXS motif, similar to ERp44

Probab=87.71  E-value=2.6  Score=30.83  Aligned_cols=50  Identities=12%  Similarity=0.211  Sum_probs=38.1

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      ++.+.+.|.+. +-..++..|++..||++.++.+  | .+.++.|..+.+.+.+
T Consensus        49 ~~~~~~vd~~~-~~~~l~~~~~V~~~PT~~lf~~--g-~~~~~~G~~~~~~l~~   98 (100)
T cd02999          49 QIRHLAIEESS-IKPSLLSRYGVVGFPTILLFNS--T-PRVRYNGTRTLDSLAA   98 (100)
T ss_pred             cCceEEEECCC-CCHHHHHhcCCeecCEEEEEcC--C-ceeEecCCCCHHHHHh
Confidence            46677777652 2246889999999999999963  5 6788999988887754

CXXS is still a redox active motif; however, the mixed disulfide formed with the substrate is more stable than those formed by CXXC motif proteins. PDI-related proteins are usually involved in the oxidative protein folding in the ER by acting as catalysts and folding assistants. ERp44 is involved in thiol-mediated retention in the ER.

>cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins

Probab=87.24  E-value=0.73  Score=33.13  Aligned_cols=30  Identities=17%  Similarity=0.396  Sum_probs=24.9

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeC
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCG   63 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G   63 (248)
                      ..++..|++..+|.+.|+++. |.++....|
T Consensus        87 ~~~~~~~~~~~~P~~~l~d~~-g~v~~~~~g  116 (116)
T cd02966          87 GELAKAYGVRGLPTTFLIDRD-GRIRARHVG  116 (116)
T ss_pred             chHHHhcCcCccceEEEECCC-CcEEEEecC
Confidence            568889999999999999864 888877665

TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.

>cd02993 PDI_a_APS_reductase PDIa family, 5'-Adenylylsulfate (APS) reductase subfamily; composed of plant-type APS reductases containing a C-terminal redox active TRX domain and an N-terminal reductase domain which is part of a superfamily that includes N type ATP PPases

Probab=86.85  E-value=3.6  Score=30.31  Aligned_cols=59  Identities=15%  Similarity=0.223  Sum_probs=40.0

Q ss_pred             HHHHhhc-ceEEEEEecCChHHHHHHH-hcCCCCCceEEEEeCCCCceEEeeeCC-CChHHHHH
Q 025774           12 VSQTIST-NFIFWQVYDDTSEGKKVCT-YYKLDSIPVVLVVDPITGQKMRSWCGM-VQPESLLE   72 (248)
Q Consensus        12 v~~~l~~-~fV~w~~d~~~~eg~~~~~-~~~~~~~P~l~ii~~~~g~~l~~~~G~-~~~e~l~~   72 (248)
                      +.+.+.. ++.+...|.+... ..++. .|++..||++.++.+. +..+..+.|. .+.+.++.
T Consensus        46 la~~~~~~~~~~~~vd~d~~~-~~~~~~~~~v~~~Pti~~f~~~-~~~~~~y~g~~~~~~~l~~  107 (109)
T cd02993          46 LAEKLAGSNVKVAKFNADGEQ-REFAKEELQLKSFPTILFFPKN-SRQPIKYPSEQRDVDSLLM  107 (109)
T ss_pred             HHHHhccCCeEEEEEECCccc-hhhHHhhcCCCcCCEEEEEcCC-CCCceeccCCCCCHHHHHh
Confidence            3334444 5889898887532 34554 6999999999999653 4456668884 57777643

APS reductase catalyzes the reduction of activated sulfate to sulfite, a key step in the biosynthesis of sulfur-containing metabolites. Sulfate is first activated by ATP sulfurylase, forming APS, which can be phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Depending on the organism, either APS or PAPS can be used for sulfate reduction. Prokaryotes and fungi use PAPS, whereas plants use both APS and PAPS. Since plant-type APS reductase uses glutathione (GSH) as its electron donor, the C-terminal domain may function like glutaredoxin, a GSH-dependent member of the TRX superfamily. The flow of reducing equivalents goes from GSH - C-terminal TRX domain - N-terminal reductase domain - APS. Plant-type APS red

>cd02957 Phd_like Phosducin (Phd)-like family; composed of Phd and Phd-like proteins (PhLP), characterized as cytosolic regulators of G protein functions

Probab=86.80  E-value=2.6  Score=31.42  Aligned_cols=41  Identities=17%  Similarity=0.429  Sum_probs=33.2

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCC
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGM   64 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~   64 (248)
                      +..|..+|++..   .+++.|++.++|++.++-  +|..+.++.|.
T Consensus        55 ~v~f~~vd~~~~---~l~~~~~i~~~Pt~~~f~--~G~~v~~~~G~   95 (113)
T cd02957          55 ETKFVKINAEKA---FLVNYLDIKVLPTLLVYK--NGELIDNIVGF   95 (113)
T ss_pred             CcEEEEEEchhh---HHHHhcCCCcCCEEEEEE--CCEEEEEEecH
Confidence            456777777644   889999999999998884  58999999884

Phd and PhLPs specifically bind G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane and impeding G protein-mediated signal transduction by inhibiting the formation of a functional G protein trimer (G protein alphabetagamma). Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-te

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=86.41  E-value=3.3  Score=28.83  Aligned_cols=55  Identities=18%  Similarity=0.095  Sum_probs=37.3

Q ss_pred             CCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          188 LRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       188 ~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ..+.||.+|...+......++....+|.-.+..+.  +  ..+.||.+.|+. +++|.|+
T Consensus        20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~--L--~d~~tL~~~gv~~g~~lyvK   75 (77)
T cd01801          20 SGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKS--L--KDDDTLVDLGVGAGATLYVR   75 (77)
T ss_pred             CCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcc--c--CCcccHhhcCCCCCCEEEEe
Confidence            45679999999997764333456666765555543  5  346789999997 4555553

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.

>cd02996 PDI_a_ERp44 PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident protein, induced during stress, involved in thiol-mediated ER retention

Probab=86.00  E-value=2.7  Score=30.78  Aligned_cols=50  Identities=20%  Similarity=0.380  Sum_probs=38.1

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCc-eEEeeeCCCChHHHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQ-KMRSWCGMVQPESLLE   72 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~-~l~~~~G~~~~e~l~~   72 (248)
                      ++.+...|.+..  ..++..|++.+||++.++-  +|. ......|..+.++++.
T Consensus        56 ~~~~~~vd~d~~--~~l~~~~~v~~~Ptl~~~~--~g~~~~~~~~g~~~~~~l~~  106 (108)
T cd02996          56 KVVWGKVDCDKE--SDIADRYRINKYPTLKLFR--NGMMMKREYRGQRSVEALAE  106 (108)
T ss_pred             cEEEEEEECCCC--HHHHHhCCCCcCCEEEEEe--CCcCcceecCCCCCHHHHHh
Confidence            467777888754  3588999999999998883  476 4466888888887754

It contains an N-terminal TRX domain, similar to that of PDIa, with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. The CXFS motif in the N-terminal domain allows ERp44 to form stable reversible mixed disulfides with its substrates. Through this activity, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. It also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol.

>PTZ00443 Thioredoxin domain-containing protein; Provisional

Probab=85.91  E-value=5.5  Score=33.92  Aligned_cols=59  Identities=12%  Similarity=0.120  Sum_probs=43.0

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ...+.+...|.+.  ...++..|++..||++.++.  +|..+....|..+.+++..-+.+-+.
T Consensus        82 ~~~v~~~~VD~~~--~~~l~~~~~I~~~PTl~~f~--~G~~v~~~~G~~s~e~L~~fi~~~~~  140 (224)
T PTZ00443         82 KGQVNVADLDATR--ALNLAKRFAIKGYPTLLLFD--KGKMYQYEGGDRSTEKLAAFALGDFK  140 (224)
T ss_pred             CCCeEEEEecCcc--cHHHHHHcCCCcCCEEEEEE--CCEEEEeeCCCCCHHHHHHHHHHHHH
Confidence            3445565566653  35688999999999999986  58877778888888888665555543

>COG5100 NPL4 Nuclear pore protein [Nuclear structure]

Probab=84.83  E-value=3.8  Score=37.75  Aligned_cols=74  Identities=16%  Similarity=0.230  Sum_probs=52.5

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhc-CCCCCcCeEEEccCCCCc-cccCCCcCCCccccCCc-CceEEEEe
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQL-EGSEMKPFRLTHAIPGAT-KSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~-~~~~~~~f~L~~~~Pr~~-~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      -++||-++|.+ .-.|..+|.+..|..-+...+ .++++.+|.+.++ |... -.+....++|+.|+||. +.++.+.+
T Consensus         2 i~rfRsk~G~~-Rve~qe~d~lg~l~~kll~~~~~n~~~e~~svc~~-p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~y   78 (571)
T COG5100           2 IFRFRSKEGQR-RVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSA-PDGQGEIFSLLKDQTPDDLGLRHGQMLYLEY   78 (571)
T ss_pred             eEEEecCCCce-eeeccccchhhhhhHHHHhhhccCCCccceEEEeC-CCCCceeeecccccChhhhccccCcEEEEEe
Confidence            37899999974 457889999987766555543 3677899999886 4322 12223578999999998 55566654

>TIGR02187 GlrX_arch Glutaredoxin-like domain protein

Probab=84.75  E-value=3.7  Score=34.42  Aligned_cols=56  Identities=14%  Similarity=0.239  Sum_probs=43.8

Q ss_pred             EEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceE-EeeeCCCChHHHHHHHhhhhh
Q 025774           22 FWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKM-RSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        22 ~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l-~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +-..+++..+...++..|++..+|+++++.  +|..+ .++.|..+.+++...|...+.
T Consensus        56 i~~v~vd~~~~~~l~~~~~V~~~Pt~~~f~--~g~~~~~~~~G~~~~~~l~~~i~~~~~  112 (215)
T TIGR02187        56 LEIYDFDTPEDKEEAEKYGVERVPTTIILE--EGKDGGIRYTGIPAGYEFAALIEDIVR  112 (215)
T ss_pred             EEEEecCCcccHHHHHHcCCCccCEEEEEe--CCeeeEEEEeecCCHHHHHHHHHHHHH
Confidence            445666666788999999999999999985  47776 489998888887666665543

This family of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different.

>PLN02560 enoyl-CoA reductase

Probab=84.57  E-value=6.7  Score=35.09  Aligned_cols=72  Identities=19%  Similarity=0.162  Sum_probs=48.7

Q ss_pred             EEEEEcCCCceE---EEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEcc----CCCCccccCCCcCCCccccCCc-CceE
Q 025774          172 RVGVRLPDGRRM---QRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHA----IPGATKSLDYDSKLTFEDSGLA-NAMI  243 (248)
Q Consensus       172 ~i~iRlp~G~r~---~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~----~Pr~~~~l~~d~~~tl~d~gl~-~~~v  243 (248)
                      +|.|+..+|+.+   .-....+.||.+|..-+........+..-+|...    =|+.. .+  ++++||+|.|+. .++|
T Consensus         2 ~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~-~L--~d~ktL~d~gv~~gstL   78 (308)
T PLN02560          2 KVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPT-VL--DDSKSLKDYGLGDGGTV   78 (308)
T ss_pred             EEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCcc-cc--CCCCCHHhcCCCCCceE
Confidence            467787889876   4577889999999999987633224556666532    12221 23  567899999997 4556


Q ss_pred             EEE
Q 025774          244 SVT  246 (248)
Q Consensus       244 ~v~  246 (248)
                      .|+
T Consensus        79 y~k   81 (308)
T PLN02560         79 VFK   81 (308)
T ss_pred             EEE
Confidence            554

>cd03017 PRX_BCP Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides

Probab=84.18  E-value=3  Score=31.80  Aligned_cols=38  Identities=18%  Similarity=0.349  Sum_probs=29.5

Q ss_pred             HHHHhcCCCCC---------ceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           34 KVCTYYKLDSI---------PVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        34 ~~~~~~~~~~~---------P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      .++..|++..+         |+..||++ +|.++..+.|..+...+-+
T Consensus        91 ~~~~~~gv~~~~~~~~~~~~p~~~lid~-~G~v~~~~~g~~~~~~~~~  137 (140)
T cd03017          91 KLAKAYGVWGEKKKKYMGIERSTFLIDP-DGKIVKVWRKVKPKGHAEE  137 (140)
T ss_pred             HHHHHhCCccccccccCCcceeEEEECC-CCEEEEEEecCCccchHHH
Confidence            57778888777         89999985 5899999999886555533

The protein was named BCP based on its electrophoretic mobility before its function was known. BCP shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides. BCP contains the peroxidatic cysteine but appears not to possess a resolving cysteine (some sequences, not all, contain a second cysteine but its role is still unknown). Unlike other PRXs, BCP exists as a monomer. The plant homolog of BCP is PRX Q, which is expressed only in leaves and is cellularly localized in the chloroplasts and the guard cells of stomata. Also included in this subfamily is the fungal nuclear protein, Dot5p (for disrupter of telomere silencing protein 5), w

>smart00295 B41 Band 4

Probab=84.07  E-value=9.1  Score=31.18  Aligned_cols=70  Identities=20%  Similarity=0.121  Sum_probs=48.7

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA  239 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~  239 (248)
                      ...|+|.||||+...-++..+.++++|.+-|...+.-....-|.|...-+........+...+|.+..-.
T Consensus         3 ~~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~   72 (207)
T smart00295        3 PRVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVK   72 (207)
T ss_pred             cEEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHHhcCC
Confidence            3679999999999999999999999999999888643335667776532222110112456677766643

1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.

>cd03001 PDI_a_P5 PDIa family, P5 subfamily; composed of eukaryotic proteins similar to human P5, a PDI-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain)

Probab=83.71  E-value=8.6  Score=27.41  Aligned_cols=52  Identities=12%  Similarity=0.149  Sum_probs=37.1

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      ..+.+...|.+.  ...++..|++..+|.+.++.+. ......+.|..+.++++.
T Consensus        49 ~~~~~~~id~~~--~~~~~~~~~i~~~P~~~~~~~~-~~~~~~~~g~~~~~~l~~  100 (103)
T cd03001          49 GIVKVGAVDADV--HQSLAQQYGVRGFPTIKVFGAG-KNSPQDYQGGRTAKAIVS  100 (103)
T ss_pred             CCceEEEEECcc--hHHHHHHCCCCccCEEEEECCC-CcceeecCCCCCHHHHHH
Confidence            355666666653  4467889999999999998642 235666888888887754

Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. Some members of this subfamily are P5-like proteins containing only one redox active TRX domain.

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=83.20  E-value=3.8  Score=30.42  Aligned_cols=56  Identities=13%  Similarity=0.010  Sum_probs=41.2

Q ss_pred             eeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEEe
Q 025774          186 NFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTW  247 (248)
Q Consensus       186 ~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~~  247 (248)
                      .-+.++||.+|-.-|..++ +..+..-.|...  ..  .| .|.+.||.+.|+.+.+++.-|
T Consensus        20 ~V~~~~TVg~LK~lImQ~f-~V~P~dQkL~~d--G~--~L-~DDsrTLssyGv~sgSvl~Ll   75 (107)
T cd01795          20 LVSANQTLKELKIQIMHAF-SVAPFDQNLSID--GK--IL-SDDCATLGTLGVIPESVILLK   75 (107)
T ss_pred             EeCccccHHHHHHHHHHHh-cCCcccceeeec--Cc--ee-ccCCccHHhcCCCCCCEEEEE
Confidence            3678999999999887765 434555578776  43  37 488999999999976665433

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,

>KOG0907 consensus Thioredoxin [Posttranslational modification, protein turnover, chaperones]

Probab=82.90  E-value=5.7  Score=29.69  Aligned_cols=51  Identities=14%  Similarity=0.287  Sum_probs=41.5

Q ss_pred             HHHHHhhc--ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC
Q 025774           11 AVSQTIST--NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV   65 (248)
Q Consensus        11 ~v~~~l~~--~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~   65 (248)
                      -+.++-.+  +-+|+..|++.  ...+++.|++...|++.++  +.|+.+..+.|..
T Consensus        42 ~~~~La~~y~~v~Flkvdvde--~~~~~~~~~V~~~PTf~f~--k~g~~~~~~vGa~   94 (106)
T KOG0907|consen   42 KFEKLAEKYPDVVFLKVDVDE--LEEVAKEFNVKAMPTFVFY--KGGEEVDEVVGAN   94 (106)
T ss_pred             HHHHHHHHCCCCEEEEEeccc--CHhHHHhcCceEeeEEEEE--ECCEEEEEEecCC
Confidence            34444443  58999999987  8999999999999999999  5689888888854

>PTZ00051 thioredoxin; Provisional

Probab=82.87  E-value=4.7  Score=28.65  Aligned_cols=47  Identities=26%  Similarity=0.352  Sum_probs=35.6

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESL   70 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l   70 (248)
                      ++.|...|.+  +...++..|++..+|++.++  .+|..+.++.|. .++++
T Consensus        49 ~~~~~~vd~~--~~~~~~~~~~v~~~Pt~~~~--~~g~~~~~~~G~-~~~~~   95 (98)
T PTZ00051         49 KMVFVKVDVD--ELSEVAEKENITSMPTFKVF--KNGSVVDTLLGA-NDEAL   95 (98)
T ss_pred             CcEEEEEECc--chHHHHHHCCCceeeEEEEE--eCCeEEEEEeCC-CHHHh
Confidence            4677777765  45678899999999998776  468999999995 44443

>cd02975 PfPDO_like_N Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI), which are both involved in oxidative protein folding

Probab=82.41  E-value=9  Score=28.61  Aligned_cols=57  Identities=12%  Similarity=0.186  Sum_probs=39.9

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEE--eeeCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMR--SWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~--~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .+-+...|++.  ...++..|++.+.|++++...  |....  ++.|..+.++|.+.|...+.
T Consensus        53 ~i~~~~vd~d~--~~~l~~~~~v~~vPt~~i~~~--g~~~~~~~~~G~~~~~el~~~i~~i~~  111 (113)
T cd02975          53 KLKLEIYDFDE--DKEKAEKYGVERVPTTIFLQD--GGKDGGIRYYGLPAGYEFASLIEDIVR  111 (113)
T ss_pred             ceEEEEEeCCc--CHHHHHHcCCCcCCEEEEEeC--CeecceEEEEecCchHHHHHHHHHHHh
Confidence            34566677753  457889999999999999863  32211  58898888887776665543

PfPDO contains two redox active CXXC motifs in two contiguous TRX-fold subdomains. The active site in the N-terminal TRX-fold subdomain is required for isomerase but not for reductase activity of PfPDO. The exclusive presence of PfPDO-like proteins in extremophiles may suggest that they have a special role in adaptation to extreme conditions.

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

Probab=82.38  E-value=15  Score=26.02  Aligned_cols=73  Identities=18%  Similarity=0.167  Sum_probs=50.7

Q ss_pred             eEEEEEcC-CCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCC-cc--ccCCCcCCCccccCCc-CceEEE
Q 025774          171 CRVGVRLP-DGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGA-TK--SLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       171 ~~i~iRlp-~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~-~~--~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ++|.|.-+ ++...+|||..+.||+.|-.=+... .|.++..-+|.- |..+ ..  .+ ++.+++|...|+. +..|+|
T Consensus         2 v~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~-~G~~~~~mrL~l-~~~~~~~~~~l-~~d~~~L~~y~~~dg~~IhV   78 (84)
T cd01789           2 VTVNITSSADSFSFEKKYSRGLTIAELKKKLELV-VGTPASSMRLQL-FDGDDKLVSKL-DDDDALLGSYPVDDGCRIHV   78 (84)
T ss_pred             EEEEEEeCCCceeeeEecCCCCcHHHHHHHHHHH-HCCCccceEEEE-EcCCCCeEeec-CCCccEeeeccCCCCCEEEE
Confidence            34556654 3557899999999999999988765 466677777742 2222 11  13 4778999999998 555665


Q ss_pred             E
Q 025774          246 T  246 (248)
Q Consensus       246 ~  246 (248)
                      .
T Consensus        79 v   79 (84)
T cd01789          79 I   79 (84)
T ss_pred             E
Confidence            3

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.

>cd03008 TryX_like_RdCVF Tryparedoxin (TryX)-like family, Rod-derived cone viability factor (RdCVF) subfamily; RdCVF is a thioredoxin (TRX)-like protein specifically expressed in photoreceptors

Probab=81.25  E-value=4.2  Score=32.25  Aligned_cols=49  Identities=12%  Similarity=0.252  Sum_probs=30.9

Q ss_pred             HHHHHhhcceEEEEE-ecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEe
Q 025774           11 AVSQTISTNFIFWQV-YDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS   60 (248)
Q Consensus        11 ~v~~~l~~~fV~w~~-d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~   60 (248)
                      .+.+|+...=+.|.. ......+..++..|++..+|+++||++. |.++.+
T Consensus        79 ~~~~f~~~~~~~~~~~p~~~~~~~~l~~~y~v~~iPt~vlId~~-G~Vv~~  128 (146)
T cd03008          79 QQESFLKDMPKKWLFLPFEDEFRRELEAQFSVEELPTVVVLKPD-GDVLAA  128 (146)
T ss_pred             HHHHHHHHCCCCceeecccchHHHHHHHHcCCCCCCEEEEECCC-CcEEee
Confidence            355666654222211 1222234478889999999999999975 887654

RdCVF was isolated and identified as a factor that supports cone survival in retinal cultures. Cone photoreceptor loss is responsible for the visual handicap resulting from the inherited disease, retinitis pigmentosa. RdCVF shows 33% similarity to TRX but does not exhibit any detectable thiol oxidoreductase activity.

>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=80.98  E-value=4.2  Score=27.67  Aligned_cols=59  Identities=20%  Similarity=0.287  Sum_probs=37.0

Q ss_pred             cCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCce
Q 025774          177 LPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAM  242 (248)
Q Consensus       177 lp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~  242 (248)
                      .++|.|..-+...+.+|.+|.+=+-.+. +.++..|.|...  ++  .+  |.+.++.=+||.|.+
T Consensus         3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~-~l~~~~~~L~h~--~k--~l--dlslp~R~snL~n~a   61 (65)
T PF11470_consen    3 CYNFRRFKVKVTPNTTLNQVLEEACKKF-GLDPSSYDLKHN--NK--PL--DLSLPFRLSNLPNNA   61 (65)
T ss_dssp             -TTS-EEEE---TTSBHHHHHHHHHHHT-T--GGG-EEEET--TE--EE--SSS-BHHHH---SS-
T ss_pred             ccCCcEEEEEECCCCCHHHHHHHHHHHc-CCCccceEEEEC--CE--Ee--ccccceeecCCCCCC
Confidence            4789999999999999999998876654 556779999886  33  25  889999999998654

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.

>cd02987 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions

Probab=80.95  E-value=5.2  Score=32.63  Aligned_cols=42  Identities=14%  Similarity=0.367  Sum_probs=34.7

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV   65 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~   65 (248)
                      ++.|..+|++..   .++..|++...|+++|+-  +|..+.++.|..
T Consensus       114 ~vkF~kVd~d~~---~l~~~f~v~~vPTlllyk--~G~~v~~~vG~~  155 (175)
T cd02987         114 AVKFCKIRASAT---GASDEFDTDALPALLVYK--GGELIGNFVRVT  155 (175)
T ss_pred             CeEEEEEeccch---hhHHhCCCCCCCEEEEEE--CCEEEEEEechH
Confidence            578888888753   789999999999999884  599998888853

It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.

>cd02995 PDI_a_PDI_a'_C PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1

Probab=80.81  E-value=8.2  Score=27.45  Aligned_cols=49  Identities=18%  Similarity=0.324  Sum_probs=36.7

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCc--eEEeeeCCCChHHHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQ--KMRSWCGMVQPESLLE   72 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~--~l~~~~G~~~~e~l~~   72 (248)
                      ++.+...|.+..   .++..+++..+|.+.++.+  |.  ......|..+.++|+.
T Consensus        52 ~~~~~~id~~~~---~~~~~~~~~~~Pt~~~~~~--~~~~~~~~~~g~~~~~~l~~  102 (104)
T cd02995          52 NVVIAKMDATAN---DVPSEFVVDGFPTILFFPA--GDKSNPIKYEGDRTLEDLIK  102 (104)
T ss_pred             CEEEEEEeCcch---hhhhhccCCCCCEEEEEcC--CCcCCceEccCCcCHHHHHh
Confidence            588888888764   3667788899999999853  43  4566888888777654

PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. PDI and ERp57 have the abb'a' domain structure (where a and a' are redox active TRX domains while b and b' are redox inactive TRX-like domains). PDI also contains an acidic region (c domain) after the a' domain that is absent in ERp57. ERp72 has an additional a domain at the N-terminus (a"abb'a' domain structure). ERp57 interacts with the lectin chaperones, calnexin and calreticu

>cd02989 Phd_like_TxnDC9 Phosducin (Phd)-like family, Thioredoxin (TRX) domain containing protein 9 (TxnDC9) subfamily; composed of predominantly uncharacterized eukaryotic proteins, containing a TRX-like domain without the redox active CXXC motif

Probab=80.59  E-value=7  Score=29.23  Aligned_cols=42  Identities=14%  Similarity=0.342  Sum_probs=33.6

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCC
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGM   64 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~   64 (248)
                      +..|+..|++..  ..+++.|++...|+++++.  +|..+.++.|.
T Consensus        53 ~i~f~~Vd~~~~--~~l~~~~~v~~vPt~l~fk--~G~~v~~~~g~   94 (113)
T cd02989          53 ETKFIKVNAEKA--PFLVEKLNIKVLPTVILFK--NGKTVDRIVGF   94 (113)
T ss_pred             CCEEEEEEcccC--HHHHHHCCCccCCEEEEEE--CCEEEEEEECc
Confidence            467777777553  3688999999999998884  68999888885

The gene name for the human protein is TxnDC9. The two characterized members are described as Phd-like proteins, PLP1 of Saccharomyces cerevisiae and PhLP3 of Dictyostelium discoideum. Gene disruption experiments show that both PLP1 and PhLP3 are non-essential proteins. Unlike Phd and most Phd-like proteins, members of this group do not contain the Phd N-terminal helical domain which is implicated in binding to the G protein betagamma subunit.

>cd02983 P5_C P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain)

Probab=80.46  E-value=11  Score=29.11  Aligned_cols=62  Identities=10%  Similarity=0.090  Sum_probs=41.7

Q ss_pred             hcc-eEEEEEecCChHHHHHHHhcCCC--CCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           17 STN-FIFWQVYDDTSEGKKVCTYYKLD--SIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        17 ~~~-fV~w~~d~~~~eg~~~~~~~~~~--~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      +.. +.|--.|.+....  +...+++.  .||.++++.+.++ .-....|.++.+.+..-+..+++..
T Consensus        54 kgk~i~Fv~vd~~~~~~--~~~~fgl~~~~~P~v~i~~~~~~-KY~~~~~~~t~e~i~~Fv~~~l~Gk  118 (130)
T cd02983          54 KKKPWGWLWTEAGAQLD--LEEALNIGGFGYPAMVAINFRKM-KFATLKGSFSEDGINEFLRELSYGR  118 (130)
T ss_pred             cCCcEEEEEEeCcccHH--HHHHcCCCccCCCEEEEEecccC-ccccccCccCHHHHHHHHHHHHcCC
Confidence            345 4544445544433  88889984  5999999998654 3222778889988877777776653

Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. The C-terminal domain is likely involved in substrate binding, similar to the b and b' domains of PDI.

>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]

Probab=80.38  E-value=2.2  Score=21.43  Aligned_cols=16  Identities=44%  Similarity=0.551  Sum_probs=13.6

Q ss_pred             chHHHHHHHHHHhhHh
Q 025774          111 IENEELLQALAASMET  126 (248)
Q Consensus       111 ~eeee~~~A~~~sl~~  126 (248)
                      .+|+++++|++.|++.
T Consensus         2 ~Ed~~L~~Al~~S~~e   17 (18)
T PF02809_consen    2 DEDEDLQRALEMSLEE   17 (18)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHhhhcc
Confidence            5788899999999874

In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains []. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (IPR015940 from INTERPRO), UBX (IPR001012 from INTERPRO), ENTH, EH (IPR000261 from INTERPRO), VHS (IPR002014 from INTERPRO), SH3 (IPR001452 from INTERPRO), HECT (IPR000569 from INTERPRO), VWFA (IPR002035 from INTERPRO), EF-hand calcium-binding, WD-40 (IPR001680 from INTERPRO), F-box (IPR001810 from INTERPRO), LIM (IPR001781 from INTERPRO), protein kinase (IPR000719 from INTERPRO), ankyrin (IPR002110 from INTERPRO), PX (IPR001683 from INTERPRO), phosphatidylinositol 3- and 4-kinase (IPR000403 from INTERPRO), C2 (IPR000008 from INTERPRO), OTU (IPR003323 from INTERPRO), dnaJ (IPR001623 from INTERPRO), RING-finger (IPR001841 from INTERPRO) or FYVE-finger (IPR017455 from INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [, , ]. The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds []. Some proteins known to contain an UIM are listed below: Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome. Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD). Vertebrate epsin and epsin2. Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation. Mammalian epidermal growth factor receptor substrate EPS15R. Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin. Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole. ; PDB: 2KDE_A 2KDF_A 1YX6_A 1YX5_A 1YX4_A 1P9C_A 1UEL_B 1P9D_S 2KLZ_A.

>TIGR01295 PedC_BrcD bacteriocin transport accessory protein, putative

Probab=80.23  E-value=16  Score=27.77  Aligned_cols=61  Identities=10%  Similarity=0.293  Sum_probs=40.3

Q ss_pred             CHHHHHHhhc-ceEEEEEecCCh---------HHHHHHHhcCCC----CCceEEEEeCCCCceEEeeeCC-CChHHHH
Q 025774            9 NEAVSQTIST-NFIFWQVYDDTS---------EGKKVCTYYKLD----SIPVVLVVDPITGQKMRSWCGM-VQPESLL   71 (248)
Q Consensus         9 ~~~v~~~l~~-~fV~w~~d~~~~---------eg~~~~~~~~~~----~~P~l~ii~~~~g~~l~~~~G~-~~~e~l~   71 (248)
                      .|.+.++.++ +.-++..|++..         +-..+...|++.    ..|+++++  .+|..+.++.|. .+.++|.
T Consensus        42 ~P~l~~~~~~~~~~~y~vdvd~~~~~~~~~~~~~~~~~~~~~i~~~i~~~PT~v~~--k~Gk~v~~~~G~~~~~~~l~  117 (122)
T TIGR01295        42 SGTLSGVVAQTKAPIYYIDSENNGSFEMSSLNDLTAFRSRFGIPTSFMGTPTFVHI--TDGKQVSVRCGSSTTAQELQ  117 (122)
T ss_pred             hHHHHHHHHhcCCcEEEEECCCccCcCcccHHHHHHHHHHcCCcccCCCCCEEEEE--eCCeEEEEEeCCCCCHHHHH
Confidence            3456666665 344666666532         344566776654    49999988  469999999994 4566663

This model describes a small family of proteins believed to aid in the export of various class II bacteriocins, which are ribosomally-synthesized, non-lantibiotic bacterial peptide antibiotics. Members of this family are found in operons for pediocin PA-1 from Pediococcus acidilactici and brochocin-C from Brochothrix campestris.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	248
2dlx_A	153	Solution Structure Of The Uas Domain Of Human Ubx D		3e-15

>pdb|2DLX|A Chain A, Solution Structure Of The Uas Domain Of Human Ubx Domain- Containing Protein 7 Length = 153

Iteration: 1
 Score = 78.6 bits (192), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 35/77 (45%), Positives = 48/77 (62%), Gaps = 1/77 (1%)
Query: 2   LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSW 61
           LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  W
Sbjct: 60  LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEW 119
Query: 62  CGMVQPESLLEDLVPFM 78
              +   S L+ +  F+
Sbjct: 120 -HQLDVSSFLDQVTGFL 135

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	248
2dlx_A	153	UBX domain-containing protein 7; UAS domain, prote	8e-28
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	2e-17
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	1e-13
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	3e-10
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	1e-09
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	3e-08

>2dlx_A UBX domain-containing protein 7; UAS domain, protein KIAA0794, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: c.47.1.24 Length = 153

 Score =  103 bits (257), Expect = 8e-28
 Identities = 35/79 (44%), Positives = 48/79 (60%), Gaps = 1/79 (1%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
            LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  
Sbjct: 59  CLNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVE 118

Query: 61  WCGMVQPESLLEDLVPFMD 79
           W  +    S L+ +  F+ 
Sbjct: 119 WHQL-DVSSFLDQVTGFLG 136

>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 = 74.4 bits (183), Expect = 2e-17
 Identities = 24/93 (25%), Positives = 43/93 (46%), Gaps = 4/93 (4%)

Query: 148 ASATEKPAYPILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGS 207
            S+      P LPEEP      +  V +R P+GR ++R F ++   Q+L  +      G 
Sbjct: 1   GSSGSSGEVPDLPEEPSETAEEVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV--GY 58

Query: 208 EMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN 240
               +RL+ + P   ++L+ +   + ED G+  
Sbjct: 59  HKSLYRLSTSFPR--RALEVEGGSSLEDIGITV 89

>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 = 65.0 bits (158), Expect = 1e-13
 Identities = 19/102 (18%), Positives = 35/102 (34%), Gaps = 4/102 (3%)

Query: 147 EASATEKPAYPILPEEPKVDRSL-LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLE 205
            + A +            ++ +     + +RL DG R+ + F  +  I  +  +      
Sbjct: 28  SSPAQQAENEAKASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARP 87

Query: 206 GSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTW 247
                 F L    P   K L  D   T +++ L NA+I    
Sbjct: 88  AMAATSFVLMTTFPN--KELA-DENQTLKEANLLNAVIVQRL 126

>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 = 55.7 bits (134), Expect = 3e-10
 Identities = 19/107 (17%), Positives = 35/107 (32%), Gaps = 12/107 (11%)

Query: 141 ASTDKDEASATEKPAYPILPEEPK-------VDRSLLCRVGVRLPDGRRMQRNFLRTDPI 193
            +    +           +P E                ++ +R PDG+R Q        +
Sbjct: 7   GTATNHQGLPAVDSEILEMPPEKADGVVEGIDVNGPKAQLMLRYPDGKREQITLPEQAKL 66

Query: 194 QLLWSYCYSQLEGSEMKPFRLTHAIPGATKSL-DYDSKLTFEDSGLA 239
             L  +  S  +G   + F L    P   + L   D  +T +++GL 
Sbjct: 67  LALVKHVQS--KGYPNERFELLTNFP--RRKLSHLDYDITLQEAGLC 109

>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 = 53.0 bits (128), Expect = 1e-09
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSL-DYDS 229
            ++ +R P G  ++R FL ++ +Q+++ +  S  +G     ++L    P   + +   D 
Sbjct: 8   SKLRIRTPSGEFLERRFLASNKLQIVFDFVAS--KGFPWDEYKLLSTFP--RRDVTQLDP 63

Query: 230 KLTFEDSGLA 239
             +  +  L 
Sbjct: 64  NKSLLEVKLF 73

>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 = 49.9 bits (119), Expect = 3e-08
 Identities = 21/101 (20%), Positives = 35/101 (34%), Gaps = 13/101 (12%)

Query: 148 ASATEKPAYPILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGS 207
            S+               DRS + R+  RLPDG      F    P++    +  +Q  G+
Sbjct: 1   GSSGSSGR----------DRSTIARIQFRLPDGSSFTNQFPSDAPLEEARQFA-AQTVGN 49

Query: 208 EMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW 247
               F L    P    + +   +    D  LA +A + +  
Sbjct: 50  TYGNFSLATMFPRREFTREDYKR-RLLDLELAPSASVVLLP 89

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	248
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	99.9
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	99.84
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	99.84
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	99.83
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	99.8
2ec4_A	178	FAS-associated factor 1; UAS domain, protein FAF1,	99.72
2dlx_A	153	UBX domain-containing protein 7; UAS domain, prote	99.49
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	98.68
2lst_A	130	Thioredoxin; structural genomics, NEW YORK structu	97.05
2kuc_A	130	Putative disulphide-isomerase; structural genomics	97.7
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	97.58
2pjh_A	80	Protein NPL4, nuclear protein localization protein	97.56
2ju5_A	154	Thioredoxin disulfide isomerase; protein, oxidored	97.52
3f9u_A	172	Putative exported cytochrome C biogenesis-related;	97.39
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	97.39
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	97.35
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	97.31
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	97.28
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	97.27
2fwh_A	134	Thiol:disulfide interchange protein DSBD; thioredo	97.24
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	97.19
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	97.17
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	97.17
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	97.14
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	97.12
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	97.12
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	97.08
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	97.07
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	97.06
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	97.05
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	97.04
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	97.03
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	97.01
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	96.96
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	96.92
2l57_A	126	Uncharacterized protein; structural genomics, unkn	96.91
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	96.78
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	96.77
3gnj_A	111	Thioredoxin domain protein; APC92103, STR genomics	96.77
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	96.75
1thx_A	115	Thioredoxin, thioredoxin 2; oxido-reductase, elect	96.71
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	96.7
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	96.69
2i4a_A	107	Thioredoxin; acidophIle, disulfide exchange, oxido	96.66
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	96.65
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	96.64
1we6_A	111	Splicing factor, putative; structural genomics, ub	96.62
2qsi_A	137	Putative hydrogenase expression/formation protein;	96.61
3tco_A	109	Thioredoxin (TRXA-1); disulfide oxidoreductase, ox	96.59
2trx_A	108	Thioredoxin; electron transport; 1.68A {Escherichi	96.59
2voc_A	112	Thioredoxin; electron transport, homodimer, disulf	96.57
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	96.57
2yzu_A	109	Thioredoxin; redox protein, electron transport, st	96.56
1nsw_A	105	Thioredoxin, TRX; thermostability, electron transp	96.55
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	96.55
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	96.55
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	96.53
1w4v_A	119	Thioredoxin, mitochondrial; antioxidant enzyme, mi	96.53
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	96.52
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	96.52
1oaz_A	123	Thioredoxin 1; immune system, antibody/complex, an	96.51
3fk8_A	133	Disulphide isomerase; APC61824.1, xylella fastidio	96.5
3ul3_B	128	Thioredoxin, thioredoxin-2; PTEX, oxidoreductase;	96.5
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	96.49
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	96.49
1dby_A	107	Chloroplast thioredoxin M CH2; thioredoxin CH2, ch	96.48
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	96.45
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	96.44
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	96.43
4euy_A	105	Uncharacterized protein; structural genomics, PSI-	96.41
1t00_A	112	Thioredoxin, TRX; redox regulation, multifunction	96.38
1v98_A	140	Thioredoxin; oxidoreductase, structural genomics,	96.38
3p2a_A	148	Thioredoxin 2, putative thioredoxin-like protein;	96.37
3ira_A	173	Conserved protein; methanosarcina mazei,structural	96.34
2o8v_B	128	Thioredoxin 1; disulfide crosslinked complex, oxid	96.33
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	96.29
1fb6_A	105	Thioredoxin M; electron transport; 2.10A {Spinacia	96.29
3die_A	106	Thioredoxin, TRX; electron transport, SWAP domain,	96.29
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	96.26
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	96.26
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	96.25
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	96.25
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	96.24
3hxs_A	141	Thioredoxin, TRXP; electron transport; 2.00A {Bact	96.23
2qgv_A	140	Hydrogenase-1 operon protein HYAE; alpha-beta prot	96.2
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	96.18
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	96.17
2e0q_A	104	Thioredoxin; electron transport; 1.49A {Sulfolobus	96.15
3hz4_A	140	Thioredoxin; NYSGXRC, PSI-II, reduced form, protei	96.14
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	96.09
2ppt_A	155	Thioredoxin-2; thiredoxin, zinc finger, oxidoreduc	96.08
3ph9_A	151	Anterior gradient protein 3 homolog; thioredoxin f	96.07
2l5l_A	136	Thioredoxin; structural genomics, electron transpo	96.06
1x5d_A	133	Protein disulfide-isomerase A6; PDIA6, ERP5, TXNDC	96.05
2b5x_A	148	YKUV protein, TRXY; thioredoxin-like, oxidoreducta	96.05
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	96.03
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	96.01
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	95.98
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	95.94
2es7_A	142	Q8ZP25_salty, putative thiol-disulfide isomerase a	95.93
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	95.92
3eyt_A	158	Uncharacterized protein SPOA0173; thioredoxin-like	95.92
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	95.91
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	95.9
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	95.88
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	95.85
3qfa_C	116	Thioredoxin; protein-protein complex, rossmann fol	95.84
3raz_A	151	Thioredoxin-related protein; structural genomics,	95.84
3dml_A	116	Putative uncharacterized protein; thioredoxin, oxi	95.83
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	95.83
2dml_A	130	Protein disulfide-isomerase A6; thioredoxin domain	95.82
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	95.8
1ep7_A	112	Thioredoxin CH1, H-type; electron transport; 2.10A	95.8
1xwb_A	106	Thioredoxin; dimerization, redox regulation, THI X	95.78
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	95.77
2i1u_A	121	Thioredoxin, TRX, MPT46; redox protein, electron t	95.76
2f9s_A	151	Thiol-disulfide oxidoreductase RESA; thioredoxin-l	95.72
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	95.72
3zzx_A	105	Thioredoxin; oxidoreductase; 1.88A {Litopenaeus va	95.7
1lu4_A	136	Soluble secreted antigen MPT53; thioredoxin-like f	95.65
2dj1_A	140	Protein disulfide-isomerase A4; protein ERP-72, ER	95.65
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	95.65
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	95.65
3ia1_A	154	THIO-disulfide isomerase/thioredoxin; oxidoreducta	95.63
1zzo_A	136	RV1677; thioredoxin fold, structural genomics, PSI	95.57
2ggt_A	164	SCO1 protein homolog, mitochondrial; copper chaper	95.56
2lja_A	152	Putative thiol-disulfide oxidoreductase; structura	95.54
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	95.53
1r26_A	125	Thioredoxin; redox-active disulfide, electron tran	95.5
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	95.5
2l6c_A	110	Thioredoxin; oxidoreductase; NMR {Desulfovibrio vu	95.49
2h30_A	164	Thioredoxin, peptide methionine sulfoxide reductas	95.49
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	95.49
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	95.48
1syr_A	112	Thioredoxin; SGPP, structural genomics, PSI, prote	95.47
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	95.47
3uvt_A	111	Thioredoxin domain-containing protein 5; thioredox	95.45
1xfl_A	124	Thioredoxin H1; AT3G51030, structural genomics, pr	95.42
3m9j_A	105	Thioredoxin; oxidoreductase; 1.10A {Homo sapiens}	95.42
3emx_A	135	Thioredoxin; structural genomics, oxidoreductase,	95.41
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	95.41
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	95.37
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	95.36
3apq_A	210	DNAJ homolog subfamily C member 10; thioredoxin fo	95.35
3d6i_A	112	Monothiol glutaredoxin-3; thioredoxin-like, electr	95.35
3erw_A	145	Sporulation thiol-disulfide oxidoreductase A; thio	95.34
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	95.33
2l5o_A	153	Putative thioredoxin; structural genomics, unknown	95.32
3kh7_A	176	Thiol:disulfide interchange protein DSBE; TRX-like	95.32
4evm_A	138	Thioredoxin family protein; structural genomics, n	95.27
1x5e_A	126	Thioredoxin domain containing protein 1; TMX, TXND	95.23
2xc2_A	117	Thioredoxinn; oxidoreductase, protein disulfide re	95.23
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	94.21
2vm1_A	118	Thioredoxin, thioredoxin H isoform 1.; oxidoreduct	95.12
2vim_A	104	Thioredoxin, TRX; thioredoxin fold, oxidoreductase	95.11
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	95.1
2b1k_A	168	Thiol:disulfide interchange protein DSBE; C-termin	95.06
1nho_A	85	Probable thioredoxin; beta sheet, alpha helix, oxi	95.04
1kng_A	156	Thiol:disulfide interchange protein CYCY; thioredo	95.02
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	94.98
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	94.98
3lor_A	160	Thiol-disulfide isomerase and thioredoxins; PSI, M	94.97
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	94.96
1ti3_A	113	Thioredoxin H, PTTRXH1; oxidoreductase; NMR {Popul	94.96
2wz9_A	153	Glutaredoxin-3; protein binding; 1.55A {Homo sapie	94.94
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	94.81
3aps_A	122	DNAJ homolog subfamily C member 10; thioredoxin fo	94.78
3kcm_A	154	Thioredoxin family protein; SGX, thioredoxin prote	94.75
1gh2_A	107	Thioredoxin-like protein; redox-active center, ele	94.74
3f3q_A	109	Thioredoxin-1; His TAG, electron transport, cytopl	94.7
2kj6_A	97	Tubulin folding cofactor B; methods development, N	94.69
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	94.68
3d22_A	139	TRXH4, thioredoxin H-type; electron transport, cyt	94.57
2vlu_A	122	Thioredoxin, thioredoxin H isoform 2.; oxidoreduct	94.56
2j23_A	121	Thioredoxin; immune protein, autoreactivity, cross	94.55
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	94.54
3gl3_A	152	Putative thiol:disulfide interchange protein DSBE;	94.48
3fkf_A	148	Thiol-disulfide oxidoreductase; structural genomic	94.47
3hcz_A	148	Possible thiol-disulfide isomerase; APC61559.2, cy	94.45
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	94.43
3lwa_A	183	Secreted thiol-disulfide isomerase; thioredoxin, P	94.4
3or5_A	165	Thiol:disulfide interchange protein, thioredoxin p	94.29
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	94.2
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	94.18
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	94.07
3cxg_A	133	Putative thioredoxin; malaria, structural GEN oxid	94.07
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	94.01
2lrt_A	152	Uncharacterized protein; structural genomics, thio	93.94
1fo5_A	85	Thioredoxin; disulfide oxidoreductase, structural	93.9
1zma_A	118	Bacterocin transport accessory protein; alpha-beta	93.86
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	93.82
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	93.82
2oe3_A	114	Thioredoxin-3; electron transport, alpha/beta sand	93.76
2pu9_C	111	TRX-F, thioredoxin F-type, chloroplast; protein-pr	93.65
3gix_A	149	Thioredoxin-like protein 4B; PRE-mRNA splicing, TX	93.55
1mek_A	120	Protein disulfide isomerase; electron transport, r	93.55
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	93.54
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	93.48
1a8l_A	226	Protein disulfide oxidoreductase; PDI, thioredoxin	93.41
1faa_A	124	Thioredoxin F; electron transport; 1.85A {Spinacia	93.32
2rli_A	171	SCO2 protein homolog, mitochondrial; copper protei	93.31
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	93.27
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	93.26
2yj7_A	106	LPBCA thioredoxin; oxidoreductase; 1.65A {Syntheti	92.37
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	93.21
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	93.12
2lrn_A	152	Thiol:disulfide interchange protein; structural ge	92.77
1ilo_A	77	Conserved hypothetical protein MTH895; beta-alpha-	92.68
1jfu_A	186	Thiol:disulfide interchange protein TLPA; thioredo	92.57
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	92.52
1qgv_A	142	Spliceosomal protein U5-15KD; snRNP, thioredoxin,	92.4
3fw2_A	150	Thiol-disulfide oxidoreductase; structural genomic	92.21
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	92.2
3hdc_A	158	Thioredoxin family protein; ATCC53774, DSM 7210, ,	92.13
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	91.86
2ywi_A	196	Hypothetical conserved protein; uncharacterized co	91.76
3q6o_A	244	Sulfhydryl oxidase 1; protein disulfide isomerase,	91.75
2av4_A	160	Thioredoxin-like protein 4A (DIM1); U5 snRNP-SPECI	91.72
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	91.71
3t58_A	519	Sulfhydryl oxidase 1; oxidoreductase; HET: FAD; 2.	91.67
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	91.62
2djj_A	121	PDI, protein disulfide-isomerase; thioredoxin fold	91.59
2f51_A	118	Thioredoxin; electron transport; 1.90A {Trichomona	91.56
2hyx_A	352	Protein DIPZ; thioredoxin fold, jelly-roll, struct	91.41
3ha9_A	165	Uncharacterized thioredoxin-like protein; PSI, MCS	91.36
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	91.19
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	90.95
3h79_A	127	Thioredoxin-like protein; thioredoxin fold, cataly	90.93
1a8l_A	226	Protein disulfide oxidoreductase; PDI, thioredoxin	90.91
3ed3_A	298	Protein disulfide-isomerase MPD1; thioredoxin-like	90.9
3eur_A	142	Uncharacterized protein; PSI2,MCSG, conserved prot	90.14
3drn_A	161	Peroxiredoxin, bacterioferritin comigratory prote	89.96
3ewl_A	142	Uncharacterized conserved protein BF1870; alpha-be	89.78
2ywm_A	229	Glutaredoxin-like protein; redox protein, structur	89.76
3iv4_A	112	Putative oxidoreductase; APC23140, meticillin-resi	89.69
3idv_A	241	Protein disulfide-isomerase A4; thioredoxin-like f	89.68
2dj3_A	133	Protein disulfide-isomerase A4; protein ERP-72, ER	89.45
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	89.43
2djk_A	133	PDI, protein disulfide-isomerase; thioredoxin fold	89.22
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	89.2
1wmj_A	130	Thioredoxin H-type; structural genomics, program f	89.19
3s9f_A	165	Tryparedoxin; thioredoxin fold, disulfide reductas	88.93
1sji_A	350	Calsequestrin 2, calsequestrin, cardiac muscle iso	88.26
2dj0_A	137	Thioredoxin-related transmembrane protein 2; AVLA2	88.14
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	87.98
1i5g_A	144	Tryparedoxin II; electron transport; HET: TS5; 1.4	87.9
1o8x_A	146	Tryparedoxin, TRYX, TXNI; tryparedoxin-I, synchrot	87.71
2dbc_A	135	PDCL2, unnamed protein product; phosducin-like pro	87.6
3me7_A	170	Putative uncharacterized protein; electron transfe	87.53
2r2j_A	382	Thioredoxin domain-containing protein 4; CRFS moti	87.3
1o73_A	144	Tryparedoxin; electron transport, trypanosomatid,	87.0
1zof_A	198	Alkyl hydroperoxide-reductase; decamer, toroide-sh	86.37
3idv_A	241	Protein disulfide-isomerase A4; thioredoxin-like f	86.33
3cmi_A	171	Peroxiredoxin HYR1; thioredoxin-like fold, oxidore	86.29
3f8u_A	481	Protein disulfide-isomerase A3ERP57; endoplasmic r	86.26
1xvw_A	160	Hypothetical protein RV2238C/MT2298; thioredoxin f	85.85
3uem_A	361	Protein disulfide-isomerase; thioredoxin-like doma	85.69
2cvb_A	188	Probable thiol-disulfide isomerase/thioredoxin; re	85.55
2bmx_A	195	Alkyl hydroperoxidase C; peroxiredoxin, antioxidan	85.03
2hls_A	243	Protein disulfide oxidoreductase; thioredoxin fold	84.97
1sen_A	164	Thioredoxin-like protein P19; endoplasmic reticulu	84.87
2b5e_A	504	Protein disulfide-isomerase; 2.40A {Saccharomyces	84.85
2qc7_A	240	ERP31, ERP28, endoplasmic reticulum protein ERP29;	84.57
1xzo_A	174	BSSCO, hypothetical protein YPMQ; thioredoxin-like	84.56
2b7k_A	200	SCO1 protein; metallochaperone, cytochrome C oxida	84.5
2k6v_A	172	Putative cytochrome C oxidase assembly protein; th	84.39
1we0_A	187	Alkyl hydroperoxide reductase C; peroxiredoxin, AH	84.27
2c0g_A	248	ERP29 homolog, windbeutel protein; PDI-dbeta, PDI,	83.48
2ywm_A	229	Glutaredoxin-like protein; redox protein, structur	82.71
3us3_A	367	Calsequestrin-1; calcium-binding protein; 1.74A {O	81.83
3a2v_A	249	Probable peroxiredoxin; thioredoxin peroxidase, hy	81.64
2v1m_A	169	Glutathione peroxidase; selenium, selenocysteine,	81.13
2h01_A	192	2-Cys peroxiredoxin; thioredoxin peroxidase, struc	80.8
2obi_A	183	PHGPX, GPX-4, phospholipid hydroperoxide glutathio	80.8
3evi_A	118	Phosducin-like protein 2; alpha beta, 3-layer(ABA)	80.69
1uul_A	202	Tryparedoxin peroxidase homologue; peroxiredoxin,	80.04

>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=99.90  E-value=8.9e-24  Score=159.39  Aligned_cols=86  Identities=27%  Similarity=0.484  Sum_probs=77.4

Q ss_pred             CCCCCCCCCCCCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccc
Q 025774          156 YPILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFED  235 (248)
Q Consensus       156 ~~~l~~eP~~~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d  235 (248)
                      ...||+||..+.+++|+|+||||||+|++|||+.+++|++||+||.++  ++.+..|.|+++|||+.  +..|.++||+|
T Consensus         9 ~~~lp~EP~~~~~~~~~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~--~~~~~~f~L~t~fPrk~--l~~d~~~TL~e   84 (109)
T 2cr5_A            9 VPDLPEEPSETAEEVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV--GYHKSLYRLSTSFPRRA--LEVEGGSSLED   84 (109)
T ss_dssp             CCCCCCCCCSSCSSEEEEEEECTTSCEEEEEEESSSBTHHHHHHHHHH--TCCTTTEEEECSSSCCB--CCCCSSCBHHH
T ss_pred             cccCCCCCCCCCCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc--CCCCCCeEEEeCCCCcC--CCCCCCCCHHH
Confidence            568999999888899999999999999999999999999999999986  55688999999999987  55578999999


Q ss_pred             cCCcCceEEE
Q 025774          236 SGLANAMISV  245 (248)
Q Consensus       236 ~gl~~~~v~v  245 (248)
                      +||.|+++|+
T Consensus        85 ~gL~p~a~L~   94 (109)
T 2cr5_A           85 IGITVDTVLN   94 (109)
T ss_dssp             HTCSSCEEEE
T ss_pred             cCCCCCeEEE
Confidence            9999877654

>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=99.84  E-value=3.9e-21  Score=148.61  Aligned_cols=79  Identities=22%  Similarity=0.334  Sum_probs=71.6

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVT  246 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~  246 (248)
                      ..++|+||||||||+|++++|+.+++|++||+||.++..++....|.|+++||++.  +. |.++||+|+||.|++|+++
T Consensus        49 ~~~~t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~~f~L~t~fPrk~--l~-d~~~TL~eagL~psavl~k  125 (127)
T 1s3s_G           49 AEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKE--LA-DENQTLKEANLLNAVIVQR  125 (127)
T ss_dssp             TSCCCCEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCSGGGTSCEEEEETTTTEE--CC-STTCBHHHHTCSSCEEEEE
T ss_pred             CCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCcCCCCCCeEEecCCCCCC--CC-CCCCcHHHCCCcCceEEEE
Confidence            35689999999999999999999999999999999986555578999999999986  64 6799999999999999999


Q ss_pred             eC
Q 025774          247 WE  248 (248)
Q Consensus       247 ~~  248 (248)
                      |+
T Consensus       126 ~~  127 (127)
T 1s3s_G          126 LT  127 (127)
T ss_dssp             EC
T ss_pred             eC
Confidence            95

>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=99.84  E-value=1.3e-20  Score=135.62  Aligned_cols=76  Identities=17%  Similarity=0.378  Sum_probs=66.5

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v  245 (248)
                      .+++|+|+||||||++++|+|+.+++|++||+||.+.  ++.+.+|.|+++||++.++ ..|.++||+|+||.|+++|+
T Consensus         4 ~~~~~~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~~--~~~~~~f~L~t~fPrk~l~-~~d~~~TL~e~gL~p~a~L~   79 (84)
T 3qx1_A            4 MEPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASK--GFPWDEYKLLSTFPRRDVT-QLDPNKSLLEVKLFPQETLF   79 (84)
T ss_dssp             CCCEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHT--TCCTTTEEEECSSSCCBGG-GSCTTSBTTTTTCCSEEEEE
T ss_pred             CCCeEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHc--CCCCCCeEEEeCCCCCCCc-CCCCCCCHHHCCCCCCCEEE
Confidence            3579999999999999999999999999999999985  5578999999999999743 24789999999999766553

>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=99.83  E-value=2e-20  Score=140.91  Aligned_cols=84  Identities=24%  Similarity=0.350  Sum_probs=70.5

Q ss_pred             CCCCCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCce
Q 025774          163 PKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAM  242 (248)
Q Consensus       163 P~~~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~  242 (248)
                      |.++.++.|+||||||||++++++|+.+++|++||+||.++. +....+|.|+++|||+.+.. .|.++||+|+||.|++
T Consensus         6 p~~~~~~~t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~-~~~~~~f~L~t~fPrk~l~~-~d~~~TL~elgL~psa   83 (109)
T 2dzk_A            6 SGRDRSTIARIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTV-GNTYGNFSLATMFPRREFTR-EDYKRRLLDLELAPSA   83 (109)
T ss_dssp             CCCCCSCCEEEEEECSSSCEEEEEECTTSBHHHHHHHHHHHH-TTSSCSCEEECSSSCCBCCT-TTTTSBTGGGTCSSEE
T ss_pred             CCCCCCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhcc-CCCCCceEEEcCCCCcCCcc-cccCCCHHHCCCCCce
Confidence            344456789999999999999999999999999999999985 34568999999999997333 3679999999999854


Q ss_pred             -EEEEeC
Q 025774          243 -ISVTWE  248 (248)
Q Consensus       243 -v~v~~~  248 (248)
                       |+|+|.
T Consensus        84 ~L~v~~~   90 (109)
T 2dzk_A           84 SVVLLPA   90 (109)
T ss_dssp             EEEEECC
T ss_pred             EEEEEEC
Confidence             668774

>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=2.2e-19  Score=138.06  Aligned_cols=82  Identities=23%  Similarity=0.291  Sum_probs=70.1

Q ss_pred             CCCCCCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccC-CCcCCCccccCCcC
Q 025774          162 EPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLD-YDSKLTFEDSGLAN  240 (248)
Q Consensus       162 eP~~~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~-~d~~~tl~d~gl~~  240 (248)
                      .|.++.++.|+|+||||||+|++|||+.+++|++||+||.++  ++.+.+|.|+++|||+.  +. .|.++||+|+||.|
T Consensus        35 ~~~d~~~~~t~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~--~~~~~~F~L~t~fPrk~--l~~~d~~~TL~e~gL~p  110 (124)
T 1wj4_A           35 EGIDVNGPKAQLMLRYPDGKREQITLPEQAKLLALVKHVQSK--GYPNERFELLTNFPRRK--LSHLDYDITLQEAGLCP  110 (124)
T ss_dssp             CCCCCSSCEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHH--HCCTTTEEEECSSSCCE--ETSSCSSSCTTTTTCCS
T ss_pred             cccCCCCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc--CCCCCCeEEecCCCCcC--CccCCCCCCHHHCCCCC
Confidence            344456789999999999999999999999999999999987  55678999999999997  43 37899999999997


Q ss_pred             -ceEEEEe
Q 025774          241 -AMISVTW  247 (248)
Q Consensus       241 -~~v~v~~  247 (248)
                       ++|+|++
T Consensus       111 sa~Liv~~  118 (124)
T 1wj4_A          111 QETVFVQE  118 (124)
T ss_dssp             SBCCEEEE
T ss_pred             ceEEEEEE
Confidence             5566654

>2ec4_A FAS-associated factor 1; UAS domain, protein FAF1, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=7.9e-18  Score=137.38  Aligned_cols=81  Identities=20%  Similarity=0.267  Sum_probs=74.3

Q ss_pred             CcccccCCCHHHHHHhhcceEEEEEecCChH-------------HHHHHHh---cCCCCCceEEEEeCCCC--ceEEeee
Q 025774            1 MLNRDTWANEAVSQTISTNFIFWQVYDDTSE-------------GKKVCTY---YKLDSIPVVLVVDPITG--QKMRSWC   62 (248)
Q Consensus         1 ~~~r~vl~~~~v~~~l~~~fV~w~~d~~~~e-------------g~~~~~~---~~~~~~P~l~ii~~~~g--~~l~~~~   62 (248)
                      .|||+||||+.|++||++|||+|+||+++++             |+++++.   |++++||+++||+++.+  +++.+++
T Consensus        72 ~f~~~~L~~~~V~~~l~~nfV~w~~dv~~~e~~~~~~~~~~~~~g~~~a~~~~~~~~~~~P~l~ii~~~~~~~~vl~~~~  151 (178)
T 2ec4_A           72 VFCSQMLCAESIVSYLSQNFITWAWDLTKDSNRARFLTMCNRHFGSVVAQTIRTQKTDQFPLFLIIMGKRSSNEVLNVIQ  151 (178)
T ss_dssp             HHHHHTTTCHHHHHHHHHTEEEEEEECCSHHHHHHHHHHHHHHTCHHHHHHHHHSCSTTCSEEEEECCCSSCCCEEEEEC
T ss_pred             HHHHHhcCCHHHHHHHHcCEEEEEEeCCCchhhhhhhhhhhhhhHHHHHHHHhhcCCCCCCeEEEEEcCCCceEEEEEEe
Confidence            3899999999999999999999999999999             6678766   89999999999998743  3689999


Q ss_pred             CCCChHHHHHHHhhhhhcC
Q 025774           63 GMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        63 G~~~~e~l~~~L~~~~~~~   81 (248)
                      |.+++++|+..|+.+++++
T Consensus       152 G~~~~~~ll~~L~~~~e~~  170 (178)
T 2ec4_A          152 GNTTVDELMMRLMAAMEIF  170 (178)
T ss_dssp             SCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHh
Confidence            9999999999999999987

>2dlx_A UBX domain-containing protein 7; UAS domain, protein KIAA0794, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: c.47.1.24

Probab=99.49  E-value=5.7e-14  Score=111.76  Aligned_cols=81  Identities=43%  Similarity=0.849  Sum_probs=76.1

Q ss_pred             CcccccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774            1 MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus         1 ~~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      +|+|+||+|+.|.++|+++||+|++|++++++..+++.|++..+|++++|++.+|+.+.++.| +++++|+..|..+++.
T Consensus        59 ~me~~vf~d~~V~~~l~~~fv~v~~d~~~~~~~~l~~~y~v~~~P~~~fld~~~G~~l~~~~g-~~~~~fl~~L~~~l~~  137 (153)
T 2dlx_A           59 CLNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEWHQ-LDVSSFLDQVTGFLGE  137 (153)
T ss_dssp             HHHHHTTTCHHHHHHHHHTEEEEEEESSSHHHHHHHHHHTCCSSSEEEEECTTTCCCCEEESS-CCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCHHHHHHHHcCeEEEEEecCCHhHHHHHHHcCCCCCCEEEEEeCCCCcEeeecCC-CCHHHHHHHHHHHHHh
Confidence            378999999999999999999999999999999999999999999999999988888888877 9999999999999998


Q ss_pred             CC
Q 025774           81 GP   82 (248)
Q Consensus        81 ~~   82 (248)
                      +.
T Consensus       138 ~~  139 (153)
T 2dlx_A          138 HG  139 (153)
T ss_dssp             TC
T ss_pred             cC
Confidence            73

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

Probab=98.68  E-value=3.7e-08  Score=70.27  Aligned_cols=72  Identities=18%  Similarity=0.217  Sum_probs=58.0

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +|+||.++|+.+...|..++||.+|..+|.... +.++..++|..+||++...+ .+.++||+++||.+ ++|+|
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 RVRCKAKGGTHLLQGLSSRTRLRELQGQIAAIT-GIAPGSQRILVGYPPECLDL-SDRDITLGDLPIQSGDMLIV   74 (86)
T ss_dssp             CEEEEETTEEEEECSCCTTCBHHHHHHHHHHHT-CCCTTTCCCEESSCCCCCCC-CCSSCBTTTSSCCTTCEEEC
T ss_pred             EEEEEcCCCCEEeeecCCCCCHHHHHHHHHHHh-CCCccceEEEeCCCCccccc-CCCCCCHHHcCCCCCCEEEE
Confidence            589999999877655999999999999998864 55678899999999875222 24789999999985 55554

>2lst_A Thioredoxin; structural genomics, NEW YORK structural genomics research consortium, oxidoreductase; NMR {Thermus thermophilus}

Probab=97.05  E-value=2.2e-06  Score=64.44  Aligned_cols=76  Identities=21%  Similarity=0.361  Sum_probs=65.6

Q ss_pred             cCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCce--EEeeeCCCChHHHHHHHhhhhhcC
Q 025774            6 TWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQK--MRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus         6 vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~--l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ++.++.+.+.+..+++++.+|++..+...++..|++..+|+++++++.+|..  +.++.|..++++|...|...+...
T Consensus        41 ~~~~~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~v~~~Pt~~~~d~~~G~~~~~~~~~G~~~~~~l~~~l~~~~~~~  118 (130)
T 2lst_A           41 VLSDPGVSRLLEARFVVASVSVDTPEGQELARRYRVPGTPTFVFLVPKAGAWEEVGRLFGSRPRAEFLKELRQVCVKG  118 (130)
Confidence            3455777788888899999999878888999999999999999999888888  889999999999988888777654

>2kuc_A Putative disulphide-isomerase; structural genomics, thioredo PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=97.70  E-value=0.00021  Score=53.24  Aligned_cols=71  Identities=15%  Similarity=0.326  Sum_probs=61.1

Q ss_pred             CHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774            9 NEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus         9 ~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ++.+.++++.+++++..|.+..+...++..|++..+|+++++++ +|..+.++.|..+.++|...|...+..
T Consensus        52 ~~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~v~~~Pt~~~~d~-~G~~~~~~~G~~~~~~l~~~l~~~~~~  122 (130)
T 2kuc_A           52 DSLVADYFNRHFVNLKMDMEKGEGVELRKKYGVHAYPTLLFINS-SGEVVYRLVGAEDAPELLKKVKLGVES  122 (130)
T ss_dssp             CHHHHHHHHHHSEEEEECSSSTTHHHHHHHTTCCSSCEEEEECT-TSCEEEEEESCCCHHHHHHHHHHHHSC
T ss_pred             cHHHHHHHhcCeEEEEEecCCcchHHHHHHcCCCCCCEEEEECC-CCcEEEEecCCCCHHHHHHHHHHHHHh
Confidence            35677788889999999998777888999999999999999974 688999999999999998888877654

>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=97.58  E-value=0.00029  Score=51.79  Aligned_cols=80  Identities=23%  Similarity=0.353  Sum_probs=59.1

Q ss_pred             CCCCCCCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-
Q 025774          161 EEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-  239 (248)
Q Consensus       161 ~eP~~~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-  239 (248)
                      +||..+.....+|.||..+|+.+.-.+..++||.+|..-+... .+.++...+|+..  .+.  +  +.+.||.++|+. 
T Consensus        14 ~~~~~~~~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~-~gip~~~qrLi~~--Gk~--L--~D~~tL~~ygI~~   86 (106)
T 1ttn_A           14 PEPPPNSGYECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAA-EGVEPGSQRWFFS--GRP--L--TDKMKFEELKIPK   86 (106)
T ss_dssp             -------CCSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHT-TCCCSTTCEEEET--TEE--C--CTTSHHHHCCCSS
T ss_pred             CCCCCCCCCeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHH-HCcCcccEEEEEC--CEE--C--CCCCcHHHcCCCC
Confidence            5666556667899999999999999999999999999999875 4667788888753  442  5  458999999998 


Q ss_pred             CceEEEEe
Q 025774          240 NAMISVTW  247 (248)
Q Consensus       240 ~~~v~v~~  247 (248)
                      +++|.+..
T Consensus        87 g~ti~lv~   94 (106)
T 1ttn_A           87 DYVVQVIV   94 (106)
T ss_dssp             SCEEEEEC
T ss_pred             CCEEEEEE
Confidence            56666653

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

Probab=97.56  E-value=8e-05  Score=52.15  Aligned_cols=73  Identities=8%  Similarity=0.071  Sum_probs=55.6

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ..||||-|+|..... ...++++.+|++.|...+. .+...|.|..+||+.. .+..+.+.||+++||. ++.|.+.
T Consensus         5 m~lRvrs~~G~~Ri~-v~~~~t~~~L~~~I~~~~~-i~~~~~~l~~~~~p~~-~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A            5 IIIRVQSPDGVKRIT-ATKRETAATFLKKVAKEFG-FQNNGFSVYINRNKTG-EITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             CCCEEECSSEEEECC-CCSSCCHHHHHHHHHHHTC-CCTTTCCCCCSCCGGG-GSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             EEEEEECCCCCEEEE-cCCcChHHHHHHHHHHHcC-CCCCcceEEecCCCCC-cccCCCCCCHHHcCCCCCCEEEEe
Confidence            569999999974433 7789999999999998763 4567889988998732 3433578999999997 5666553

>2ju5_A Thioredoxin disulfide isomerase; protein, oxidoreductase; NMR {Chlamydophila pneumoniae}

Probab=97.52  E-value=0.00053  Score=53.24  Aligned_cols=71  Identities=10%  Similarity=0.234  Sum_probs=58.8

Q ss_pred             CCCHHHHHHhhcceEEEEEecCCh---------HHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC--ChHHHHHHHh
Q 025774            7 WANEAVSQTISTNFIFWQVYDDTS---------EGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV--QPESLLEDLV   75 (248)
Q Consensus         7 l~~~~v~~~l~~~fV~w~~d~~~~---------eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~--~~e~l~~~L~   75 (248)
                      +.++.+.++.+.+|++..+|++..         ....++..|++..+|+++|+++ +|.++.++ |..  +.++++..|.
T Consensus        71 ~~~~~~~~~~~~~~~~v~vd~~~~~~~~~~~~~~~~~l~~~~~v~~~Pt~~~~d~-~G~~~~~~-G~~~~~~~~l~~~l~  148 (154)
T 2ju5_A           71 LQSSEFKHFAGVHLHMVEVDFPQKNHQPEEQRQKNQELKAQYKVTGFPELVFIDA-EGKQLARM-GFEPGGGAAYVSKVK  148 (154)
T ss_dssp             TTSHHHHHHHHHHCEEEEEECCSSCCCCHHHHHHHHHHHHHTTCCSSSEEEEECT-TCCEEEEE-CCCTTCHHHHHHHHH
T ss_pred             hcCHHHHHHhcCcEEEEEecCccccCCChhhHhhHHHHHHHcCCCCCCEEEEEcC-CCCEEEEe-cCCCCCHHHHHHHHH
Confidence            334667777778999999999763         4568899999999999999985 68999999 998  8999988888


Q ss_pred             hhhh
Q 025774           76 PFMD   79 (248)
Q Consensus        76 ~~~~   79 (248)
                      ..+.
T Consensus       149 ~~l~  152 (154)
T 2ju5_A          149 SALK  152 (154)
T ss_dssp             HHHT
T ss_pred             HHHh
Confidence            7664

>3f9u_A Putative exported cytochrome C biogenesis-related; exported cytochrome C biogenesis-related protein, bacteroide fragilis; 2.20A {Bacteroides fragilis nctc 9343}

Probab=97.39  E-value=0.00031  Score=55.23  Aligned_cols=76  Identities=13%  Similarity=0.273  Sum_probs=63.0

Q ss_pred             ccCCCHHHHHHhhcceEEEEEecCChH------------------------HHHHHHhcCCCCCceEEEEeCCCCceEEe
Q 025774            5 DTWANEAVSQTISTNFIFWQVYDDTSE------------------------GKKVCTYYKLDSIPVVLVVDPITGQKMRS   60 (248)
Q Consensus         5 ~vl~~~~v~~~l~~~fV~w~~d~~~~e------------------------g~~~~~~~~~~~~P~l~ii~~~~g~~l~~   60 (248)
                      .+|.++.+.++++.+|++...|++...                        +...+..|++..+|+++|+++ +|.++.+
T Consensus        68 ~~~~~~~~~~~~~~~~~~v~v~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~Pt~~lid~-~G~~~~~  146 (172)
T 3f9u_A           68 AVWTDPKVSSIINNDYVLITLYVDNKTPLTEPVKIMENGTERTLRTVGDKWSYLQRVKFGANAQPFYVLIDN-EGNPLNK  146 (172)
T ss_dssp             HTTTSHHHHHHHHHHCEEEEEETTCCCEEEEEEEEEETTEEEEEEEHHHHHHHHHHHHHSCCCSSEEEEECT-TSCBSSC
T ss_pred             HhcCCHHHHHHhcCCEEEEEEecCcccccchhhhhhhcchhhhhhhhhhhhhHHHHHHcCCCCcceEEEECC-CCCEEee
Confidence            457789999999999999999986543                        112268899999999999985 5999999


Q ss_pred             eeCCCC-hHHHHHHHhhhhhcC
Q 025774           61 WCGMVQ-PESLLEDLVPFMDGG   81 (248)
Q Consensus        61 ~~G~~~-~e~l~~~L~~~~~~~   81 (248)
                      +.|..+ +++|...|...++.+
T Consensus       147 ~~G~~~~~~~l~~~l~~~l~~~  168 (172)
T 3f9u_A          147 SYAYDEDISKYINFLQTGLENY  168 (172)
T ss_dssp             CBCSCCCHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCHHHHHHHHHHHHHHh
Confidence            999998 999999998888754

>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=97.39  E-value=0.00086  Score=48.86  Aligned_cols=71  Identities=20%  Similarity=0.118  Sum_probs=58.9

Q ss_pred             CCceEEEEEcCC----CceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-Cce
Q 025774          168 SLLCRVGVRLPD----GRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAM  242 (248)
Q Consensus       168 ~~~~~i~iRlp~----G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~  242 (248)
                      .++++|.||+|+    |+.+.-....++||.+|-.-|... .+.++...+|+.+  .+.  +  +++.||.+.|+. +++
T Consensus        13 tg~ati~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k-~gip~~qQrLI~~--GKi--L--~D~~TL~~y~I~~gst   85 (100)
T 1wju_A           13 TGIATIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAET-FGLQENYIKIVIN--KKQ--L--QLGKTLEEQGVAHNVK   85 (100)
T ss_dssp             CCEEEEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHH-TTCCSTTCEEEET--TEE--C--CTTSBHHHHTCCSSEE
T ss_pred             cceEEEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHH-HCcCHHHeEEEeC--CeE--C--CCCCcHHHcCCCCCCE
Confidence            568999999999    878999999999999999999886 4677888999854  543  5  567999999998 555


Q ss_pred             EEE
Q 025774          243 ISV  245 (248)
Q Consensus       243 v~v  245 (248)
                      |+|
T Consensus        86 i~v   88 (100)
T 1wju_A           86 AMV   88 (100)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            644

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

Probab=97.35  E-value=0.0018  Score=45.86  Aligned_cols=72  Identities=17%  Similarity=0.168  Sum_probs=58.1

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +...+|.||..+|+.+.-.+..++||.+|-.-+.... +.++...+|+..  .+  .+  +++.||.++|+. +++|.+.
T Consensus        15 ~~~m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrL~~~--Gk--~L--~D~~tL~~~gi~~g~~i~l~   87 (91)
T 3v6c_B           15 RGSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GK--QL--EDGRTLSDYNIQKESTLHLV   87 (91)
T ss_dssp             CCSEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHH-CCCGGGCEEEET--TE--EC--CTTCBTGGGTCCTTCEEEEE
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhh-CCChhhEEEEEC--Ce--EC--CCcCcHHHCCCCCCCEEEEE
Confidence            4578999999999999999999999999999998764 667777888764  33  25  457999999998 5666654

>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=97.31  E-value=0.0017  Score=43.88  Aligned_cols=68  Identities=15%  Similarity=0.226  Sum_probs=54.6

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +|.||.++|+.+.-.+..++||.+|..-+.... +.++...+|...  .+.  +  +++.||.+.|+. +++|.+.
T Consensus         2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~-~i~~~~q~L~~~--g~~--L--~d~~tL~~~~i~~g~~i~l~   70 (76)
T 1ndd_A            2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKE-GIPPQQQRLIYS--GKQ--M--NDEKTAADYKILGGSVLHLV   70 (76)
T ss_dssp             EEEEECTTSCEEEEECCTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTSBGGGGTCCTTCEEEEE
T ss_pred             EEEEECCCCCEEEEEECCCChHHHHHHHHHHHH-CcChHHEEEEEC--CEE--C--CCCCcHHHcCCCCCCEEEEE
Confidence            688999999999999999999999999998764 566778888753  442  5  457999999998 5666554

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

Probab=97.28  E-value=0.0026  Score=43.67  Aligned_cols=72  Identities=15%  Similarity=0.191  Sum_probs=57.3

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +...+|.||.++|+.+.-.+..++||.+|..-+... .+.++...+|...  .+.  +  +++.||.++|+. +++|.+.
T Consensus         5 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~-~~i~~~~qrL~~~--gk~--L--~d~~tL~~~~i~~g~~i~l~   77 (81)
T 2dzi_A            5 SSGMQLTVKALQGRECSLQVPEDELVSTLKQLVSEK-LNVPVRQQRLLFK--GKA--L--ADGKRLSDYSIGPNSKLNLV   77 (81)
T ss_dssp             SSSEEEEEEETTSCEEEEEECSSCBHHHHHHHHHHH-TCCCTTTCEEEET--TEE--C--CTTSBGGGGTCCSSBCCEEE
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHH-HCcCHHHEEEEEC--CeE--C--CCCCcHHHcCCCCCCEEEEE
Confidence            456889999999998889999999999999999875 3667788888753  443  5  457999999998 5666554

>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=97.27  E-value=0.0023  Score=45.09  Aligned_cols=72  Identities=11%  Similarity=0.032  Sum_probs=57.8

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~  246 (248)
                      +...+|.||..+|+.+.-.+..++||.+|-..|.... +.++...+|+..  .+  .+  +++.||.++|+.+++|.+.
T Consensus         3 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~-gip~~~qrLi~~--Gk--~L--~d~~tL~~~~i~g~~i~l~   74 (90)
T 4dwf_A            3 PDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASV-SIPSEKQRLIYQ--GR--VL--QDDKKLQEYNVGGKVIHLV   74 (90)
T ss_dssp             CCEEEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHH-TCCGGGEEEEET--TE--EC--CTTSBGGGGTCTTEEEEEE
T ss_pred             CcEEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHh-CCCHHHEEEEEC--Ce--EC--CCCCCHHHcCCCCcEEEEE
Confidence            4578999999999999889999999999999998764 666778888763  33  25  4589999999965666554

>2fwh_A Thiol:disulfide interchange protein DSBD; thioredoxin-like, C-terminal domain, reduced form at PH7, oxidoreductase; 0.99A {Escherichia coli} SCOP: c.47.1.1 PDB: 2fwe_A 2fwf_A 2fwg_A 1vrs_D 1uc7_A

Probab=97.24  E-value=0.0013  Score=49.62  Aligned_cols=69  Identities=14%  Similarity=0.281  Sum_probs=55.2

Q ss_pred             CCCHHHHHHhhcceEEEEEecCC--hHHHHHHHhcCCCCCceEEEEeCCCCceE--EeeeCCCChHHHHHHHhhh
Q 025774            7 WANEAVSQTISTNFIFWQVYDDT--SEGKKVCTYYKLDSIPVVLVVDPITGQKM--RSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus         7 l~~~~v~~~l~~~fV~w~~d~~~--~eg~~~~~~~~~~~~P~l~ii~~~~g~~l--~~~~G~~~~e~l~~~L~~~   77 (248)
                      +.++.+.+.+. ++++...|++.  .+...++..|++..+|+++++++ +|..+  .++.|..+.++|...|..+
T Consensus        54 ~~~~~l~~~~~-~~~~~~vd~~~~~~~~~~l~~~~~v~~~Pt~~~~d~-~G~~v~~~~~~G~~~~~~l~~~l~~~  126 (134)
T 2fwh_A           54 FSDPQVQKALA-DTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDG-QGQEHPQARVTGFMDAETFSAHLRDR  126 (134)
T ss_dssp             TTSHHHHHHTT-TSEEEEEECTTCCHHHHHHHHHTTCCSSSEEEEECT-TSCBCGGGCBCSCCCHHHHHHHHHHC
T ss_pred             cCCHHHHHHhc-CcEEEEEeCCCCcchHHHHHHHcCCCCCCEEEEECC-CCCEeeeeeeeeccCHHHHHHHHHhc
Confidence            34456666555 59999999865  56778999999999999999984 58877  7899999999987776655

>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=97.19  E-value=0.0025  Score=42.96  Aligned_cols=69  Identities=17%  Similarity=0.229  Sum_probs=55.0

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      +|.||.++|+.+.-.+..++||.+|...+.... +.++...+|...  .+.  +  +++.||.++|+. +++|.+..
T Consensus         2 ~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~-~i~~~~q~L~~~--g~~--L--~d~~tL~~~~i~~g~~i~l~~   71 (76)
T 3a9j_A            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQRESTLHLVL   71 (76)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTCBTGGGTCCTTCEEEEEE
T ss_pred             EEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHH-CcCHHHeEEEEC--CeE--C--CCCCcHHHcCCCCCCEEEEEE
Confidence            588999999999999999999999999998864 556778888753  443  5  347999999998 56666543

>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=97.17  E-value=0.0025  Score=44.14  Aligned_cols=70  Identities=16%  Similarity=0.166  Sum_probs=56.6

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ..+|.|+.++|+.+.-.+..++||.+|..-+.... +.++...+|+.  ..+.  +  +++.||.++|+. +++|.+.
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~-~i~~~~qrL~~--~g~~--L--~d~~tL~~~~i~~~~~l~l~   73 (85)
T 3mtn_B            3 HMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIF--AGKQ--L--EDGRTLSDYNIQKWSTLFLL   73 (85)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHH-CCCGGGCEEEE--TTEE--C--CTTSBTGGGTCCTTCEEEEE
T ss_pred             eEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHH-CcChHHEEEEE--CCEE--C--CCCCCHHHcCCCCCCEEEEE
Confidence            46899999999999999999999999999998864 56778888875  3443  5  457999999998 5666554

>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=97.17  E-value=0.0035  Score=43.51  Aligned_cols=72  Identities=10%  Similarity=0.178  Sum_probs=57.9

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhc--CCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQL--EGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~--~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ...+|.||..+|+.+.-.+..++||.+|..-+...+  .+.++...+|+..  .+.  +  +++.||.++|+. +++|.+
T Consensus         4 ~~m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~--Gk~--L--~D~~tL~~~~i~~g~~i~l   77 (85)
T 2wyq_A            4 MAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYA--GKI--L--SDDVPIRDYRIDEKNFVVV   77 (85)
T ss_dssp             CCEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEET--TEE--C--CTTSBGGGGCCCTTSEEEE
T ss_pred             ceEEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEEC--CEE--C--cCCCCHHHcCCCCCCEEEE
Confidence            467899999999999999999999999999998862  5667788888754  442  5  457999999998 566655


Q ss_pred             E
Q 025774          246 T  246 (248)
Q Consensus       246 ~  246 (248)
                      .
T Consensus        78 ~   78 (85)
T 2wyq_A           78 M   78 (85)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=97.14  E-value=0.0031  Score=44.05  Aligned_cols=72  Identities=22%  Similarity=0.156  Sum_probs=57.8

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ++..+|.|+.++|+.+.-.+..++||.+|..-+... .+.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus         5 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~-~gi~~~~qrL~~~--Gk~--L--~d~~tL~~~~i~~g~~i~l~   77 (87)
T 1wh3_A            5 SSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQ-QGLPKKQQQLEFQ--GQV--L--QDWLGLGIYGIQDSDTLILS   77 (87)
T ss_dssp             SSSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHH-TCCCTTTEEEEET--TEE--C--CSSSBHHHHTCCTTEEEEEE
T ss_pred             CCCEEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHH-hCCChHHEEEEEC--CEE--c--cCCCCHHHCCCCCCCEEEEE
Confidence            346889999999999999999999999999999876 4667888888753  432  5  457999999998 5666554

>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=97.12  E-value=0.0035  Score=44.82  Aligned_cols=69  Identities=12%  Similarity=0.173  Sum_probs=55.4

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhc--CCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQL--EGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~--~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +|.||.++|+.+.-.+..++||.+|..-+....  .+.++...+|+..  .+.  +  +++.||.+.|+. +++|.+.
T Consensus         2 ~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~--Gk~--L--~D~~tL~~ygI~~g~~i~l~   73 (95)
T 1uel_A            2 QVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYA--GKI--L--NDDTALKEYKIDEKNFVVVM   73 (95)
T ss_dssp             EEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEET--TEE--C--CTTSBGGGGTCCSSSEEEEE
T ss_pred             EEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEEC--CEE--C--CCcCcHHHCCCCCCCEEEEE
Confidence            588999999999999999999999999998864  4667888888753  443  5  457999999998 5666554

>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=97.12  E-value=0.0036  Score=43.71  Aligned_cols=71  Identities=14%  Similarity=0.185  Sum_probs=56.9

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      .....|.|+.++|+.+.-.+..++||.+|-.-+.... +.++...+|+..  .+  .+  +++.||.++|+. +++|.+
T Consensus        10 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~-gip~~~qrL~~~--G~--~L--~d~~tL~~~~i~~~~~i~l   81 (88)
T 3dbh_I           10 GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKE-GIPPQQQRLIYS--GK--QM--NDEKTAADYKILGGSVLHL   81 (88)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHH-CCCGGGCCEEET--TE--EC--CTTSBGGGGTCCTTCEEEE
T ss_pred             CCcEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHH-CcCHHHEEEEEC--Ce--EC--CCCCcHHHcCCCCCCEEEE
Confidence            4568999999999999999999999999999998764 666777888763  33  25  458999999998 556654

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

Probab=97.08  E-value=0.005  Score=42.12  Aligned_cols=70  Identities=23%  Similarity=0.256  Sum_probs=56.4

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ...|.||.++|+.+.-.+..++||.+|-.-+... .+.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus         4 ~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~-~gip~~~qrL~~~--G~~--L--~d~~tL~~~~i~~~~~l~l~   74 (79)
T 3phx_B            4 PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGL-EGVQDDLFWLTFE--GKP--L--EDQLPLGEYGLKPLSTVFMN   74 (79)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-HTCCGGGEEEEET--TEE--C--CTTSBGGGGTCCTTCEEEEE
T ss_pred             CEEEEEEeCCCCEEEEEECCcChHHHHHHHHHhh-cCCCHHHEEEEEC--CEE--C--CCCCcHHHCCCCCCCEEEEE
Confidence            4689999999999988999999999999999875 3667788888764  332  5  458999999998 5666554

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

Probab=97.07  E-value=0.0037  Score=42.38  Aligned_cols=68  Identities=12%  Similarity=0.121  Sum_probs=54.1

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      .+|.|+. +|+.+.-.+..++||.+|..-+.... +.++...+|..  ..+.  +  +++.||.+.|+. +++|.+.
T Consensus         5 m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~-~i~~~~qrL~~--~gk~--L--~d~~tL~~~~i~~g~~i~l~   73 (77)
T 2bwf_A            5 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKAN-GIPVANQRLIY--SGKI--L--KDDQTVESYHIQDGHSVHLV   73 (77)
T ss_dssp             EEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHH-CCCGGGEEEEE--TTEE--C--CTTSBTGGGTCCTTCEEEEE
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHh-CCCHHHEEEEE--CCeE--c--CCCCCHHHcCCCCCCEEEEE
Confidence            5788888 99999999999999999999998764 66778888874  3443  5  446999999998 5666654

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

Probab=97.06  E-value=0.0035  Score=45.01  Aligned_cols=68  Identities=18%  Similarity=0.236  Sum_probs=54.6

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +|.||.++|+.+.-.+..++||.+|..-|.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus         2 ~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~-gi~~~~qrL~~~--Gk~--L--~D~~tL~~~gi~~g~~i~l~   70 (98)
T 1yx5_B            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHLV   70 (98)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHT-CCCGGGEEEEET--TEE--C--CTTSBTGGGTCCTTCEEEEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHH-CcChhhEEEEEC--CEE--C--CCCCCHHHcCCCCCCEEEEE
Confidence            688999999989999999999999999998764 667788888753  443  5  448999999998 5666544

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

Probab=97.05  E-value=0.0042  Score=44.61  Aligned_cols=78  Identities=12%  Similarity=0.204  Sum_probs=61.3

Q ss_pred             CCceEEEEEcC---CCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEcc---CCCCccccCCCcCCCccccCCc-C
Q 025774          168 SLLCRVGVRLP---DGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHA---IPGATKSLDYDSKLTFEDSGLA-N  240 (248)
Q Consensus       168 ~~~~~i~iRlp---~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~---~Pr~~~~l~~d~~~tl~d~gl~-~  240 (248)
                      .+.++|.|+.|   +|..+.++|..+.||+.|-.-+.... +.++...+|...   +|.....+ .+.+.||...|+. +
T Consensus         7 ~~~v~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~-gip~~~q~L~~~~~~~~~~~~~L-~~d~~~L~~y~i~~G   84 (97)
T 1wjn_A            7 GQLLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLL-KVPVSELLLSYESSKMPGREIEL-ENDLQPLQFYSVENG   84 (97)
T ss_dssp             SCEEEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTT-TCCTTTCEEEEECTTSCSCEEEC-CCSSSBSGGGTCCTT
T ss_pred             CccEEEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHH-CCChhHeEEEEEcCCCCceeecc-CCCcccHhhcCCCCC
Confidence            45788999876   68899999999999999999998754 667778888643   55443224 4789999999998 6


Q ss_pred             ceEEEEe
Q 025774          241 AMISVTW  247 (248)
Q Consensus       241 ~~v~v~~  247 (248)
                      ..|+|.+
T Consensus        85 ~~I~V~d   91 (97)
T 1wjn_A           85 DCLLVRW   91 (97)
T ss_dssp             CEEEEEC
T ss_pred             CEEEEEe
Confidence            7788876

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

Probab=97.04  E-value=0.004  Score=43.83  Aligned_cols=70  Identities=23%  Similarity=0.256  Sum_probs=56.6

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ..+|.||.++|+.+.-.+..++||.+|..-+... .+.++...+|+..  .+.  +  ++++||.++|+. +++|.+.
T Consensus         4 ~m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~-~gip~~~qrL~~~--Gk~--L--~D~~tL~~~~I~~g~~i~l~   74 (88)
T 2hj8_A            4 PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGL-EGVQDDLFWLTFE--GKP--L--EDQLPLGEYGLKPLSTVFMN   74 (88)
T ss_dssp             EEEEEEEETTSCEEEEEEESSSBHHHHHHHHHHH-TCSCTTTEEEESS--SSC--C--CTTSBHHHHHCSTTCEEEEE
T ss_pred             cEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHH-hCCChhHEEEEEC--CEE--C--CCCCcHHHcCCCCCCEEEEE
Confidence            5789999999999999999999999999999875 4667888888753  443  5  457999999998 5666554

>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=97.03  E-value=0.0035  Score=45.58  Aligned_cols=74  Identities=12%  Similarity=0.128  Sum_probs=59.9

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ..+...|-|+.++|+.+.-....++||.+|..-|... .+.++...+|+..  .+.  +  +++.||.+.|+. .++|.+
T Consensus        25 ~~~mm~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k-~Gip~~qQrLi~~--Gk~--L--~D~~TL~dygI~~gstlhL   97 (100)
T 1uh6_A           25 AATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQ-TGTRWNKIVLKKW--YTI--F--KDHVSLGDYEIHDGMNLEL   97 (100)
T ss_dssp             CCCEEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHH-HCCCGGGCEEEET--TEE--C--CSSCBHHHHTCCTTEEEEE
T ss_pred             CCCeEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHH-hCCCHHHEEEEEC--CEE--C--CCCCCHHHcCCCCCCEEEE
Confidence            3457899999999999999999999999999999886 4677888888754  553  5  458999999998 466666


Q ss_pred             Ee
Q 025774          246 TW  247 (248)
Q Consensus       246 ~~  247 (248)
                      .+
T Consensus        98 ~~   99 (100)
T 1uh6_A           98 YY   99 (100)
T ss_dssp             EC
T ss_pred             Ee
Confidence            54

>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=97.01  E-value=0.0034  Score=45.13  Aligned_cols=72  Identities=17%  Similarity=0.208  Sum_probs=57.7

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +....|.|+..+|+.+.-....++||..|...+.... +.++...+|+..  .+.  |  +.+.||+++|+. +++|.+.
T Consensus        19 ~~~m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~-gip~~~qrLif~--Gk~--L--~d~~tl~dy~i~~g~~I~l~   91 (97)
T 1wyw_B           19 GEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQ-GVPMNSLRFLFE--GQR--I--ADNHTPKELGMEEEDVIEVY   91 (97)
T ss_dssp             CCEEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHH-TCCGGGEEEEET--TEE--C--CTTCCHHHHTCCTTCEEEEE
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHH-CCChhhEEEEEC--CeE--c--CCCCCHHHCCCCCCCEEEEE
Confidence            4568999999999999999999999999999998764 667788888764  443  5  457999999998 5666543

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

Probab=96.96  E-value=0.0056  Score=42.85  Aligned_cols=72  Identities=11%  Similarity=0.032  Sum_probs=57.6

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~  246 (248)
                      +...+|.||..+|+.+.-.+..++||.+|-..+.... +.++...+|+..  .+  .+  +++.||.++|+.+++|.+.
T Consensus        15 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~-gip~~~qrLi~~--Gk--~L--~D~~tL~~~~i~g~~i~lv   86 (88)
T 4eew_A           15 PDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASV-SIPSEKQRLIYQ--GR--VL--QDDKKLQEYNVGGKVIHLV   86 (88)
T ss_dssp             CCEEEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHH-TCCGGGEEEEET--TE--EC--CTTSBGGGGTCTTEEEEEE
T ss_pred             CCeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHh-CCCHHHEEEEEC--CE--EC--CCCCcHHHcCCCCcEEEEE
Confidence            3468999999999998889999999999999998764 667788888753  33  25  4489999999966666654

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

Probab=96.92  E-value=0.0041  Score=44.73  Aligned_cols=72  Identities=18%  Similarity=0.204  Sum_probs=56.5

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +...+|.||..+|+.+.-.+..+++|.+|-.-|.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus        20 ~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrLi~~--Gk~--L--~D~~tL~~~~i~~g~~i~l~   92 (98)
T 4hcn_B           20 GRPMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHLV   92 (98)
T ss_dssp             --CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHH-CCCGGGCEEEET--TEE--C--CTTCBSGGGTCCTTEEEEEE
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHh-CCChhHEEEEEC--CEE--C--CCCCcHHHCCCCCCCEEEEE
Confidence            3468999999999999999999999999999998764 567788888753  442  5  568999999998 4555554

>2l57_A Uncharacterized protein; structural genomics, unknown function, thioredoxin-like, PSI protein structure initiative; NMR {Clostridium perfringens}

Probab=96.91  E-value=0.0085  Score=44.12  Aligned_cols=62  Identities=13%  Similarity=0.223  Sum_probs=51.4

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .++.+...|++..+...++..|++..+|+++++++ +|..+.++.|..+.++|...|...+..
T Consensus        57 ~~v~~~~v~~~~d~~~~~~~~~~v~~~Pt~~~~~~-~G~~~~~~~G~~~~~~l~~~l~~~~~~  118 (126)
T 2l57_A           57 GKFNIYYARLEEEKNIDLAYKYDANIVPTTVFLDK-EGNKFYVHQGLMRKNNIETILNSLGVK  118 (126)
T ss_dssp             SSCEEEEEETTSSHHHHHHHHTTCCSSSEEEEECT-TCCEEEEEESCCCHHHHHHHHHHHCCC
T ss_pred             CCeEEEEEeCCCCchHHHHHHcCCcceeEEEEECC-CCCEEEEecCCCCHHHHHHHHHHHhcc
Confidence            57899999944455667899999999999999985 688899999999999988777776554

>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=96.78  E-value=0.0077  Score=42.79  Aligned_cols=69  Identities=17%  Similarity=0.228  Sum_probs=55.1

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      .+|.||..+|+.+.-.+..++||.+|-.-|.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus         2 m~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~-gip~~~qrL~~~--G~~--L--~d~~tL~~~~i~~~~~i~l~   71 (96)
T 3k9o_B            2 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHLV   71 (96)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTSBTGGGTCCTTCEEEEE
T ss_pred             cEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhh-CCChhHEEEEEC--CEE--C--CCCCcHHHcCCCCCCEEEEE
Confidence            3688999999999999999999999999998864 667788888753  442  5  457899999998 5666554

>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=96.77  E-value=0.0055  Score=42.34  Aligned_cols=70  Identities=20%  Similarity=0.210  Sum_probs=55.8

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ..+|.||.++|+.+.-.+..++||.+|..-+.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~-~ip~~~qrL~~~--g~~--L--~d~~tL~~~~i~~~~~i~l~   73 (85)
T 3n3k_B            3 HMRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIHNHSALYLL   73 (85)
T ss_dssp             -CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHH-CCCGGGEEEEET--BEE--C--CTTCBTTTTTCCTTCEEEEE
T ss_pred             eEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHH-CCCHHHEEEEEC--CeE--C--CCCCCHHHCCCCCCCEEEEE
Confidence            46899999999999999999999999999998864 667788888764  332  5  457899999998 5666554

>3gnj_A Thioredoxin domain protein; APC92103, STR genomics, PSI-2, protein structure initiative, midwest CENT structural genomics; 1.99A {Desulfitobacterium hafniense dcb-2} SCOP: c.47.1.0

Probab=96.77  E-value=0.0089  Score=42.61  Aligned_cols=60  Identities=17%  Similarity=0.325  Sum_probs=49.3

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +..++.|...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.+++...|...+.
T Consensus        51 ~~~~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~--~~g~~~~~~~g~~~~~~l~~~l~~~l~  110 (111)
T 3gnj_A           51 YEESFGFYYVDVEEE--KTLFQRFSLKGVPQILYF--KDGEYKGKMAGDVEDDEVEQMIADVLE  110 (111)
T ss_dssp             TTTTSEEEEEETTTC--HHHHHHTTCCSSCEEEEE--ETTEEEEEEESSCCHHHHHHHHHHHHH
T ss_pred             cCCceEEEEEECCcC--hhHHHhcCCCcCCEEEEE--ECCEEEEEEeccCCHHHHHHHHHHHhc
Confidence            334688888888654  367899999999999998  468899999999999999888877654

>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=96.75  E-value=0.0096  Score=40.50  Aligned_cols=71  Identities=21%  Similarity=0.171  Sum_probs=55.3

Q ss_pred             ceEEEEEcCCCceE-EEe-eCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRM-QRN-FLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~-~r~-F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ..+|.||.++|+.+ .-. +..++||.+|-.-+.... +.++...+|...  .+.  +  +++.||.+.|+. +++|.+.
T Consensus         2 ~m~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~-gip~~~qrL~~~--g~~--L--~d~~tL~~~~i~~g~~i~l~   74 (78)
T 2faz_A            2 SMWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELF-HVEPGLQRLFYR--GKQ--M--EDGHTLFDYEVRLNDTIQLL   74 (78)
T ss_dssp             CEEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTCBTTTTTCCTTCEEEEE
T ss_pred             cEEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHH-CcChhhEEEEEC--CEE--C--CCCCCHHHcCCCCCCEEEEE
Confidence            46789999999875 677 999999999999998764 667788888753  442  5  457999999998 5666654


Q ss_pred             e
Q 025774          247 W  247 (248)
Q Consensus       247 ~  247 (248)
                      .
T Consensus        75 ~   75 (78)
T 2faz_A           75 V   75 (78)
T ss_dssp             E
T ss_pred             E
Confidence            3

>1thx_A Thioredoxin, thioredoxin 2; oxido-reductase, electron transport; 1.60A {Nostoc SP} SCOP: c.47.1.1

Probab=96.71  E-value=0.0099  Score=42.56  Aligned_cols=60  Identities=20%  Similarity=0.274  Sum_probs=49.0

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +..++.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.++|...|...+.
T Consensus        54 ~~~~v~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~g~~~~~~l~~~l~~~l~  113 (115)
T 1thx_A           54 YSDRLKVVKLEIDPN--PTTVKKYKVEGVPALRLV--KGEQILDSTEGVISKDKLLSFLDTHLN  113 (115)
T ss_dssp             TTTTCEEEEEESTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHHC
T ss_pred             hCCcEEEEEEEcCCC--HHHHHHcCCCceeEEEEE--cCCEEEEEecCCCCHHHHHHHHHHHhc
Confidence            334688888888653  367889999999999999  469999999999999999888877654

>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=96.70  E-value=0.016  Score=42.22  Aligned_cols=72  Identities=18%  Similarity=0.213  Sum_probs=56.0

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ++...+|.||..+|+ +.-.+..++||.+|...|.... +.+....+|+..  .+.  |  ++++||.++|+. +++|.+
T Consensus        14 ~~~~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrLi~~--Gk~--L--~D~~tL~~~gi~~g~~i~l   85 (106)
T 1wx7_A           14 DPHLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRF-KAHPDQLVLIFA--GKI--L--KDPDSLAQCGVRDGLTVHL   85 (106)
T ss_dssp             CSSEEEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHH-TCCTTTEEEEET--TEE--C--CTTSCHHHHTCCTTEEEEE
T ss_pred             CCceEEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHH-CcChhhEEEEEC--CEE--C--CCcCcHHHcCCCCCCEEEE
Confidence            356789999999996 6888999999999999998764 566788888754  332  5  457999999998 455555


Q ss_pred             E
Q 025774          246 T  246 (248)
Q Consensus       246 ~  246 (248)
                      .
T Consensus        86 ~   86 (106)
T 1wx7_A           86 V   86 (106)
T ss_dssp             E
T ss_pred             E
Confidence            4

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

Probab=96.69  E-value=0.019  Score=43.28  Aligned_cols=72  Identities=15%  Similarity=0.231  Sum_probs=56.3

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +....+|.|+.. |+.+.-.+..++||.+|..-|.... +.+....+|+..  .+.  |  ++++||.++|+.+ ++|.+
T Consensus        29 ~~~~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~QrLi~~--Gk~--L--~D~~tL~dygI~~gstI~l  100 (125)
T 1j8c_A           29 EPKIIKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRF-KSQTDQLVLIFA--GKI--L--KDQDTLIQHGIHDGLTVHL  100 (125)
T ss_dssp             CCCCEEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHH-CSCSSSEEEEET--TEE--E--STTSCGGGTTCSSSEEEEE
T ss_pred             CCCcEEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHH-CcCcceEEEEEC--CEE--c--CCCCCHHHcCCCCCCEEEE
Confidence            345788999998 8899999999999999999998764 566788888753  332  5  4579999999984 55544


Q ss_pred             E
Q 025774          246 T  246 (248)
Q Consensus       246 ~  246 (248)
                      .
T Consensus       101 v  101 (125)
T 1j8c_A          101 V  101 (125)
T ss_dssp             E
T ss_pred             E
Confidence            3

>2i4a_A Thioredoxin; acidophIle, disulfide exchange, oxidoreductase; 1.00A {Acetobacter aceti}

Probab=96.66  E-value=0.011  Score=41.72  Aligned_cols=58  Identities=17%  Similarity=0.221  Sum_probs=46.7

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +..++.+...|++...  .++..|++..+|++.++  .+|..+.++.|..+.+++...|...
T Consensus        49 ~~~~~~~~~v~~~~~~--~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~  106 (107)
T 2i4a_A           49 FAGKVTVAKVNIDDNP--ETPNAYQVRSIPTLMLV--RDGKVIDKKVGALPKSQLKAWVESA  106 (107)
T ss_dssp             HTTSEEEEEEETTTCC--HHHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHT
T ss_pred             hCCcEEEEEEECCCCH--HHHHhcCCCccCEEEEE--eCCEEEEEecCCCCHHHHHHHHHhc
Confidence            3447899999986543  57889999999999999  4699999999999999887766543

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

Probab=96.65  E-value=0.015  Score=42.73  Aligned_cols=71  Identities=18%  Similarity=0.235  Sum_probs=57.3

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ...+|.|+.++|+.+.-.+..++||.+|..-+.... +.++...+|+..  .+.  +  +.++||.++|+. +++|.+.
T Consensus        34 ~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrLi~~--Gk~--L--~D~~tL~~~gI~~gs~I~l~  105 (111)
T 2ojr_A           34 LAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHLV  105 (111)
T ss_dssp             SCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHH-CCCTTTEEEEET--TEE--C--CSSCBTTTTTCCTTCEEEEE
T ss_pred             CeEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHH-CcCcccEEEEEC--CEE--C--CCCCcHHHcCCCCCCEEEEE
Confidence            468899999999999999999999999999998764 567788888763  332  5  458999999998 5666554

>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=96.64  E-value=0.01  Score=40.51  Aligned_cols=70  Identities=17%  Similarity=0.225  Sum_probs=55.4

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ...|.|+..+|+.+.-....++||..|.+-+.... +.++...+|...  .+.  +  +++.||+++|+. +++|.+.
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~-gi~~~~qrL~~~--G~~--L--~d~~tl~~~~i~~~~~i~l~   73 (79)
T 2uyz_B            3 YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQ-GVPMNSLRFLFE--GQR--I--ADNHTPKELGMEEEDVIEVY   73 (79)
T ss_dssp             EEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHH-TCCGGGEEEEET--TEE--C--CTTCCHHHHTCCTTEEEEEE
T ss_pred             eEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHH-CCCcccEEEEEC--CEE--e--CCCCCHHHcCCCCCCEEEEE
Confidence            46789999999999999999999999999998763 666778888653  443  5  457999999998 4555443

>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=96.62  E-value=0.016  Score=42.58  Aligned_cols=71  Identities=11%  Similarity=0.176  Sum_probs=56.9

Q ss_pred             CceEEEEEcC---CCceEEEeeCC-CCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceE
Q 025774          169 LLCRVGVRLP---DGRRMQRNFLR-TDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMI  243 (248)
Q Consensus       169 ~~~~i~iRlp---~G~r~~r~F~~-~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v  243 (248)
                      +.++|.|+.|   +|+.+.-.+.. ++||.+|-.-|... .+.++...+|+..  .+.  +  +++.||.+.|+. +++|
T Consensus        26 ~~i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~-~gip~~~QrL~~~--Gk~--L--~D~~tL~~y~I~~g~~l   98 (111)
T 1we6_A           26 GPATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGE-IQIPANKQKLSGK--AGF--L--KDNMSLAHYNVGAGEIL   98 (111)
T ss_dssp             SCEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHH-TTCCTTTSEEECS--SSB--C--CTTSBTTTTTCSSSCEE
T ss_pred             CcEEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHH-HCCCHHHeEEEEC--CEE--C--CCCCcHHHCCCCCCCEE
Confidence            4589999999   89999999997 99999999999876 4667788888763  332  4  458999999998 5666


Q ss_pred             EEE
Q 025774          244 SVT  246 (248)
Q Consensus       244 ~v~  246 (248)
                      .+.
T Consensus        99 ~l~  101 (111)
T 1we6_A           99 TLS  101 (111)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            554

>2qsi_A Putative hydrogenase expression/formation protein; HUPG, MCS SAD, structural genomics, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=96.61  E-value=0.0084  Score=46.10  Aligned_cols=58  Identities=10%  Similarity=0.159  Sum_probs=50.5

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .+.|+.+|++  +...++..|++.+.|+++++  ++|+.+.++.|..+.+++...|...+++
T Consensus        67 ~v~~~KVdvD--e~~~la~~ygV~siPTlilF--kdG~~v~~~vG~~~k~~l~~~l~~~l~~  124 (137)
T 2qsi_A           67 RLVAAEVAAE--AERGLMARFGVAVCPSLAVV--QPERTLGVIAKIQDWSSYLAQIGAMLAE  124 (137)
T ss_dssp             TEEEEEECGG--GHHHHHHHHTCCSSSEEEEE--ECCEEEEEEESCCCHHHHHHHHHHHHHH
T ss_pred             CcEEEEEECC--CCHHHHHHcCCccCCEEEEE--ECCEEEEEEeCCCCHHHHHHHHHHHhcc
Confidence            5788888874  56789999999999999999  5799999999999999998888877754

>3tco_A Thioredoxin (TRXA-1); disulfide oxidoreductase, oxidoreductase; 1.90A {Sulfolobus solfataricus} SCOP: c.47.1.0

Probab=96.59  E-value=0.0091  Score=42.24  Aligned_cols=58  Identities=22%  Similarity=0.432  Sum_probs=47.4

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ..++.+...|++.  ...++..|++..+|++.++  .+|..+.++.|..+.++|...|...+
T Consensus        51 ~~~~~~~~v~~~~--~~~~~~~~~i~~~Pt~~~~--~~g~~~~~~~g~~~~~~l~~~l~~~l  108 (109)
T 3tco_A           51 KGKAVFGRLNVDE--NQKIADKYSVLNIPTTLIF--VNGQLVDSLVGAVDEDTLESTVNKYL  108 (109)
T ss_dssp             TTTSEEEEEETTT--CHHHHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHC
T ss_pred             CCCceEEEEcccc--CHHHHHhcCcccCCEEEEE--cCCcEEEeeeccCCHHHHHHHHHHHh
Confidence            3467888888754  3467899999999999999  46999999999999999988777654

>2trx_A Thioredoxin; electron transport; 1.68A {Escherichia coli} SCOP: c.47.1.1 PDB: 1skr_B* 1skw_B* 1sl0_B* 1sks_B* 1sl2_B* 1t7p_B* 1t8e_B* 1tk0_B* 1tk5_B* 1tk8_B* 1tkd_B* 1sl1_B* 1x9s_B* 1x9w_B* 1xoa_A 1xob_A 1zyq_B* 2ajq_B* 2bto_T* 2h6x_A ...

Probab=96.59  E-value=0.011  Score=41.85  Aligned_cols=59  Identities=17%  Similarity=0.211  Sum_probs=47.4

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      +..++.+...|++...  .++..|++..+|++.++  .+|..+.++.|..+.++|...|...+
T Consensus        49 ~~~~~~~~~v~~~~~~--~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~l  107 (108)
T 2trx_A           49 YQGKLTVAKLNIDQNP--GTAPKYGIRGIPTLLLF--KNGEVAATKVGALSKGQLKEFLDANL  107 (108)
T ss_dssp             TTTTEEEEEEETTTCT--THHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHH
T ss_pred             hCCCcEEEEEECCCCH--HHHHHcCCcccCEEEEE--eCCEEEEEEecCCCHHHHHHHHHHhh
Confidence            3346889898886533  57789999999999998  46999999999999998877776654

>2voc_A Thioredoxin; electron transport, homodimer, disulfide, transport, redox-active center; 1.50A {Bacillus subtilis} PDB: 2ipa_A 2gzy_A 2gzz_A

Probab=96.57  E-value=0.011  Score=42.70  Aligned_cols=63  Identities=21%  Similarity=0.284  Sum_probs=49.5

Q ss_pred             HHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           14 QTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        14 ~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      +-+..++.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.++|...|...+..
T Consensus        44 ~~~~~~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~~~~  106 (112)
T 2voc_A           44 QEMGDKLKIVKIDVDEN--QETAGKYGVMSIPTLLVL--KDGEVVETSVGFKPKEALQELVNKHLLE  106 (112)
T ss_dssp             HHHTTTCEEEEEETTTC--CSHHHHTTCCSBSEEEEE--ETTEEEEEEESCCCHHHHHHHHHTTSCS
T ss_pred             HHhCCCcEEEEEECCCC--HHHHHHcCCCcccEEEEE--eCCEEEEEEeCCCCHHHHHHHHHHHHHh
Confidence            33445789999998653  357889999999999999  4699999999999999887766665543

>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=96.57  E-value=0.017  Score=41.26  Aligned_cols=71  Identities=18%  Similarity=0.245  Sum_probs=57.9

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      ++.+.|-|+.++|+.+.-.+..+|||.+|-.-|... .|.++..-+|...  .+.  +  +++.||+|.|+.+ ++|.+
T Consensus        19 ~~mIqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k-~Gip~~qQrLif~--Gk~--L--kD~~TL~dY~I~dgstLhL   90 (93)
T 3plu_A           19 SHMIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQ-IGTQPNKIVLQKG--GSV--L--KDHISLEDYEVHDQTNLEL   90 (93)
T ss_dssp             -CEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHH-HTCCGGGEEEEET--TEE--C--CTTSBTGGGTCCTTCEEEE
T ss_pred             CceEEEEEECCCCCEEEEEECCcCHHHHHHHHHHHH-hCCCHHHEEEEeC--CEE--c--cCcCCHHHcCCCCCCEEEE
Confidence            568999999999999999999999999999999876 3667888899764  343  5  5589999999984 55544

>2yzu_A Thioredoxin; redox protein, electron transport, structural genomics; 1.90A {Thermus thermophilus} PDB: 2cvk_A

Probab=96.56  E-value=0.013  Score=41.29  Aligned_cols=59  Identities=17%  Similarity=0.280  Sum_probs=47.5

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ..++.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.+++...|...+.
T Consensus        48 ~~~~~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~g~~~~~~~g~~~~~~l~~~l~~~l~  106 (109)
T 2yzu_A           48 EGKLLVAKLDVDEN--PKTAMRYRVMSIPTVILF--KDGQPVEVLVGAQPKRNYQAKIEKHLP  106 (109)
T ss_dssp             BTTBEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHTTC-
T ss_pred             hCceEEEEEECCCC--HhHHHhCCCCcCCEEEEE--eCCcEeeeEeCCCCHHHHHHHHHHHhh
Confidence            34689999998654  357889999999999998  468889999999999988777766543

>1nsw_A Thioredoxin, TRX; thermostability, electron transport; 1.90A {Alicyclobacillus acidocaldarius} SCOP: c.47.1.1 PDB: 1rqm_A 1quw_A 1nw2_A

Probab=96.55  E-value=0.01  Score=41.91  Aligned_cols=58  Identities=16%  Similarity=0.287  Sum_probs=46.2

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ..++.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.+++...|...+
T Consensus        47 ~~~v~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~l  104 (105)
T 1nsw_A           47 ADKVTVAKLNVDEN--PETTSQFGIMSIPTLILF--KGGRPVKQLIGYQPKEQLEAQLADVL  104 (105)
T ss_dssp             TTTCEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHTTTTT
T ss_pred             cCCcEEEEEECcCC--HHHHHHcCCccccEEEEE--eCCeEEEEEecCCCHHHHHHHHHHHh
Confidence            34588888888643  467889999999999999  46888999999999988876665543

>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=96.55  E-value=0.023  Score=39.64  Aligned_cols=72  Identities=22%  Similarity=0.204  Sum_probs=56.5

Q ss_pred             CCceEEEEEcCCC-ceEEE-eeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEE
Q 025774          168 SLLCRVGVRLPDG-RRMQR-NFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMIS  244 (248)
Q Consensus       168 ~~~~~i~iRlp~G-~r~~r-~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~  244 (248)
                      .....|.||.++| +.+.- .+..++||.+|..-|... .+.++...+|+..  .+.  +  +++.||.++|+. +++|.
T Consensus         5 ~~~m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~-~gip~~~qrL~~~--gk~--L--~d~~tL~~~~i~~g~~i~   77 (89)
T 1wy8_A            5 SSGMWIQVRTIDGSKTCTIEDVSRKATIEELRERVWAL-FDVRPECQRLFYR--GKQ--L--ENGYTLFDYDVGLNDIIQ   77 (89)
T ss_dssp             SSCEEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHH-SCCCTTTEEEEET--TEE--C--CSSSBHHHHTCCTTCEEE
T ss_pred             CCcEEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHH-HCcChhhEEEEEC--CeE--C--CCCCCHHHCCCCCCCEEE
Confidence            3568899999999 67877 599999999999999876 4667888888764  332  5  457999999998 56665


Q ss_pred             EE
Q 025774          245 VT  246 (248)
Q Consensus       245 v~  246 (248)
                      +.
T Consensus        78 l~   79 (89)
T 1wy8_A           78 LL   79 (89)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>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=96.55  E-value=0.013  Score=41.21  Aligned_cols=68  Identities=15%  Similarity=0.227  Sum_probs=54.3

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +|.||..+|+.+.-.+..++||.+|-.-+.... +.++...+|+..  .+  .+  +++.||.++|+. +++|.+.
T Consensus         2 ~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrLi~~--Gk--~L--~D~~tL~~~~i~~g~~l~l~   70 (88)
T 4fbj_B            2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKE-GIPPQQQRLIYS--GK--QM--NDEKTAADYKILGGSVLHLV   70 (88)
T ss_dssp             EEEEEETTCCEEEEECCTTCBHHHHHHHHHHHH-CCCGGGCEEEET--TE--EC--CTTSBTTTTTCCTTCEEEEE
T ss_pred             EEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHH-CcChhHEEEEEC--Ce--EC--CCCCcHHHcCCCCCCEEEEE
Confidence            588999999999999999999999999998764 567778888763  33  25  458999999998 5566553

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

Probab=96.53  E-value=0.017  Score=43.81  Aligned_cols=77  Identities=10%  Similarity=0.158  Sum_probs=58.1

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCC-------------------------cccc-
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGA-------------------------TKSL-  225 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~-------------------------~~~l-  225 (248)
                      .|.||+|||...+-+-..+.+|..+...|...+.-.....|.|+...|..                         ...+ 
T Consensus        13 ~LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kigI~n~~ey~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~k~kL~   92 (128)
T 2kc2_A           13 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKDEGTGTLRKDKTLLRDEKKMEKLKQKLH   92 (128)
T ss_dssp             EEEEECTTSCEEEEEEEECSSHHHHHHHHHHHHTCCCCSSEEEEEECCCCCCCCCSSCCSSSSSCSCCSCCSCSSCCSCC
T ss_pred             cEEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhCCCCcccccccccccccccccCchhhccccccccchhHHHHHHHHhc
Confidence            49999999999999999999999999998887654445678988654421                         0011 


Q ss_pred             ------CCCcCCCccccCCc-CceEEEEeC
Q 025774          226 ------DYDSKLTFEDSGLA-NAMISVTWE  248 (248)
Q Consensus       226 ------~~d~~~tl~d~gl~-~~~v~v~~~  248 (248)
                            ..|.++||.+-|+. +++|+++++
T Consensus        93 ~dd~~~WLD~srtL~EQGI~e~~tllLRrK  122 (128)
T 2kc2_A           93 TDDELNWLDHGRTLREQGVEEHETLLLRRK  122 (128)
T ss_dssp             CSSSEEEECSSSCHHHHTCCTTSEEEEEES
T ss_pred             ccCCCCcccCCCcHHHcCCCCCCEEEEEEE
Confidence                  12458999999998 788887763

>1w4v_A Thioredoxin, mitochondrial; antioxidant enzyme, mitochondrion, electron TRA oxidoreductase; 1.80A {Homo sapiens} PDB: 1uvz_A 1w89_A

Probab=96.53  E-value=0.015  Score=42.43  Aligned_cols=57  Identities=18%  Similarity=0.342  Sum_probs=47.0

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      .++.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.++|...|...+
T Consensus        62 ~~v~~~~vd~d~~--~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~l  118 (119)
T 1w4v_A           62 GKVVMAKVDIDDH--TDLAIEYEVSAVPTVLAM--KNGDVVDKFVGIKDEDQLEAFLKKLI  118 (119)
T ss_dssp             TSSEEEEEETTTT--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCC--HHHHHHcCCCcccEEEEE--eCCcEEEEEcCCCCHHHHHHHHHHHh
Confidence            4688999988653  368899999999999988  46998999999999998877776654

>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=96.52  E-value=0.011  Score=42.03  Aligned_cols=70  Identities=17%  Similarity=0.144  Sum_probs=53.9

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ....+|.||..+|+.+.-.+..+++|.+|..-+....    +...+|+..  .+.  | .|.+.||.++|+. +++|.+.
T Consensus         5 ~~~m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~----~~~qrLi~~--Gk~--L-~D~~~tL~~y~i~~g~~i~l~   75 (95)
T 1wia_A            5 SSGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ----ESQMKLIYQ--GRL--L-QDPARTLSSLNITNNCVIHCH   75 (95)
T ss_dssp             CCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST----TTTCEEEET--TEE--C-CCSSCBTTTTTCCTTEEEEEE
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC----cCcEEEEEC--CEE--c-cCCcCCHHHcCCCCCCEEEEE
Confidence            3468899999999999999999999999999987652    667778643  443  5 2444999999998 4556554

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

Probab=96.52  E-value=0.016  Score=41.91  Aligned_cols=74  Identities=18%  Similarity=0.245  Sum_probs=55.7

Q ss_pred             CCCceEEEEEcCCCceEEE--eeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCC-c-Cce
Q 025774          167 RSLLCRVGVRLPDGRRMQR--NFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGL-A-NAM  242 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r--~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl-~-~~~  242 (248)
                      .++..+|-|+..+|+.+.-  .+..++||..|-.-+.....+.++...+|+..  ++.  |  +.+.||+++|+ . +++
T Consensus        16 ~~~~m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~--Gk~--L--~D~~tL~dy~I~~~g~t   89 (98)
T 4a20_A           16 DNAAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLK--GKV--L--HDNLFLSDLKVTPANST   89 (98)
T ss_dssp             --CCEEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEET--TEE--E--CTTCBGGGSCCBTTBCE
T ss_pred             CCCCEEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcCCChhhEEEEEC--CEE--C--cCcCCHHHcCcCCCCCE
Confidence            3557899999999987655  56699999999999944455777888898764  443  5  45799999999 6 666


Q ss_pred             EEEE
Q 025774          243 ISVT  246 (248)
Q Consensus       243 v~v~  246 (248)
                      |++.
T Consensus        90 i~lm   93 (98)
T 4a20_A           90 ITVM   93 (98)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6554

>1oaz_A Thioredoxin 1; immune system, antibody/complex, antibody, allergy, IGE, conformational diversity, multispecficity, redox-active center; 2.77A {Escherichia coli} SCOP: c.47.1.1

Probab=96.51  E-value=0.0034  Score=46.69  Aligned_cols=58  Identities=17%  Similarity=0.198  Sum_probs=45.2

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +..++.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.+++...|...
T Consensus        64 ~~~~~~~~~vd~d~~--~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~  121 (123)
T 1oaz_A           64 YQGKLTVAKLNIDQN--PGTAPKYGIRGIPTLLLF--KNGEVAATKVGALSKGQLKEFLDAN  121 (123)
T ss_dssp             ----CEEEEEETTSC--TTTGGGGTCCBSSEEEEE--ESSSEEEEEESCCCHHHHHHHHTTT
T ss_pred             hcCCeEEEEEECCCC--HHHHHHcCCCccCEEEEE--ECCEEEEEEeCCCCHHHHHHHHHHH
Confidence            344688999998754  357889999999999998  4699999999999999887776654

>3fk8_A Disulphide isomerase; APC61824.1, xylella fastidiosa temecul structural genomics, PSI-2, protein structure initiative; 1.30A {Xylella fastidiosa}

Probab=96.50  E-value=0.0067  Score=45.15  Aligned_cols=69  Identities=17%  Similarity=0.255  Sum_probs=52.6

Q ss_pred             CCCHHHHHHhhcceEEEEEecCC-hHHHHHHHhcCC---CCCceEEEEeCCCCceEEeeeC-------CCChHHHHHHHh
Q 025774            7 WANEAVSQTISTNFIFWQVYDDT-SEGKKVCTYYKL---DSIPVVLVVDPITGQKMRSWCG-------MVQPESLLEDLV   75 (248)
Q Consensus         7 l~~~~v~~~l~~~fV~w~~d~~~-~eg~~~~~~~~~---~~~P~l~ii~~~~g~~l~~~~G-------~~~~e~l~~~L~   75 (248)
                      |.+..+.+.++.++.+...|++. .+...++..|++   ..+|+++++++ +|..+.+..|       ..+.+++...|.
T Consensus        51 l~~~~~~~~~~~~~~~~~vd~~~~~~~~~l~~~~~v~~~~~~Pt~~~~d~-~G~~~~~~~g~~~~~~~~~~~~~l~~~l~  129 (133)
T 3fk8_A           51 LRNQKNTALIAKHFEVVKIDVGNFDRNLELSQAYGDPIQDGIPAVVVVNS-DGKVRYTTKGGELANARKMSDQGIYDFFA  129 (133)
T ss_dssp             HTSHHHHHHHHHHCEEEEEECTTTTSSHHHHHHTTCGGGGCSSEEEEECT-TSCEEEECCSCTTTTGGGSCHHHHHHHHH
T ss_pred             hCCHHHHHHhcCCEEEEEEeCCcccchHHHHHHhCCccCCccceEEEECC-CCCEEEEecCCcccccccCCHHHHHHHHH
Confidence            33456666776789999999943 345678999999   99999999984 5899998888       667776655554


Q ss_pred             h
Q 025774           76 P   76 (248)
Q Consensus        76 ~   76 (248)
                      .
T Consensus       130 ~  130 (133)
T 3fk8_A          130 K  130 (133)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3ul3_B Thioredoxin, thioredoxin-2; PTEX, oxidoreductase; 2.90A {Plasmodium falciparum}

Probab=96.50  E-value=0.013  Score=43.37  Aligned_cols=60  Identities=10%  Similarity=0.203  Sum_probs=48.2

Q ss_pred             HHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           13 SQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        13 ~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      .+-+..++.+...|++..  ..++..|++..+|+++++  .+|..+.++.|..+.+++...|.+
T Consensus        68 ~~~~~~~v~~~~vd~d~~--~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~  127 (128)
T 3ul3_B           68 QKYYGKRIYLLKVDLDKN--ESLARKFSVKSLPTIILL--KNKTMLARKDHFVSSNDLIALIKK  127 (128)
T ss_dssp             HHHHGGGEEEEEEEGGGC--HHHHHHTTCCSSSEEEEE--ETTEEEEEESSCCCHHHHHHHHTT
T ss_pred             HHHhcCCeEEEEEECCCC--HHHHHHcCCCCcCEEEEE--ECCEEEEEecCCCCHHHHHHHHHh
Confidence            334445789999998654  378899999999999999  368999999999999988776643

>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=96.49  E-value=0.015  Score=42.85  Aligned_cols=71  Identities=18%  Similarity=0.235  Sum_probs=57.0

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ...+|.||..+|+.+.-.+..++||..|-..+.... +.++...+|+..  .+.  +  +.+.||.++|+. +++|.+.
T Consensus        34 ~~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~QrLi~~--Gk~--L--~D~~tL~~~gI~~gs~I~l~  105 (111)
T 3vdz_A           34 LAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHLV  105 (111)
T ss_dssp             GCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTSBTTTTTCCTTCEEEEE
T ss_pred             ccEEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHh-CCChHHEEEEEC--CEE--C--CCCCcHHHCCCCCCCEEEEE
Confidence            357899999999999999999999999999998864 667778888753  442  5  457899999998 5666554

>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=96.49  E-value=0.01  Score=42.29  Aligned_cols=71  Identities=15%  Similarity=0.200  Sum_probs=55.1

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      ++...+|.|+.. |+.+.-.+..++||.+|..-|.... +.++...+|+..  .+.  +  +++.||.++|+.+ ++|.+
T Consensus        14 ~~~~m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~-gip~~~qrL~~~--Gk~--L--~D~~tL~~~gi~~g~~i~l   85 (96)
T 1wx8_A           14 SSRIIRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYL-HCNADRLVLIFT--GKI--L--RDQDILSQRGILDGSTVHV   85 (96)
T ss_dssp             CSCEEEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHT-CSCTTTBCCEET--TEE--C--CTTSCHHHHTCCTTEEEEC
T ss_pred             CCCcEEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHh-CCCHHHEEEEEC--CEE--C--CCcCCHHHCCCCCCCEEEE
Confidence            356788999998 8899999999999999999998863 556777777653  332  5  4579999999985 55544

>1dby_A Chloroplast thioredoxin M CH2; thioredoxin CH2, chloroplastic thioredoxin, oxidoreductase; NMR {Chlamydomonas reinhardtii} SCOP: c.47.1.1

Probab=96.48  E-value=0.017  Score=40.89  Aligned_cols=58  Identities=21%  Similarity=0.410  Sum_probs=46.4

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ..++.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.+++...|...+
T Consensus        49 ~~~~~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~l  106 (107)
T 1dby_A           49 KDKLKCVKLNTDES--PNVASEYGIRSIPTIMVF--KGGKKCETIIGAVPKATIVQTVEKYL  106 (107)
T ss_dssp             TTTCEEEEEETTTC--HHHHHHHTCCSSCEEEEE--SSSSEEEEEESCCCHHHHHHHHHHHC
T ss_pred             CCceEEEEEECCCC--HHHHHHCCCCcCCEEEEE--eCCEEEEEEeCCCCHHHHHHHHHHHh
Confidence            34688888888643  357889999999998877  46899999999999998877776654

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

Probab=96.45  E-value=0.019  Score=40.94  Aligned_cols=72  Identities=21%  Similarity=0.257  Sum_probs=55.6

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v~  246 (248)
                      .....|.||.++| .+.-.+..++||.+|..-|... .+.++...+|+.  ..+.  +. |.+.||.++|+.+ ++|.+.
T Consensus        13 ~~~~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~-~gip~~~QrLi~--~Gk~--L~-D~~~tL~~ygI~~gstl~lv   85 (94)
T 2kan_A           13 VRKIHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIV-ENTPIKRMQLYY--SGIE--LA-DDYRNLNEYGITEFSEIVVF   85 (94)
T ss_dssp             SCCEEEEEECSSC-EEEEEECTTCBHHHHHHHHHHH-SSSCTTTEEEEE--TTEE--EC-CTTSBHHHHTCCTTEEEEEE
T ss_pred             CCCEEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHH-HCcCHHHEEEEE--CCEE--CC-CCcccHHHCCCCCCCEEEEE
Confidence            3458899999999 7888999999999999999886 466788888874  3543  52 4339999999984 555443

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

Probab=96.44  E-value=0.024  Score=40.91  Aligned_cols=70  Identities=16%  Similarity=0.231  Sum_probs=55.2

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ...+|.|+.. |+.+.-.+..++||.+|..-|.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus        24 ~~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrLi~~--Gk~--L--~D~~tL~~~gI~~g~~I~l~   94 (101)
T 2klc_A           24 KIMKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRF-KSHTDQLVLIFA--GKI--L--KDQDTLSQHGIHDGLTVHLV   94 (101)
T ss_dssp             CCEEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHH-TCCGGGEEEEET--TEE--E--CTTCCTGGGTCCTTCEEEEE
T ss_pred             CeEEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHH-CcChhhEEEEEC--CEE--C--CCcCcHHHcCCCCCCEEEEE
Confidence            4688999998 8888899999999999999998764 666778888653  443  5  457999999998 5555554

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

Probab=96.43  E-value=0.017  Score=40.52  Aligned_cols=69  Identities=17%  Similarity=0.232  Sum_probs=55.3

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ..|-++..+|+.+.-.+..++||.+|..-+.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus        10 ~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrL~~~--Gk~--L--~D~~tL~~~gi~~g~~i~l~   79 (88)
T 1sif_A           10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHLV   79 (88)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHH-CCCGGGCEEEET--TEE--C--CTTSBSGGGTCCTTCEEEEE
T ss_pred             eEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHH-CcChhhEEEEEC--CEE--C--CCCCcHHHcCCCCCCEEEEE
Confidence            5788999999999999999999999999998764 567788888753  443  5  347999999998 4555553

>4euy_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, unknown function; 2.90A {Bacillus cereus}

Probab=96.41  E-value=0.013  Score=41.76  Aligned_cols=64  Identities=14%  Similarity=0.177  Sum_probs=43.0

Q ss_pred             HHHHHhhc--ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           11 AVSQTIST--NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        11 ~v~~~l~~--~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      .+.++.+.  ++.|...|++...  .++..|++..+|++.++.  +|..+.++.|..+.++|...|...+
T Consensus        39 ~~~~~~~~~~~~~~~~vd~~~~~--~l~~~~~v~~~Pt~~~~~--~G~~~~~~~g~~~~~~l~~~l~~~~  104 (105)
T 4euy_A           39 KVNYVLENYNYVEKIEILLQDMQ--EIAGRYAVFTGPTVLLFY--NGKEILRESRFISLENLERTIQLFE  104 (105)
T ss_dssp             HHHHHHHTCTTEEEEEEEECCC-----------CCCCEEEEEE--TTEEEEEEESSCCHHHHHHHHHTTC
T ss_pred             HHHHHHHHcCCceEEEEECCCCH--HHHHhcCCCCCCEEEEEe--CCeEEEEEeCCcCHHHHHHHHHHhh
Confidence            34444443  6888888886443  678899999999999994  6999999999999999988777654

>1t00_A Thioredoxin, TRX; redox regulation, multifunction macromolecule, electron transport; 1.51A {Streptomyces coelicolor}

Probab=96.38  E-value=0.018  Score=41.14  Aligned_cols=58  Identities=19%  Similarity=0.283  Sum_probs=47.1

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .++.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.+++...|...+.
T Consensus        54 ~~~~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~l~  111 (112)
T 1t00_A           54 DKIEIVKLNIDEN--PGTAAKYGVMSIPTLNVY--QGGEVAKTIVGAKPKAAIVRDLEDFIA  111 (112)
T ss_dssp             TTCEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHTHHHHC
T ss_pred             CCeEEEEEEcCCC--HHHHHhCCCCcccEEEEE--eCCEEEEEEeCCCCHHHHHHHHHHHhh
Confidence            4688888888653  457889999999998877  468999999999999988877766653

>1v98_A Thioredoxin; oxidoreductase, structural genomics, riken structural genomics/proteomics initiative, RSGI; 1.82A {Thermus thermophilus}

Probab=96.38  E-value=0.023  Score=42.64  Aligned_cols=58  Identities=21%  Similarity=0.434  Sum_probs=48.4

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .++.|...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.++|...|...++
T Consensus        81 ~~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~i~~~l~  138 (140)
T 1v98_A           81 GRLKVVKVNVDEH--PGLAARYGVRSVPTLVLF--RRGAPVATWVGASPRRVLEERLRPYLE  138 (140)
T ss_dssp             TTEEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHHT
T ss_pred             CceEEEEEECCCC--HHHHHHCCCCccCEEEEE--eCCcEEEEEeCCCCHHHHHHHHHHHHc
Confidence            4689999998653  468899999999999988  469999999999999988888777664

>3p2a_A Thioredoxin 2, putative thioredoxin-like protein; structural genomics, center for structural genomics of infec diseases, csgid; 2.19A {Yersinia pestis}

Probab=96.37  E-value=0.022  Score=43.24  Aligned_cols=61  Identities=16%  Similarity=0.277  Sum_probs=50.8

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ..++.|...|++..  ..++..|++..+|+++++.  +|..+.++.|..+.++|...|...+...
T Consensus        85 ~~~~~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~--~G~~~~~~~G~~~~~~l~~~l~~~l~~~  145 (148)
T 3p2a_A           85 AGKVRFVKVNTEAE--PALSTRFRIRSIPTIMLYR--NGKMIDMLNGAVPKAPFDNWLDEQLSRD  145 (148)
T ss_dssp             TTTCEEEEEETTTC--HHHHHHTTCCSSSEEEEEE--TTEEEEEESSCCCHHHHHHHHHHHHHSC
T ss_pred             CCceEEEEEECcCC--HHHHHHCCCCccCEEEEEE--CCeEEEEEeCCCCHHHHHHHHHHHhccc
Confidence            34688888888654  3678999999999998883  6999999999999999998888887753

>3ira_A Conserved protein; methanosarcina mazei,structural genomics, MCSG, protein structure initiative, midwest center for STRU genomics; 2.10A {Methanosarcina mazei}

Probab=96.34  E-value=0.006  Score=48.77  Aligned_cols=74  Identities=12%  Similarity=0.197  Sum_probs=51.2

Q ss_pred             cccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhc--------CCCCCceEEEEeCCCCceEEeee-----CCCChHHH
Q 025774            4 RDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYY--------KLDSIPVVLVVDPITGQKMRSWC-----GMVQPESL   70 (248)
Q Consensus         4 r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~--------~~~~~P~l~ii~~~~g~~l~~~~-----G~~~~e~l   70 (248)
                      ..+|.++.|.++++.+||+...|.+...  .++..|        ++..+|++++++|. |..+....     |..+.+.|
T Consensus        59 ~~~f~~~~va~~l~~~fv~ikVD~de~~--~l~~~y~~~~q~~~gv~g~Pt~v~l~~d-G~~v~~~ty~p~~~~~~~~~f  135 (173)
T 3ira_A           59 HESFEDEEVAGLMNEAFVSIKVDREERP--DIDNIYMTVCQIILGRGGWPLNIIMTPG-KKPFFAGTYIPKNTRFNQIGM  135 (173)
T ss_dssp             HHTTTCHHHHHHHHHHCEEEEEETTTCH--HHHHHHHHHHHHHHSCCCSSEEEEECTT-SCEEEEESSCCSSCBTTBCCH
T ss_pred             ccccCCHHHHHHHHhcCceeeeCCcccC--cHHHHHHHHHHHHcCCCCCcceeeECCC-CCceeeeeeCCCCcCCCCCCH
Confidence            3488999999999999999999997432  233334        89999999999874 88766432     12233445


Q ss_pred             HHHHhhhhhc
Q 025774           71 LEDLVPFMDG   80 (248)
Q Consensus        71 ~~~L~~~~~~   80 (248)
                      ...|..+.+.
T Consensus       136 ~~~L~~v~~~  145 (173)
T 3ira_A          136 LELVPRIKEI  145 (173)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5555555443

>2o8v_B Thioredoxin 1; disulfide crosslinked complex, oxidoreductase; 3.00A {Escherichia coli}

Probab=96.33  E-value=0.011  Score=44.16  Aligned_cols=59  Identities=17%  Similarity=0.211  Sum_probs=47.7

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      +..++.|...|++...  .++..|++..+|++.++  .+|..+.++.|..+.++|...|...+
T Consensus        69 ~~~~v~~~~vd~~~~~--~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~l  127 (128)
T 2o8v_B           69 YQGKLTVAKLNIDQNP--GTAPKYGIRGIPTLLLF--KNGEVAATKVGALSKGQLKEFLDANL  127 (128)
T ss_dssp             TTTTEEEEEEETTTCC--TTSGGGTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHH
T ss_pred             hcCCeEEEEEECCCCH--HHHHHcCCCccCEEEEE--eCCEEEEEEcCCCCHHHHHHHHHHhh
Confidence            3447889999886433  57789999999999998  46999999999999998887776654

>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=96.29  E-value=0.024  Score=41.89  Aligned_cols=71  Identities=15%  Similarity=0.206  Sum_probs=56.1

Q ss_pred             CceEEEEEcCC----------CceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCC
Q 025774          169 LLCRVGVRLPD----------GRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGL  238 (248)
Q Consensus       169 ~~~~i~iRlp~----------G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl  238 (248)
                      +.++|.|++|+          |+.+.-.+..++||.+|-.-|... .+.++...+|+..  .+.  +  +++.||.+.|+
T Consensus        24 ~~i~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~-~gip~~~QrL~~~--Gk~--L--~D~~tL~~y~i   96 (115)
T 1we7_A           24 GPVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEA-TGMPAGKQKLQYE--GIF--I--KDSNSLAYYNM   96 (115)
T ss_dssp             SCEEEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHH-SSCCTTTEEEEET--TEE--E--CTTSBHHHHTC
T ss_pred             CCEEEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHH-HCCChHHEEEEEC--CEE--C--CCCCCHHHCCC
Confidence            46899999995          778888999999999999999875 4667788888753  432  5  45799999999


Q ss_pred             c-CceEEEE
Q 025774          239 A-NAMISVT  246 (248)
Q Consensus       239 ~-~~~v~v~  246 (248)
                      . +++|.+.
T Consensus        97 ~~g~~i~lv  105 (115)
T 1we7_A           97 ASGAVIHLA  105 (115)
T ss_dssp             CSSCEEEEE
T ss_pred             CCCCEEEEE
Confidence            8 5666554

>1fb6_A Thioredoxin M; electron transport; 2.10A {Spinacia oleracea} SCOP: c.47.1.1 PDB: 1fb0_A 1gl8_A 2puk_C

Probab=96.29  E-value=0.021  Score=40.04  Aligned_cols=58  Identities=24%  Similarity=0.447  Sum_probs=46.0

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +..++.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.+++...|...
T Consensus        47 ~~~~~~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~g~~~~~~~G~~~~~~l~~~l~~~  104 (105)
T 1fb6_A           47 YSGKIAVYKLNTDEA--PGIATQYNIRSIPTVLFF--KNGERKESIIGAVPKSTLTDSIEKY  104 (105)
T ss_dssp             TTTTCEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEEECCCHHHHHHHHHHH
T ss_pred             hcCceEEEEEcCcch--HHHHHhCCCCcccEEEEE--eCCeEEEEEecCCCHHHHHHHHHhh
Confidence            334688888888643  467899999999998777  3689999999999999887776654

>3die_A Thioredoxin, TRX; electron transport, SWAP domain, redox enzymology, oxidoreductase, redox-active center, transport; 1.85A {Staphylococcus aureus} SCOP: c.47.1.1 PDB: 2o7k_A 2o85_A 2o89_A 2o87_A

Probab=96.29  E-value=0.027  Score=39.51  Aligned_cols=58  Identities=22%  Similarity=0.272  Sum_probs=46.5

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +..++.+...|++..  ..++..|++..+|++.++.  +|..+.++.|..+.+++...|...
T Consensus        48 ~~~~~~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~~--~G~~~~~~~g~~~~~~l~~~l~~~  105 (106)
T 3die_A           48 YEGKADILKLDVDEN--PSTAAKYEVMSIPTLIVFK--DGQPVDKVVGFQPKENLAEVLDKH  105 (106)
T ss_dssp             TTTTCEEEEEETTTC--HHHHHHTTCCSBSEEEEEE--TTEEEEEEESCCCHHHHHHHHHTT
T ss_pred             hcCCcEEEEEECCcC--HHHHHhCCCcccCEEEEEe--CCeEEEEEeCCCCHHHHHHHHHHh
Confidence            334588888888643  4578999999999999884  699999999999999887776654

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

Probab=96.26  E-value=0.019  Score=40.53  Aligned_cols=71  Identities=20%  Similarity=0.259  Sum_probs=55.2

Q ss_pred             eEEEEEcCCCceEEEe--eCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCC--cCceEEEE
Q 025774          171 CRVGVRLPDGRRMQRN--FLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGL--ANAMISVT  246 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~--F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl--~~~~v~v~  246 (248)
                      ..|-||..+|+.+.-.  +..++||..|-.-+.+...|.++...+|+..  .+.  +  +++.||+++|+  .+++|.|.
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~--Gk~--L--~D~~tL~~y~I~~~~stl~v~   75 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLK--GKV--L--HDNLFLSDLKVTPANSTITVM   75 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSCSSSTTEEEEET--TEE--C--CTTCBHHHHCCCGGGCEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcCCChHHEEEEEC--CEE--C--cCcCCHHHcCCCCCCCEEEEE
Confidence            4688999999877765  5599999999999933356778889999864  443  5  45799999999  36777775


Q ss_pred             e
Q 025774          247 W  247 (248)
Q Consensus       247 ~  247 (248)
                      +
T Consensus        76 ~   76 (87)
T 2lxa_A           76 I   76 (87)
T ss_dssp             E
T ss_pred             c
Confidence            4

>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=96.26  E-value=0.032  Score=39.75  Aligned_cols=73  Identities=19%  Similarity=0.206  Sum_probs=56.6

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +..+.|.|+-.+|+.+..+...+++++.|++...... +.++..++|...  .+.  +  +.+.|.+++++. +.+|-|.
T Consensus        15 ~~~i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~-gi~~~~~rf~fd--G~~--l--~~~~Tp~dl~medgD~Idv~   87 (93)
T 2d07_B           15 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQ-GLSMRQIRFRFD--GQP--I--NETDTPAQLEMEDEDTIDVF   87 (93)
T ss_dssp             CCEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHH-TCCGGGEEEEET--TEE--C--CTTCCTTTTTCCTTEEEEEE
T ss_pred             CCeEEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHh-CCCccceEEEEC--CEE--c--CCCCCHHHcCCCCCCEEEEE
Confidence            4578899998999999999999999999999876653 556677887654  433  5  567899999998 5666555


Q ss_pred             e
Q 025774          247 W  247 (248)
Q Consensus       247 ~  247 (248)
                      +
T Consensus        88 ~   88 (93)
T 2d07_B           88 Q   88 (93)
T ss_dssp             E
T ss_pred             e
Confidence            4

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

Probab=96.25  E-value=0.014  Score=42.27  Aligned_cols=72  Identities=14%  Similarity=0.134  Sum_probs=53.0

Q ss_pred             CCceEEEEEcCCCc--eEEEeeCCCCchHHHHHHHHhhcCCCC-CcCeEEEccCCCCccccCCCcCCCcccc--CCcC-c
Q 025774          168 SLLCRVGVRLPDGR--RMQRNFLRTDPIQLLWSYCYSQLEGSE-MKPFRLTHAIPGATKSLDYDSKLTFEDS--GLAN-A  241 (248)
Q Consensus       168 ~~~~~i~iRlp~G~--r~~r~F~~~~~l~~l~~fv~~~~~~~~-~~~f~L~~~~Pr~~~~l~~d~~~tl~d~--gl~~-~  241 (248)
                      +..+.|.||.++|+  .+.-....++||..|-.-|...+++.+ +...+|+..  .+.  |  +++.||.+.  |+.+ +
T Consensus        21 ~~~m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~--Gk~--L--~D~~tL~~y~~~I~~~~   94 (99)
T 2kdb_A           21 GHPVTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYS--GRL--L--PDHLQLKDILRKQDEYH   94 (99)
T ss_dssp             --CEEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEET--TEE--E--CTTSBTHHHHTTTCSEE
T ss_pred             CCeEEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEEC--CEE--C--CCCCCHHHHhcCCCCCC
Confidence            45689999999998  455556999999999999988655544 377888753  443  5  457999999  9985 4


Q ss_pred             eEEE
Q 025774          242 MISV  245 (248)
Q Consensus       242 ~v~v  245 (248)
                      +|.+
T Consensus        95 tihL   98 (99)
T 2kdb_A           95 MVHL   98 (99)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            5543

>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=96.25  E-value=0.027  Score=40.63  Aligned_cols=71  Identities=18%  Similarity=0.218  Sum_probs=55.8

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +...+|.|+..+|+ +.-.+..++||.+|..-|.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus        20 ~~~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~-gip~~~QrLi~~--Gk~--L--~D~~tL~~ygI~~gstI~l~   91 (100)
T 1yqb_A           20 PHLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRF-KAHPDQLVLIFA--GKI--L--KDPDSLAQCGVRDGLTVHLV   91 (100)
T ss_dssp             TTEEEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHH-TCCGGGEEEEET--TEE--C--CTTSBHHHHTCCTTCEEEEE
T ss_pred             CCeEEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHH-CcChhhEEEEEC--CEE--C--CCcCcHHHCCCCCCCEEEEE
Confidence            45789999999996 6788999999999999998764 666778888753  442  5  457999999998 5566554

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

Probab=96.24  E-value=0.017  Score=42.20  Aligned_cols=69  Identities=12%  Similarity=0.122  Sum_probs=54.2

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      .+|.||..+|+.+.-.+..++||.+|-..|... .+.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~-~gip~~~QrLi~~--Gk~--L--~D~~tL~~~~i~~g~~i~lv   71 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQS-ISCEESQIKLIYS--GKV--L--QDSKTVSECGLKDGDQVVFM   71 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHT-TTSCGGGCEEEET--TEE--C--CTTSBTTTTTCCTTCEEEEE
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHH-HCCChhhEEEEEC--CEE--C--CCcCCHHHcCCCCCCEEEEE
Confidence            468899999999999999999999999999875 4666777888753  332  5  448999999998 5666554

>3hxs_A Thioredoxin, TRXP; electron transport; 2.00A {Bacteroides fragilis} PDB: 3hyp_A

Probab=96.23  E-value=0.024  Score=42.37  Aligned_cols=60  Identities=17%  Similarity=0.247  Sum_probs=47.8

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +..++.++..|++..  ..++..|++..+|+++++++ .|..+ ...|..+.++|...|...+.
T Consensus        80 ~~~~~~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~~~-~g~~~-~~~G~~~~~~l~~~l~~~l~  139 (141)
T 3hxs_A           80 YAGKIYIYKVNVDKE--PELARDFGIQSIPTIWFVPM-KGEPQ-VNMGALSKEQLKGYIDKVLL  139 (141)
T ss_dssp             TTTTCEEEEEETTTC--HHHHHHTTCCSSSEEEEECS-SSCCE-EEESCCCHHHHHHHHHHTTC
T ss_pred             hcCceEEEEEECCCC--HHHHHHcCCCCcCEEEEEeC-CCCEE-EEeCCCCHHHHHHHHHHHHc
Confidence            344789999998654  46889999999999999974 46665 78999999999887776654

>2qgv_A Hydrogenase-1 operon protein HYAE; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 2.70A {Shigella flexneri 2A} PDB: 2hfd_A

Probab=96.20  E-value=0.011  Score=45.51  Aligned_cols=57  Identities=11%  Similarity=0.095  Sum_probs=48.8

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      +.|..+|++  +...++..|++.++|+++++  ++|+.+.++.|..+.+++...|...+..
T Consensus        70 v~~~KVdvD--e~~~lA~~ygV~sIPTlilF--k~G~~v~~~~G~~~k~~l~~~i~~~l~~  126 (140)
T 2qgv_A           70 WQVAIADLE--QSEAIGDRFGAFRFPATLVF--TGGNYRGVLNGIHPWAELINLMRGLVEP  126 (140)
T ss_dssp             CEEEECCHH--HHHHHHHHHTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHHC-
T ss_pred             EEEEEEECC--CCHHHHHHcCCccCCEEEEE--ECCEEEEEEecCCCHHHHHHHHHHHhcC
Confidence            778877774  66789999999999999988  5799999999999999998888887743

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

Probab=96.18  E-value=0.034  Score=39.79  Aligned_cols=76  Identities=8%  Similarity=0.030  Sum_probs=58.3

Q ss_pred             CCceEEEEEcCCCc--eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCc-cccCCCcCCCccccCCcC-ceE
Q 025774          168 SLLCRVGVRLPDGR--RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGAT-KSLDYDSKLTFEDSGLAN-AMI  243 (248)
Q Consensus       168 ~~~~~i~iRlp~G~--r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~-~~l~~d~~~tl~d~gl~~-~~v  243 (248)
                      ++.++|.|+.++++  .+.++|..++||..|-.-|... .|.++..-+|....+.+. ..+ .++++||.+.|+.+ ++|
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 SDFIKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEIL-TGGCAGTMKVQVFKGDTCVSTM-DNNDAQLGYYANSDGLRL   90 (95)
T ss_dssp             CCEEEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHH-HCSCTTTEEEEEEETTEEEEEC-CCTTSBHHHHCCSSSCEE
T ss_pred             CCeEEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHH-HCcCHHHeEEEEecCCccccee-CCCCCCHhHCCcCCCCEE
Confidence            56889999998775  7999999999999999999885 467788888876543321 013 36789999999984 555


Q ss_pred             EE
Q 025774          244 SV  245 (248)
Q Consensus       244 ~v  245 (248)
                      .+
T Consensus        91 hl   92 (95)
T 2kjr_A           91 HV   92 (95)
T ss_dssp             EE
T ss_pred             EE
Confidence            44

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

Probab=96.17  E-value=0.023  Score=44.91  Aligned_cols=73  Identities=19%  Similarity=0.250  Sum_probs=57.2

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ++....|.|+..+|+.+.-....++||.+|-.-|... .+.++...+|+..  .+.  +  +++.||.++|+. +++|.+
T Consensus        17 ~~~~m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~-~gip~~~QrL~~~--g~~--L--~d~~tL~~~~i~~~~~l~l   89 (172)
T 3u30_A           17 RGSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK-EGIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHL   89 (172)
T ss_dssp             --CCEEEEEEETTTEEEEEEECTTCBHHHHHHHHHHH-HCCCGGGEEEEET--TEE--C--CTTCBTGGGTCCTTCEEEE
T ss_pred             CCCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHH-HCcChHHEEEEEC--Ccc--c--cccCCHhHcCCcccceeee
Confidence            3456899999999999999999999999999999875 3667778888753  332  5  558999999998 566655


Q ss_pred             E
Q 025774          246 T  246 (248)
Q Consensus       246 ~  246 (248)
                      .
T Consensus        90 ~   90 (172)
T 3u30_A           90 V   90 (172)
T ss_dssp             E
T ss_pred             e
Confidence            3

>2e0q_A Thioredoxin; electron transport; 1.49A {Sulfolobus tokodaii} PDB: 3hhv_A

Probab=96.15  E-value=0.034  Score=38.62  Aligned_cols=56  Identities=18%  Similarity=0.309  Sum_probs=46.1

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +.+...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.+++...|...+.
T Consensus        48 ~~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~g~~~~~~~g~~~~~~l~~~l~~~l~  103 (104)
T 2e0q_A           48 VGFGKLNSDEN--PDIAARYGVMSLPTVIFF--KDGEPVDEIIGAVPREEIEIRIKNLLG  103 (104)
T ss_dssp             SEEEEEETTTC--HHHHHHTTCCSSCEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHHT
T ss_pred             ceEEEEECCCC--HHHHHhCCccccCEEEEE--ECCeEhhhccCCCCHHHHHHHHHHHhc
Confidence            78888887643  467889999999999988  468989999999999988887776654

>3hz4_A Thioredoxin; NYSGXRC, PSI-II, reduced form, protein structure initiative, structural genomics; 2.30A {Methanosarcina mazei}

Probab=96.14  E-value=0.02  Score=43.16  Aligned_cols=64  Identities=13%  Similarity=0.222  Sum_probs=52.1

Q ss_pred             HHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           13 SQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        13 ~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .+-+..++.|...|++..  ..++..|++..+|+++++  .+|..+.++.|..+.++|...|...+..
T Consensus        50 ~~~~~~~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~l~~  113 (140)
T 3hz4_A           50 AKEYGSSAVFGRINIATN--PWTAEKYGVQGTPTFKFF--CHGRPVWEQVGQIYPSILKNAVRDMLQH  113 (140)
T ss_dssp             HHHHTTTSEEEEEETTTC--HHHHHHHTCCEESEEEEE--ETTEEEEEEESSCCHHHHHHHHHHHHHH
T ss_pred             HHHhCCceEEEEEECCcC--HhHHHHCCCCcCCEEEEE--eCCcEEEEEcCCCCHHHHHHHHHHHhcc
Confidence            333445688888988654  467889999999998888  4689999999999999998888888764

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

Probab=96.09  E-value=0.062  Score=39.15  Aligned_cols=72  Identities=19%  Similarity=0.222  Sum_probs=55.7

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ...+.|.|+-.+|+.+..+...+++|..|++...... +.++..++|+..  .+.  +  +.+.|.+++++. +.+|-|.
T Consensus        22 ~~~I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~-gi~~~~~rf~Fd--G~~--l--~~~~Tp~dl~medgD~Idv~   94 (104)
T 1wz0_A           22 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQ-GLSMRQIRFRFD--GQP--I--NETDTPAQLEMEDEDTIDVF   94 (104)
T ss_dssp             SCCEEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHH-TCCTTTSCEESS--SSB--C--CTTSCTTTTTCCTTEEEEEC
T ss_pred             CCeEEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHh-CCCcceEEEEEC--CEE--c--CCCCCHHHcCCCCCCEEEEE
Confidence            4568899999999999999999999999999876654 445667777653  443  5  567899999998 5555554

>2ppt_A Thioredoxin-2; thiredoxin, zinc finger, oxidoreductase; 1.92A {Rhodobacter capsulatus}

Probab=96.08  E-value=0.031  Score=43.16  Aligned_cols=60  Identities=10%  Similarity=0.183  Sum_probs=49.0

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +..++.|...|++..  ..++..|++..+|++.++  .+|..+.++.|..+.++|...|...+.
T Consensus        93 ~~~~v~~~~vd~~~~--~~l~~~~~i~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~l~~~l~  152 (155)
T 2ppt_A           93 LAGQVRLAKIDTQAH--PAVAGRHRIQGIPAFILF--HKGRELARAAGARPASELVGFVRGKLG  152 (155)
T ss_dssp             HTTTCEEEEEETTTS--THHHHHTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHHC
T ss_pred             ccCCEEEEEEeCCcc--HHHHHHcCCCcCCEEEEE--eCCeEEEEecCCCCHHHHHHHHHHHhc
Confidence            344788999988654  357899999999999988  369999999999999998887777654

>3ph9_A Anterior gradient protein 3 homolog; thioredoxin fold, protein disulfide isomerase, endoplasmic R isomerase; 1.83A {Homo sapiens} SCOP: c.47.1.0 PDB: 2lns_A 2lnt_A

Probab=96.07  E-value=0.0028  Score=49.46  Aligned_cols=72  Identities=17%  Similarity=0.200  Sum_probs=54.7

Q ss_pred             cCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCC-------C---ChHHHHHHHh
Q 025774            6 TWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGM-------V---QPESLLEDLV   75 (248)
Q Consensus         6 vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~-------~---~~e~l~~~L~   75 (248)
                      ++.++.+.++++.+||....|.+..+   .+..|++..+|+++++++ +|..+.++.|.       .   +.+.++..+.
T Consensus        66 ~~~~~~~~~~~~~~fv~V~vD~e~~~---~~~~~~v~~~PT~~f~~~-~G~~v~~~~G~~~~~~~~~~~~~~~~ll~~~~  141 (151)
T 3ph9_A           66 FAQNEEIQEMAQNKFIMLNLMHETTD---KNLSPDGQYVPRIMFVDP-SLTVRADIAGRYSNRLYTYEPRDLPLLIENMK  141 (151)
T ss_dssp             HHHCHHHHHHHHHTCEEEEESSCCSC---GGGCTTCCCSSEEEEECT-TSCBCTTCCCSCTTSTTCCCGGGHHHHHHHHH
T ss_pred             HhcCHHHHHHhhcCeEEEEecCCchh---hHhhcCCCCCCEEEEECC-CCCEEEEEeCCcCCcccccchhhHHHHHHHHH
Confidence            44456778888889999998754333   356788999999999985 58989999997       4   4456777788


Q ss_pred             hhhhcC
Q 025774           76 PFMDGG   81 (248)
Q Consensus        76 ~~~~~~   81 (248)
                      .++.++
T Consensus       142 ~al~~~  147 (151)
T 3ph9_A          142 KALRLI  147 (151)
T ss_dssp             HHHSCC
T ss_pred             HHHHHH
Confidence            777765

>2l5l_A Thioredoxin; structural genomics, electron transport, PSI-2, protein STRU initiative; NMR {Bacteroides vulgatus}

Probab=96.06  E-value=0.053  Score=40.46  Aligned_cols=61  Identities=15%  Similarity=0.293  Sum_probs=49.0

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ..++.|...|++..  ..++..|++..+|++.++++ +|..+ ...|..+.++|...|...+...
T Consensus        68 ~~~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~~-~G~~~-~~~G~~~~~~l~~~l~~~~~~~  128 (136)
T 2l5l_A           68 DGQIVIYKVDTEKE--QELAGAFGIRSIPSILFIPM-EGKPE-MAQGAMPKASFKKAIDEFLLKK  128 (136)
T ss_dssp             TTTCEEEEEETTTC--HHHHHHTTCCSSCEEEEECS-SSCCE-EEESCCCHHHHHHHHHHHHTSC
T ss_pred             cCCEEEEEEeCCCC--HHHHHHcCCCCCCEEEEECC-CCcEE-EEeCCCCHHHHHHHHHHHhhcc
Confidence            34688999998654  36788999999999999974 57766 6889999999988888776654

>1x5d_A Protein disulfide-isomerase A6; PDIA6, ERP5, TXNDC7, thioredoxin like domain, redox, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.05  E-value=0.039  Score=40.57  Aligned_cols=59  Identities=8%  Similarity=0.208  Sum_probs=50.0

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .++.|...|++..  ..++..|++..+|++.++.+  |..+.++.|..+.++|...|...+..
T Consensus        60 ~~~~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~~--g~~~~~~~G~~~~~~l~~~l~~~~~~  118 (133)
T 1x5d_A           60 GKVKLAAVDATVN--QVLASRYGIRGFPTIKIFQK--GESPVDYDGGRTRSDIVSRALDLFSD  118 (133)
T ss_dssp             TSEEEEEEETTTC--CHHHHHHTCCSSSEEEEEET--TEEEEEECSCCSHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEECCCC--HHHHHhCCCCeeCeEEEEeC--CCceEEecCCCCHHHHHHHHHHHhhc
Confidence            5788888888643  35778899999999999975  88888999999999998888888765

>2b5x_A YKUV protein, TRXY; thioredoxin-like, oxidoreductase; NMR {Bacillus subtilis} SCOP: c.47.1.10 PDB: 2b5y_A

Probab=96.05  E-value=0.026  Score=42.00  Aligned_cols=47  Identities=17%  Similarity=0.182  Sum_probs=40.6

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ..++..|++..+|+++||++ +|.++.+..|..+.+++...|...+..
T Consensus       100 ~~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~~l~~  146 (148)
T 2b5x_A          100 HALTDAFENEYVPAYYVFDK-TGQLRHFQAGGSGMKMLEKRVNRVLAE  146 (148)
T ss_dssp             CHHHHHTCCCCSSEEEEECT-TCBEEEEEESCSTTHHHHHHHHHHHTT
T ss_pred             hhHHHHhCCCCCCEEEEECC-CCcEEEEecCCCCHHHHHHHHHHHHhc
Confidence            46788999999999999985 599999999999999998888877764

>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=96.03  E-value=0.037  Score=42.29  Aligned_cols=70  Identities=16%  Similarity=0.194  Sum_probs=56.3

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ...|.|+.++|+.+...+..++||.+|-.-+.... +.++...+|..  ..+.  +  +++.||.+.|+. +++|.+.
T Consensus        76 ~~~i~Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~-gi~~~~qrL~~--~g~~--L--~d~~tL~~~~i~~~~~i~l~  146 (152)
T 3b08_A           76 GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIF--AGKQ--L--EDGRTLSDYNIQKESTLHLV  146 (152)
T ss_dssp             CEEEEEEESSSCEEEEEECTTCBHHHHHHHHHHHH-CCCGGGEEEEE--TTEE--C--CTTSBTGGGTCCTTCEEEEE
T ss_pred             ccceeeeecCCCEEEEEeCCCCcHHHHHHHHHHHh-CcChhhEEEEE--CCEE--C--CCCCCHHHcCCCCCCEEEEE
Confidence            46888999999999999999999999999998764 66788888875  3443  5  458999999998 5666554

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

Probab=96.01  E-value=0.042  Score=41.47  Aligned_cols=71  Identities=17%  Similarity=0.155  Sum_probs=55.1

Q ss_pred             CCCCCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhc-----CCC--CCcCeEEEccCCCCccccCCCcCCCccc
Q 025774          163 PKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQL-----EGS--EMKPFRLTHAIPGATKSLDYDSKLTFED  235 (248)
Q Consensus       163 P~~~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~-----~~~--~~~~f~L~~~~Pr~~~~l~~d~~~tl~d  235 (248)
                      .++-+.....|.||+.+|+.+.-.|..++||.+|-+-|...+     ++.  ++...+|+..  .+.  |  +++.||++
T Consensus        10 ~~~~~~~~m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~--GK~--L--eD~~TL~~   83 (125)
T 2gow_A           10 SSNVPADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQ--GRF--L--HGNVTLGA   83 (125)
T ss_dssp             CCSCCTTCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESS--SSE--E--ESSCBTGG
T ss_pred             ccCCCCCeEEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEEC--CcC--C--CCCCcHHH
Confidence            333345568999999999999999999999999999998743     233  2567788765  443  5  45799999


Q ss_pred             cCCc
Q 025774          236 SGLA  239 (248)
Q Consensus       236 ~gl~  239 (248)
                      .|+.
T Consensus        84 y~I~   87 (125)
T 2gow_A           84 LKLP   87 (125)
T ss_dssp             GCCC
T ss_pred             cCCC
Confidence            9997

>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=95.98  E-value=0.023  Score=41.58  Aligned_cols=72  Identities=18%  Similarity=0.186  Sum_probs=56.1

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCC---------------CcCeEEEccCCCCccccCCCcCCCc
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSE---------------MKPFRLTHAIPGATKSLDYDSKLTF  233 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~---------------~~~f~L~~~~Pr~~~~l~~d~~~tl  233 (248)
                      ...+|.|+.-+|+.+.-....++||.+|-.-|.... +.+               +..|.|+  |..+.  |. |+++||
T Consensus         6 ~~M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~-~i~~~~q~g~~~isw~~~w~q~~Li--~~Gk~--L~-dD~~tL   79 (105)
T 1v2y_A            6 SGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYV-QLKQEREGGVQHISWSYVWRTYHLT--SAGEK--LT-EDRKKL   79 (105)
T ss_dssp             CSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHH-HHHHHHTTCCCCCCHHHHHTTEEEE--SSSCE--EC-CSSSBH
T ss_pred             CcEEEEEEecCCCEEEEEECCCChHHHHHHHHHHHh-CCCcccccCcceeeeeecceeEEEE--eCCcC--cc-CCcCCH
Confidence            457899999999999999999999999999988763 111               2478998  55654  63 678999


Q ss_pred             cccCCc-CceEEEE
Q 025774          234 EDSGLA-NAMISVT  246 (248)
Q Consensus       234 ~d~gl~-~~~v~v~  246 (248)
                      ++.|+. +++|.++
T Consensus        80 ~dygI~~g~~l~lv   93 (105)
T 1v2y_A           80 RDYGIRNRDEVSFI   93 (105)
T ss_dssp             HHHTCCSSEEEEEE
T ss_pred             HHcCCCCCCEEEEE
Confidence            999998 5666554

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

Probab=95.94  E-value=0.044  Score=40.47  Aligned_cols=71  Identities=17%  Similarity=0.174  Sum_probs=57.1

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +...|.++..+|+.+.-.+..++||.+|..-+.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus         8 ~~~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrLi~~--Gk~--L--~D~~tL~~ygI~~gstI~l~   79 (114)
T 2kdi_A            8 GEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKE-GIPPDQQRLIWA--GKQ--L--EDGRTLSDYNIQRESTLHLV   79 (114)
T ss_dssp             CCCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTCBTTTTTCCSSCEEEEE
T ss_pred             CcEEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHH-CcChHHEEEEEC--CEE--C--CCCCcHHHCCCCCCCEEEEE
Confidence            346899999999999999999999999999998764 667788888754  442  5  457999999998 5666554

>2es7_A Q8ZP25_salty, putative thiol-disulfide isomerase and thioredoxi; structural genomics, PSI, protein structure initiative; 2.80A {Salmonella typhimurium} SCOP: c.47.1.20 PDB: 2gzp_A 2jzt_A

Probab=95.93  E-value=0.018  Score=44.11  Aligned_cols=66  Identities=14%  Similarity=0.223  Sum_probs=47.6

Q ss_pred             HHHHHhh--cceE--EEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           11 AVSQTIS--TNFI--FWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        11 ~v~~~l~--~~fV--~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .+.++.+  .++.  |...|++  +...++..|++.++|++.++  ++|..+.++.|..+.+++...|...+..
T Consensus        57 ~l~~la~~~~~v~~~~~~Vd~d--~~~~la~~~~V~~iPT~~~f--k~G~~v~~~~G~~~~~~l~~~i~~~l~~  126 (142)
T 2es7_A           57 MIAELLREFPQFDWQVAVADLE--QSEAIGDRFNVRRFPATLVF--TDGKLRGALSGIHPWAELLTLMRSIVDT  126 (142)
T ss_dssp             HHHHHHHTCTTSCCEEEEECHH--HHHHHHHTTTCCSSSEEEEE--SCC----CEESCCCHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHhcccceeEEEEECC--CCHHHHHhcCCCcCCeEEEE--eCCEEEEEEeCCCCHHHHHHHHHHHhcc
Confidence            3444444  3566  7788774  45678899999999999999  5799999999999999988888877754

>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=95.92  E-value=0.076  Score=38.85  Aligned_cols=72  Identities=19%  Similarity=0.246  Sum_probs=55.0

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ++..+.|.|+- +|+.+..+...+++|+.|++...... +.+...++|...  .+.  +  +.+.|.+++|+. +.+|-|
T Consensus        28 ~~~~I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~-gi~~~~~rF~Fd--G~r--l--~~~~Tp~dl~medgD~Idv   99 (106)
T 2eke_C           28 PETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQ-GKEMDSLRFLYD--GIR--I--QADQTPEDLDMEDNDIIEA   99 (106)
T ss_dssp             CCSEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHH-TCCGGGEEEEET--TEE--C--CTTCCTTTTTCCTTEEEEE
T ss_pred             CCCeEEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHh-CCCcccEEEEEC--CeE--c--CCCCCHHHcCCCCCCEEEE
Confidence            34568888888 99999999999999999999876653 556677888654  332  5  567899999998 455544


Q ss_pred             E
Q 025774          246 T  246 (248)
Q Consensus       246 ~  246 (248)
                      .
T Consensus       100 ~  100 (106)
T 2eke_C          100 H  100 (106)
T ss_dssp             E
T ss_pred             E
Confidence            3

>3eyt_A Uncharacterized protein SPOA0173; thioredoxin-like superfamily protein SPOA0173, silicibacter DSS, structural genomics, PSI-2; 1.95A {Silicibacter pomeroyi}

Probab=95.92  E-value=0.0088  Score=45.60  Aligned_cols=46  Identities=17%  Similarity=0.337  Sum_probs=40.8

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .++..|++..+|+++||++ +|.++.++.|..+.+++...|...+..
T Consensus       108 ~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~i~~ll~~  153 (158)
T 3eyt_A          108 RTMAAYQMRGTPSLLLIDK-AGDLRAHHFGDVSELLLGAEIATLLGE  153 (158)
T ss_dssp             HHHHHTTCCSSSEEEEECT-TSEEEEEEESCCCHHHHHHHHHHHHTS
T ss_pred             HHHHHcCCCCCCEEEEECC-CCCEEEEEeCCCCHHHHHHHHHHHhcc
Confidence            5788999999999999995 599999999999999998888888764

>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=95.91  E-value=0.053  Score=38.70  Aligned_cols=73  Identities=19%  Similarity=0.206  Sum_probs=56.4

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +..++|.|+-.+|+.+..+...+++++.|++...... +.++..++|...  .+.  +  +.+.|.+++++. +++|-|.
T Consensus         5 ~~~i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~-gi~~~~~rf~Fd--G~~--l--~~~~Tp~dl~medgD~Idv~   77 (94)
T 2io1_B            5 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQ-GLSMRQIRFRFD--GQP--I--NETDTPAQLEMEDEDTIDVF   77 (94)
T ss_dssp             -CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHH-TCCGGGEEEEET--TEE--C--CTTCCTTTTTCCTTCEEEEE
T ss_pred             CCeEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHh-CCCcccEEEEEC--CEE--c--CCCCCHHHcCCCCCCEEEEE
Confidence            4567888998999999999999999999999877653 556778888654  443  5  567899999998 5666554


Q ss_pred             e
Q 025774          247 W  247 (248)
Q Consensus       247 ~  247 (248)
                      .
T Consensus        78 ~   78 (94)
T 2io1_B           78 Q   78 (94)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=95.90  E-value=0.038  Score=39.40  Aligned_cols=69  Identities=13%  Similarity=0.027  Sum_probs=52.4

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +..++|.|++ +|+.+.-.+..++||.+|-.-|.... +.++...+|+  |..+.  +  | +.||.++|+.+ ++|++
T Consensus        15 ~~~~~i~Vk~-~g~~~~i~v~~~~TV~~LK~~I~~~t-gip~~~QrL~--~~Gk~--L--d-d~tL~~~~i~~g~~i~l   84 (95)
T 1v86_A           15 KELVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSIT-GLPPAMQKVM--YKGLV--P--E-DKTLREIKVTSGAKIMV   84 (95)
T ss_dssp             CCCEEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHH-CSCSTTCCCB--SSSBC--C--S-SSBHHHHCCCTTEEEEE
T ss_pred             CceEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHH-CcCHHHeEEE--ECCee--C--C-cCcHHHCCCCCCCEEEE
Confidence            4568888985 68888899999999999999998864 5667777776  55553  5  3 34999999985 55543

>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=95.88  E-value=0.072  Score=37.79  Aligned_cols=71  Identities=20%  Similarity=0.236  Sum_probs=55.7

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ..++|.|+-.+|+.+..+...+++++.|++..... .+.++..++|...  .+.  +  +.+.|.+++|+. +.+|-|.
T Consensus         4 ~~i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~-~gi~~~~~rf~Fd--G~~--l--~~~~Tp~dl~medgD~Idv~   75 (91)
T 2io0_B            4 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCER-QGLSMRQIRFRFD--GQP--I--NETDTPAQLEMEDEDTIDVF   75 (91)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHH-TTCCSTTEEEEET--TEE--C--CTTCCTTTTTCCTTEEEEEE
T ss_pred             CeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHH-hCCCcccEEEEEC--CEE--c--CCCCCHHHcCCCCCCEEEEE
Confidence            35789999999999999999999999999987665 3556778888654  333  5  567899999998 5555454

>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=95.85  E-value=0.068  Score=37.57  Aligned_cols=71  Identities=13%  Similarity=0.068  Sum_probs=54.3

Q ss_pred             CceEEEEEcCCCceEEEeeCCC-----CchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-Cce
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRT-----DPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAM  242 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~-----~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~  242 (248)
                      ...+|.|+.+ |+.+.-.+..+     +||.+|..-+... .+.++...+|+..  .+.  + .|.++||.++|+. ++.
T Consensus         6 ~~~~v~Vk~~-~~~~~i~v~~~~~~~~~TV~~LK~~i~~~-~gip~~~qrL~~~--Gk~--L-~D~~~~L~~~~i~~g~~   78 (92)
T 1wxv_A            6 SGLTVTVTHS-NEKHDLHVTSQQGSSEPVVQDLAQVVEEV-IGVPQSFQKLIFK--GKS--L-KEMETPLSALGIQDGCR   78 (92)
T ss_dssp             SSEEEEEECS-SSEEEEEECCCSSSSSCBHHHHHHHHHHH-TCCCTTTCEEEET--TEE--E-CCSSSBHHHHTCCSSEE
T ss_pred             CeEEEEEEEC-CEEEEEEECCCcCcccCcHHHHHHHHHHH-HCcCHHHEEEEEC--Cee--c-CCCcccHHHCCCCCCCE
Confidence            4688999984 77888899985     9999999999875 4667888888753  442  6 3568899999998 455


Q ss_pred             EEEE
Q 025774          243 ISVT  246 (248)
Q Consensus       243 v~v~  246 (248)
                      |++.
T Consensus        79 i~l~   82 (92)
T 1wxv_A           79 VMLI   82 (92)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            5543

>3qfa_C Thioredoxin; protein-protein complex, rossmann fold, HO pyridine nucleotide disulfide oxidoreductase, electron TRAN oxidoreductase; HET: FAD; 2.20A {Homo sapiens} PDB: 3qfb_C*

Probab=95.84  E-value=0.06  Score=39.05  Aligned_cols=54  Identities=26%  Similarity=0.390  Sum_probs=44.3

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.|...|++.  ...++..|++..+|++.++  .+|..+.++.|. ++++|...|...
T Consensus        62 ~v~~~~vd~d~--~~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~-~~~~l~~~l~~~  115 (116)
T 3qfa_C           62 NVIFLEVDVDD--CQDVASECEVKSMPTFQFF--KKGQKVGEFSGA-NKEKLEATINEL  115 (116)
T ss_dssp             TSEEEEEETTT--THHHHHHTTCCSSSEEEEE--SSSSEEEEEESC-CHHHHHHHHHHH
T ss_pred             CCEEEEEECCC--CHHHHHHcCCccccEEEEE--eCCeEEEEEcCC-CHHHHHHHHHHh
Confidence            47888888864  3578899999999998888  469999999999 888887777654

>3raz_A Thioredoxin-related protein; structural genomics, PSI-2, protein structure initiative; 2.00A {Neisseria meningitidis serogroup B}

Probab=95.84  E-value=0.041  Score=41.60  Aligned_cols=49  Identities=16%  Similarity=0.222  Sum_probs=41.1

Q ss_pred             HHHHHHhcC--CCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           32 GKKVCTYYK--LDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        32 g~~~~~~~~--~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ...++..|+  +..+|+++||++ +|.++.++.|..+++++...|.......
T Consensus        92 ~~~~~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~l~~~~  142 (151)
T 3raz_A           92 SRNFMKTYGNTVGVLPFTVVEAP-KCGYRQTITGEVNEKSLTDAVKLAHSKC  142 (151)
T ss_dssp             HHHHHHTTTCCSCCSSEEEEEET-TTTEEEECCSCCCHHHHHHHHHHHHTC-
T ss_pred             hHHHHHHhCCccCCCCEEEEECC-CCcEEEEECCCCCHHHHHHHHHHHHHHh
Confidence            455778888  899999999995 5999999999999999988888877654

>3dml_A Putative uncharacterized protein; thioredoxin, oxidoreductase, sulfur oxidation, thiol- disulfide oxidoreductase; HET: MSE; 1.90A {Paracoccus denitrificans} PDB: 3d4t_A*

Probab=95.83  E-value=0.0063  Score=45.46  Aligned_cols=60  Identities=5%  Similarity=-0.056  Sum_probs=51.8

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      +.+...|++......++..|++...|+++++.  +|+.+.++.|+++++.|...|...+...
T Consensus        53 ~~l~~vdv~~~~~~~la~~~~V~g~PT~i~f~--~G~ev~Ri~G~~~~~~f~~~L~~~l~~~  112 (116)
T 3dml_A           53 APVQRLQMRDPLPPGLELARPVTFTPTFVLMA--GDVESGRLEGYPGEDFFWPMLARLIGQA  112 (116)
T ss_dssp             SCEEEEETTSCCCTTCBCSSCCCSSSEEEEEE--TTEEEEEEECCCCHHHHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCchhHHHHCCCCCCCEEEEEE--CCEEEeeecCCCCHHHHHHHHHHHHhhc
Confidence            67778888876666678899999999999997  6999999999999999999998887654

>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=95.83  E-value=0.049  Score=41.61  Aligned_cols=68  Identities=18%  Similarity=0.236  Sum_probs=54.4

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +|.|+.++|+.+.-.+..++||.+|..-+.... +.++....|...  .+.  +  +++.||.+.|+. +++|.+.
T Consensus         2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~-gip~~~q~L~~~--g~~--L--~d~~tL~~~~i~~~~~l~l~   70 (152)
T 3b08_A            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHLV   70 (152)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTSBTGGGTCCTTCEEEEE
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHH-CcChHHeEEEEC--CeE--C--cCcccHHHhccCCCCeeEEE
Confidence            578999999999999999999999999998864 566777888753  442  5  458999999998 5666554

>2dml_A Protein disulfide-isomerase A6; thioredoxin domain-containing protein 7, endoplasmic reticulum, redox-active center, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=95.82  E-value=0.039  Score=40.52  Aligned_cols=63  Identities=13%  Similarity=0.242  Sum_probs=49.6

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      +..++.|...|++..  ..++..|++..+|++.++.+ .|..+..+.|..+.++|+..|...+...
T Consensus        64 ~~~~~~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~~-~~~~~~~~~G~~~~~~l~~~l~~~l~~~  126 (130)
T 2dml_A           64 LKDVVKVGAVNADKH--QSLGGQYGVQGFPTIKIFGA-NKNKPEDYQGGRTGEAIVDAALSALRSG  126 (130)
T ss_dssp             TTTTSEEEEEETTTC--HHHHHHHTCCSSSEEEEESS-CTTSCEECCSCCSHHHHHHHHHHHHHHS
T ss_pred             hcCceEEEEEeCCCC--HHHHHHcCCCccCEEEEEeC-CCCeEEEeecCCCHHHHHHHHHHHHhcC
Confidence            344588888888643  45788999999999999974 3445788999999999999888887654

>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=95.80  E-value=0.098  Score=39.46  Aligned_cols=66  Identities=21%  Similarity=0.265  Sum_probs=51.6

Q ss_pred             CceEEEEEcCCCceE-EEeeCCCCchHHHHHHHHhhcC----CCCC--cCeEEEccCCCCccccCCCcCCCccccCCcC
Q 025774          169 LLCRVGVRLPDGRRM-QRNFLRTDPIQLLWSYCYSQLE----GSEM--KPFRLTHAIPGATKSLDYDSKLTFEDSGLAN  240 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~-~r~F~~~~~l~~l~~fv~~~~~----~~~~--~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~  240 (248)
                      ....|.||+.+|+.+ .-.|..++||..|-.-|...++    +.++  ..-+|+.+  .+.  |  +++.||++.++..
T Consensus        15 ~~~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~--GK~--L--eD~~TLsdy~I~~   87 (126)
T 1se9_A           15 NQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISA--GKV--L--ENSKTVKDYRSPV   87 (126)
T ss_dssp             CCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEET--TEE--C--CTTSBGGGGSCCT
T ss_pred             ccEEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEEC--CeE--C--cCCCcHHHcCCCc
Confidence            468999999999888 6899999999999999976542    2232  56778764  443  5  5689999999984

>1ep7_A Thioredoxin CH1, H-type; electron transport; 2.10A {Chlamydomonas reinhardtii} SCOP: c.47.1.1 PDB: 1tof_A 1ep8_A

Probab=95.80  E-value=0.041  Score=39.13  Aligned_cols=56  Identities=20%  Similarity=0.213  Sum_probs=44.9

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      .++.|...|++.  ...++..|++..+|++.++  .+|..+.++.|. +++++...|...+
T Consensus        55 ~~~~~~~vd~~~--~~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~-~~~~l~~~l~~~l  110 (112)
T 1ep7_A           55 GKVIFLKVDVDA--VAAVAEAAGITAMPTFHVY--KDGVKADDLVGA-SQDKLKALVAKHA  110 (112)
T ss_dssp             TTSEEEEEETTT--THHHHHHHTCCBSSEEEEE--ETTEEEEEEESC-CHHHHHHHHHHHH
T ss_pred             CCeEEEEEECCc--hHHHHHHcCCCcccEEEEE--ECCeEEEEEcCC-CHHHHHHHHHHHh
Confidence            378899998864  3467889999999997776  468989999998 8888877776654

>1xwb_A Thioredoxin; dimerization, redox regulation, THI X-RAY electron transport; 2.20A {Drosophila melanogaster} SCOP: c.47.1.1 PDB: 1xw9_A 1xwc_A 1xwa_A

Probab=95.78  E-value=0.064  Score=37.52  Aligned_cols=55  Identities=18%  Similarity=0.373  Sum_probs=42.9

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      .++.+...|++..  ..++..|++..+|++.++  .+|..+.++.| .+++++...|...
T Consensus        51 ~~~~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~g-~~~~~l~~~i~~~  105 (106)
T 1xwb_A           51 DNVVVLKVDVDEC--EDIAMEYNISSMPTFVFL--KNGVKVEEFAG-ANAKRLEDVIKAN  105 (106)
T ss_dssp             TTEEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEES-CCHHHHHHHHHHT
T ss_pred             CCeEEEEEeccch--HHHHHHcCCCcccEEEEE--cCCcEEEEEcC-CCHHHHHHHHHHh
Confidence            4688888888643  467889999999998777  36888999999 6888776665543

>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=95.77  E-value=0.061  Score=37.92  Aligned_cols=72  Identities=15%  Similarity=0.064  Sum_probs=53.6

Q ss_pred             CceEEEEEcCCCc--eEEEeeCCCCchHHHHHHHHhhc-CCCCCcCeEEEccCCCCccccCCCcCCCcccc--CCcC-ce
Q 025774          169 LLCRVGVRLPDGR--RMQRNFLRTDPIQLLWSYCYSQL-EGSEMKPFRLTHAIPGATKSLDYDSKLTFEDS--GLAN-AM  242 (248)
Q Consensus       169 ~~~~i~iRlp~G~--r~~r~F~~~~~l~~l~~fv~~~~-~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~--gl~~-~~  242 (248)
                      ....|.||.++|+  .+.-....++||.+|-.-|.... .+.++...+|+..  .+.  +  +++.||.+.  |+.+ ++
T Consensus         6 ~~m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~--Gk~--L--~D~~tL~~~~~~i~~~~~   79 (93)
T 1wgd_A            6 SGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYS--GKL--L--LDHQCLRDLLPKQEKRHV   79 (93)
T ss_dssp             CCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEET--TEE--C--CSSSCHHHHSCSSSCSEE
T ss_pred             cEEEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEEC--CEE--C--cCcCCHHHHhcCCCCCCE
Confidence            4588999999998  44445559999999999998864 2567788888753  443  5  457899999  9984 55


Q ss_pred             EEEE
Q 025774          243 ISVT  246 (248)
Q Consensus       243 v~v~  246 (248)
                      |++.
T Consensus        80 i~lv   83 (93)
T 1wgd_A           80 LHLV   83 (93)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            5543

>2i1u_A Thioredoxin, TRX, MPT46; redox protein, electron transport; 1.30A {Mycobacterium tuberculosis} PDB: 3nof_A 3o6t_A* 2l4q_A 2l59_A

Probab=95.76  E-value=0.042  Score=39.66  Aligned_cols=58  Identities=21%  Similarity=0.375  Sum_probs=45.8

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ..++.|...|++..  ..++..|++..+|+++++.  +|..+.++.|..+.++|...|...+
T Consensus        60 ~~~~~~~~v~~~~~--~~~~~~~~i~~~Pt~~~~~--~g~~~~~~~G~~~~~~l~~~l~~~l  117 (121)
T 2i1u_A           60 ATDLTVAKLDVDTN--PETARNFQVVSIPTLILFK--DGQPVKRIVGAKGKAALLRELSDVV  117 (121)
T ss_dssp             TTTCEEEEEETTTC--HHHHHHTTCCSSSEEEEEE--TTEEEEEEESCCCHHHHHHHTCSCC
T ss_pred             cCCeEEEEEECCCC--HHHHHhcCCCcCCEEEEEE--CCEEEEEecCCCCHHHHHHHHHHHH
Confidence            34688888888643  3578899999999998873  6889999999999998866655443

>2f9s_A Thiol-disulfide oxidoreductase RESA; thioredoxin-like protein; HET: MSE; 1.40A {Bacillus subtilis} SCOP: c.47.1.10 PDB: 1st9_A 1su9_A 2h1d_A 2h1b_A 2h1a_A 2h19_A 2h1g_A 3c71_A 3c73_A

Probab=95.72  E-value=0.053  Score=40.84  Aligned_cols=47  Identities=15%  Similarity=0.395  Sum_probs=40.5

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      .++..|++..+|+++||++ +|.++.++.|..+.+++...|...+...
T Consensus        94 ~~~~~~~v~~~P~~~lid~-~G~i~~~~~G~~~~~~l~~~l~~ll~~~  140 (151)
T 2f9s_A           94 QVLDAYDVSPLPTTFLINP-EGKVVKVVTGTMTESMIHDYMNLIKPGE  140 (151)
T ss_dssp             HHHHHTTCCSSCEEEEECT-TSEEEEEEESCCCHHHHHHHHHHHSCC-
T ss_pred             HHHHhcCCCCCCeEEEECC-CCcEEEEEeCCCCHHHHHHHHHHHHhhh
Confidence            5788899999999999985 5999999999999999988888887653

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

Probab=95.72  E-value=0.055  Score=37.63  Aligned_cols=70  Identities=14%  Similarity=0.097  Sum_probs=56.2

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccc-cCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKS-LDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~-l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      -.+|-|+..+|+.+.-.+..++||.+|-.-+.... +.++...+|+..  .+  . +  +++.||++.|+. +++|.+.
T Consensus        10 ~~~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~QrLi~~--Gk--~lL--~D~~tL~~y~I~~gs~i~lv   81 (84)
T 2kk8_A           10 HMKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQ-HIPVSKQTLIVD--GI--VIL--REDLTVEQCQIVPTSDIQLE   81 (84)
T ss_dssp             CEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHH-TCCGGGEEEEET--TE--ECC--CSSSBHHHHTCCTTSCEEEE
T ss_pred             ceEEEEEecCCcEEEEEECCCChHHHHHHHHHHHH-CcChHHEEEEEC--CE--Eec--CCcCCHHHcCCCCCCEEEEE
Confidence            46899999999999999999999999999998864 667888888753  33  3 4  558999999998 5656554

>3zzx_A Thioredoxin; oxidoreductase; 1.88A {Litopenaeus vannamei}

Probab=95.70  E-value=0.052  Score=39.15  Aligned_cols=51  Identities=25%  Similarity=0.428  Sum_probs=40.8

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      +++|...|++.  ...++..|++.++|++.++  .+|..+.++.|. ++++|...|
T Consensus        51 ~~~~~~vd~d~--~~~l~~~~~V~~~PT~~~~--~~G~~v~~~~G~-~~~~l~~~i  101 (105)
T 3zzx_A           51 DVVFLKVDVDE--CEDIAQDNQIACMPTFLFM--KNGQKLDSLSGA-NYDKLLELV  101 (105)
T ss_dssp             TEEEEEEETTT--CHHHHHHTTCCBSSEEEEE--ETTEEEEEEESC-CHHHHHHHH
T ss_pred             CeEEEEEeccc--CHHHHHHcCCCeecEEEEE--ECCEEEEEEeCc-CHHHHHHHH
Confidence            68888888864  4568999999999998888  469999999994 777665444

>1lu4_A Soluble secreted antigen MPT53; thioredoxin-like fold, structural genomics, PSI, protein structure initiative; 1.12A {Mycobacterium tuberculosis} SCOP: c.47.1.10

Probab=95.65  E-value=0.042  Score=40.25  Aligned_cols=44  Identities=9%  Similarity=0.144  Sum_probs=36.5

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeee---CCCChHHHHHHHhhhh
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWC---GMVQPESLLEDLVPFM   78 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~---G~~~~e~l~~~L~~~~   78 (248)
                      ..++..|++..+|++.|+++ +|.++ ++.   |..+++++...|...+
T Consensus        89 ~~~~~~~~i~~~P~~~lid~-~G~i~-~~~~~~g~~~~~~l~~~l~~ll  135 (136)
T 1lu4_A           89 GVIWARYNVPWQPAFVFYRA-DGTST-FVNNPTAAMSQDELSGRVAALT  135 (136)
T ss_dssp             SHHHHHTTCCSSSEEEEECT-TSCEE-EECCSSSCCCHHHHHHHHHHC-
T ss_pred             hhHHHhcCCCCCCEEEEECC-CCcEE-EEEcCCCccCHHHHHHHHHHHh
Confidence            45778899999999999985 58888 888   9999999888777654

>2dj1_A Protein disulfide-isomerase A4; protein ERP-72, ERP72, CAI, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=95.65  E-value=0.057  Score=40.16  Aligned_cols=57  Identities=9%  Similarity=0.222  Sum_probs=47.3

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      +.|...|++..  ..++..|++..+|++.++  .+|. +.++.|..+.++|...|...+...
T Consensus        70 v~~~~vd~~~~--~~~~~~~~v~~~Pt~~~~--~~G~-~~~~~g~~~~~~l~~~l~~~~~~~  126 (140)
T 2dj1_A           70 IAVAKIDATSA--SMLASKFDVSGYPTIKIL--KKGQ-AVDYDGSRTQEEIVAKVREVSQPD  126 (140)
T ss_dssp             CEEEEECTTTC--HHHHHHTTCCSSSEEEEE--ETTE-EEECCSCCCHHHHHHHHHHHHSSS
T ss_pred             eEEEEEeCccc--HHHHHHCCCCccCeEEEE--ECCc-EEEcCCCCCHHHHHHHHHHhcCCC
Confidence            88888888654  568889999999999999  3577 778899999999988888887653

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=95.65  E-value=0.065  Score=39.46  Aligned_cols=72  Identities=21%  Similarity=0.269  Sum_probs=55.8

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +..+.|.|+-.+|+.+..+...+++++.|++...... +.++..++|+..  .+.  +  +.+.|.+++++. +.+|-|.
T Consensus        24 ~~~I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~-gi~~~~~rfiFd--G~~--L--~~~~Tp~dl~mEDgD~Idv~   96 (110)
T 2k8h_A           24 TALVAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQ-GISRNSVRFLFD--GTP--I--DETKTPEELGMEDDDVIDAM   96 (110)
T ss_dssp             CCCEEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHH-TCCSSSCEEESS--SCB--C--CSSSHHHHHHCSSEEEEEEE
T ss_pred             CCeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHh-CCCcccEEEEEC--CEE--c--CCCCCHHHcCCCCCCEEEEE
Confidence            4568899999999999999999999999999876653 556777888653  443  5  567899999998 4555444

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

Probab=95.65  E-value=0.062  Score=37.37  Aligned_cols=67  Identities=15%  Similarity=0.123  Sum_probs=50.3

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +.+.+. .+|+.+.-.+..++||.+|..-+.... +.++...+|+.  -.+.  +  +++.||.++|+.+ ++|.+
T Consensus        13 ~~~~~~-~~g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrL~~--~Gk~--L--~D~~tL~~~gi~~g~~l~l   80 (85)
T 2kd0_A           13 IKLTVK-FGGKSIPLSVSPDCTVKDLKSQLQPIT-NVLPRGQKLIF--KGKV--L--VETSTLKQSDVGSGAKLML   80 (85)
T ss_dssp             EEEEEE-ETTEEEEEEECTTSBHHHHHHHHHHHH-CCCTTTCEEEE--TTEE--C--CTTCBTTTTTCCTTEEEEE
T ss_pred             EEEEEE-ECCEEEEEEECCCCcHHHHHHHHHHHH-CcChHHEEEEE--CCeE--C--CCcCCHHHCCCCCCCEEEE
Confidence            444444 488888899999999999999998764 66778888874  3442  5  4579999999985 55544

>3ia1_A THIO-disulfide isomerase/thioredoxin; oxidoreductase, PSI-2, NYSGXRC, structu genomics, protein structure initiative; 1.76A {Thermus thermophilus}

Probab=95.63  E-value=0.033  Score=42.07  Aligned_cols=49  Identities=24%  Similarity=0.345  Sum_probs=42.4

Q ss_pred             HHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           31 EGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        31 eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ....++..|++..+|+++||++ +|.++.++.|..+++++...|......
T Consensus        97 ~~~~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~~~~~  145 (154)
T 3ia1_A           97 RPHEVAARFKVLGQPWTFVVDR-EGKVVALFAGRAGREALLDALLLAGAD  145 (154)
T ss_dssp             CHHHHHTTSSBCSSCEEEEECT-TSEEEEEEESBCCHHHHHHHHHHTTCC
T ss_pred             chHHHHHHhCCCcccEEEEECC-CCCEEEEEcCCCCHHHHHHHHHhccCc
Confidence            5677889999999999999995 599999999999999998888777654

>1zzo_A RV1677; thioredoxin fold, structural genomics, PSI, protein structure initiative, TB structural genomics consortium, TBSGC; 1.60A {Mycobacterium tuberculosis} SCOP: c.47.1.10 PDB: 3ios_A

Probab=95.57  E-value=0.043  Score=40.04  Aligned_cols=45  Identities=18%  Similarity=0.287  Sum_probs=37.4

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ..++..|++..+|++.||++ +|.++ .+.|..+.+++...|...+.
T Consensus        91 ~~~~~~~~i~~~P~~~~id~-~g~i~-~~~g~~~~~~l~~~l~~~l~  135 (136)
T 1zzo_A           91 GSVWANFGVTQQPAYAFVDP-HGNVD-VVRGRMSQDELTRRVTALTS  135 (136)
T ss_dssp             CHHHHHTTCCSSSEEEEECT-TCCEE-EEESCCCHHHHHHHHHHHC-
T ss_pred             cHHHHHcCCCCCceEEEECC-CCCEE-EEecCCCHHHHHHHHHHHhc
Confidence            45778899999999999985 58888 99999999998888876653

>2ggt_A SCO1 protein homolog, mitochondrial; copper chaperone, Cu-binding protein, mitochondrial assembly factor, redox, nickel, disuplhide, mitochondrion; 2.40A {Homo sapiens} SCOP: c.47.1.10 PDB: 2gqk_A 2gql_A 2gqm_A 2gt5_A 2gt6_A 2gvp_A 2hrf_A 2hrn_A 1wp0_A

Probab=95.56  E-value=0.08  Score=40.27  Aligned_cols=48  Identities=13%  Similarity=0.281  Sum_probs=41.0

Q ss_pred             HHHHHhcCCCCCc---------------eEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           33 KKVCTYYKLDSIP---------------VVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        33 ~~~~~~~~~~~~P---------------~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ..+++.|++...|               .++||++ +|.++.++.|..+++++...|...+..+
T Consensus       101 ~~~~~~~~v~~~p~~~~~~~~~~~~~~~~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~ll~~~  163 (164)
T 2ggt_A          101 DQVARAYRVYYSPGPKDEDEDYIVDHTIIMYLIGP-DGEFLDYFGQNKRKGEIAASIATHMRPY  163 (164)
T ss_dssp             HHHHHTTTCCEEEEEECTTSCEEEEECCEEEEECT-TSCEEEEEETTCCHHHHHHHHHHHHGGG
T ss_pred             HHHHHhcCeEEEecCCCCCCCeeEeccceEEEECC-CCeEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            4588899999899               7899985 5999999999999999999988887654

>2lja_A Putative thiol-disulfide oxidoreductase; structural genomics, unknown function, thioredoxin-like; NMR {Bacteroides vulgatus}

Probab=95.54  E-value=0.07  Score=40.06  Aligned_cols=62  Identities=13%  Similarity=0.211  Sum_probs=50.2

Q ss_pred             ceEEEEEecCChHH---------------------HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEG---------------------KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg---------------------~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.+...+++....                     ..++..|++..+|+++||++ +|.++.+..|..+.+++...|...
T Consensus        63 ~~~~v~v~~d~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~~  141 (152)
T 2lja_A           63 DIHFVSLSCDKNKKAWENMVTKDQLKGIQLHMGTDRTFMDAYLINGIPRFILLDR-DGKIISANMTRPSDPKTAEKFNEL  141 (152)
T ss_dssp             SEEEEEEECCSCHHHHHHHHHHHTCCSEEEECSSCTHHHHHTTCCSSCCEEEECT-TSCEEESSCCCTTCHHHHHHHHHH
T ss_pred             CeEEEEEEccCcHHHHHHHHHhcCCCCceeecCcchhHHHHcCcCCCCEEEEECC-CCeEEEccCCCCCHHHHHHHHHHH
Confidence            57788877765431                     26788999999999999985 599999999999999998888888


Q ss_pred             hhcC
Q 025774           78 MDGG   81 (248)
Q Consensus        78 ~~~~   81 (248)
                      ...+
T Consensus       142 ~~~~  145 (152)
T 2lja_A          142 LGLE  145 (152)
T ss_dssp             HTCC
T ss_pred             hccc
Confidence            7765

>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=95.53  E-value=0.076  Score=41.14  Aligned_cols=69  Identities=16%  Similarity=0.273  Sum_probs=55.2

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccC-CCCccccCCCcCCCccccCCc-CceEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAI-PGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~-Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      .+|.|+..+|+.+.-.+..++||.+|-.-+.... +.++...+|+. | +.+.  +  +++.||.+.|+. +++|.+
T Consensus         3 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~-gip~~~QrL~~-~~~g~~--L--~d~~tL~~y~i~~~~~l~l   73 (159)
T 3rt3_B            3 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKI-GVHAFQQRLAV-HPSGVA--L--QDRVPLASQGLGPGSTVLL   73 (159)
T ss_dssp             CEEEEEETTSCEEEEECCTTCCHHHHHHHHHHHH-CCCGGGEEEEE-ETTCCB--C--CTTSCGGGGTCCTTCEEEE
T ss_pred             eEEEEEECCCCEEEEEeCCCCcHHHHHHHHHHHh-CCCHHHEEEEE-cCCCCC--C--CCCCCHHHcCCCCCCEEEE
Confidence            4688999999999999999999999999998864 66777888873 4 3443  5  568999999998 566654

>1r26_A Thioredoxin; redox-active disulfide, electron transport; 1.40A {Trypanosoma} SCOP: c.47.1.1

Probab=95.50  E-value=0.082  Score=39.09  Aligned_cols=56  Identities=16%  Similarity=0.335  Sum_probs=45.3

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ++.|...|++..  ..++..|++..+|+++++  .+|..+.++.| .++++|...|...+.
T Consensus        68 ~v~~~~vd~d~~--~~l~~~~~v~~~Pt~~i~--~~G~~~~~~~G-~~~~~l~~~l~~~l~  123 (125)
T 1r26_A           68 TVKFAKVDADNN--SEIVSKCRVLQLPTFIIA--RSGKMLGHVIG-ANPGMLRQKLRDIIK  123 (125)
T ss_dssp             TSEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEES-SCHHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCC--HHHHHHcCCCcccEEEEE--eCCeEEEEEeC-CCHHHHHHHHHHHhc
Confidence            688999988643  458889999999998777  46899999999 688888777776654

>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=95.50  E-value=0.12  Score=38.38  Aligned_cols=66  Identities=18%  Similarity=0.194  Sum_probs=52.9

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhc-----CCC--CCcCeEEEccCCCCccccCCCcCCCccccCCc
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQL-----EGS--EMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA  239 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~-----~~~--~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~  239 (248)
                      +..+.|.||+.+|+.+.-.+..++||..|-.-|....     ++.  ++...+|+..  .+.  |  +++.||.++++.
T Consensus        14 ~~~m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~--GK~--L--eD~~TL~~y~I~   86 (116)
T 1wgh_A           14 ADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQ--GRF--L--HGNVTLGALKLP   86 (116)
T ss_dssp             SSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEET--TEE--E--CSSCBTTTTTCC
T ss_pred             CCeEEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEEC--CcC--C--CCCCcHHHcCCC
Confidence            3468899999999999999999999999999998742     232  4677888765  443  5  567999999986

>2l6c_A Thioredoxin; oxidoreductase; NMR {Desulfovibrio vulgaris} PDB: 2l6d_A

Probab=95.49  E-value=0.057  Score=38.71  Aligned_cols=57  Identities=11%  Similarity=0.281  Sum_probs=44.9

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ++.|...|++  +...++..|++..+|++.++  .+|..+.++.|..++++|...|..+..
T Consensus        50 ~v~~~~vd~~--~~~~l~~~~~v~~~Pt~~~~--~~G~~v~~~~G~~~~~~l~~~~~~~~~  106 (110)
T 2l6c_A           50 QVAISSVDSE--ARPELMKELGFERVPTLVFI--RDGKVAKVFSGIMNPRELQALYASIHH  106 (110)
T ss_dssp             TSCEEEEEGG--GCHHHHHHTTCCSSCEEEEE--ESSSEEEEEESCCCHHHHHHHHHTC--
T ss_pred             CcEEEEEcCc--CCHHHHHHcCCcccCEEEEE--ECCEEEEEEcCCCCHHHHHHHHHHHhh
Confidence            4677777774  34567889999999999998  469999999999999998777766644

>2h30_A Thioredoxin, peptide methionine sulfoxide reductase MSRA/MSRB; reduced, thiol-disulfide exchange, oxidoreductase; 1.60A {Neisseria gonorrhoeae} PDB: 2jzr_A 2jzs_A 2k9f_A 2fy6_A

Probab=95.49  E-value=0.02  Score=43.70  Aligned_cols=47  Identities=11%  Similarity=0.104  Sum_probs=39.6

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ..++..|++..+|+++||++ +|.++.++.|..+.+++...|...+..
T Consensus       111 ~~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~i~~~~~~  157 (164)
T 2h30_A          111 GTIAQNLNISVYPSWALIGK-DGDVQRIVKGSINEAQALALIRNPNAD  157 (164)
T ss_dssp             CHHHHHTTCCSSSEEEEECT-TSCEEEEEESCCCHHHHHHHHHCTTCC
T ss_pred             hHHHHHcCCCccceEEEECC-CCcEEEEEcCCCCHHHHHHHHHHHHHH
Confidence            46788999999999999985 589999999999999887777766543

>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=95.49  E-value=0.099  Score=40.48  Aligned_cols=70  Identities=23%  Similarity=0.256  Sum_probs=56.8

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ...|.|+.++|+.+.-.+..++||.+|-.-+... .+.++...+|+..  .+.  +  +++.||.+.|+. +++|.+.
T Consensus        81 ~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~-~gip~~~q~L~~~--G~~--L--~d~~tL~~y~i~~g~~l~l~  151 (159)
T 3rt3_B           81 PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGL-EGVQDDLFWLTFE--GKP--L--EDQLPLGEYGLKPLSTVFMN  151 (159)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-HTCCGGGEEEEET--TEE--C--CTTSBGGGGTCCTTCEEEEE
T ss_pred             cEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHH-HCCCHHHEEEEEC--Cee--c--CCCCCHHHcCCCCCCEEEEE
Confidence            4789999999999999999999999999999875 3667888999764  332  5  458999999998 5666554

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

Probab=95.48  E-value=0.14  Score=35.12  Aligned_cols=71  Identities=21%  Similarity=0.260  Sum_probs=54.2

Q ss_pred             CCceEEEEEcCCCc-eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          168 SLLCRVGVRLPDGR-RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       168 ~~~~~i~iRlp~G~-r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +..+.|.|+-.+|+ .+..+...+++++.|++...... +.++..++|...  .+.  +  +.+.|.+++|+.. .+|-|
T Consensus         5 ~~~i~ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~-gi~~~~~rf~fd--G~~--l--~~~~Tp~~l~medgD~Idv   77 (79)
T 3a4r_A            5 SQELRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAM-GLSGHKLSFFFD--GTK--L--SGKELPADLGLESGDLIEV   77 (79)
T ss_dssp             CCCEEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHH-TCTTCCCEEEET--TEE--C--CSCCCHHHHTCCTTCEEEE
T ss_pred             CCEEEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHh-CCCcccEEEEEC--CEE--c--CCCCCHHHcCCCCCCEEEE
Confidence            34689999999996 89999999999999999876653 555677777653  332  4  5688999999985 44433

>1syr_A Thioredoxin; SGPP, structural genomics, PSI, protein structure initiative structural genomics of pathogenic protozoa consortium; 2.95A {Plasmodium falciparum} SCOP: c.47.1.1

Probab=95.47  E-value=0.081  Score=37.83  Aligned_cols=54  Identities=19%  Similarity=0.292  Sum_probs=43.3

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.|...|++..  ..++..|++..+|++.++  .+|..+.++.|. +.++|...|...
T Consensus        57 ~v~~~~vd~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~-~~~~l~~~l~~~  110 (112)
T 1syr_A           57 KMVFIKVDVDEV--SEVTEKENITSMPTFKVY--KNGSSVDTLLGA-NDSALKQLIEKY  110 (112)
T ss_dssp             TSEEEEEETTTT--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESC-CHHHHHHHHHTT
T ss_pred             CCEEEEEECCCC--HHHHHHcCCCcccEEEEE--ECCcEEEEEeCC-CHHHHHHHHHHh
Confidence            588888888653  367889999999998776  368999999998 888887666554

>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=95.47  E-value=0.056  Score=38.94  Aligned_cols=72  Identities=11%  Similarity=0.065  Sum_probs=54.5

Q ss_pred             CceEEEEEcCCC----ceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceE
Q 025774          169 LLCRVGVRLPDG----RRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMI  243 (248)
Q Consensus       169 ~~~~i~iRlp~G----~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v  243 (248)
                      ...+|.|+.++|    +.+.-.+..++||.+|..-|... .+.++...+|+..  .+.  + .|..+||.++|+. +++|
T Consensus         6 ~~m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~-~gip~~~qrL~~~--gk~--L-~D~~~tL~~ygI~~g~~l   79 (102)
T 1v5o_A            6 SGMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELE-SGVPAEEAQIVYM--EQL--L-TDDHCSLGSYGLKDGDMV   79 (102)
T ss_dssp             CCEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHH-TCCCGGGBCEEET--TEE--E-CCSSSBHHHHTCCTTEEE
T ss_pred             CeEEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHH-HCcChHHeEEEEC--CEE--C-CCCcccHHHCCCCCCCEE
Confidence            457888999865    67778899999999999999876 4667778888754  342  5 3556899999998 4555


Q ss_pred             EEE
Q 025774          244 SVT  246 (248)
Q Consensus       244 ~v~  246 (248)
                      ++.
T Consensus        80 ~l~   82 (102)
T 1v5o_A           80 VLL   82 (102)
T ss_dssp             EEC
T ss_pred             EEE
Confidence            553

>3uvt_A Thioredoxin domain-containing protein 5; thioredoxin-like fold, isomerase; 2.00A {Homo sapiens} PDB: 2diz_A 3uj1_A

Probab=95.45  E-value=0.11  Score=36.61  Aligned_cols=54  Identities=19%  Similarity=0.328  Sum_probs=43.9

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      ++.+...|.+..  ..++..|++..+|++.++  .+|..+..+.|..+.++|...|..
T Consensus        56 ~~~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~--~~g~~~~~~~g~~~~~~l~~~l~~  109 (111)
T 3uvt_A           56 GVKIAEVDCTAE--RNICSKYSVRGYPTLLLF--RGGKKVSEHSGGRDLDSLHRFVLS  109 (111)
T ss_dssp             CEEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEECSCCSHHHHHHHHHH
T ss_pred             ceEEEEEecccc--HhHHHhcCCCcccEEEEE--eCCcEEEeccCCcCHHHHHHHHHh
Confidence            578888888643  458899999999998888  468889999999999988776653

>1xfl_A Thioredoxin H1; AT3G51030, structural genomics, protein structure initiative, CESG, center for eukaryotic structural genomics; NMR {Arabidopsis thaliana} SCOP: c.47.1.1

Probab=95.42  E-value=0.095  Score=38.53  Aligned_cols=61  Identities=16%  Similarity=0.351  Sum_probs=46.4

Q ss_pred             HHHHhhc--ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           12 VSQTIST--NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        12 v~~~l~~--~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +.++.+.  ++.|...|++.  ...++..|++..+|+++++  .+|..+.++.| .+++++...|...
T Consensus        60 l~~l~~~~~~v~~~~vd~d~--~~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G-~~~~~l~~~l~~~  122 (124)
T 1xfl_A           60 FADLAKKLPNVLFLKVDTDE--LKSVASDWAIQAMPTFMFL--KEGKILDKVVG-AKKDELQSTIAKH  122 (124)
T ss_dssp             HHHHHHHCSSEEEEEEETTT--SHHHHHHTTCCSSSEEEEE--ETTEEEEEEES-CCHHHHHHHHHHH
T ss_pred             HHHHHHHCCCcEEEEEECcc--CHHHHHHcCCCccCEEEEE--ECCEEEEEEeC-CCHHHHHHHHHHh
Confidence            3444443  68899998864  3468899999999998877  46999999999 4888887766654

>3m9j_A Thioredoxin; oxidoreductase; 1.10A {Homo sapiens} SCOP: c.47.1.1 PDB: 3m9k_A 2hsh_A 1erv_A 2ifq_A 2ifq_B 1auc_A 1eru_A 1ert_A 3kd0_A 1aiu_A 3trx_A 4trx_A 1trs_A 1tru_A 1trv_A 1trw_A 3e3e_A* 1cqg_A 1cqh_A 1mdi_A ...

Probab=95.42  E-value=0.073  Score=37.18  Aligned_cols=54  Identities=26%  Similarity=0.382  Sum_probs=43.7

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.|...|.+.  ...++..|++..+|++.++  .+|..+.++.|. +++++...|...
T Consensus        51 ~~~~~~vd~~~--~~~~~~~~~v~~~Pt~~~~--~~g~~~~~~~g~-~~~~l~~~l~~~  104 (105)
T 3m9j_A           51 NVIFLEVDVDD--CQDVASESEVKSMPTFQFF--KKGQKVGEFSGA-NKEKLEATINEL  104 (105)
T ss_dssp             TSEEEEEETTT--CHHHHHHTTCCBSSEEEEE--ETTEEEEEEESS-CHHHHHHHHHHH
T ss_pred             CeEEEEEEhhh--hHHHHHHcCCCcCcEEEEE--ECCeEEEEEeCC-CHHHHHHHHHHh
Confidence            47888888754  3468899999999999999  358899999999 888887766554

>3emx_A Thioredoxin; structural genomics, oxidoreductase, PSI-2, protein structure initiative, NEW YORK SGX research center for structural genomics; 2.25A {Aeropyrum pernix}

Probab=95.41  E-value=0.084  Score=39.40  Aligned_cols=68  Identities=10%  Similarity=0.090  Sum_probs=51.2

Q ss_pred             HHHHHhhc-ceEEEEEecCC-------hHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           11 AVSQTIST-NFIFWQVYDDT-------SEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        11 ~v~~~l~~-~fV~w~~d~~~-------~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .+.++.+. .+.|...|++.       .+...++..|++..+|+++++.  +|..+.++.|..+.+.+...+...++.
T Consensus        52 ~l~~l~~~~~v~~~~vd~~~~~~~~~~d~~~~l~~~~~v~~~Pt~~~~~--~G~~v~~~~G~~~~~~~~~~i~~~~~~  127 (135)
T 3emx_A           52 QLIQASKEVDVPIVMFIWGSLIGERELSAARLEMNKAGVEGTPTLVFYK--EGRIVDKLVGATPWSLKVEKAREIYGG  127 (135)
T ss_dssp             HHHHHHTTCCSCEEEEEECTTCCHHHHHHHHHHHHHHTCCSSSEEEEEE--TTEEEEEEESCCCHHHHHHHHHHHC--
T ss_pred             hHHHHHHHCCCEEEEEECCCchhhhhhhhhHHHHHHcCCceeCeEEEEc--CCEEEEEEeCCCCHHHHHHHHHHHhCC
Confidence            44445444 36777777743       4567889999999999888886  699999999999998887777777664

>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=95.41  E-value=0.068  Score=38.88  Aligned_cols=71  Identities=17%  Similarity=0.189  Sum_probs=53.7

Q ss_pred             ceEEEEEcCCC---ceEEEeeCC---------CCchHHHHHHHHhhcC-CCCCcC-eEEEccCCCCccccCCCcCCCccc
Q 025774          170 LCRVGVRLPDG---RRMQRNFLR---------TDPIQLLWSYCYSQLE-GSEMKP-FRLTHAIPGATKSLDYDSKLTFED  235 (248)
Q Consensus       170 ~~~i~iRlp~G---~r~~r~F~~---------~~~l~~l~~fv~~~~~-~~~~~~-f~L~~~~Pr~~~~l~~d~~~tl~d  235 (248)
                      ..+|.||..+|   +.+.-.|..         ++||.+|-..|..... +.++.. .+|+..  .+.  +  +++.||.+
T Consensus        12 ~~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~--Gk~--L--~D~~tL~~   85 (107)
T 1x1m_A           12 DWHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYC--GRK--L--KDDQTLDF   85 (107)
T ss_dssp             SCCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEET--TEE--C--CTTCBHHH
T ss_pred             ceEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEEEC--CeE--C--CCCCcHHH
Confidence            47899999999   777778665         5999999999988642 566777 888743  443  5  45799999


Q ss_pred             cCCc-CceEEEE
Q 025774          236 SGLA-NAMISVT  246 (248)
Q Consensus       236 ~gl~-~~~v~v~  246 (248)
                      +|+. +++|.+.
T Consensus        86 y~i~~g~~i~lv   97 (107)
T 1x1m_A           86 YGIQPGSTVHVL   97 (107)
T ss_dssp             HTCCTTCEEEEE
T ss_pred             cCCCCCCEEEEE
Confidence            9998 5556553

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=95.37  E-value=0.066  Score=45.12  Aligned_cols=59  Identities=20%  Similarity=0.334  Sum_probs=48.5

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      +..+++|..+|++..  ..++..|++..+|++.++  .+|..+.++.|..+.+.+...|...+
T Consensus        55 ~~~~~~~~~vd~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~g~~~~~~l~~~l~~~l  113 (287)
T 3qou_A           55 YNGQFILAKLDCDAE--QMIAAQFGLRAIPTVYLF--QNGQPVDGFQGPQPEEAIRALLDXVL  113 (287)
T ss_dssp             HTSSSEEEEEETTTC--HHHHHTTTCCSSSEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHS
T ss_pred             cCCCeEEEEEeCccC--HHHHHHcCCCCCCeEEEE--ECCEEEEEeeCCCCHHHHHHHHHHHc
Confidence            334699999999754  478899999999999999  36899999999999888877776654

>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=95.36  E-value=0.16  Score=34.06  Aligned_cols=68  Identities=21%  Similarity=0.276  Sum_probs=52.9

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +.|.|+-.+|+.+..+...+++++.|++...... +.++..++|...  .+.  +  +.+.|.+++|+.. .+|-|
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~-gi~~~~~rf~fd--G~~--l--~~~~Tp~~l~medgD~Idv   70 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQ-GLSMRQIRFRFD--GQP--I--NETDTPAQLEMEDEDTIDV   70 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHH-TCCTTTCEEEET--TEE--C--CTTCCTTTTTCCTTEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHh-CCCcceEEEEEC--CEE--c--CCCCCHHHcCCCCCCEEEE
Confidence            5788888999999999999999999999876653 556778888654  333  5  5678999999985 44433

>3apq_A DNAJ homolog subfamily C member 10; thioredoxin fold, DNAJ domain, endoplasmic reticulum, oxidor; 1.84A {Mus musculus}

Probab=95.35  E-value=0.068  Score=43.11  Aligned_cols=63  Identities=14%  Similarity=0.204  Sum_probs=51.3

Q ss_pred             HhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           15 TISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        15 ~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      -+..++.|..+|++..  ..++..|++..+|++.++  .+|..+.++.|..+.++|...|...+...
T Consensus       142 ~~~~~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~~~~~l~~~i~~~l~~~  204 (210)
T 3apq_A          142 EVDGLLRIGAVNCGDD--RMLCRMKGVNSYPSLFIF--RSGMAAVKYNGDRSKESLVAFAMQHVRST  204 (210)
T ss_dssp             HTBTTBEEEEEETTTC--HHHHHHTTCCSSSEEEEE--CTTSCCEECCSCCCHHHHHHHHHHHHHCC
T ss_pred             HhcCceEEEEEECCcc--HHHHHHcCCCcCCeEEEE--ECCCceeEecCCCCHHHHHHHHHHhCccc
Confidence            3344688888888654  468889999999999988  56888899999999999988888887653

>3d6i_A Monothiol glutaredoxin-3; thioredoxin-like, electron transport, redox- active center, transport, oxidoreductase; HET: CME; 1.50A {Saccharomyces cerevisiae}

Probab=95.35  E-value=0.11  Score=36.94  Aligned_cols=55  Identities=15%  Similarity=0.416  Sum_probs=42.9

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ++.|...|++..  ..++..|++..+|++.++  .+|..+.++.|. .+++|...|...+
T Consensus        54 ~~~~~~vd~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~-~~~~l~~~l~~~~  108 (112)
T 3d6i_A           54 NVSFLSIDADEN--SEISELFEISAVPYFIII--HKGTILKELSGA-DPKEYVSLLEDCK  108 (112)
T ss_dssp             TSEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEECSC-CHHHHHHHHHHHH
T ss_pred             CEEEEEEecccC--HHHHHHcCCCcccEEEEE--ECCEEEEEecCC-CHHHHHHHHHHHH
Confidence            688999998654  367889999999998887  469999999997 4556666666554

>3erw_A Sporulation thiol-disulfide oxidoreductase A; thioredoxin-like fold, RESA-like fold, dithiol, STOA, redox-active center; 2.50A {Bacillus subtilis} SCOP: c.47.1.0

Probab=95.34  E-value=0.037  Score=40.99  Aligned_cols=41  Identities=20%  Similarity=0.310  Sum_probs=35.6

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      ..++..|++..+|+++||++ +|.++.++.|..+.++|...|
T Consensus       104 ~~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l  144 (145)
T 3erw_A          104 GELMKEYHIITIPTSFLLNE-KGEIEKTKIGPMTAEQLKEWT  144 (145)
T ss_dssp             SHHHHHTTCCEESEEEEECT-TCCEEEEEESCCCHHHHHHHH
T ss_pred             hhHHHhcCcCccCeEEEEcC-CCcEEEEEcCCcCHHHHHHhh
Confidence            36788999999999999985 599999999999999887654

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

Probab=95.33  E-value=0.065  Score=37.92  Aligned_cols=68  Identities=16%  Similarity=0.120  Sum_probs=52.2

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ..+|.||.  |+.+.-.+..++||.+|..-+.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus        19 ~m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~qrLi~~--Gk~--L--~D~~tL~~y~I~~gstI~lv   87 (93)
T 2l7r_A           19 SMQLFVRA--QELHTFEVTGQETVAQIKAHVASLE-GIAPEDQVVLLA--GAP--L--EDEATLGQCGVEALTTLEVA   87 (93)
T ss_dssp             -CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHH-TCCGGGCEEEET--TEE--C--CTTSBHHHHTCCSSCEEEEE
T ss_pred             cEEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHh-CcChhHEEEEEC--CEE--C--CCCCcHHHCCCCCCCEEEEE
Confidence            46777776  8888889999999999999998764 567788888754  443  5  457999999998 5666554

>2l5o_A Putative thioredoxin; structural genomics, unknown function, PSI-2, protein struct initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.32  E-value=0.032  Score=42.07  Aligned_cols=48  Identities=13%  Similarity=0.272  Sum_probs=42.1

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ..++..|++..+|+++||++ +|.++..+.|..+.+++...|...+...
T Consensus        96 ~~~~~~~~i~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~ll~~~  143 (153)
T 2l5o_A           96 KAVGQAFGTQVYPTSVLIGK-KGEILKTYVGEPDFGKLYQEIDTAWRNS  143 (153)
T ss_dssp             CHHHHHHTCCSSSEEEEECS-SSCCCEEEESSCCHHHHHHHHHHHHHCC
T ss_pred             HHHHHHcCCCccCeEEEECC-CCcEEEEEcCCCCHHHHHHHHHHHHHhh
Confidence            35788899999999999985 5888899999999999999999988864

>3kh7_A Thiol:disulfide interchange protein DSBE; TRX-like, thiol-disulfide exchange, cell inner membrane, CYT C-type biogenesis, disulfide bond; 1.75A {Pseudomonas aeruginosa} PDB: 3kh9_A

Probab=95.32  E-value=0.039  Score=43.28  Aligned_cols=46  Identities=17%  Similarity=0.258  Sum_probs=40.1

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .++..|++..+|+++||++ +|.++.++.|..+.+++...|...++.
T Consensus       123 ~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~~l~~  168 (176)
T 3kh7_A          123 TLGLDLGVYGAPETYLIDK-QGIIRHKIVGVVDQKVWREQLAPLYQQ  168 (176)
T ss_dssp             HHHHHHTCCSSCEEEEECT-TCBEEEEEESCCCHHHHHHHTHHHHHH
T ss_pred             hHHHHcCCCCCCeEEEECC-CCeEEEEEcCCCCHHHHHHHHHHHHHH
Confidence            5677889999999999995 599999999999999998888888764

>4evm_A Thioredoxin family protein; structural genomics, niaid, national institute of allergy AN infectious diseases; 1.51A {Streptococcus pneumoniae}

Probab=95.27  E-value=0.042  Score=39.99  Aligned_cols=42  Identities=21%  Similarity=0.447  Sum_probs=36.6

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      .++..|++..+|+++||++ +|.++.++.|..+++++...|..
T Consensus        95 ~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~  136 (138)
T 4evm_A           95 KLLETYGVRSYPTQAFIDK-EGKLVKTHPGFMEKDAILQTLKE  136 (138)
T ss_dssp             HHHHHTTCCSSSEEEEECT-TCCEEEEEESCCCHHHHHHHHHH
T ss_pred             HHHHHcCcccCCeEEEECC-CCcEEEeecCCCcHHHHHHHHHh
Confidence            5788999999999999995 59999999999999988777654

>1x5e_A Thioredoxin domain containing protein 1; TMX, TXNDC1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.23  E-value=0.11  Score=37.93  Aligned_cols=57  Identities=9%  Similarity=0.124  Sum_probs=46.0

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ++.|...|++..  ..++..|++..+|++.++  .+|. +.++.|..+.++|...|...+..
T Consensus        55 ~v~~~~vd~~~~--~~~~~~~~v~~~Pt~~~~--~~G~-~~~~~G~~~~~~l~~~l~~~~~~  111 (126)
T 1x5e_A           55 EVNIAKVDVTEQ--PGLSGRFIINALPTIYHC--KDGE-FRRYQGPRTKKDFINFISDKEWK  111 (126)
T ss_dssp             TCEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTE-EEECCSCCCHHHHHHHHHTCGGG
T ss_pred             CeEEEEEECcCC--HHHHHHcCCcccCEEEEE--eCCe-EEEeecCCCHHHHHHHHHHHhhc
Confidence            789999988644  357889999999999999  4577 57899999999888777776543

>2xc2_A Thioredoxinn; oxidoreductase, protein disulfide reductase; 1.56A {Schistosoma mansoni} PDB: 2xbq_A 2xbi_A

Probab=95.23  E-value=0.11  Score=37.36  Aligned_cols=62  Identities=16%  Similarity=0.295  Sum_probs=45.4

Q ss_pred             HHHHHhhc-ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           11 AVSQTIST-NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        11 ~v~~~l~~-~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      .+.++.+. ++.+...|++.  ...++..|++..+|++.++  .+|..+.++.| .+++++...|...
T Consensus        54 ~~~~~~~~~~~~~~~vd~~~--~~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G-~~~~~l~~~l~~~  116 (117)
T 2xc2_A           54 LFKELSEKYDAIFVKVDVDK--LEETARKYNISAMPTFIAI--KNGEKVGDVVG-ASIAKVEDMIKKF  116 (117)
T ss_dssp             HHHHHHTTSSSEEEEEETTT--SHHHHHHTTCCSSSEEEEE--ETTEEEEEEES-SCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCcEEEEEECCc--cHHHHHHcCCCccceEEEE--eCCcEEEEEeC-CCHHHHHHHHHHh
Confidence            34444444 67888888854  3468889999999998877  46899999999 5788776666543

>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=94.21  E-value=0.0033  Score=42.66  Aligned_cols=67  Identities=21%  Similarity=0.266  Sum_probs=51.4

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +|.||.++|+.+.-.+..++||.+|..-+... .+.++...+|...  .+.  +  +++.||.++|+. +++|.+
T Consensus         2 ~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~-~gi~~~~qrL~~~--gk~--L--~d~~tL~~~~i~~g~~i~l   69 (76)
T 3b1l_X            2 IVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQ-QGVPADQLRVIFA--GKE--L--PNHLTVQNCDLEQQSIVHI   69 (76)
Confidence            47788999998888999999999999999875 3556677777543  443  5  457999999998 455543

>2vm1_A Thioredoxin, thioredoxin H isoform 1.; oxidoreductase, protein disulfide reductase, thioredoxin-FOL; 1.7A {Hordeum vulgare var} PDB: 2vm2_A

Probab=95.12  E-value=0.11  Score=37.17  Aligned_cols=64  Identities=23%  Similarity=0.404  Sum_probs=48.4

Q ss_pred             HHHHhhc--ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           12 VSQTIST--NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        12 v~~~l~~--~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      +.++.+.  ++.|...|++.  ...++..|++..+|++.++  .+|..+.++.| .+++++...|...+..
T Consensus        50 l~~~~~~~~~~~~~~v~~~~--~~~~~~~~~v~~~Pt~~~~--~~g~~~~~~~g-~~~~~l~~~l~~~~~~  115 (118)
T 2vm1_A           50 FAEYAKKFPGAIFLKVDVDE--LKDVAEAYNVEAMPTFLFI--KDGEKVDSVVG-GRKDDIHTKIVALMGS  115 (118)
T ss_dssp             HHHHHHHCTTSEEEEEETTT--SHHHHHHTTCCSBSEEEEE--ETTEEEEEEES-CCHHHHHHHHHHHHC-
T ss_pred             HHHHHHHCCCcEEEEEEccc--CHHHHHHcCCCcCcEEEEE--eCCeEEEEecC-CCHHHHHHHHHHHhcc
Confidence            3444443  68888888864  3467889999999998887  46898999999 5888888888777653

>2vim_A Thioredoxin, TRX; thioredoxin fold, oxidoreductase; 1.38A {Fasciola hepatica}

Probab=95.11  E-value=0.15  Score=35.40  Aligned_cols=54  Identities=17%  Similarity=0.388  Sum_probs=42.5

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.|...|++..  ..++..|++..+|++.++.  +|..+.++.| .+++++...|...
T Consensus        50 ~~~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~~--~g~~~~~~~G-~~~~~l~~~l~~~  103 (104)
T 2vim_A           50 EVEFAKVDVDQN--EEAAAKYSVTAMPTFVFIK--DGKEVDRFSG-ANETKLRETITRH  103 (104)
T ss_dssp             TSEEEEEETTTC--HHHHHHTTCCSSSEEEEEE--TTEEEEEEES-SCHHHHHHHHHHH
T ss_pred             CCEEEEEeccCC--HHHHHHcCCccccEEEEEe--CCcEEEEEeC-CCHHHHHHHHHhh
Confidence            688888888643  4678899999999988774  6889999999 5888876666543

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

Probab=95.10  E-value=0.14  Score=40.51  Aligned_cols=68  Identities=19%  Similarity=0.240  Sum_probs=54.9

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +|.||..+|+.+.-....++||.+|-.-+.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+.
T Consensus         2 qI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~-gip~~~QrLi~~--Gk~--L--~D~~tL~~y~I~~gstI~Lv   70 (169)
T 3l0w_B            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHLV   70 (169)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHH-CCCTTTEEEEET--TEE--C--CTTSBGGGGTCCTTCEEEEE
T ss_pred             EEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHH-CcCHHHEEEEEC--Ccc--c--cCcCcHHHcCCCCCCEEEEE
Confidence            588999999999999999999999999998764 667888888764  332  5  458999999998 5666554

>2b1k_A Thiol:disulfide interchange protein DSBE; C-terminal thioredoxin-like domain, N-terminal beta-sheet, fingerprint rigion, oxidoreductase; 1.90A {Escherichia coli} PDB: 3k8n_A 2g0f_A 1z5y_E 2b1l_A

Probab=95.06  E-value=0.036  Score=42.63  Aligned_cols=47  Identities=15%  Similarity=0.234  Sum_probs=39.1

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ..++..|++..+|+++||++ +|.++.++.|..+++.+...|...++.
T Consensus       115 ~~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~~l~~  161 (168)
T 2b1k_A          115 GMLGLDLGVYGAPETFLIDG-NGIIRYRHAGDLNPRVWEEEIKPLWEK  161 (168)
T ss_dssp             CHHHHHHTCCSSSEEEEECT-TSBEEEEEESCCCHHHHHHTTHHHHHH
T ss_pred             hHHHHHcCccccCEEEEECC-CCeEEEEEeCCCCHHHHHHHHHHHHHH
Confidence            35778899999999999985 599999999999999888777776653

>1nho_A Probable thioredoxin; beta sheet, alpha helix, oxidoreductase; NMR {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: c.47.1.1

Probab=95.04  E-value=0.059  Score=36.17  Aligned_cols=52  Identities=17%  Similarity=0.227  Sum_probs=41.6

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ++.+...|++...  .++..|++..+|++.+    +|..  ++.|..+.+++...|...+
T Consensus        33 ~~~~~~vd~~~~~--~~~~~~~v~~~Pt~~~----~G~~--~~~G~~~~~~l~~~l~~~l   84 (85)
T 1nho_A           33 KIDVEKIDIMVDR--EKAIEYGLMAVPAIAI----NGVV--RFVGAPSREELFEAINDEM   84 (85)
T ss_dssp             SCCEEEECTTTCG--GGGGGTCSSCSSEEEE----TTTE--EEECSSCCHHHHHHHHHHC
T ss_pred             CeEEEEEECCCCH--HHHHhCCceeeCEEEE----CCEE--EEccCCCHHHHHHHHHHHh
Confidence            7888888886443  5778999999999988    4766  7889889999887777654

>1kng_A Thiol:disulfide interchange protein CYCY; thioredoxin fold, cytochrome C maturation, atomic resolution oxidoreductase; 1.14A {Bradyrhizobium japonicum} SCOP: c.47.1.10

Probab=95.02  E-value=0.052  Score=40.91  Aligned_cols=45  Identities=22%  Similarity=0.429  Sum_probs=38.6

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .++..|++..+|+++||++ +|.++.++.|..+.+++...|...+.
T Consensus       108 ~~~~~~~v~~~P~~~~id~-~G~i~~~~~g~~~~~~l~~~l~~~l~  152 (156)
T 1kng_A          108 RASIEWGVYGVPETFVVGR-EGTIVYKLVGPITPDNLRSVLLPQME  152 (156)
T ss_dssp             HHHHHTTCCSSCEEEEECT-TSBEEEEEESCCCHHHHHHTHHHHHH
T ss_pred             HHHHhcCcCccCeEEEEcC-CCCEEEEEeCCCCHHHHHHHHHHHHH
Confidence            5778899999999999985 58999999999999988887777665

>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=94.98  E-value=0.11  Score=36.36  Aligned_cols=71  Identities=14%  Similarity=0.143  Sum_probs=52.8

Q ss_pred             CceEEEEEcCCCceEEE-eeCCCCchHHHHHHHHhhcCCCCCcCeEEEcc-CCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          169 LLCRVGVRLPDGRRMQR-NFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHA-IPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r-~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~-~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ...+|.|+. +|+.+.- ....++||.+|-.-|... .+.++..-+|+-. |-.+  .+  +++.||.++|+. +++|++
T Consensus         6 ~~m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~-~gip~~~QkLi~~k~~Gk--~L--~D~~~L~~~~i~~g~~l~l   79 (90)
T 1v5t_A            6 SGLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTL-TGVLPERQKLLGLKVKGK--PA--ENDVKLGALKLKPNTKIMM   79 (90)
T ss_dssp             CSCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHH-TCCCTTTCEEESCEETTE--EC--CTTSBHHHHTCCTTEEEEE
T ss_pred             ceEEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHH-HCcCHHHeEEEeeccCCc--Cc--CCCCCHHHcCCCCCCEEEE
Confidence            356788886 7887776 778899999999999875 5677888888832 3233  24  457899999998 455554

>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=94.98  E-value=0.16  Score=35.46  Aligned_cols=68  Identities=15%  Similarity=0.059  Sum_probs=55.6

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA  239 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~  239 (248)
                      +.++|+.|-+|--.+..-|-...-+|++|+--|-.+- ++++..+.|....-..   .+.|.++||.|+||.
T Consensus         8 E~TvRLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kc-efdp~~~~Ll~d~~~~---e~LdLskSLndlgir   75 (91)
T 2daj_A            8 EKTVRVVINFKKTQKTIVRVSPHASLQELAPIICSKC-EFDPLHTLLLKDYQSQ---EPLDLTKSLNDLGLR   75 (91)
T ss_dssp             CSCEEEEEEETTTEEEEEEECSSSCTTTHHHHHHHHT-TCCTTSEEEESCSSCC---CBCCTTSCHHHHTCS
T ss_pred             ccEEEEEEeecCcceeEEEeCCCCcHHHHHHHHhhcc-cCChhhEEEecCCCCC---cccchhcchhhhhhh
Confidence            4689999999988888889999999999999886653 4568899998764333   223889999999997

>3lor_A Thiol-disulfide isomerase and thioredoxins; PSI, MCSG, structural genomics, midwest CE structural genomics; HET: MSE; 2.20A {Corynebacterium glutamicum}

Probab=94.97  E-value=0.026  Score=42.91  Aligned_cols=45  Identities=20%  Similarity=0.271  Sum_probs=40.0

Q ss_pred             HHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           35 VCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        35 ~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ++..|++..+|+++||++ +|.++.++.|..+.+++...|...+..
T Consensus       112 ~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~i~~ll~~  156 (160)
T 3lor_A          112 TMKKYRLEGTPSIILADR-KGRIRQVQFGQVDDFVLGLLLGSLLSE  156 (160)
T ss_dssp             HHHHTTCCSSSEEEEECT-TSBEEEEEESCCCHHHHHHHHHHHHTC
T ss_pred             HHHhcccCccceEEEECC-CCcEEEEecCcCCHHHHHHHHHHHHhc
Confidence            788999999999999995 599999999999999998888888764

>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=94.96  E-value=0.065  Score=38.27  Aligned_cols=68  Identities=12%  Similarity=0.214  Sum_probs=51.6

Q ss_pred             CceEEEEEcCCCceE-EEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          169 LLCRVGVRLPDGRRM-QRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~-~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ...+|.|+. +|+.+ .-.+..++||.+|-.-|... .+.++...+|+  |..+.  +. | + ||.++|+. +++|++
T Consensus         6 ~~m~i~Vk~-~g~~~~~l~v~~~~TV~~lK~~I~~~-tgip~~~QkLi--~~Gk~--L~-D-~-tL~~~~I~~g~~i~l   75 (96)
T 1wgg_A            6 SGYSVTVKW-GKEKFEGVELNTDEPPMVFKAQLFAL-TGVQPARQKVM--VKGGT--LK-D-D-DWGNIKMKNGMTVLM   75 (96)
T ss_dssp             CEEEEEEEE-TTEEEEEEEEESSSCHHHHHHHHHHH-TCCCTTTSCCE--ETTEE--CC-S-S-CCCSCCCCSSCEEEC
T ss_pred             cEEEEEEEE-CCEEEEEEEECCCCcHHHHHHHHHHH-HCcCHHHeEEE--ECCcC--CC-C-C-CHHHCCCCCCCEEEE
Confidence            467788886 67777 47899999999999999875 56677788887  45553  53 3 5 99999998 455543

>1ti3_A Thioredoxin H, PTTRXH1; oxidoreductase; NMR {Populus tremula} SCOP: c.47.1.1

Probab=94.96  E-value=0.1  Score=36.98  Aligned_cols=55  Identities=18%  Similarity=0.308  Sum_probs=44.0

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ++.|...|++..  ..++..|++..+|++.++  .+|..+.++.| .++++|...|...+
T Consensus        57 ~v~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~g-~~~~~l~~~l~~~~  111 (113)
T 1ti3_A           57 NVTFLKVDVDEL--KAVAEEWNVEAMPTFIFL--KDGKLVDKTVG-ADKDGLPTLVAKHA  111 (113)
T ss_dssp             SEEEEEEETTTC--HHHHHHHHCSSTTEEEEE--ETTEEEEEEEC-CCTTHHHHHHHHHH
T ss_pred             CcEEEEEEcccc--HHHHHhCCCCcccEEEEE--eCCEEEEEEec-CCHHHHHHHHHHhh
Confidence            688888888643  457888999999999888  46899999999 58888877776654

>2wz9_A Glutaredoxin-3; protein binding; 1.55A {Homo sapiens} PDB: 2diy_A

Probab=94.94  E-value=0.15  Score=38.91  Aligned_cols=57  Identities=18%  Similarity=0.306  Sum_probs=46.6

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ++.|..+|++..  ..++..|++..+|++.++.  +|..+.++.|. +++++...|...+..
T Consensus        63 ~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~--~G~~~~~~~G~-~~~~l~~~i~~~l~~  119 (153)
T 2wz9_A           63 QVSFVKLEAEGV--PEVSEKYEISSVPTFLFFK--NSQKIDRLDGA-HAPELTKKVQRHASS  119 (153)
T ss_dssp             TSEEEEEETTTS--HHHHHHTTCCSSSEEEEEE--TTEEEEEEESS-CHHHHHHHHHHHSCT
T ss_pred             CeEEEEEECCCC--HHHHHHcCCCCCCEEEEEE--CCEEEEEEeCC-CHHHHHHHHHHHhcc
Confidence            688999988653  3578899999999999997  69999999995 778887777777654

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

Probab=94.81  E-value=0.051  Score=39.23  Aligned_cols=68  Identities=12%  Similarity=0.117  Sum_probs=52.3

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      .++|.|+. +|+.+.-.+..++||.+|-.-|.... +.++...+|+..  .+  .+  +++.||.++|+.+ ++|.+
T Consensus        28 ~i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~-gip~~~QrLi~~--Gk--~L--~D~~tL~~~gI~~g~tI~l   96 (101)
T 3m63_B           28 SLNIHIKS-GQDKWEVNVAPESTVLQFKEAINKAN-GIPVANQRLIYS--GK--IL--KDDQTVESYHIQDGHSVHL   96 (101)
T ss_dssp             -CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHH-SCCSTTCCEEET--TE--EC--CTTSBTTTTTCCTTEEEEE
T ss_pred             EEEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHH-CcChHHEEEEEC--CE--EC--CCcCcHHHCCCCCCCEEEE
Confidence            46788886 88888889999999999999998864 666777788753  33  25  4589999999984 55544

>3aps_A DNAJ homolog subfamily C member 10; thioredoxin fold, CXXC motif, endoplasmic reticulum, oxidore; 1.90A {Mus musculus}

Probab=94.78  E-value=0.075  Score=38.47  Aligned_cols=63  Identities=10%  Similarity=0.027  Sum_probs=47.8

Q ss_pred             HhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCC----CChHHHHHHHhhhhhcC
Q 025774           15 TISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGM----VQPESLLEDLVPFMDGG   81 (248)
Q Consensus        15 ~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~----~~~e~l~~~L~~~~~~~   81 (248)
                      .+..++.|...|++..  ..++..|++..+|++.++..  |..+.++.|.    .+++++...|...+...
T Consensus        49 ~~~~~~~~~~vd~~~~--~~~~~~~~v~~~Pt~~~~~~--~~~~~~~~g~~~~~~~~~~l~~~l~~~l~~~  115 (122)
T 3aps_A           49 MIKGKVRAGKVDCQAY--PQTCQKAGIKAYPSVKLYQY--ERAKKSIWEEQINSRDAKTIAALIYGKLETL  115 (122)
T ss_dssp             HHTTTCEEEEEETTTC--HHHHHHTTCCSSSEEEEEEE--EGGGTEEEEEEECCSCHHHHHHHHHHHHHCC
T ss_pred             HhcCCeEEEEEeCcCC--HHHHHHcCCCccceEEEEeC--CCccceeeccccCcCCHHHHHHHHHHHHHhh
Confidence            3344799999998654  35788999999999999964  3335666665    78999988888887754

>3kcm_A Thioredoxin family protein; SGX, thioredoxin protein, PSI, structural genomics, protein initiative; 2.45A {Geobacter metallireducens gs-15}

Probab=94.75  E-value=0.21  Score=37.36  Aligned_cols=62  Identities=19%  Similarity=0.272  Sum_probs=45.4

Q ss_pred             ceEEEEEecCCh--HH-------------------HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC--ChHHHHHHHh
Q 025774           19 NFIFWQVYDDTS--EG-------------------KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV--QPESLLEDLV   75 (248)
Q Consensus        19 ~fV~w~~d~~~~--eg-------------------~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~--~~e~l~~~L~   75 (248)
                      ++.+...+++..  +.                   ..++..|++..+|+++||++ +|.++.++.|..  +.+++...|.
T Consensus        61 ~~~~v~v~~d~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~~~l~~~l~  139 (154)
T 3kcm_A           61 PFRMLCVSIDEGGKVAVEEFFRKTGFTLPVLLDADKRVGKLYGTTGVPETFVIDR-HGVILKKVVGAMEWDHPEVIAFLN  139 (154)
T ss_dssp             SEEEEEEECCTTHHHHHHHHHHHHCCCCCEEECTTCHHHHHHTCCSBCEEEEECT-TSBEEEEEESCCCTTSHHHHHHHH
T ss_pred             CeEEEEEEcCCcchHHHHHHHHHcCCCeeEEecCchHHHHHhCCCCCCeEEEECC-CCcEEEEEcCCCccccHHHHHHHH
Confidence            577777777653  22                   23788899999999999995 699999999986  6668887777


Q ss_pred             hhhhcC
Q 025774           76 PFMDGG   81 (248)
Q Consensus        76 ~~~~~~   81 (248)
                      ......
T Consensus       140 ~l~~~~  145 (154)
T 3kcm_A          140 NELSKA  145 (154)
T ss_dssp             TC----
T ss_pred             HHHHHh
Confidence            776554

>1gh2_A Thioredoxin-like protein; redox-active center, electron transport; 2.22A {Homo sapiens} SCOP: c.47.1.1

Probab=94.74  E-value=0.2  Score=35.28  Aligned_cols=54  Identities=11%  Similarity=0.169  Sum_probs=41.4

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.|...|++..  ..++..|++..+|++.++  .+|..+.++.|.. +++|...|...
T Consensus        52 ~~~~~~vd~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~-~~~l~~~l~~~  105 (107)
T 1gh2_A           52 QAVFLEVDVHQC--QGTAATNNISATPTFQFF--RNKVRIDQYQGAD-AVGLEEKIKQH  105 (107)
T ss_dssp             TSEEEEEETTTS--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESSC-HHHHHHHHHHH
T ss_pred             CcEEEEEECccC--HHHHHhcCCCcccEEEEE--ECCeEEEEEeCCC-HHHHHHHHHHh
Confidence            688888888643  457889999999999888  4688899999954 45566555544

>3f3q_A Thioredoxin-1; His TAG, electron transport, cytoplasm, deoxyribonucleotide synthesis, golgi apparatus, membrane, nucleus; 1.76A {Saccharomyces cerevisiae} PDB: 3f3r_A* 2i9h_A 2fa4_A 2hsy_A 3pin_A 4dss_B

Probab=94.70  E-value=0.21  Score=35.51  Aligned_cols=53  Identities=15%  Similarity=0.348  Sum_probs=41.6

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      ++.|...|++.  ...++..|++..+|++.++.  +|..+.++.|. +++++...|..
T Consensus        55 ~~~~~~vd~~~--~~~l~~~~~v~~~Pt~~~~~--~G~~~~~~~G~-~~~~l~~~i~~  107 (109)
T 3f3q_A           55 QADFYKLDVDE--LGDVAQKNEVSAMPTLLLFK--NGKEVAKVVGA-NPAAIKQAIAA  107 (109)
T ss_dssp             TSEEEEEETTT--CHHHHHHTTCCSSSEEEEEE--TTEEEEEEESS-CHHHHHHHHHH
T ss_pred             CCEEEEEECCC--CHHHHHHcCCCccCEEEEEE--CCEEEEEEeCC-CHHHHHHHHHh
Confidence            47777777754  34588999999999999986  69999999998 67777665544

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

Probab=94.69  E-value=0.28  Score=35.09  Aligned_cols=76  Identities=7%  Similarity=0.010  Sum_probs=56.9

Q ss_pred             CCceEEEEEcCCCc--eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccC--CCCccccCCCcCCCccccCCc-Cce
Q 025774          168 SLLCRVGVRLPDGR--RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAI--PGATKSLDYDSKLTFEDSGLA-NAM  242 (248)
Q Consensus       168 ~~~~~i~iRlp~G~--r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~--Pr~~~~l~~d~~~tl~d~gl~-~~~  242 (248)
                      ++.++|.|..++.+  .++++|..++||..|-.-|... .|.++...+|...-  ++....+ .++++||.+.|+. +++
T Consensus        12 ~~~v~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~-~Gip~~~QrLi~~g~~g~~~~~L-~~D~~tL~~Y~I~~g~~   89 (97)
T 2kj6_A           12 DDSVHLHITHANLKSFSADARFSPQMSVEAVKEKLWKK-CGTSVNSMALELYDDSGSKVAVL-SDDSRPLGFFSPFDGFR   89 (97)
T ss_dssp             CCCEEEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHH-HCCCTTSEEEEEECSSSCBCCCS-SGGGSCHHHHCCCSCCE
T ss_pred             CceEEEEEEECCCCceEEEEEeCCCChHHHHHHHHHHH-HCcCHHHeEEEEecCCCccccee-cCCcCCHHHCCCCCCCE
Confidence            46789999987764  7999999999999999999886 47778888887532  1211012 3678999999998 455


Q ss_pred             EEE
Q 025774          243 ISV  245 (248)
Q Consensus       243 v~v  245 (248)
                      |.+
T Consensus        90 Ihl   92 (97)
T 2kj6_A           90 LHI   92 (97)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            544

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

Probab=94.68  E-value=0.12  Score=41.86  Aligned_cols=68  Identities=16%  Similarity=0.216  Sum_probs=54.9

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ..|.||..+|+.+.-.+..++||.+|-.-|.... +.++...+|+.  ..+.  |  +++.||.++|+. +++|.+
T Consensus       106 MqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~-gIp~~~QrLi~--~Gk~--L--~D~~tL~dygI~~gstI~L  174 (189)
T 3q3f_A          106 GQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIF--AGKQ--L--EDGRTLSDYNIQKESTLHL  174 (189)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHH-CCCGGGCCEEE--TTEE--C--CTTCBGGGGTCCTTCEEEE
T ss_pred             eeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhcc-CCCHHHEEEEE--CCEE--C--CCCCCHHHCCCCCCCEEEE
Confidence            6899999999999999999999999999998764 66677788874  3443  5  448999999998 566654

>3d22_A TRXH4, thioredoxin H-type; electron transport, cytoplasm, redox-active center, transport, oxidoreductase; 1.60A {Populus trichocarpa x populusdeltoides} PDB: 3d21_A

Probab=94.57  E-value=0.18  Score=37.35  Aligned_cols=57  Identities=14%  Similarity=0.344  Sum_probs=46.8

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ++.|...|++.  ...++..|++..+|++.++  .+|..+.++.|. ++++|...|...+..
T Consensus        77 ~v~~~~v~~~~--~~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~-~~~~l~~~l~~~~~~  133 (139)
T 3d22_A           77 SLMFLVIDVDE--LSDFSASWEIKATPTFFFL--RDGQQVDKLVGA-NKPELHKKITAILDS  133 (139)
T ss_dssp             TSEEEEEETTT--SHHHHHHTTCCEESEEEEE--ETTEEEEEEESC-CHHHHHHHHHHHHHT
T ss_pred             CCEEEEEeCcc--cHHHHHHcCCCcccEEEEE--cCCeEEEEEeCC-CHHHHHHHHHHHhcc
Confidence            58888888864  3468899999999998877  469999999998 888888878777664

>2vlu_A Thioredoxin, thioredoxin H isoform 2.; oxidoreductase, thioredoxin-fold, protein disulfide reductase; 1.70A {Hordeum vulgare var} PDB: 2vlt_A 2vlv_A 2iwt_A*

Probab=94.56  E-value=0.18  Score=36.39  Aligned_cols=56  Identities=20%  Similarity=0.319  Sum_probs=44.5

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ++.|...|++..  ..++..|++..+|++.++  .+|..+.++.|.. .++|...|...+.
T Consensus        65 ~~~~~~vd~~~~--~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~-~~~l~~~l~~~l~  120 (122)
T 2vlu_A           65 NAVFLKVDVDEL--KPIAEQFSVEAMPTFLFM--KEGDVKDRVVGAI-KEELTAKVGLHAA  120 (122)
T ss_dssp             TSEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESSC-HHHHHHHHHHHHS
T ss_pred             CcEEEEEECCCC--HHHHHHcCCCcccEEEEE--eCCEEEEEEeCcC-HHHHHHHHHHHhc
Confidence            478888888643  467889999999998777  4689899999988 8888777776654

>2j23_A Thioredoxin; immune protein, autoreactivity, cross-reactivity, IGE, fungi, epitope, allergen; 1.41A {Malassezia sympodialis}

Probab=94.55  E-value=0.088  Score=38.35  Aligned_cols=54  Identities=19%  Similarity=0.367  Sum_probs=43.4

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      +.+...|++..  ..++..|++..+|++.++.  +|..+.++.|. ++++|...|...+
T Consensus        67 v~~~~vd~d~~--~~~~~~~~v~~~Pt~~~~~--~G~~~~~~~G~-~~~~l~~~l~~~l  120 (121)
T 2j23_A           67 VGFYKVDVDEQ--SQIAQEVGIRAMPTFVFFK--NGQKIDTVVGA-DPSKLQAAITQHS  120 (121)
T ss_dssp             SEEEEEETTTC--HHHHHHHTCCSSSEEEEEE--TTEEEEEEESS-CHHHHHHHHHHHT
T ss_pred             EEEEEEECcCC--HHHHHHcCCCcccEEEEEE--CCeEEeeEcCC-CHHHHHHHHHHhh
Confidence            88888888653  3578899999999998873  68899999998 8888877666543

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=94.54  E-value=0.073  Score=43.89  Aligned_cols=65  Identities=18%  Similarity=0.142  Sum_probs=49.7

Q ss_pred             eEEEeeCCCCchHHHHHHHHhhcCCCCC-cCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          182 RMQRNFLRTDPIQLLWSYCYSQLEGSEM-KPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       182 r~~r~F~~~~~l~~l~~fv~~~~~~~~~-~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      .++..|...+|++.|+..+...+ +.+. ..++|..-+....+.+..+.++||+|++|. +..|+++.
T Consensus       141 ~~~~~~Sk~~ti~~l~~~~~~~~-~i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~illE~  207 (217)
T 4a3p_A          141 VVTRRFSKADTIDTIEKEIRKIF-SIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQ  207 (217)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHT-TCCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEEEEE
T ss_pred             ceEEEEcccchHHHHHHHHHHHh-CCCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEEEEE
Confidence            47799999999999999998865 3344 479998755444445556778999999998 67777763

>3gl3_A Putative thiol:disulfide interchange protein DSBE; oxidoreductase, PSI-II, structural genomics, protein structure initiative; 2.09A {Chlorobium tepidum tls}

Probab=94.48  E-value=0.37  Score=35.91  Aligned_cols=47  Identities=17%  Similarity=0.438  Sum_probs=36.7

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCCh--HHHHHHHhhhhhcC
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQP--ESLLEDLVPFMDGG   81 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~--e~l~~~L~~~~~~~   81 (248)
                      .++..|++..+|.++||++ +|.++.++.|..+.  +++...|.+.+...
T Consensus        96 ~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~~~~~l~~~i~~~~~~~  144 (152)
T 3gl3_A           96 QTPRLYGVKGMPTSFLIDR-NGKVLLQHVGFRPADKEALEQQILAALGGN  144 (152)
T ss_dssp             HHHHHTTCCSSSEEEEECT-TSBEEEEEESCCTTTHHHHHHHHHHHTC--
T ss_pred             hhHHHcCCCCCCeEEEECC-CCCEEEEEccCCCcCHHHHHHHHHHHHccc
Confidence            5778899999999999995 69999999997644  67777777766543

>3fkf_A Thiol-disulfide oxidoreductase; structural genomics, PSI-2, structure initiative, midwest center for structural genomic oxidoreductase; 2.20A {Bacteroides fragilis}

Probab=94.47  E-value=0.15  Score=37.72  Aligned_cols=57  Identities=21%  Similarity=0.367  Sum_probs=43.1

Q ss_pred             ceEEEEEecCChH-----------------------HHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           19 NFIFWQVYDDTSE-----------------------GKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        19 ~fV~w~~d~~~~e-----------------------g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ++.+...+++...                       ...++..|++..+|+++||++ +|.++.+..   +.+++...|.
T Consensus        67 ~~~~v~v~~d~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~v~~~P~~~lid~-~G~i~~~~~---~~~~l~~~l~  142 (148)
T 3fkf_A           67 NFAMLGISLDIDREAWETAIKKDTLSWDQVCDFTGLSSETAKQYAILTLPTNILLSP-TGKILARDI---QGEALTGKLK  142 (148)
T ss_dssp             TEEEEEEECCSCHHHHHHHHHHTTCCSEEECCSCGGGCHHHHHTTCCSSSEEEEECT-TSBEEEESC---CHHHHHHHHH
T ss_pred             CeEEEEEECCCCHHHHHHHHHHcCCCceEEEccCCcchHHHHhcCCCCcCEEEEECC-CCeEEEecC---CHHHHHHHHH
Confidence            4788888776544                       447889999999999999985 588776654   7777777777


Q ss_pred             hhhh
Q 025774           76 PFMD   79 (248)
Q Consensus        76 ~~~~   79 (248)
                      ..+.
T Consensus       143 ~ll~  146 (148)
T 3fkf_A          143 ELLK  146 (148)
T ss_dssp             HHC-
T ss_pred             HHHc
Confidence            6653

>3hcz_A Possible thiol-disulfide isomerase; APC61559.2, cytophaga hutchinsoni structural genomics, PSI-2, protein structure initiative; 1.88A {Cytophaga hutchinsonii}

Probab=94.45  E-value=0.11  Score=38.60  Aligned_cols=44  Identities=16%  Similarity=0.228  Sum_probs=37.4

Q ss_pred             HHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           35 VCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        35 ~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ++..|++..+|+++||++ +|.++.++.|..+.++++..+...+.
T Consensus       103 ~~~~~~i~~~P~~~lid~-~G~i~~~~~g~~~~~~~l~~l~~~l~  146 (148)
T 3hcz_A          103 FKITYDIYATPVLYVLDK-NKVIIAKRIGYENLDDFLVQYEKSLK  146 (148)
T ss_dssp             HHHHHCCCSSCEEEEECT-TCBEEEESCCGGGHHHHHHHHHHHHH
T ss_pred             HHHhcCcCCCCEEEEECC-CCcEEEecCCHHHHHHHHHHHHHHhc
Confidence            788899999999999995 59999999998888888888776543

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

Probab=94.43  E-value=0.15  Score=35.79  Aligned_cols=71  Identities=11%  Similarity=-0.028  Sum_probs=51.3

Q ss_pred             eEEEEEcCCCceEE--E-eeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          171 CRVGVRLPDGRRMQ--R-NFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       171 ~~i~iRlp~G~r~~--r-~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      ..|-|+...|+...  - ....++||.+|..-|....++.++..-+|...+=.+  .+  +++.||++.|+.+ ++|.|
T Consensus        11 M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~~~~Gk--~L--~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           11 YEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGK--SL--KDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             EEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEESSTTSC--CC--CTTCBTTTSSCCSEEEEEE
T ss_pred             EEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEecCCCc--Cc--CCCCCHHHcCCCCCCEEEE
Confidence            56778888887653  3 678999999999999874456667777786543233  25  5589999999985 44444

>3lwa_A Secreted thiol-disulfide isomerase; thioredoxin, PSI, MCSG, structural genomics, midwest center for structural genomics; 1.75A {Corynebacterium glutamicum}

Probab=94.40  E-value=0.27  Score=38.24  Aligned_cols=39  Identities=21%  Similarity=0.388  Sum_probs=33.8

Q ss_pred             CCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           40 KLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        40 ~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ++..+|+++||++ .|.++.++.|..+++++...|...+.
T Consensus       143 ~v~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~ll~  181 (183)
T 3lwa_A          143 PASVIPTTIVLDK-QHRPAAVFLREVTSKDVLDVALPLVD  181 (183)
T ss_dssp             CTTCCSEEEEECT-TSCEEEEECSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCeEEEECC-CCcEEEEEcCCCCHHHHHHHHHHHHh
Confidence            5688999999995 59999999999999999888887765

>3or5_A Thiol:disulfide interchange protein, thioredoxin protein; PSI-II, structural genomics, protein structure initiative; 1.66A {Chlorobaculum tepidum} SCOP: c.47.1.0

Probab=94.29  E-value=0.14  Score=38.78  Aligned_cols=41  Identities=15%  Similarity=0.186  Sum_probs=35.4

Q ss_pred             CCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           40 KLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        40 ~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ++..+|.++||++ +|.++..+.|..+++++...|...+...
T Consensus       113 ~i~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~~l~~~  153 (165)
T 3or5_A          113 GITGIPTSFVIDA-SGNVSGVIVGPRSKADFDRIVKMALGAK  153 (165)
T ss_dssp             CSCSSSEEEEECT-TSBEEEEECSCCCHHHHHHHHHHHHC--
T ss_pred             CCCCCCeEEEECC-CCcEEEEEcCCCCHHHHHHHHHHHHhhh
Confidence            7899999999995 5999999999999999999999888765

>3jyu_A Ubiquitin carboxyl-terminal hydrolase; domain in ubiquitin-specific peptidases (DUSP), proto- oncogene, ubiquitin-fold, UBL, protease, thioesterase; HET: 1PS; 2.37A {Mus musculus}

Probab=94.20  E-value=0.18  Score=41.92  Aligned_cols=64  Identities=16%  Similarity=0.130  Sum_probs=48.2

Q ss_pred             eEEEeeCCCCchHHHHHHHHhhcCCCCC-cCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          182 RMQRNFLRTDPIQLLWSYCYSQLEGSEM-KPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       182 r~~r~F~~~~~l~~l~~fv~~~~~~~~~-~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      .++.+|...+|++.|+..+...+ +.+. ..++|..-+-...+.+..+.++||+|++|. +..|+++
T Consensus       153 ~~~~~~Sk~~ti~~l~~~~~~~~-~i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~illE  218 (231)
T 3jyu_A          153 VLSCHFSKADTIATIEKEMRKLF-NIPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIE  218 (231)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHT-TCCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEEE
T ss_pred             eEEEEecccCcHHHHHHHHHHHh-CCCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEEE
Confidence            36689999999999999998865 4444 479998755443344445788999999998 5666665

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=94.18  E-value=0.2  Score=34.99  Aligned_cols=71  Identities=8%  Similarity=0.045  Sum_probs=51.6

Q ss_pred             ceEEEEEcC--CCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEcc-----CCCCccccCCCcCCCccccCCc-Cc
Q 025774          170 LCRVGVRLP--DGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHA-----IPGATKSLDYDSKLTFEDSGLA-NA  241 (248)
Q Consensus       170 ~~~i~iRlp--~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~-----~Pr~~~~l~~d~~~tl~d~gl~-~~  241 (248)
                      +++|.|.-.  ++....+||..++||..|-.-+... .|.++..-+|...     |..+   + .+.++||.+.|+. ++
T Consensus         2 ~V~v~iths~~~~~~~E~r~~~s~TI~~lK~ki~~~-~Gip~~~QrLi~~~~~~~~~g~---~-l~d~~tL~~Y~i~~g~   76 (86)
T 4b6w_A            2 VVKVSLTHSASRMRVPEKRYGLAQTIESIKENVFTH-FATPPEYMQLQLIDDRGITIEK---N-MANDKQLGYYQCRDEF   76 (86)
T ss_dssp             EEEEEEEETTCSCCEEEEEEETTSBHHHHHHHHHTT-SCCCGGGEEEEEECTTSCEEES---S-CCTTSBGGGGTCCTTC
T ss_pred             EEEEEEEEcCCCCeEEEEEcCccCcHHHHHHHHHHH-HCCCHHHEEEEEecCCCCceee---E-cCCCCCHHHCCCCCCC
Confidence            456666543  3445699999999999999999874 5777888888642     2222   2 3678999999998 56


Q ss_pred             eEEE
Q 025774          242 MISV  245 (248)
Q Consensus       242 ~v~v  245 (248)
                      +|.+
T Consensus        77 ~ihl   80 (86)
T 4b6w_A           77 VIHV   80 (86)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6644

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

Probab=94.07  E-value=0.07  Score=38.87  Aligned_cols=74  Identities=18%  Similarity=0.140  Sum_probs=50.2

Q ss_pred             eEEEEEcCCCceEEEeeC-CCCchHHHHHHHHhhcCCCCCcCeEEEc-cCC------CCccccC--CCcCCCccccCCc-
Q 025774          171 CRVGVRLPDGRRMQRNFL-RTDPIQLLWSYCYSQLEGSEMKPFRLTH-AIP------GATKSLD--YDSKLTFEDSGLA-  239 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~-~~~~l~~l~~fv~~~~~~~~~~~f~L~~-~~P------r~~~~l~--~d~~~tl~d~gl~-  239 (248)
                      ..|+||-++|+. .-... .+++|.+|..-|.... +.++...+|.. +.|      .....+.  .+.++||.++||. 
T Consensus         8 M~irvrs~~G~~-~v~v~~~~~Tv~~LK~kI~~~~-gip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~   85 (107)
T 1wf9_A            8 TMLRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQL-QIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAH   85 (107)
T ss_dssp             EEEEEECSSCEE-EEEECCTTSBHHHHHHHHHHHS-CCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCT
T ss_pred             EEEEEECCCCCE-EEEECCCCCcHHHHHHHHHHHh-CcCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCC
Confidence            569999999975 33566 8899999999998864 55677777743 221      1000120  3678999999998 


Q ss_pred             CceEEEE
Q 025774          240 NAMISVT  246 (248)
Q Consensus       240 ~~~v~v~  246 (248)
                      .++|.+.
T Consensus        86 G~~L~l~   92 (107)
T 1wf9_A           86 GSMVYLA   92 (107)
T ss_dssp             TCEEECC
T ss_pred             CCEEEEE
Confidence            4555543

>3cxg_A Putative thioredoxin; malaria, structural GEN oxidoreductase, structural genomics consortium, SGC; 2.00A {Plasmodium falciparum}

Probab=94.07  E-value=0.17  Score=37.66  Aligned_cols=58  Identities=7%  Similarity=0.089  Sum_probs=44.5

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCc--eEEeeeCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQ--KMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~--~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +++|...|++..  ..++..|++..+|++.++...+|.  .+.++.|. ++++|...|...+.
T Consensus        70 ~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~~~~g~g~~~~~~~G~-~~~~l~~~l~~~l~  129 (133)
T 3cxg_A           70 YVTLVDIDVDIH--PKLNDQHNIKALPTFEFYFNLNNEWVLVHTVEGA-NQNDIEKAFQKYCL  129 (133)
T ss_dssp             ECEEEEEETTTC--HHHHHHTTCCSSSEEEEEEEETTEEEEEEEEESC-CHHHHHHHHHHHSE
T ss_pred             CEEEEEEeccch--HHHHHhcCCCCCCEEEEEEecCCCeEEEEEEcCC-CHHHHHHHHHHHHH
Confidence            468888887643  467889999999999998322466  88899998 88888777776654

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

Probab=94.01  E-value=0.38  Score=35.69  Aligned_cols=70  Identities=20%  Similarity=0.282  Sum_probs=55.8

Q ss_pred             CceEEEEE-cCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          169 LLCRVGVR-LPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       169 ~~~~i~iR-lp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ..++|.|. .|+|.+++-.|..+.+|.+|-+-+.... +.+...-+|+.+  .+.  +  .++.||++.|+. +.+|.+
T Consensus        14 ~~itvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~-~iP~e~qrLIy~--GKi--L--KD~eTL~~~gIk~g~TIhL   85 (118)
T 2daf_A           14 SLATVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLL-GIPHSVLQIRYS--GKI--L--KNNETLVQHGVKPQEIVQV   85 (118)
T ss_dssp             SCEEEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHH-TCCTTTEEEEET--TEE--E--CSSCCHHHHSCCSSCEEEE
T ss_pred             ccEEEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhh-CCChHHEEEEEC--CeE--c--CCcchHHHcCCCCCCEEEE
Confidence            34678887 7899999999999999999999998875 557778888665  453  6  457899999997 566643

>2lrt_A Uncharacterized protein; structural genomics, thioredoxin-like, NEW YORK structural G research consortium, nysgrc, PSI-biology; NMR {Bacteroides vulgatus}

Probab=93.94  E-value=0.5  Score=35.68  Aligned_cols=59  Identities=15%  Similarity=0.232  Sum_probs=47.4

Q ss_pred             ceEEEEEecCChHHH---------------------HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGK---------------------KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~---------------------~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.+.+.+++.....                     .++..|++..+|+++||++ +|.++.++.|..+.++.+..+.+-
T Consensus        68 ~~~vv~i~~d~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~v~~~P~~~lid~-~G~i~~~~~g~~~~e~~~~~~~~~  146 (152)
T 2lrt_A           68 GFEIYQISLDGDEHFWKTSADNLPWVCVRDANGAYSSYISLYNVTNLPSVFLVNR-NNELSARGENIKDLDEAIKKLLEG  146 (152)
T ss_dssp             TEEEEEEECSCCHHHHHHHHTTCSSEEEECSSGGGCHHHHHHTCCSCSEEEEEET-TTEEEEETTTCSCHHHHHHHHHGG
T ss_pred             CeEEEEEEccCCHHHHHHHHhCCCceEEECCCCcchHHHHHcCcccCceEEEECC-CCeEEEecCCHHHHHHHHHHHHhc
Confidence            588888888755431                     2788999999999999995 599999999999988887776655


Q ss_pred             h
Q 025774           78 M   78 (248)
Q Consensus        78 ~   78 (248)
                      .
T Consensus       147 ~  147 (152)
T 2lrt_A          147 H  147 (152)
T ss_dssp             G
T ss_pred             c
Confidence            4

>1fo5_A Thioredoxin; disulfide oxidoreductase, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; NMR {Methanocaldococcus jannaschii} SCOP: c.47.1.1

Probab=93.90  E-value=0.098  Score=35.01  Aligned_cols=51  Identities=14%  Similarity=0.225  Sum_probs=40.4

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.+...|++...  .++..|++..+|++.+    +|..  ++.|..+.+++...|...
T Consensus        34 ~~~~~~vd~~~~~--~~~~~~~v~~~Pt~~~----~G~~--~~~G~~~~~~l~~~l~~~   84 (85)
T 1fo5_A           34 AVEVEYINVMENP--QKAMEYGIMAVPTIVI----NGDV--EFIGAPTKEALVEAIKKR   84 (85)
T ss_dssp             SEEEEEEESSSSC--CTTTSTTTCCSSEEEE----TTEE--ECCSSSSSHHHHHHHHHH
T ss_pred             ceEEEEEECCCCH--HHHHHCCCcccCEEEE----CCEE--eeecCCCHHHHHHHHHHh
Confidence            7888888886543  4678899999999988    4765  788988999887777654

>1zma_A Bacterocin transport accessory protein; alpha-beta-alpha-sandwich, structural genomics, PSI, protein structure initiative; HET: MSE; 1.25A {Streptococcus pneumoniae} SCOP: c.47.1.1

Probab=93.86  E-value=0.18  Score=36.27  Aligned_cols=42  Identities=10%  Similarity=0.137  Sum_probs=35.1

Q ss_pred             HHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHH
Q 025774           31 EGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        31 eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L   74 (248)
                      +...++..|++..+|+++++.  +|..+.++.|..+.++|...|
T Consensus        75 ~~~~~~~~~~i~~~Pt~~~~~--~G~~~~~~~G~~~~~~l~~~l  116 (118)
T 1zma_A           75 DLQAFRSRYGIPTVPGFVHIT--DGQINVRCDSSMSAQEIKDFA  116 (118)
T ss_dssp             HHHHHHHHHTCCSSCEEEEEE--TTEEEEECCTTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCCeEEEEE--CCEEEEEecCCCCHHHHHHHh
Confidence            345788999999999998884  688889999999998886654

>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=93.82  E-value=0.21  Score=44.55  Aligned_cols=69  Identities=7%  Similarity=0.143  Sum_probs=54.9

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhc--CCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQL--EGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMI  243 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~--~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v  243 (248)
                      ...+|.||..+|+.+.-.+..++||.+|...|....  .+.+....+|+.  -.+.  |  ++++||.++|+. +++|
T Consensus         6 ~~M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy--~GK~--L--~D~~tL~dygI~~gstI   77 (368)
T 1oqy_A            6 SAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIY--AGKI--L--SDDVPIRDYRIDEKNFV   77 (368)
T ss_dssp             CCCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEES--SSSE--E--CSSSBTTTTCCCTTSCE
T ss_pred             ceEEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEE--CCee--c--CCcCCHHHcCCCCCCEE
Confidence            457899999999999989999999999999998742  356677888875  3553  6  457999999998 4555

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

Probab=93.82  E-value=0.32  Score=42.23  Aligned_cols=72  Identities=17%  Similarity=0.195  Sum_probs=57.6

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ++..+|.||..+|+.+.-.+..++||.+|-.-|.... +.++...+|+..  .+.  |  ++++||.+.|+. +++|.+.
T Consensus       231 ~~~MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~-GIp~~~QRLi~~--Gk~--L--~D~~TLsdygI~~gstL~Lv  303 (307)
T 3ai5_A          231 TGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHLV  303 (307)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHH-CCCGGGCEEEET--TEE--C--CTTSBTGGGTCCTTCEEEEE
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHH-CcChHHEEEEeC--Cee--c--CCCCCHHHcCCCCCCEEEEE
Confidence            3567899999999999999999999999999998764 667778888753  443  5  458999999998 5666553

>2oe3_A Thioredoxin-3; electron transport, alpha/beta sandwich, oxidized, dimer; 1.80A {Saccharomyces cerevisiae} PDB: 2oe1_A 2oe0_A

Probab=93.76  E-value=0.3  Score=35.12  Aligned_cols=52  Identities=17%  Similarity=0.268  Sum_probs=40.8

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ++.|...|++..  ..++..|++..+|+++++  .+|..+.++.|.. +++|...|.
T Consensus        61 ~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~-~~~l~~~l~  112 (114)
T 2oe3_A           61 DVRFVKCDVDES--PDIAKECEVTAMPTFVLG--KDGQLIGKIIGAN-PTALEKGIK  112 (114)
T ss_dssp             TSEEEEEETTTC--HHHHHHTTCCSBSEEEEE--ETTEEEEEEESSC-HHHHHHHHH
T ss_pred             CCEEEEEECCCC--HHHHHHCCCCcccEEEEE--eCCeEEEEEeCCC-HHHHHHHHH
Confidence            378888888643  358899999999998876  4689999999988 777765554

>2pu9_C TRX-F, thioredoxin F-type, chloroplast; protein-protein complex, iron-sulfur, electron transport; 1.65A {Spinacia oleracea} PDB: 2pvo_C 1f9m_A

Probab=93.65  E-value=0.34  Score=34.19  Aligned_cols=55  Identities=16%  Similarity=0.221  Sum_probs=41.6

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.|...|++. +...++..|++..+|++++ . .+|..+.++.|.. ++++...|..+
T Consensus        55 ~v~~~~vd~~~-~~~~~~~~~~v~~~Pt~~~-~-~~G~~~~~~~G~~-~~~l~~~l~~~  109 (111)
T 2pu9_C           55 DVIFLKLDCNQ-ENKTLAKELGIRVVPTFKI-L-KENSVVGEVTGAK-YDKLLEAIQAA  109 (111)
T ss_dssp             TSEEEEEECSS-TTHHHHHHHCCSBSSEEEE-E-SSSSEEEEEESSC-HHHHHHHHHHH
T ss_pred             CeEEEEEecCc-chHHHHHHcCCCeeeEEEE-E-eCCcEEEEEcCCC-HHHHHHHHHHh
Confidence            48888888863 3356888999999999554 4 5688899999984 77777666554

>3gix_A Thioredoxin-like protein 4B; PRE-mRNA splicing, TXNL4B, DLP, cell cycle, mRNA processing, mRNA splicing, nucleus, phosphoprotein, splicing; HET: SUC; 1.33A {Homo sapiens} SCOP: c.47.1.0 PDB: 1xbs_A

Probab=93.55  E-value=0.12  Score=39.47  Aligned_cols=59  Identities=17%  Similarity=0.326  Sum_probs=47.3

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceE---------EeeeC-CCChHHHHHHHhhhhhc
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKM---------RSWCG-MVQPESLLEDLVPFMDG   80 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l---------~~~~G-~~~~e~l~~~L~~~~~~   80 (248)
                      ..+.|+..|++..  ..++..|++..+|++.+..  +|..+         .++.| ..+.++|...|...+..
T Consensus        54 ~~~~~~~vd~d~~--~~l~~~~~v~~~Pt~~~~~--~G~~v~~~~g~~~~~~~~G~~~~~~~l~~~l~~~~~~  122 (149)
T 3gix_A           54 KMAAIYLVDVDQT--AVYTQYFDISYIPSTVFFF--NGQHMKVDYGSPDHTKFVGSFKTKQDFIDLIEVIYRG  122 (149)
T ss_dssp             TTEEEEEEETTTC--CHHHHHTTCCSSSEEEEEE--TTEEEEEECSSSCCSCEESCCSSHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCcC--HHHHHHcCCCccCeEEEEE--CCeEEEeecCCCCCCeEeeecCCHHHHHHHHHHHHHH
Confidence            3489999998643  4588999999999999553  58888         88999 88999988888777653

>1mek_A Protein disulfide isomerase; electron transport, redox-active center, endoplasmic reticulum; NMR {Homo sapiens} SCOP: c.47.1.2

Probab=93.55  E-value=0.082  Score=37.69  Aligned_cols=56  Identities=9%  Similarity=0.179  Sum_probs=43.2

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceE--EeeeCCCChHHHHHHHhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKM--RSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l--~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ++++...|.+...  .++..|++..+|++.++.  +|..+  ..+.|..+.++|...|...+
T Consensus        59 ~v~~~~vd~~~~~--~~~~~~~v~~~Pt~~~~~--~g~~~~~~~~~g~~~~~~l~~~l~~~~  116 (120)
T 1mek_A           59 EIRLAKVDATEES--DLAQQYGVRGYPTIKFFR--NGDTASPKEYTAGREADDIVNWLKKRT  116 (120)
T ss_dssp             CCBCEEEETTTCC--SSHHHHTCCSSSEEEEEE--SSCSSSCEECCCCSSHHHHHHHHHTTS
T ss_pred             cEEEEEEcCCCCH--HHHHHCCCCcccEEEEEe--CCCcCCcccccCccCHHHHHHHHHhcc
Confidence            5778888876432  567889999999999993  57766  78899999998877766554

>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=93.54  E-value=0.013  Score=44.27  Aligned_cols=67  Identities=19%  Similarity=0.265  Sum_probs=0.0

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +|.|+..+|+.+.-.+..++||.+|-.-|... .+.++...+|+.  -.+.  +  +++.||.+.|+. +++|.+
T Consensus         2 ~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~-~gip~~~QrLi~--~Gk~--L--~D~~tL~~~~I~~gsti~l   69 (128)
T 3u5e_m            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDK-EGIPPDQQRLIF--AGKQ--L--EDGRTLSDYNIQKESTLHL   69 (128)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             EEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHH-hCcChHHEEEEE--CCEE--C--CCCCchhhhccCCCCEEEE
Confidence            46788899999888999999999999998875 355677777764  3443  5  558999999998 455544

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

Probab=93.48  E-value=0.31  Score=38.25  Aligned_cols=69  Identities=17%  Similarity=0.207  Sum_probs=55.3

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ...|.|+..+|+.+.-++..++||.+|-.-|.... +.++...+|+..  .+.  +  +++.||.+.|+. +++|.+
T Consensus        96 g~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~-gip~~~q~L~~~--g~~--L--~D~~tL~~y~i~~g~tl~l  165 (172)
T 3u30_A           96 GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHL  165 (172)
T ss_dssp             CEEEEEEESSCCEEEEEECTTCBHHHHHHHHHHHH-CCCGGGCCEEET--TEE--C--CTTSBSGGGTCCTTCEEEE
T ss_pred             cccceeecccCcceeEEecCCCCHHHHHHHHHHHh-CCCceeEEEEEC--Ccc--C--CCCCcHHHhCCCCCCEEEE
Confidence            46788899999999999999999999999998764 667888888753  332  5  458899999998 566654

>1a8l_A Protein disulfide oxidoreductase; PDI, thioredoxin fold; 1.90A {Pyrococcus furiosus} SCOP: c.47.1.2 c.47.1.2 PDB: 1j08_A

Probab=93.41  E-value=0.36  Score=38.84  Aligned_cols=57  Identities=14%  Similarity=0.187  Sum_probs=46.1

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      .++.+...|++..  ..++..|++..+|++.++.  +|..+.++.|..+.++|...|...+
T Consensus       169 ~~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~--~G~~~~~~~G~~~~~~l~~~l~~~l  225 (226)
T 1a8l_A          169 GKILGDMVEAIEY--PEWADQYNVMAVPKIVIQV--NGEDRVEFEGAYPEKMFLEKLLSAL  225 (226)
T ss_dssp             CCEEEEEEEGGGC--HHHHHHTTCCSSCEEEEEE--TTEEEEEEESCCCHHHHHHHHHHHH
T ss_pred             CcEEEEEEEcccC--HHHHHhCCCcccCeEEEEe--CCceeEEEcCCCCHHHHHHHHHHhh
Confidence            3788888888643  4578899999999987773  6888889999999998888777654

>1faa_A Thioredoxin F; electron transport; 1.85A {Spinacia oleracea} SCOP: c.47.1.1

Probab=93.32  E-value=0.35  Score=34.89  Aligned_cols=55  Identities=16%  Similarity=0.256  Sum_probs=41.8

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ++.+...|++. +...++..|++..+|++.+.  .+|..+.++.|.. ++++...|...
T Consensus        68 ~~~~~~vd~~~-~~~~~~~~~~v~~~Pt~~~~--~~G~~~~~~~G~~-~~~l~~~i~~~  122 (124)
T 1faa_A           68 DVIFLKLDCNQ-ENKTLAKELGIRVVPTFKIL--KENSVVGEVTGAK-YDKLLEAIQAA  122 (124)
T ss_dssp             TSEEEEEECSS-TTHHHHHHHCCSSSSEEEEE--ETTEEEEEEESSC-HHHHHHHHHHH
T ss_pred             CCEEEEEecCc-chHHHHHHcCCCeeeEEEEE--eCCcEEEEEcCCC-HHHHHHHHHHh
Confidence            47888888853 34568889999999996665  4688899999975 77776666554

>2rli_A SCO2 protein homolog, mitochondrial; copper protein, thioredoxin fold, metal transport, structural genomics, spine2-complexes; NMR {Homo sapiens}

Probab=93.31  E-value=0.24  Score=37.88  Aligned_cols=48  Identities=10%  Similarity=0.166  Sum_probs=40.8

Q ss_pred             HHHHHhcCCCCCc---------------eEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           33 KKVCTYYKLDSIP---------------VVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        33 ~~~~~~~~~~~~P---------------~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ..++..|++...|               .++||++ +|.++.++.|..+++++...|...+..+
T Consensus       104 ~~~~~~~~v~~~p~~~~~~~~~~~~~~~~~~lid~-~G~i~~~~~g~~~~~~l~~~l~~ll~~~  166 (171)
T 2rli_A          104 AQASHSYRVYYNAGPKDEDQDYIVDHSIAIYLLNP-DGLFTDYYGRSRSAEQISDSVRRHMAAF  166 (171)
T ss_dssp             HHHHHHSCCCCEECCCCSSCCCCEECCCEEEEECT-TSCEEEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCeEEEecCCCCCCCeEEeccceEEEECC-CCeEEEEECCCCCHHHHHHHHHHHHHHH
Confidence            4688899998888               8899995 5999999999999999999988887754

>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=93.27  E-value=0.62  Score=34.43  Aligned_cols=71  Identities=17%  Similarity=0.220  Sum_probs=54.8

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ...+.|.|+-.+|+.+.-+...++++..|++...... +.+...++|...  ...  +  +.+.|.+++|+. +..|-|
T Consensus        38 ~~~I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~-Gl~~~~irFlFD--G~r--I--~~~~TP~dL~MEDgD~IdV  109 (115)
T 3kyd_D           38 GEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQ-GVPMNSLRFLFE--GQR--I--ADNHTPKELGMEEEDVIEV  109 (115)
T ss_dssp             -CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHH-TCCTTSEEEEET--TEE--C--CTTCCTTTTTCCTTCEEEE
T ss_pred             CCeEEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHh-CCChhhEEEEEC--CeE--C--CCCCCHHHcCCCCCCEEEE
Confidence            4578899999999999999999999999998776653 556778888654  332  5  568999999998 455533

>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=93.26  E-value=0.49  Score=33.37  Aligned_cols=74  Identities=14%  Similarity=-0.013  Sum_probs=54.2

Q ss_pred             ceEEEEEcCCCc-eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCC-CCcc-ccCCCcCCCccccCCcC-ceEEE
Q 025774          170 LCRVGVRLPDGR-RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIP-GATK-SLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       170 ~~~i~iRlp~G~-r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~P-r~~~-~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      .++|.|+..++. .+.+++..++||..|-.-+... .|.++...+|....+ .+.. .+ .++++||.+.|+.+ ++|.|
T Consensus         7 ~v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~-~gip~~~qrL~~~~~~g~~~~~l-~~D~~tL~~y~i~~g~~l~v   84 (95)
T 1v6e_A            7 GVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELV-VGSPASCMELELYGADDKFYSKL-DQEDALLGSYPVDDGCRIHV   84 (95)
T ss_dssp             CEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHH-TCSCTTTCBCEEECSSSCEEEEC-CCSSSBTTSSSCCTTCEEEE
T ss_pred             EEEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHH-HCCCHHHeEEEEeCCCCcccccc-CCCcCCHhHCCCCCCCEEEE
Confidence            477888876654 6899999999999999999886 577788888876532 2210 12 25689999999984 55544

>2yj7_A LPBCA thioredoxin; oxidoreductase; 1.65A {Synthetic construct}

Probab=92.37  E-value=0.015  Score=40.63  Aligned_cols=55  Identities=24%  Similarity=0.306  Sum_probs=42.1

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      .++.+...|++.  ...++..|++..+|++.++  .+|..+.++.|..+.+++...|..
T Consensus        50 ~~~~~~~v~~~~--~~~~~~~~~v~~~Pt~~~~--~~g~~~~~~~g~~~~~~l~~~l~~  104 (106)
T 2yj7_A           50 GKVKVVKVNVDE--NPNTAAQYGIRSIPTLLLF--KNGQVVDRLVGAQPKEALKERIDK  104 (106)
Confidence            356777776643  4467889999999999988  468888889998888877665554

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=93.21  E-value=0.26  Score=40.09  Aligned_cols=63  Identities=17%  Similarity=0.246  Sum_probs=50.6

Q ss_pred             HhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           15 TISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        15 ~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      -+..++.|..+|++..  ..++..|++..+|+++++.  +|..+.++.|..+.++|...|...+...
T Consensus        58 ~~~~~v~~~~vd~d~~--~~l~~~~~v~~~Pt~~~~~--~G~~~~~~~G~~~~~~l~~~l~~~l~~~  120 (222)
T 3dxb_A           58 EYQGKLTVAKLNIDQN--PGTAPKYGIRGIPTLLLFK--NGEVAATKVGALSKGQLKEFLDANLAGS  120 (222)
T ss_dssp             HTTTTCEEEEEETTTC--TTTGGGGTCCSBSEEEEEE--TTEEEEEEESCCCHHHHHHHHHHHSCCS
T ss_pred             HhcCCcEEEEEECCCC--HHHHHHcCCCcCCEEEEEE--CCeEEEEeccccChHHHHHHHHhhcccc
Confidence            3344688888888643  2467899999999999884  6889999999999999998888887654

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

Probab=93.12  E-value=0.5  Score=34.00  Aligned_cols=70  Identities=9%  Similarity=0.041  Sum_probs=51.2

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISVT  246 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v~  246 (248)
                      ...+.+++ +|+.+.-.+..++||.+|-.-|... .+.++..-+|. .||...  +  +++.+|.++|+.+ ++|++.
T Consensus         9 m~~~~vk~-~Gk~~~v~v~~~~TV~~LK~~I~~~-tgIpp~~QkLi-~~~~gk--L--~D~~tLs~~~I~~gstL~lv   79 (100)
T 2dzm_A            9 MLDFRVEY-RDRNVDVVLEDTCTVGEIKQILENE-LQIPVSKMLLK-GWKTGD--V--EDSTVLKSLHLPKNNSLYVL   79 (100)
T ss_dssp             EEEEEEEC-SSCEEEEEEETTSBHHHHHHHHHHH-HCCCTTTCCEE-CCSSSC--C--CTTSBHHHHCCCSEEEEEEC
T ss_pred             eEEEEEEe-CCeEEEEEECCCCcHHHHHHHHHHH-HCCChhHeEEE-ccCCCC--C--CCcCCHHHcCCCCCCEEEEE
Confidence            45677777 6677778899999999999999875 46566666663 355553  5  4589999999985 555553

>2lrn_A Thiol:disulfide interchange protein; structural genomics, thioredoxin-like, NEW YORK structural G research consortium, oxidoreductase; NMR {Bacteroides SP}

Probab=92.77  E-value=0.78  Score=34.25  Aligned_cols=59  Identities=25%  Similarity=0.485  Sum_probs=43.6

Q ss_pred             ceEEEEEecCChH-----------------------HHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           19 NFIFWQVYDDTSE-----------------------GKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        19 ~fV~w~~d~~~~e-----------------------g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ++.+.+.+++...                       ...++..|++..+|+++||++ +|.++.+.   ++++++...|.
T Consensus        62 ~~~vv~v~~d~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~v~~~P~~~lid~-~G~i~~~~---~~~~~l~~~l~  137 (152)
T 2lrn_A           62 GFTIYGVSTDRREEDWKKAIEEDKSYWNQVLLQKDDVKDVLESYCIVGFPHIILVDP-EGKIVAKE---LRGDDLYNTVE  137 (152)
T ss_dssp             TEEEEEEECCSCHHHHHHHHHHHTCCSEEEEECHHHHHHHHHHTTCCSSCEEEEECT-TSEEEEEC---CCTTHHHHHHH
T ss_pred             CeEEEEEEccCCHHHHHHHHHHhCCCCeEEecccchhHHHHHHhCCCcCCeEEEECC-CCeEEEee---CCHHHHHHHHH
Confidence            4888888876422                       467889999999999999995 58887765   35567766676


Q ss_pred             hhhhcC
Q 025774           76 PFMDGG   81 (248)
Q Consensus        76 ~~~~~~   81 (248)
                      ..+...
T Consensus       138 ~l~~~~  143 (152)
T 2lrn_A          138 KFVNGA  143 (152)
T ss_dssp             HHHTSS
T ss_pred             HHHhhc
Confidence            666643

>1ilo_A Conserved hypothetical protein MTH895; beta-alpha-beta-alpha-beta-BETA-alpha motif, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus str} SCOP: c.47.1.1

Probab=92.68  E-value=0.29  Score=32.02  Aligned_cols=46  Identities=17%  Similarity=0.130  Sum_probs=34.9

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC-ChHHHHHH
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV-QPESLLED   73 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~-~~e~l~~~   73 (248)
                      ..++.+...|     ...++..|++..+|++.+    +|..+..  |.. +.+++...
T Consensus        29 ~~~~~~~~v~-----~~~~~~~~~v~~~Pt~~~----~G~~~~~--G~~~~~~~l~~~   75 (77)
T 1ilo_A           29 GIDAEFEKIK-----EMDQILEAGLTALPGLAV----DGELKIM--GRVASKEEIKKI   75 (77)
T ss_dssp             TCCEEEEEEC-----SHHHHHHHTCSSSSCEEE----TTEEEEC--SSCCCHHHHHHH
T ss_pred             CCceEEEEec-----CHHHHHHCCCCcCCEEEE----CCEEEEc--CCCCCHHHHHHH
Confidence            3467777777     345788999999999988    5877665  987 88877654

>1jfu_A Thiol:disulfide interchange protein TLPA; thioredoxin-like, double disulfide bridge, membrane protein; 1.60A {Bradyrhizobium japonicum} SCOP: c.47.1.10

Probab=92.57  E-value=0.97  Score=35.00  Aligned_cols=62  Identities=23%  Similarity=0.302  Sum_probs=45.1

Q ss_pred             cceEEEEEecCCh---HHHHHHHhcCCC-----------------------CCceEEEEeCCCCceEEeeeCCCC--hHH
Q 025774           18 TNFIFWQVYDDTS---EGKKVCTYYKLD-----------------------SIPVVLVVDPITGQKMRSWCGMVQ--PES   69 (248)
Q Consensus        18 ~~fV~w~~d~~~~---eg~~~~~~~~~~-----------------------~~P~l~ii~~~~g~~l~~~~G~~~--~e~   69 (248)
                      .++.+.+.+++..   ....++..|++.                       .+|+++||++ +|.++.++.|..+  .++
T Consensus        92 ~~~~vv~v~~d~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~P~~~lid~-~G~i~~~~~g~~~~~~~~  170 (186)
T 1jfu_A           92 PNFEVVAINIDTRDPEKPKTFLKEANLTRLGYFNDQKAKVFQDLKAIGRALGMPTSVLVDP-QGCEIATIAGPAEWASED  170 (186)
T ss_dssp             TTEEEEEEECCCSCTTHHHHHHHHTTCCTTCCEECTTCHHHHHHHTTTCCSSSSEEEEECT-TSBEEEEEESCCCTTSHH
T ss_pred             CCcEEEEEECCCCCHHHHHHHHHHcCCCCCceEECCcchHHHHhccccccCCCCEEEEECC-CCCEEEEEecCCccCHHH
Confidence            3677777776543   345666666653                       7999999995 5999999999875  778


Q ss_pred             HHHHHhhhhhc
Q 025774           70 LLEDLVPFMDG   80 (248)
Q Consensus        70 l~~~L~~~~~~   80 (248)
                      +...|...+..
T Consensus       171 l~~~l~~ll~~  181 (186)
T 1jfu_A          171 ALKLIRAATGK  181 (186)
T ss_dssp             HHHHHHHHHC-
T ss_pred             HHHHHHHHhcc
Confidence            88777777653

>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=92.52  E-value=1  Score=33.38  Aligned_cols=76  Identities=13%  Similarity=0.127  Sum_probs=55.3

Q ss_pred             CceEEEEEcCCCc-eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccC-CCCcc-ccCCCcCCCccccCCcC-ceEE
Q 025774          169 LLCRVGVRLPDGR-RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAI-PGATK-SLDYDSKLTFEDSGLAN-AMIS  244 (248)
Q Consensus       169 ~~~~i~iRlp~G~-r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~-Pr~~~-~l~~d~~~tl~d~gl~~-~~v~  244 (248)
                      +.++|.|+-.++. .+.++|..++||..|-.-|... .|.++...+|...- ..+.. .+ .+.++||.+.|+.+ ++|+
T Consensus         5 ~~v~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~-~Gip~~~qrL~~~g~~~~~~~~l-~~D~~tL~~y~i~~g~~ih   82 (122)
T 1t0y_A            5 EVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELV-VGTTVDSMRIQLFDGDDQLKGEL-TDGAKSLKDLGVRDGYRIH   82 (122)
T ss_dssp             CEEEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHH-HCCCTTTEEEEEECSSSSEEEEC-CCCSSBTTTTTCCSSEEEE
T ss_pred             CEEEEEEEECCCCccEEEEeCCCCcHHHHHHHHHHH-hCCCHHHeEEEEecCCCcccccc-CCCcCCHHHCCCCCCCEEE
Confidence            3678888877664 6899999999999999999886 47778888887532 11210 12 25689999999984 5565


Q ss_pred             EE
Q 025774          245 VT  246 (248)
Q Consensus       245 v~  246 (248)
                      |+
T Consensus        83 vv   84 (122)
T 1t0y_A           83 AV   84 (122)
T ss_dssp             EE
T ss_pred             EE
Confidence            53

>1qgv_A Spliceosomal protein U5-15KD; snRNP, thioredoxin, transcription; 1.40A {Homo sapiens} SCOP: c.47.1.8 PDB: 1syx_A 1pqn_A

Probab=92.40  E-value=0.31  Score=36.81  Aligned_cols=61  Identities=8%  Similarity=0.089  Sum_probs=45.5

Q ss_pred             hhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEE---------eeeCCCC-hHHHHHHHhhhhhc
Q 025774           16 ISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMR---------SWCGMVQ-PESLLEDLVPFMDG   80 (248)
Q Consensus        16 l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~---------~~~G~~~-~e~l~~~L~~~~~~   80 (248)
                      +..++.|...|++...  .++..|++..+|++.++.  +|..+.         ++.|.++ .++|...|...+..
T Consensus        52 ~~~~v~~~~vd~d~~~--~~~~~~~i~~~Pt~~~~~--~G~~v~~~~g~~~~~~~~g~~~~~~~l~~~i~~~~~~  122 (142)
T 1qgv_A           52 VKNFAVIYLVDITEVP--DFNKMYELYDPCTVMFFF--RNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRG  122 (142)
T ss_dssp             HTTTEEEEEEETTTCC--TTTTSSCSCSSCEEEEEE--TTEEEEEECC------CCSCCSCHHHHHHHHHHHHHH
T ss_pred             hCCCeEEEEEccccCH--HHHHHcCCCCCCEEEEEE--CCcEEEEecCCCCcceeeeecCcHHHHHHHHHHHHHH
Confidence            3346899999987543  478899999999999884  577665         4667664 88888888877764

>3fw2_A Thiol-disulfide oxidoreductase; structural genomics, APC61456.1, thiol-disulfide oxidoreduct TLPA-like family, PSI-2; 1.74A {Bacteroides thetaiotaomicron}

Probab=92.21  E-value=0.5  Score=35.29  Aligned_cols=43  Identities=16%  Similarity=0.344  Sum_probs=34.2

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ..++..|++..+|++.||++ +|.++.+..   +++++...|...+.
T Consensus       106 ~~~~~~~~v~~~P~~~lid~-~G~i~~~~~---~~~~l~~~l~~ll~  148 (150)
T 3fw2_A          106 SEVAKQYSIYKIPANILLSS-DGKILAKNL---RGEELKKKIENIVE  148 (150)
T ss_dssp             CHHHHHTTCCSSSEEEEECT-TSBEEEESC---CHHHHHHHHHHHHH
T ss_pred             hHHHHHcCCCccCeEEEECC-CCEEEEccC---CHHHHHHHHHHHHh
Confidence            36888999999999999995 588877653   77888777776654

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=92.20  E-value=0.87  Score=36.99  Aligned_cols=71  Identities=20%  Similarity=0.266  Sum_probs=54.1

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +...+.|+|+. +|+.+..+...++++..|++..... .|.+...++|...  .+.  +  +.+.|.+++|+. +.+|-|
T Consensus        26 ~~~~I~LkV~~-~g~~v~fkIk~~t~l~kL~~ay~er-~Gi~~~~~RF~Fd--G~r--I--~~~~TP~dL~MEdgD~Idv   97 (200)
T 3pge_A           26 PETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKR-QGKEMDSLRFLYD--GIR--I--QADQTPEDLDMEDNDIIEA   97 (200)
T ss_dssp             CCCCEEEEEEC-SSCEEEEEECTTSCTHHHHHHHHHH-HSSCGGGEEEEET--TEE--C--CTTCCTTTTTCCTTEEEEE
T ss_pred             CCCeEEEEEec-CCCEEEEEEecCCHHHHHHHHHHHH-hCCChhhEEEEEC--CEE--c--CCCCCHHHcCCCCCCEEEE
Confidence            35578899986 9999999999999999999876554 3666778888654  433  5  568999999998 455544

>3hdc_A Thioredoxin family protein; ATCC53774, DSM 7210, , structural genomics, PSI-2, protein structure initiative; 1.77A {Geobacter metallireducens gs-15}

Probab=92.13  E-value=0.47  Score=35.86  Aligned_cols=58  Identities=16%  Similarity=0.256  Sum_probs=44.1

Q ss_pred             cceEEEEEecCC-----------------hHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCC--hHHHHHHHhh
Q 025774           18 TNFIFWQVYDDT-----------------SEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQ--PESLLEDLVP   76 (248)
Q Consensus        18 ~~fV~w~~d~~~-----------------~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~--~e~l~~~L~~   76 (248)
                      .++.+...+.+.                 .....++..|++..+|+++||++ +|.++.++.|..+  .++++..+..
T Consensus        73 ~~~~~v~v~~d~~~~~~~~~~~~~~~~~~d~~~~~~~~~~v~~~P~~~lid~-~G~i~~~~~G~~~~~~~~~~~~~~~  149 (158)
T 3hdc_A           73 GDLVVLAVNVEKRFPEKYRRAPVSFNFLSDATGQVQQRYGANRLPDTFIVDR-KGIIRQRVTGGIEWDAPKVVSYLKS  149 (158)
T ss_dssp             TSEEEEEEECSSSCCGGGGGCCCSCEEEECTTSHHHHHTTCCSSSEEEEECT-TSBEEEEEESCCCTTSHHHHHHHHT
T ss_pred             CCeEEEEEeCCHHHHHHHHHcCCCceEEECchHHHHHHhCCCCcceEEEEcC-CCCEEEEEeCCCccchHHHHHHHHh
Confidence            368888888765                 12346889999999999999995 6999999999764  4566665544

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

Probab=91.86  E-value=0.49  Score=33.41  Aligned_cols=65  Identities=20%  Similarity=0.243  Sum_probs=53.5

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMI  243 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v  243 (248)
                      .|-|..|||.|.+-+...+.++.+|.+=+-.+. +.++..|.|...  ++  .+  |.+..+-=.||.| +.|
T Consensus        11 ~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~-gl~~~~~~Lkh~--~k--~l--DLSlpfRlsgLpnnAkL   76 (90)
T 2al3_A           11 AVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQ-DFNPSEYDLKFQ--RT--VL--DLSLQWRFANLPNNAKL   76 (90)
T ss_dssp             CEEEECTTSCEEEECCCTTSBHHHHHHHHHHHT-TCCGGGCEEEET--TE--EE--SSSCBHHHHCCCSSCEE
T ss_pred             EEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHh-CCChhhCeEEeC--CE--ec--cccceeEecCCCCCCEE
Confidence            789999999999999999999999887665554 667899999875  33  25  8899999999985 444

>2ywi_A Hypothetical conserved protein; uncharacterized conserved protein, NPPSFA, national project protein structural and functional analyses; 1.60A {Geobacillus kaustophilus}

Probab=91.76  E-value=0.51  Score=36.91  Aligned_cols=47  Identities=19%  Similarity=0.179  Sum_probs=38.9

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEe---------eeCCCChHHHHHHHhhhhhcC
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRS---------WCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~---------~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      .++..|++..+|+++||++ +|.++.+         ..|..+.+++...|...+...
T Consensus       121 ~~~~~~~v~~~P~~~lid~-~G~i~~~~~~~~~~~~~~g~~~~~~l~~~i~~ll~~~  176 (196)
T 2ywi_A          121 EVAKAYDAACTPDFYIFDR-DLKCVYRGQLDDSRPNNGIPVTGESIRAALDALLEGR  176 (196)
T ss_dssp             HHHHHHTCCEESEEEEEET-TCBEEEEECSSSCCTTTCCCCCCHHHHHHHHHHHHTC
T ss_pred             HHHHHhCCCCCCeEEEEcC-CCeEEEccccCcccccccCccCHHHHHHHHHHHHcCC
Confidence            5778899999999999995 5888877         457788999999888888754

>3q6o_A Sulfhydryl oxidase 1; protein disulfide isomerase, thioredoxin, thioredoxin fold, oxidoreductase, reductive methylation; HET: MLY; 2.05A {Homo sapiens}

Probab=91.75  E-value=0.7  Score=37.84  Aligned_cols=61  Identities=15%  Similarity=0.300  Sum_probs=49.7

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCC--C--CceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPI--T--GQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~--~--g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ++.|...|++..+...++..|++..+|++.++.+-  .  |..+ .+.| .+++.+...|...+..+
T Consensus        65 ~v~~~~vd~~~~~~~~l~~~~~v~~~Pt~~~~~~g~~~~~g~~~-~~~g-~~~~~l~~~i~~~l~~~  129 (244)
T 3q6o_A           65 ALYLAALDCAEETNSAVCRDFNIPGFPTVRFFXAFTXNGSGAVF-PVAG-ADVQTLRERLIDALESH  129 (244)
T ss_dssp             TEEEEEEETTSTTTHHHHHHTTCCSSSEEEEECTTCCSSSCEEC-CCTT-CCHHHHHHHHHHHHHTC
T ss_pred             cEEEEEEeCCchhhHHHHHHcCCCccCEEEEEeCCCcCCCCeeE-ecCC-CCHHHHHHHHHHHHHhc
Confidence            79999999987778899999999999999999852  1  2233 5667 58999999999988865

>2av4_A Thioredoxin-like protein 4A (DIM1); U5 snRNP-SPECIFIC 15KD prote structural genomics, structural genomics consortium, SGC, U function; 1.73A {Plasmodium yoelii}

Probab=91.72  E-value=0.28  Score=38.46  Aligned_cols=59  Identities=12%  Similarity=0.120  Sum_probs=47.2

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceE--E-------eeeCCCC-hHHHHHHHhhhhhc
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKM--R-------SWCGMVQ-PESLLEDLVPFMDG   80 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l--~-------~~~G~~~-~e~l~~~L~~~~~~   80 (248)
                      ...+|+.+|++..  ..++..|++.+.|+++++-  +|+.+  .       ++.|..+ .++|...|..++..
T Consensus        72 ~~v~f~kVDVDe~--~e~a~~y~V~siPT~~fFk--~G~~v~vd~Gtgd~~k~vGa~~~k~~l~~~ie~~~r~  140 (160)
T 2av4_A           72 NFCVIYLVDITEV--PDFNTMYELYDPVSVMFFY--RNKHMMIDLGTGNNNKINWPMNNKQEFIDIVETIFRG  140 (160)
T ss_dssp             TTEEEEEEETTTC--CTTTTTTTCCSSEEEEEEE--TTEEEEEECSSSCCSCBCSCCCCHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEECCCC--HHHHHHcCCCCCCEEEEEE--CCEEEEEecCCCCcCeEEeecCCHHHHHHHHHHHHHH
Confidence            4589999999743  3589999999999998884  47765  5       8999887 88888888777653

>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=91.71  E-value=0.39  Score=35.72  Aligned_cols=60  Identities=13%  Similarity=0.072  Sum_probs=46.2

Q ss_pred             EEEEcCCCc-eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc
Q 025774          173 VGVRLPDGR-RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA  239 (248)
Q Consensus       173 i~iRlp~G~-r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~  239 (248)
                      |.|+.-.|+ .+.-....++||..|-.-|... .|.++...+|+.+  .+.  +  ++++||.|.|+.
T Consensus         3 mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~-egIP~~qQrLi~~--Gk~--L--eD~~TLsdy~I~   63 (118)
T 2fnj_B            3 VFLMIRRHKTTIFTDAKESSTVFELKRIVEGI-LKRPPEEQRLYKD--DQL--L--DDGKTLGECGFT   63 (118)
T ss_dssp             EEEEEEEBTEEEEEEEETTSBHHHHHHHHHHH-HCCCGGGEEEEET--TEE--C--CTTSBHHHHTCC
T ss_pred             EEEEEecCCEEEEEEeCCcChHHHHHHHHHHH-hCCCHHHeEEEEC--CeE--C--CCCCCHHHcCcc
Confidence            444444565 4777889999999999999875 4677889999843  443  5  668999999998

>3t58_A Sulfhydryl oxidase 1; oxidoreductase; HET: FAD; 2.40A {Mus musculus} PDB: 3t59_A*

Probab=91.67  E-value=0.89  Score=42.24  Aligned_cols=63  Identities=11%  Similarity=0.150  Sum_probs=53.0

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCC--CCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPI--TGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~--~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      .+.|...|++..+...++..|++..||++.++.+-  .|..+....|..+++.+...|...+..+
T Consensus        65 ~v~~~~VD~d~d~~~~l~~~~~V~~~PTl~~f~~g~~~G~~~~~~~g~~~~~~L~~~l~~~l~~~  129 (519)
T 3t58_A           65 ALNLAVLDCAEETNSAVCREFNIAGFPTVRFFQAFTKNGSGATLPGAGANVQTLRMRLIDALESH  129 (519)
T ss_dssp             TEEEEEEETTSGGGHHHHHHTTCCSBSEEEEECTTCCSCCCEEECCSSCCHHHHHHHHHHHHTTC
T ss_pred             cEEEEEEECCccccHHHHHHcCCcccCEEEEEcCcccCCCceeEecCCCCHHHHHHHHHHHHhhc
Confidence            69999999987778899999999999999999851  3555566677789999999999988865

>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=91.62  E-value=0.033  Score=43.46  Aligned_cols=67  Identities=19%  Similarity=0.265  Sum_probs=0.0

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      .|.|+..+|+.+.-.+..++||.+|-.-|... .+.++...+|+.  -.+.  |  +++.||.+.|+. +++|.+
T Consensus         2 qI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~-~gip~~~QrLi~--~Gk~--L--~D~~tL~dygI~~gstL~L   69 (152)
T 3u5c_f            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDK-EGIPPDQQRLIF--AGKQ--L--EDGRTLSDYNIQKESTLHL   69 (152)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHHHH-hCCCHHHEEEEE--CCEE--c--cccCcHHHcCCCCCCEEEE
Confidence            57788899998888899999999999999775 355677777764  3443  5  457999999998 455544

>2djj_A PDI, protein disulfide-isomerase; thioredoxin fold; NMR {Humicola insolens} SCOP: c.47.1.2 PDB: 2kp1_A

Probab=91.59  E-value=0.26  Score=35.37  Aligned_cols=54  Identities=11%  Similarity=0.177  Sum_probs=41.4

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCce-EEeeeCCCChHHHHHHHhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQK-MRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~-l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ++.|...|++..+   ++.  ++..+|++.++.+ .|.. +.++.|..+.++|...|...+
T Consensus        62 ~v~~~~vd~~~~~---~~~--~v~~~Pt~~~~~~-~~~~~~~~~~G~~~~~~l~~~i~~~~  116 (121)
T 2djj_A           62 RVVIAKVDATAND---VPD--EIQGFPTIKLYPA-GAKGQPVTYSGSRTVEDLIKFIAENG  116 (121)
T ss_dssp             SSEEEEEETTTSC---CSS--CCSSSSEEEEECS-SCTTSCCCCCCCSCHHHHHHHHHHTS
T ss_pred             ceEEEEEECcccc---ccc--ccCcCCeEEEEeC-cCCCCceEecCCCCHHHHHHHHHhcc
Confidence            7899999987655   444  8999999999974 3443 677899999998877766554

>2f51_A Thioredoxin; electron transport; 1.90A {Trichomonas vaginalis}

Probab=91.56  E-value=0.51  Score=34.05  Aligned_cols=58  Identities=19%  Similarity=0.310  Sum_probs=42.6

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCC--CCceEEeeeCCCChHHHHHHHhhhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPI--TGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~--~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      .++.|...|++..  ..++..|++..+|++.++...  .|..+.++.|..+. ++...+..+.
T Consensus        53 ~~v~~~~vd~~~~--~~~~~~~~i~~~Pt~~~~~~~~~~G~~~~~~~G~~~~-~l~~~~~~~~  112 (118)
T 2f51_A           53 KDVTFIKVDVDKN--GNAADAYGVSSIPALFFVKKEGNEIKTLDQFVGADVS-RIKADIEKFK  112 (118)
T ss_dssp             TTSEEEEEETTTC--HHHHHHTTCCSSSEEEEEEEETTEEEEEEEEESCCHH-HHHHHHHHHC
T ss_pred             CCeEEEEEECCCC--HHHHHhcCCCCCCEEEEEeCCCCcceEEEeecCCCHH-HHHHHHHHhh
Confidence            4788999988654  457899999999999999531  27789999997654 4555554443

>2hyx_A Protein DIPZ; thioredoxin fold, jelly-roll, structural genomics, TB struct genomics consortium, TBSGC, unknown function; 1.90A {Mycobacterium tuberculosis}

Probab=91.41  E-value=0.2  Score=44.30  Aligned_cols=47  Identities=15%  Similarity=0.105  Sum_probs=40.7

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ..++..|++..+|.++||++ +|.++.++.|..+.+++...|...+..
T Consensus       154 ~~l~~~ygV~~~Pt~~lID~-~G~Iv~~~~G~~~~~~l~~~I~~lL~e  200 (352)
T 2hyx_A          154 YATWTNYRNRYWPAEYLIDA-TGTVRHIKFGEGDYNVTETLVRQLLND  200 (352)
T ss_dssp             SHHHHHTTCCEESEEEEECT-TSBEEEEEESBCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCccCEEEEEeC-CCeEEEEEcCCCCHHHHHHHHHHHHhh
Confidence            35778899999999999995 699999999999999998888888764

>3ha9_A Uncharacterized thioredoxin-like protein; PSI, MCSG, structural G midwest center for structural genomics, protein structure initiative; 1.70A {Aeropyrum pernix}

Probab=91.36  E-value=0.16  Score=38.67  Aligned_cols=63  Identities=14%  Similarity=0.203  Sum_probs=42.6

Q ss_pred             HHHHHHhhcceE-EEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC-ChHHHHHHHhhhh
Q 025774           10 EAVSQTISTNFI-FWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV-QPESLLEDLVPFM   78 (248)
Q Consensus        10 ~~v~~~l~~~fV-~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~-~~e~l~~~L~~~~   78 (248)
                      +.+.+|++++=+ -|..-.+   ...++..|++..+|+++||++ +|.++.  .|.. +.+++...|...+
T Consensus        99 ~~~~~~~~~~~~~~~~~~~d---~~~~~~~~~v~~~P~~~lid~-~G~i~~--~g~~~~~~~l~~~l~~l~  163 (165)
T 3ha9_A           99 EMFRKFIANYGDPSWIMVMD---DGSLVEKFNVRSIDYIVIMDK-SSNVLY--AGTTPSLGELESVIKSVQ  163 (165)
T ss_dssp             HHHHHHHHHHSCTTSEEEEC---CSHHHHHTTCCSSSEEEEEET-TCCEEE--EEESCCHHHHHHHHHHC-
T ss_pred             HHHHHHHHHcCCCCeeEEeC---hHHHHHHhCCCCceEEEEEcC-CCcEEE--eCCCCCHHHHHHHHHHHh
Confidence            455666665222 2222222   236888999999999999995 588777  8888 8888877776654

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}

Probab=91.19  E-value=0.81  Score=37.01  Aligned_cols=71  Identities=17%  Similarity=0.236  Sum_probs=52.5

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +...+.|.|+. +|+.+.-+...+++|..|++..... .+.+...++|...  ...  +  +.+.|.+++++.. .+|-|
T Consensus        54 p~e~InLKVk~-dG~eV~FKIKrtTpL~KLmeAYcER-qGL~~~sIRFLFD--GqR--I--~~ddTPeDLdMEDGDtIDV  125 (207)
T 3tix_A           54 PETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKR-QGKEMDSLTFLYD--GIE--I--QADQTPEDLDMEDNDIIEA  125 (207)
T ss_dssp             -CCEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHH-TTCCGGGSCEEET--TEE--C--CSSCCTTTTTCCTTEEEEE
T ss_pred             CCCcEEEEEec-CCCEEEEEEccCChHHHHHHHHHHH-hCCCcccEEEEEC--Cee--c--CCCCCHHHcCCCCCCEEEE
Confidence            35578888884 9999999999999999999877554 3556667776543  332  4  5689999999984 44433

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=90.95  E-value=1.1  Score=32.57  Aligned_cols=76  Identities=13%  Similarity=0.062  Sum_probs=53.1

Q ss_pred             CCCCCCCceEEEEEcCC--C--ceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCC
Q 025774          163 PKVDRSLLCRVGVRLPD--G--RRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGL  238 (248)
Q Consensus       163 P~~~~~~~~~i~iRlp~--G--~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl  238 (248)
                      |..-+++.++++|.+-|  |  ..+.-.+..++||..|-+-+.... |.++..-+|+.+  ++   + .+++.||.+.|+
T Consensus        15 ~~~~~~~~i~l~v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~-Gipp~~QRli~g--gk---l-l~D~~TL~~ygI   87 (105)
T 4dbg_A           15 PEVSPTQDIRLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDY-GFPPVLQQWVIG--QR---L-ARDQETLHSHGV   87 (105)
T ss_dssp             -----CCCEEEEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TE---E-ECTTCBTGGGTC
T ss_pred             CCcCCCCcEEEEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHh-CCCHHHEEEecc--Ce---E-ccCcCcHHHcCC
Confidence            33344456777777755  3  578889999999999999998764 777878887754  43   4 256899999999


Q ss_pred             c--CceEEE
Q 025774          239 A--NAMISV  245 (248)
Q Consensus       239 ~--~~~v~v  245 (248)
                      .  ++++.+
T Consensus        88 ~~~G~t~hL   96 (105)
T 4dbg_A           88 RQNGDSAYL   96 (105)
T ss_dssp             CSTTCEEEE
T ss_pred             CCCCCEEEE
Confidence            4  555543

>3h79_A Thioredoxin-like protein; thioredoxin fold, catalytic cysteines missing, unknown funct; 1.50A {Trypanosoma cruzi} SCOP: c.47.1.0

Probab=90.93  E-value=0.75  Score=33.37  Aligned_cols=56  Identities=7%  Similarity=0.067  Sum_probs=41.9

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCce-EEeeeCCCChHHHHHHHhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQK-MRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~-l~~~~G~~~~e~l~~~L~~   76 (248)
                      .++.+...|.+..  ..++..|++..||++.++.+ .+.. ...+.|..+.++|..-|..
T Consensus        69 ~~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~~-g~~~~~~~~~G~~~~~~l~~~i~~  125 (127)
T 3h79_A           69 LTFVAARIDGEKY--PDVIERMRVSGFPTMRYYTR-IDKQEPFEYSGQRYLSLVDSFVFQ  125 (127)
T ss_dssp             TTEEEEEEETTTC--HHHHHHTTCCSSSEEEEECS-SCSSSCEECCSCCCHHHHHHHHHH
T ss_pred             CCeEEEEEEcccc--HhHHHhcCCccCCEEEEEeC-CCCCCceEecCCccHHHHHHHHHh
Confidence            4688888988643  46889999999999999964 2232 2568899999888665543

>1a8l_A Protein disulfide oxidoreductase; PDI, thioredoxin fold; 1.90A {Pyrococcus furiosus} SCOP: c.47.1.2 c.47.1.2 PDB: 1j08_A

Probab=90.91  E-value=1.3  Score=35.38  Aligned_cols=60  Identities=22%  Similarity=0.356  Sum_probs=46.2

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCce-EEeeeCCCChHHHHHHHhhhhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQK-MRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~-l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .++.|...|++.++...++..|++..+|++.++.  .|.. ..++.|..+.+++...+...++
T Consensus        53 ~~v~~~~vd~~~~~~~~~~~~~~v~~~Pt~~~~~--~g~~~~~~~~G~~~~~~l~~~l~~~l~  113 (226)
T 1a8l_A           53 DKLSYEIVDFDTPEGKELAKRYRIDRAPATTITQ--DGKDFGVRYFGLPAGHEFAAFLEDIVD  113 (226)
T ss_dssp             TTEEEEEEETTSHHHHHHHHHTTCCSSSEEEEEE--TTBCCSEEEESCCCTTHHHHHHHHHHH
T ss_pred             CceEEEEEeCCCcccHHHHHHcCCCcCceEEEEc--CCceeeEEEeccCcHHHHHHHHHHHHh
Confidence            3688889999887788999999999999999984  3554 3678898777776665555443

>3ed3_A Protein disulfide-isomerase MPD1; thioredoxin-like domain, CXXC, endoplasmic reticulum, glycoprotein, redox-active center; 2.00A {Saccharomyces cerevisiae}

Probab=90.90  E-value=0.84  Score=39.01  Aligned_cols=66  Identities=14%  Similarity=0.293  Sum_probs=50.4

Q ss_pred             HHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCc-----------------eEEeeeCCCChHHHHHHH
Q 025774           12 VSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQ-----------------KMRSWCGMVQPESLLEDL   74 (248)
Q Consensus        12 v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~-----------------~l~~~~G~~~~e~l~~~L   74 (248)
                      +.+-+...+.+..++++..+...++..|++..||++.++.+  |.                 ....+.|..+.+.++.-+
T Consensus        60 la~~~~~~~~~~~v~~d~~~~~~l~~~~~I~~~Pt~~~~~~--g~~v~~~~g~~~~~~~~~~~~~~y~G~r~~~~i~~fl  137 (298)
T 3ed3_A           60 AAKRLDGVVQVAAVNCDLNKNKALCAKYDVNGFPTLMVFRP--PKIDLSKPIDNAKKSFSAHANEVYSGARTLAPIVDFS  137 (298)
T ss_dssp             HHHHTTTTSEEEEEETTSTTTHHHHHHTTCCBSSEEEEEEC--CCC-------------CCCEEEECCSCCSHHHHHHHH
T ss_pred             HHHHccCCcEEEEEEccCccCHHHHHhCCCCccceEEEEEC--CceeecccccccccccccccceeecCCcCHHHHHHHH
Confidence            33344456778888887667788999999999999999974  43                 356788999999987777


Q ss_pred             hhhhh
Q 025774           75 VPFMD   79 (248)
Q Consensus        75 ~~~~~   79 (248)
                      ...+.
T Consensus       138 ~~~~~  142 (298)
T 3ed3_A          138 LSRIR  142 (298)
T ss_dssp             HTTCC
T ss_pred             HHhcc
Confidence            66654

>3eur_A Uncharacterized protein; PSI2,MCSG, conserved protein, structural genomics, protein S initiative, midwest center for structural genomics; HET: MSE; 1.30A {Bacteroides fragilis}

Probab=90.14  E-value=0.22  Score=36.99  Aligned_cols=45  Identities=18%  Similarity=0.262  Sum_probs=33.2

Q ss_pred             cceEEEEEecCChH-H---------------------HHHHHhcCCCCCceEEEEeCCCCceEEeeeC
Q 025774           18 TNFIFWQVYDDTSE-G---------------------KKVCTYYKLDSIPVVLVVDPITGQKMRSWCG   63 (248)
Q Consensus        18 ~~fV~w~~d~~~~e-g---------------------~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G   63 (248)
                      .++.+++.+.+... .                     ..++..|++..+|+++||++ +|.++.+..|
T Consensus        66 ~~~~vi~i~~d~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~v~~~P~~~lid~-~G~i~~~~~~  132 (142)
T 3eur_A           66 KKLKVLSIYPDEELDEWKKHRNDFAKEWTNGYDKELVIKNKNLYDLRAIPTLYLLDK-NKTVLLKDAT  132 (142)
T ss_dssp             TSEEEEEEECSSCHHHHHHHGGGSCTTSEEEECTTCHHHHTTCSCCTTCSEEEEECT-TCBEEEEEEC
T ss_pred             CCeEEEEEEcCCCHHHHHHHHHhcccccccccCccchhhhhhhcCCCcCCeEEEECC-CCcEEecCCC
Confidence            46777777776542 1                     23678899999999999995 5888877654

>3drn_A Peroxiredoxin, bacterioferritin comigratory prote homolog; bacterioferritin comigratory protein, oxidore; HET: CIT; 2.15A {Sulfolobus solfataricus} SCOP: c.47.1.0

Probab=89.96  E-value=0.54  Score=35.81  Aligned_cols=60  Identities=15%  Similarity=0.296  Sum_probs=43.3

Q ss_pred             ceEEEEEecCChH-------------------HHHHHHhcCCCC----CceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           19 NFIFWQVYDDTSE-------------------GKKVCTYYKLDS----IPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        19 ~fV~w~~d~~~~e-------------------g~~~~~~~~~~~----~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ++.+.+.+.++.+                   ...++..|++..    +|.++||++ +|.++..+.|...++..+..+.
T Consensus        63 ~v~vv~vs~d~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~v~~~~~~~P~~~lid~-~G~i~~~~~g~~~~~~~~~~il  141 (161)
T 3drn_A           63 DVVVIGVSSDDINSHKRFKEKYKLPFILVSDPDKKIRELYGAKGFILPARITFVIDK-KGIIRHIYNSQMNPANHVNEAL  141 (161)
T ss_dssp             CEEEEEEESCCHHHHHHHHHHTTCCSEEEECTTSHHHHHTTCCCSSSCCCEEEEECT-TSBEEEEEECSSCTTHHHHHHH
T ss_pred             CCEEEEEeCCCHHHHHHHHHHhCCCceEEECCcHHHHHHcCCCCcCcccceEEEECC-CCEEEEEEecCCCCCcCHHHHH
Confidence            5777777776543                   236778899988    999999995 5999999999665554445544


Q ss_pred             hhhh
Q 025774           76 PFMD   79 (248)
Q Consensus        76 ~~~~   79 (248)
                      ..++
T Consensus       142 ~~l~  145 (161)
T 3drn_A          142 KALK  145 (161)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4444

>3ewl_A Uncharacterized conserved protein BF1870; alpha-beta fold, structural genomics, PSI-2, protein structu initiative; 2.00A {Bacteroides fragilis}

Probab=89.78  E-value=0.55  Score=34.53  Aligned_cols=37  Identities=16%  Similarity=0.305  Sum_probs=27.9

Q ss_pred             HHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           36 CTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        36 ~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      +..|++..+|+++||++ +|.++.   |.++.+++...|..
T Consensus       102 ~~~~~v~~~P~~~lid~-~G~i~~---~~~~~~~l~~~l~~  138 (142)
T 3ewl_A          102 RQLYDIRATPTIYLLDG-RKRVIL---KDTSMEQLIDYLAT  138 (142)
T ss_dssp             TTCSCCCSSSEEEEECT-TCBEEE---CSCCHHHHHHHHHC
T ss_pred             HHHcCCCCCCeEEEECC-CCCEEe---cCCCHHHHHHHHHH
Confidence            34899999999999995 588765   55778877665554

>2ywm_A Glutaredoxin-like protein; redox protein, structural genomics, NPPSFA, national project protein structural and functional analyses; 2.30A {Aquifex aeolicus} PDB: 2ayt_A

Probab=89.76  E-value=1.2  Score=35.89  Aligned_cols=55  Identities=5%  Similarity=0.213  Sum_probs=43.7

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ++.+...|++.  ...++..|++..+|++.+    +|. +.++.|..+.++|...|...+..
T Consensus       167 ~v~~~~vd~~~--~~~l~~~~~v~~~Pt~~~----~G~-~~~~~G~~~~~~l~~~l~~~~~~  221 (229)
T 2ywm_A          167 YITSKVIDASE--NQDLAEQFQVVGVPKIVI----NKG-VAEFVGAQPENAFLGYIMAVYEK  221 (229)
T ss_dssp             TEEEEEEEGGG--CHHHHHHTTCCSSSEEEE----GGG-TEEEESCCCHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECCC--CHHHHHHcCCcccCEEEE----CCE-EEEeeCCCCHHHHHHHHHHHhhh
Confidence            67888888754  345788999999999988    477 56799999999998888777653

>3iv4_A Putative oxidoreductase; APC23140, meticillin-resistant staphylococcus aureus, oxidor thioredoxin fold, structural genomics, PSI-2; HET: MSE; 1.50A {Staphylococcus aureus subsp}

Probab=89.69  E-value=1.1  Score=32.88  Aligned_cols=67  Identities=7%  Similarity=0.077  Sum_probs=49.3

Q ss_pred             ccCCCH------HHHHHhh-cceEEEEEecCChHH--HHHHHhcCCCC-CceEEEEeCCCCceEEe-eeCCCChHHHHHH
Q 025774            5 DTWANE------AVSQTIS-TNFIFWQVYDDTSEG--KKVCTYYKLDS-IPVVLVVDPITGQKMRS-WCGMVQPESLLED   73 (248)
Q Consensus         5 ~vl~~~------~v~~~l~-~~fV~w~~d~~~~eg--~~~~~~~~~~~-~P~l~ii~~~~g~~l~~-~~G~~~~e~l~~~   73 (248)
                      .+||-+      .+.++.+ .+.-|+..|+...-.  -.++..|++.+ -|.++++  ++|+.++. ..|.++.+.|...
T Consensus        33 atwCgpc~~~~~~~e~~~~~~~v~~~~vdVde~r~~Sn~IA~~~~V~h~sPq~il~--k~G~~v~~~SH~~I~~~~l~~~  110 (112)
T 3iv4_A           33 SETCPISANAYDQFNKFLYERDMDGYYLIVQQERDLSDYIAKKTNVKHESPQAFYF--VNGEMVWNRDHGDINVSSLAQA  110 (112)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHTCCEEEEEGGGGHHHHHHHHHHHTCCCCSSEEEEE--ETTEEEEEEEGGGCSHHHHHHH
T ss_pred             CCcCHhHHHHHHHHHHHhccCCceEEEEEeecCchhhHHHHHHhCCccCCCeEEEE--ECCEEEEEeeccccCHHHHHHh
Confidence            467765      4444543 468888888865433  45899999995 9999999  56999988 6688999877543

>3idv_A Protein disulfide-isomerase A4; thioredoxin-like fold, disulfide bond, endoplasmic reticulum isomerase, redox-active center; 1.95A {Homo sapiens} PDB: 2dj2_A

Probab=89.68  E-value=1.3  Score=35.73  Aligned_cols=56  Identities=9%  Similarity=0.254  Sum_probs=45.7

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      +.+...|.+..  ..++..|++..+|++.++.  .|..+ ...|..+.+++...+...+..
T Consensus        68 ~~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~--~g~~~-~~~g~~~~~~l~~~i~~~~~~  123 (241)
T 3idv_A           68 IPVAKIDATSA--SVLASRFDVSGYPTIKILK--KGQAV-DYEGSRTQEEIVAKVREVSQP  123 (241)
T ss_dssp             CCEEEEETTTC--HHHHHHTTCCSSSEEEEEE--TTEEE-ECCSCSCHHHHHHHHHHHHST
T ss_pred             eEEEEEeccCC--HHHHHhcCCCcCCEEEEEc--CCCcc-cccCcccHHHHHHHHhhccCc
Confidence            88888888644  4688999999999999995  47766 588999999998888777654

>2dj3_A Protein disulfide-isomerase A4; protein ERP-72, ERP72, CAI, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=89.45  E-value=0.72  Score=33.56  Aligned_cols=61  Identities=11%  Similarity=0.166  Sum_probs=43.3

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCce-EEeee-CCCChHHHHHHHhhhhhcC
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQK-MRSWC-GMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~-l~~~~-G~~~~e~l~~~L~~~~~~~   81 (248)
                      .+++|..+|++...  .++..|++..+|++.++.+ .+.+ ...+. |..+.++|...|...+...
T Consensus        58 ~~~~~~~vd~~~~~--~~~~~~~v~~~Pt~~~~~~-g~~~~~~~~~gg~~~~~~l~~~l~~~~~~~  120 (133)
T 2dj3_A           58 KDLVIAKMDATAND--ITNDQYKVEGFPTIYFAPS-GDKKNPIKFEGGNRDLEHLSKFIDEHATKR  120 (133)
T ss_dssp             SSEEEEEECTTTSC--CCCSSCCCSSSSEEEEECT-TCTTSCEECCSSCCSTTHHHHHHHHHSSSC
T ss_pred             CCEEEEEecCCcCH--HHHhhcCCCcCCEEEEEeC-CCcccceEecCCCcCHHHHHHHHHHhcccc
Confidence            36899999886543  3456799999999999963 2332 12355 6688999988888776643

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=89.43  E-value=1.1  Score=38.96  Aligned_cols=71  Identities=14%  Similarity=0.175  Sum_probs=54.9

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEcc-CCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHA-IPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~-~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ..++|.|+. +|+.+.-....++||.+|-.-+... .|.++..-+|+.. |.++.  +  +++.||.++|+. +++|++
T Consensus         4 ~~i~i~Vk~-~g~~~~v~v~~~~Tv~~lK~~I~~~-tgVpp~~QkLi~~k~~Gk~--l--~D~~~L~~~~ik~g~~l~L   76 (320)
T 3shq_A            4 KEVVVIVKW-SGKEYPVDLTDQDTVEVLRHEIFRK-TQVRPERQKLLNLKYKGKT--A--ADNVKISALELKPNFKLMM   76 (320)
T ss_dssp             CEEEEEEEE-TTEEEEEEEETTSBHHHHHHHHHHH-HCCCGGGCEETTCBSSSSB--C--CTTSBTTSSCCC--CEEEE
T ss_pred             ceEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHH-HCcCHHHeEEeecccCCcc--c--CccccHHHcCCCCCCEEEE
Confidence            357888887 7888999999999999999999875 4777888888743 44443  4  458999999998 566654

>2djk_A PDI, protein disulfide-isomerase; thioredoxin fold; NMR {Humicola insolens} SCOP: c.47.1.2 PDB: 2kp2_A

Probab=89.22  E-value=0.69  Score=34.25  Aligned_cols=59  Identities=14%  Similarity=0.127  Sum_probs=44.8

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCC--CceEEEEeCCCCceEEeee--CCCChHHHHHHHhhhhhc
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDS--IPVVLVVDPITGQKMRSWC--GMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~--~P~l~ii~~~~g~~l~~~~--G~~~~e~l~~~L~~~~~~   80 (248)
                      .+.|...|++..  ..++..|++.+  .|.++++....|.. ..+.  |.++.+.+..-|..+++.
T Consensus        54 k~~f~~vd~d~~--~~~a~~~gi~~~~iPtl~i~~~~~g~~-~~~~~~g~~~~~~l~~fi~~~l~G  116 (133)
T 2djk_A           54 VINFGTIDAKAF--GAHAGNLNLKTDKFPAFAIQEVAKNQK-FPFDQEKEITFEAIKAFVDDFVAG  116 (133)
T ss_dssp             TSEEEEECTTTT--GGGTTTTTCCSSSSSEEEEECTTTCCB-CCCCSSSCCCHHHHHHHHHHHHHT
T ss_pred             eEEEEEEchHHh--HHHHHHcCCCcccCCEEEEEecCcCcc-cCCCCccccCHHHHHHHHHHHHcC
Confidence            577778887633  35888999998  99999997434655 3554  999999888888888774

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=89.20  E-value=3.3  Score=29.47  Aligned_cols=70  Identities=16%  Similarity=0.222  Sum_probs=52.3

Q ss_pred             CCceEEEEEcCCCc-eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEE
Q 025774          168 SLLCRVGVRLPDGR-RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMIS  244 (248)
Q Consensus       168 ~~~~~i~iRlp~G~-r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~  244 (248)
                      +..++|.++-++|+ .+..+-..+.+++.|++...... +.....++|...  ...  +  +.+.|.+++|+...-++
T Consensus        23 ~~~I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~-g~~~~~vrF~FD--G~r--I--~~~~TP~dLdMEDgD~I   93 (97)
T 2jxx_A           23 SQQLQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAM-GLSGRKLSFFFD--GTK--L--SGRELPADLGMESGDLI   93 (97)
T ss_dssp             CSEEEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHT-TCSSSCCEEEET--TEE--C--CSCSCHHHHTCCTTEEE
T ss_pred             CCeEEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHH-CCCcccEEEEEC--CEE--c--CCCCCHHHcCCCCCCEE
Confidence            45788999999995 78889999999999999765543 445667777553  332  4  56889999999854444

>1wmj_A Thioredoxin H-type; structural genomics, program for RICE genome research, oxidoreductase; NMR {Oryza sativa}

Probab=89.19  E-value=0.2  Score=36.37  Aligned_cols=65  Identities=18%  Similarity=0.366  Sum_probs=47.0

Q ss_pred             HHHHHhhc--ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           11 AVSQTIST--NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        11 ~v~~~l~~--~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .+.++...  ++.|...|++..  ..++..|++..+|++.++  .+|..+.++.| .+++++...|...+..
T Consensus        57 ~l~~~~~~~~~v~~~~v~~~~~--~~~~~~~~v~~~Pt~~~~--~~g~~~~~~~g-~~~~~l~~~l~~~~~~  123 (130)
T 1wmj_A           57 VFAEYAKKFPGAVFLKVDVDEL--KEVAEKYNVEAMPTFLFI--KDGAEADKVVG-ARKDDLQNTIVKHVGA  123 (130)
T ss_dssp             HHHHHHHHCTTBCCEECCTTTS--GGGHHHHTCCSSCCCCBC--TTTTCCBCCCT-TCTTTHHHHHHHHTSS
T ss_pred             HHHHHHHHCCCCEEEEEeccch--HHHHHHcCCCccceEEEE--eCCeEEEEEeC-CCHHHHHHHHHHHHhc
Confidence            44444443  577777777543  357788999999998776  56888888999 4778887777776654

>3s9f_A Tryparedoxin; thioredoxin fold, disulfide reductase, electron transport; 1.80A {Leishmania major}

Probab=88.93  E-value=1.4  Score=33.71  Aligned_cols=29  Identities=21%  Similarity=0.455  Sum_probs=24.6

Q ss_pred             HHHHHhcCCCCCceEEEEeCCCCceEEee
Q 025774           33 KKVCTYYKLDSIPVVLVVDPITGQKMRSW   61 (248)
Q Consensus        33 ~~~~~~~~~~~~P~l~ii~~~~g~~l~~~   61 (248)
                      ..++..|++..+|+++||++.+|.++.+.
T Consensus       118 ~~l~~~~~v~~~Pt~~lid~~~G~iv~~~  146 (165)
T 3s9f_A          118 EALTKKYSVESIPTLIGLNADTGDTVTTR  146 (165)
T ss_dssp             HHHHHHTTCCSSSEEEEEETTTCCEEESC
T ss_pred             HHHHHHcCCCCCCEEEEEeCCCCEEEecc
Confidence            68899999999999999997558877653

>1sji_A Calsequestrin 2, calsequestrin, cardiac muscle isoform; glycoprotein, calcium-binding, muscle protein, metal binding protein; 2.40A {Canis lupus familiaris} PDB: 2vaf_A

Probab=88.26  E-value=2  Score=37.24  Aligned_cols=64  Identities=17%  Similarity=0.235  Sum_probs=48.6

Q ss_pred             HHHHHhhc-ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           11 AVSQTIST-NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        11 ~v~~~l~~-~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .+.+.+.. ++.+..+|++..  ..++..|++..||++.++.  .|. +....|..+.+.++..+...+.
T Consensus        58 ~~a~~~~~~~v~~~~Vd~~~~--~~l~~~~~v~~~Pt~~~~~--~g~-~~~~~G~~~~~~l~~~i~~~~~  122 (350)
T 1sji_A           58 LVAQVLEHKDIGFVMVDAKKE--AKLAKKLGFDEEGSLYVLK--GDR-TIEFDGEFAADVLVEFLLDLIE  122 (350)
T ss_dssp             HHHHHGGGSSEEEEEEETTTT--HHHHHHHTCCSTTEEEEEE--TTE-EEEECSCCCHHHHHHHHHTTSS
T ss_pred             HHHHHHhhcCcEEEEEeCCCC--HHHHHhcCCCccceEEEEE--CCc-EEEecCCCCHHHHHHHHHHhcC
Confidence            34445555 589999998754  4688999999999999993  576 5578999999988776665543

>2dj0_A Thioredoxin-related transmembrane protein 2; AVLA237, CGI-31 protein, TXNDC14, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=88.14  E-value=0.74  Score=33.95  Aligned_cols=48  Identities=17%  Similarity=0.219  Sum_probs=38.2

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCC------CCceEEEEeCCCCceEEeeeCCCChHHH
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLD------SIPVVLVVDPITGQKMRSWCGMVQPESL   70 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~------~~P~l~ii~~~~g~~l~~~~G~~~~e~l   70 (248)
                      ++.|...|++..  ..++..|++.      .+|++.++  .+|..+.++.|..+.+++
T Consensus        59 ~v~~~~vd~~~~--~~~~~~~~v~~~~~~~~~Pt~~~~--~~G~~~~~~~G~~~~~~l  112 (137)
T 2dj0_A           59 GLNFGKVDVGRY--TDVSTRYKVSTSPLTKQLPTLILF--QGGKEAMRRPQIDKKGRA  112 (137)
T ss_dssp             SCEEEECCTTTC--HHHHHHTTCCCCSSSSCSSEEEEE--SSSSEEEEESCBCSSSCB
T ss_pred             CeEEEEEeCccC--HHHHHHccCcccCCcCCCCEEEEE--ECCEEEEEecCcCchHHH
Confidence            789988888643  4578899998      99999988  468888889897766543

>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=87.98  E-value=1.2  Score=33.09  Aligned_cols=59  Identities=12%  Similarity=0.085  Sum_probs=44.5

Q ss_pred             EEcCCCc-eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC
Q 025774          175 VRLPDGR-RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN  240 (248)
Q Consensus       175 iRlp~G~-r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~  240 (248)
                      ||+..|+ .+.-....++||..|-.-|... .+.++..-+|+.+  .+.  +  ++++||+|.|+.+
T Consensus         5 l~Ikr~ktTI~ldve~sdTV~~lK~kI~~~-~giPp~qQrLI~~--Gk~--L--eD~kTL~dy~I~~   64 (118)
T 4ajy_B            5 LMIRRHKTTIFTDAKESSTVFELKRIVEGI-LKRPPDEQRLYKD--DQL--L--DDGKTLGECGFTS   64 (118)
T ss_dssp             EEEEEBTEEEEEEEETTSBHHHHHHHHHHH-HCCCGGGEEEEET--TEE--C--CTTSBTTTTTCCG
T ss_pred             EEEecCCEEEEEEcCCCChHHHHHHHHHHH-HCCCHHHeEEEeC--CeE--C--CCcCCHHHcCCCc
Confidence            3344444 6677788999999999999875 4677888899853  442  5  6699999999975

>1i5g_A Tryparedoxin II; electron transport; HET: TS5; 1.40A {Crithidia fasciculata} SCOP: c.47.1.10 PDB: 1o6j_A 1o81_A 1oc8_A 1oc9_B 1fg4_A 1oc9_A

Probab=87.90  E-value=2.1  Score=31.38  Aligned_cols=44  Identities=23%  Similarity=0.262  Sum_probs=33.2

Q ss_pred             cceEEEEEecCCh----------------------HHHHHHHhcCCCCCceEEEEeCCCCceEEee
Q 025774           18 TNFIFWQVYDDTS----------------------EGKKVCTYYKLDSIPVVLVVDPITGQKMRSW   61 (248)
Q Consensus        18 ~~fV~w~~d~~~~----------------------eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~   61 (248)
                      .++.+..++++..                      ....++..|++..+|+++||++.+|.++.+.
T Consensus        61 ~~~~vv~v~~d~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~v~~~P~~~lid~~~G~i~~~~  126 (144)
T 1i5g_A           61 KNFEVMLISWDESAEDFKDYYAKMPWLALPFEDRKGMEFLTTGFDVKSIPTLVGVEADSGNIITTQ  126 (144)
T ss_dssp             TTEEEEEEECCSSHHHHHHHHTTCSSEECCTTCHHHHHHHHHHTTCCSSSEEEEEETTTCCEEESC
T ss_pred             CCEEEEEEeCCCCHHHHHHHHHhCCccccccCchHHHHHHHHHcCCCCCCEEEEEECCCCcEEecc
Confidence            3677777777642                      2467899999999999999995568876543

>1o8x_A Tryparedoxin, TRYX, TXNI; tryparedoxin-I, synchrotron radiation, disulfide bonds tryparedoxin, thioredoxin, trypanosome; 1.3A {Crithidia fasciculata} SCOP: c.47.1.10 PDB: 1okd_A 1qk8_A 1o85_A 1o8w_A 1o7u_A 1ezk_A 1ewx_A

Probab=87.71  E-value=2  Score=31.65  Aligned_cols=30  Identities=23%  Similarity=0.444  Sum_probs=24.6

Q ss_pred             HHHHHHhcCCCCCceEEEEeCCCCceEEee
Q 025774           32 GKKVCTYYKLDSIPVVLVVDPITGQKMRSW   61 (248)
Q Consensus        32 g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~   61 (248)
                      ...++..|++..+|+++||++.+|.++.+.
T Consensus        97 ~~~~~~~~~v~~~Pt~~lid~~~G~i~~~~  126 (146)
T 1o8x_A           97 VQKLSKHFNVESIPTLIGVDADSGDVVTTR  126 (146)
T ss_dssp             HHHHHHHTTCCSSSEEEEEETTTCCEEESC
T ss_pred             HHHHHHHhCCCCCCEEEEEECCCCeEEEec
Confidence            467899999999999999995568876653

>2dbc_A PDCL2, unnamed protein product; phosducin-like protein, thioredoxin_FOLD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=87.60  E-value=1.7  Score=32.08  Aligned_cols=58  Identities=19%  Similarity=0.261  Sum_probs=40.8

Q ss_pred             HHHHHhhc--ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC-------ChHHHHHHHh
Q 025774           11 AVSQTIST--NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV-------QPESLLEDLV   75 (248)
Q Consensus        11 ~v~~~l~~--~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~-------~~e~l~~~L~   75 (248)
                      .+.++...  ++.|...|++...     ..|++..+|+++++.  +|..+.++.|..       +.++|...|.
T Consensus        51 ~l~~la~~~~~v~~~~vd~~~~~-----~~~~i~~~Pt~~~~~--~G~~v~~~~G~~~~~~~~~~~~~l~~~l~  117 (135)
T 2dbc_A           51 HLSVLARKFPETKFVKAIVNSCI-----EHYHDNCLPTIFVYK--NGQIEGKFIGIIECGGINLKLEELEWKLS  117 (135)
T ss_dssp             HHHHHHHHCSSEEEEEECCSSSC-----SSCCSSCCSEEEEES--SSSCSEEEESTTTTTCTTCCHHHHHHHHH
T ss_pred             HHHHHHHHCCCcEEEEEEhhcCc-----ccCCCCCCCEEEEEE--CCEEEEEEEeEEeeCCCcCCHHHHHHHHH
Confidence            34444443  5788888887543     689999999998884  699999999975       4555544443

>3me7_A Putative uncharacterized protein; electron transfer protein, electron transport, structural GE PSI-2, protein structure initiative; 1.50A {Aquifex aeolicus} PDB: 3me8_A

Probab=87.53  E-value=2  Score=33.06  Aligned_cols=51  Identities=18%  Similarity=0.074  Sum_probs=38.5

Q ss_pred             hHHHHHHHhcCC---------CCCceEEEEeCCCCceEEeeeCC-CChHHHHHHHhhhhhcC
Q 025774           30 SEGKKVCTYYKL---------DSIPVVLVVDPITGQKMRSWCGM-VQPESLLEDLVPFMDGG   81 (248)
Q Consensus        30 ~eg~~~~~~~~~---------~~~P~l~ii~~~~g~~l~~~~G~-~~~e~l~~~L~~~~~~~   81 (248)
                      .+...+++.|++         ...|.+.||++ .|.++..+.|. .+++++...|.+..-..
T Consensus       104 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~lID~-~G~i~~~~~g~~~~~~~i~~~l~~~~~~~  164 (170)
T 3me7_A          104 EDLFKLLDAIDFRFMTAGNDFIHPNVVVVLSP-ELQIKDYIYGVNYNYLEFVNALRLARGEG  164 (170)
T ss_dssp             HHHHHHHHHTTCCCEEETTEEECCCEEEEECT-TSBEEEEEESSSCCHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHCCeEEecCCCccccCceEEEECC-CCeEEEEEeCCCCCHHHHHHHHHHhhccc
Confidence            455677777653         45688999996 59988888986 67889988888876543

>2r2j_A Thioredoxin domain-containing protein 4; CRFS motif, chaperone, endoplasmic reticulum, S response; 2.60A {Homo sapiens}

Probab=87.30  E-value=1.9  Score=37.95  Aligned_cols=58  Identities=16%  Similarity=0.307  Sum_probs=47.1

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEE-eeeCCCChHHHHHHHhhhhhc
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMR-SWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~-~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      ++++..+|++..  ..++..|++..||++.++.  +|..+. ...|..+.+.++..+...+..
T Consensus        60 ~v~~~~Vd~~~~--~~l~~~~~v~~~Pt~~~f~--~G~~~~~~~~G~~~~~~l~~~i~~~~~~  118 (382)
T 2r2j_A           60 QVVFARVDCDQH--SDIAQRYRISKYPTLKLFR--NGMMMKREYRGQRSVKALADYIRQQKSD  118 (382)
T ss_dssp             CEEEEEEETTTC--HHHHHHTTCCEESEEEEEE--TTEEEEEECCSCCSHHHHHHHHHHHHSC
T ss_pred             ceEEEEEECCcc--HHHHHhcCCCcCCEEEEEe--CCcEeeeeecCcchHHHHHHHHHHhccC
Confidence            488888888654  5688999999999999874  588776 489999999998888877653

>1o73_A Tryparedoxin; electron transport, trypanosomatid, thioredoxin; 2.28A {Trypanosoma brucei brucei} SCOP: c.47.1.10

Probab=87.00  E-value=2.1  Score=31.28  Aligned_cols=30  Identities=17%  Similarity=0.355  Sum_probs=24.6

Q ss_pred             HHHHHHhcCCCCCceEEEEeCCCCceEEee
Q 025774           32 GKKVCTYYKLDSIPVVLVVDPITGQKMRSW   61 (248)
Q Consensus        32 g~~~~~~~~~~~~P~l~ii~~~~g~~l~~~   61 (248)
                      ...++..|++..+|+++||++.+|.++.+.
T Consensus        97 ~~~~~~~~~v~~~Pt~~lid~~~G~i~~~~  126 (144)
T 1o73_A           97 VSELGKTFGVESIPTLITINADTGAIIGTQ  126 (144)
T ss_dssp             HHHHHHHHTCCSSSEEEEEETTTCCEEESC
T ss_pred             HHHHHHHcCCCCCCEEEEEECCCCeEEecc
Confidence            467889999999999999995568876653

>1zof_A Alkyl hydroperoxide-reductase; decamer, toroide-shaped complex, oxidoreductase; 2.95A {Helicobacter pylori} SCOP: c.47.1.10

Probab=86.37  E-value=1.5  Score=34.53  Aligned_cols=44  Identities=7%  Similarity=0.166  Sum_probs=34.5

Q ss_pred             HHHHhcCCC-----CCceEEEEeCCCCceEEeeeCCC----ChHHHHHHHhhhh
Q 025774           34 KVCTYYKLD-----SIPVVLVVDPITGQKMRSWCGMV----QPESLLEDLVPFM   78 (248)
Q Consensus        34 ~~~~~~~~~-----~~P~l~ii~~~~g~~l~~~~G~~----~~e~l~~~L~~~~   78 (248)
                      .++..|++.     .+|+++||++ +|.++.++.|..    ++++++..|....
T Consensus       108 ~~~~~~~v~~~~g~~~P~~~lid~-~G~i~~~~~g~~~~~~~~~~l~~~l~~l~  160 (198)
T 1zof_A          108 SISRDYDVLFEEAIALRGAFLIDK-NMKVRHAVINDLPLGRNADEMLRMVDALL  160 (198)
T ss_dssp             HHHHHTTCEETTTEECEEEEEEET-TTEEEEEEEESSSCCCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCcccCCcccceEEEECC-CCEEEEEEecCCCCCCCHHHHHHHHHHHH
Confidence            577888998     9999999995 599999888865    5667776666554

>3idv_A Protein disulfide-isomerase A4; thioredoxin-like fold, disulfide bond, endoplasmic reticulum isomerase, redox-active center; 1.95A {Homo sapiens} PDB: 2dj2_A

Probab=86.33  E-value=3.1  Score=33.32  Aligned_cols=55  Identities=7%  Similarity=0.213  Sum_probs=43.5

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +.|...|++..  ..++..|++..+|++.++.  .|..+. ..|..+.++++..|...+.
T Consensus       183 v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~--~g~~~~-~~g~~~~~~l~~~l~~~~~  237 (241)
T 3idv_A          183 IPLAKVDATAE--TDLAKRFDVSGYPTLKIFR--KGRPYD-YNGPREKYGIVDYMIEQSG  237 (241)
T ss_dssp             CCEEEEETTTC--HHHHHHTTCCSSSEEEEEE--TTEEEE-CCSCCSHHHHHHHHHHHTT
T ss_pred             EEEEEEECCCC--HHHHHHcCCcccCEEEEEE--CCeEEE-ecCCCCHHHHHHHHHhhhC
Confidence            78888888654  3588999999999999986  477665 8899999998877766543

>3cmi_A Peroxiredoxin HYR1; thioredoxin-like fold, oxidoreductase, peroxidase, redox-ACT center; 2.02A {Saccharomyces cerevisiae}

Probab=86.29  E-value=1.1  Score=34.35  Aligned_cols=41  Identities=17%  Similarity=0.329  Sum_probs=34.5

Q ss_pred             hcCCCCCc------eEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           38 YYKLDSIP------VVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        38 ~~~~~~~P------~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .|++..+|      .++||++ +|.++.++.|..+++++...|...+.
T Consensus       122 ~~~v~~~P~i~~~~~~~lid~-~G~i~~~~~g~~~~~~l~~~i~~ll~  168 (171)
T 3cmi_A          122 KSGMLGLRGIKWNFEKFLVDK-KGKVYERYSSLTKPSSLSETIEELLK  168 (171)
T ss_dssp             SCCSSSCCSCCSTTCEEEECS-SSCEEEEECTTSCGGGGHHHHHHHHT
T ss_pred             cCCcCCCCcccccceEEEECC-CCCEEEEeCCCCCHHHHHHHHHHHHH
Confidence            46788899      8999995 59999999999999988888877765

>3f8u_A Protein disulfide-isomerase A3ERP57; endoplasmic reticulum, glycoprotein, immunoglobulin domain, microsome, protein disulfide isomerase, thioredoxin-like FO like domain; HET: NAG; 2.60A {Homo sapiens} PDB: 2dmm_A 2alb_A

Probab=86.26  E-value=1.3  Score=40.05  Aligned_cols=63  Identities=11%  Similarity=0.226  Sum_probs=49.3

Q ss_pred             HHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           13 SQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        13 ~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .+-+...+.|...|.+.  ...++..|++..||++.++  ++|..+....|..+.+.++..+...+.
T Consensus        47 a~~~~~~v~~~~vd~~~--~~~l~~~~~v~~~Ptl~~~--~~g~~~~~~~G~~~~~~l~~~~~~~~~  109 (481)
T 3f8u_A           47 ATRLKGIVPLAKVDCTA--NTNTCNKYGVSGYPTLKIF--RDGEEAGAYDGPRTADGIVSHLKKQAG  109 (481)
T ss_dssp             HHHTTTTCCEEEEETTT--CHHHHHHTTCCEESEEEEE--ETTEEEEECCSCSSHHHHHHHHHHHTS
T ss_pred             HHHhcCceEEEEEECCC--CHHHHHhcCCCCCCEEEEE--eCCceeeeecCccCHHHHHHHHHhhcc
Confidence            34444557777888764  4568899999999999988  458888889999999998888777654

>1xvw_A Hypothetical protein RV2238C/MT2298; thioredoxin fold, oxidized cystein sulfenic acid, structural genomics, PSI; 1.90A {Mycobacterium tuberculosis} SCOP: c.47.1.10 PDB: 1xxu_A

Probab=85.85  E-value=0.97  Score=33.98  Aligned_cols=49  Identities=14%  Similarity=-0.011  Sum_probs=37.0

Q ss_pred             ceEEEEEecCChH---------------------HHHHHHhcCCC----CCc--eEEEEeCCCCceEEeeeCCCChH
Q 025774           19 NFIFWQVYDDTSE---------------------GKKVCTYYKLD----SIP--VVLVVDPITGQKMRSWCGMVQPE   68 (248)
Q Consensus        19 ~fV~w~~d~~~~e---------------------g~~~~~~~~~~----~~P--~l~ii~~~~g~~l~~~~G~~~~e   68 (248)
                      ++.+++.++++.+                     ...++..|++.    .+|  .++||++ +|.++.+..|..+.+
T Consensus        70 ~~~vv~is~d~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~v~~~~~~~p~~~~~lid~-~G~i~~~~~g~~~~~  145 (160)
T 1xvw_A           70 DSAALAISVGPPPTHKIWATQSGFTFPLLSDFWPHGAVSQAYGVFNEQAGIANRGTFVVDR-SGIIRFAEMKQPGEV  145 (160)
T ss_dssp             SEEEEEEESCCHHHHHHHHHHHTCCSCEEECTTTTTHHHHHTTCEETTTTEECSEEEEECT-TSBEEEEEECCTTCC
T ss_pred             CcEEEEEeCCCHHHHHHHHHhcCCCceEEecCCcChHHHHHcCCccccCCCeeeeEEEECC-CCeEEEEEecCCCCC
Confidence            5777777776543                     34578889987    899  8999995 599999988876443

>3uem_A Protein disulfide-isomerase; thioredoxin-like domain, chaper; 2.29A {Homo sapiens} PDB: 2k18_A 1x5c_A 1bjx_A 2bjx_A

Probab=85.69  E-value=1.5  Score=38.02  Aligned_cols=53  Identities=13%  Similarity=0.179  Sum_probs=41.9

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      ++++...|.+...    +..|++..||++.++....|..+..+.|..+.++|+..|.
T Consensus       301 ~v~~~~vd~~~~~----~~~~~v~~~Pt~~~~~~~~~~~~~~~~G~~~~~~l~~~l~  353 (361)
T 3uem_A          301 NIVIAKMDSTANE----VEAVKVHSFPTLKFFPASADRTVIDYNGERTLDGFKKFLE  353 (361)
T ss_dssp             SEEEEEEETTTCB----CSSCCCCSSSEEEEECSSSSCCCEECCSCSSHHHHHHHHT
T ss_pred             cEEEEEEECCccc----hhhcCCcccCeEEEEECCCCcceeEecCCCCHHHHHHHHH
Confidence            4899999988766    5789999999999996443566788999999988855443

>2cvb_A Probable thiol-disulfide isomerase/thioredoxin; redox protein, structural genomics, riken struc genomics/proteomics initiative, RSGI; 1.80A {Thermus thermophilus} SCOP: c.47.1.10 PDB: 2ywo_A

Probab=85.55  E-value=2.2  Score=32.97  Aligned_cols=47  Identities=19%  Similarity=0.191  Sum_probs=35.8

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEe--------eeCCCChHHHHHHHhhhhhcC
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRS--------WCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~--------~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      .++..|++..+|+++||++ +|.++.+        ..|..+.+++...|...+...
T Consensus       107 ~~~~~~~v~~~P~~~lid~-~G~i~~~g~~~~~~~~~g~~~~~~l~~~i~~ll~~~  161 (188)
T 2cvb_A          107 EVAKAYRALRTPEVFLFDE-RRLLRYHGRVNDNPKDPSKVQSHDLEAAIEALLRGE  161 (188)
T ss_dssp             HHHHHTTCCEESEEEEECT-TCBEEEEECSSSCTTCGGGCCCCHHHHHHHHHHTTC
T ss_pred             hHHHHcCCCCCCeEEEECC-CCcEEEEEecCCccccccccCHHHHHHHHHHHHcCC
Confidence            5778899999999999995 5887766        113346788888888887654

>2bmx_A Alkyl hydroperoxidase C; peroxiredoxin, antioxidant defense system, oxidoreductase, structural proteomics in EURO spine; 2.4A {Mycobacterium tuberculosis} SCOP: c.47.1.10

Probab=85.03  E-value=1.1  Score=35.33  Aligned_cols=45  Identities=13%  Similarity=0.087  Sum_probs=35.9

Q ss_pred             HHHHhcCCC-----CCceEEEEeCCCCceEEeeeCCC----ChHHHHHHHhhhhh
Q 025774           34 KVCTYYKLD-----SIPVVLVVDPITGQKMRSWCGMV----QPESLLEDLVPFMD   79 (248)
Q Consensus        34 ~~~~~~~~~-----~~P~l~ii~~~~g~~l~~~~G~~----~~e~l~~~L~~~~~   79 (248)
                      .++..|++.     .+|+++||++ +|.++.++.|..    ++++++..|.....
T Consensus       117 ~~~~~~~v~~~~g~~~P~~~lid~-~G~i~~~~~g~~~~~~~~~~l~~~l~~l~~  170 (195)
T 2bmx_A          117 ELSQAAGVLNADGVADRVTFIVDP-NNEIQFVSATAGSVGRNVDEVLRVLDALQS  170 (195)
T ss_dssp             HHHHHHTCBCTTSSBCEEEEEECT-TSBEEEEEEECTTCCCCHHHHHHHHHHHHC
T ss_pred             HHHHHhCCcccCCCccceEEEEcC-CCeEEEEEecCCCCCCCHHHHHHHHHHHhh
Confidence            567778888     9999999995 599999888865    67888877776654

>2hls_A Protein disulfide oxidoreductase; thioredoxin fold; 1.93A {Aeropyrum pernix}

Probab=84.97  E-value=3.3  Score=34.06  Aligned_cols=56  Identities=16%  Similarity=0.271  Sum_probs=44.5

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      .++.+...|++...  .++..|++.++|++.+    +|..+  ..|..+.++|+..|...+..+
T Consensus       173 ~~v~~~~vd~~~~~--~~~~~~~V~~vPt~~i----~G~~~--~~G~~~~~~l~~~l~~~~~~~  228 (243)
T 2hls_A          173 PVILSEAVEAYENP--DIADKYGVMSVPSIAI----NGYLV--FVGVPYEEDFLDYVKSAAEGR  228 (243)
T ss_dssp             CCEEEEEEETTTCH--HHHHHTTCCSSSEEEE----TTEEE--EESCCCHHHHHHHHHHHHTTC
T ss_pred             CcEEEEEEECccCH--HHHHHcCCeeeCeEEE----CCEEE--EeCCCCHHHHHHHHHHHhhcc
Confidence            46888888886543  5778899999999987    57754  889999999999888887653

>1sen_A Thioredoxin-like protein P19; endoplasmic reticulum, RP19, structural genomics, PSI, protein structure initiative; 1.20A {Homo sapiens} SCOP: c.47.1.1 PDB: 2k8v_A

Probab=84.87  E-value=0.82  Score=35.22  Aligned_cols=59  Identities=19%  Similarity=0.301  Sum_probs=42.5

Q ss_pred             ceEEEEEecCChHHHHHHHhcCC--CCCceEEEEeCCCCceEEeeeCC----------CChHHHHHHHhhhhhcC
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKL--DSIPVVLVVDPITGQKMRSWCGM----------VQPESLLEDLVPFMDGG   81 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~--~~~P~l~ii~~~~g~~l~~~~G~----------~~~e~l~~~L~~~~~~~   81 (248)
                      +|+...++.....   ++..|.+  ..+|+++++++ +|..+.++.|.          .++++|+..|...++..
T Consensus        80 ~~~~v~~d~~~~~---~~~~~~~~~~~~Pt~~~~d~-~G~~~~~~~G~~~~~~~~~~~~~~~~l~~~l~~~l~~~  150 (164)
T 1sen_A           80 NFVMVNLEDEEEP---KDEDFSPDGGYIPRILFLDP-SGKVHPEIINENGNPSYKYFYVSAEQVVQGMKEAQERL  150 (164)
T ss_dssp             TSEEEEEEGGGSC---SCGGGCTTCSCSSEEEEECT-TSCBCTTCCCTTSCTTSTTCCCSHHHHHHHHHHHHHHH
T ss_pred             eEEEEEecCCchH---HHHHhcccCCcCCeEEEECC-CCCEEEEEeCCCCccchhcccCCHHHHHHHHHHHHHhc
Confidence            4555554443221   4566777  66999999984 58888888884          78899999999888764

>2b5e_A Protein disulfide-isomerase; 2.40A {Saccharomyces cerevisiae} SCOP: c.47.1.2 c.47.1.2 c.47.1.2 c.47.1.2 PDB: 3boa_A

Probab=84.85  E-value=3  Score=37.90  Aligned_cols=62  Identities=11%  Similarity=0.229  Sum_probs=49.2

Q ss_pred             HHhhc-ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCce--EEeeeCCCChHHHHHHHhhhhh
Q 025774           14 QTIST-NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQK--MRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        14 ~~l~~-~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~--l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +-+.. ++.|..+|.+..  ..++..|++..||++.++.  +|..  +....|..+.+.++..|...+.
T Consensus        58 ~~~~~~~v~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~--~g~~~~~~~~~G~~~~~~l~~~l~~~~~  122 (504)
T 2b5e_A           58 ETLVEKNITLAQIDCTEN--QDLCMEHNIPGFPSLKIFK--NSDVNNSIDYEGPRTAEAIVQFMIKQSQ  122 (504)
T ss_dssp             HHTTTTTCEEEEEETTTC--HHHHHHTTCCSSSEEEEEE--TTCTTCEEECCSCCSHHHHHHHHHHHTS
T ss_pred             HHhccCCeEEEEEECCCC--HHHHHhcCCCcCCEEEEEe--CCccccceeecCCCCHHHHHHHHHHhcC
Confidence            33444 488999998654  5689999999999999985  4765  8889999999999888776654

>2qc7_A ERP31, ERP28, endoplasmic reticulum protein ERP29; B domain (residues 33-153), D domain (residues 154-261), CHA; 2.90A {Homo sapiens} PDB: 1g7e_A 1g7d_A

Probab=84.57  E-value=2.6  Score=34.99  Aligned_cols=58  Identities=21%  Similarity=0.235  Sum_probs=44.7

Q ss_pred             ceEEEEEecCC---hHHHHHHHhcCCC--CCceEEEEeCCCCc--eEEeeeCCCChHHHHHHHhhhh
Q 025774           19 NFIFWQVYDDT---SEGKKVCTYYKLD--SIPVVLVVDPITGQ--KMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        19 ~fV~w~~d~~~---~eg~~~~~~~~~~--~~P~l~ii~~~~g~--~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      +++|..+|++.   .+-..++..|++.  .||++.++.  .|.  .+..+.|..+.+.|+..|....
T Consensus        54 ~v~~akVDvd~~g~~~~~~l~~~~~V~~~~~PTl~~f~--~G~~~~~~~y~G~~~~~~L~~fi~~~~  118 (240)
T 2qc7_A           54 DLLVAEVGISDYGDKLNMELSEKYKLDKESYPVFYLFR--DGDFENPVPYTGAVKVGAIQRWLKGQG  118 (240)
T ss_dssp             TEEEEEECCCCSSSCCSHHHHHHTTCCGGGCSEEEEEE--TTCSSCCEECCSCSCHHHHHHHHHHTT
T ss_pred             CeEEEEEeCCcccchhhHHHHHHcCCCCCCCCEEEEEe--CCCcCcceeecCCCCHHHHHHHHHHhc
Confidence            68999999753   2346689999999  999999985  355  3567889999988877766553

>1xzo_A BSSCO, hypothetical protein YPMQ; thioredoxin-like fold, structural genomics, montreal-kingsto bacterial structural genomics initiative, BSGI; 1.70A {Bacillus subtilis} SCOP: c.47.1.10 PDB: 1on4_A

Probab=84.56  E-value=4.3  Score=30.57  Aligned_cols=40  Identities=13%  Similarity=0.295  Sum_probs=31.5

Q ss_pred             cCCCCCceEEEEeCCCCceEEeeeCCC--ChHHHHHHHhhhhh
Q 025774           39 YKLDSIPVVLVVDPITGQKMRSWCGMV--QPESLLEDLVPFMD   79 (248)
Q Consensus        39 ~~~~~~P~l~ii~~~~g~~l~~~~G~~--~~e~l~~~L~~~~~   79 (248)
                      |.+...|.++||++ +|.++.++.|..  ++++++..|...+.
T Consensus       131 ~~~~~~p~~~lid~-~G~i~~~~~g~~~~~~~~l~~~l~~ll~  172 (174)
T 1xzo_A          131 DQVIHQSSFYLVGP-DGKVLKDYNGVENTPYDDIISDVKSAST  172 (174)
T ss_dssp             CSCCSCCEEEEECT-TSEEEEEEESSSSCCHHHHHHHHHHHTC
T ss_pred             CeeeeeeEEEEECC-CCeEEEEEcCCCCCCHHHHHHHHHHHHh
Confidence            34567899999995 599999999976  47888888877654

>2b7k_A SCO1 protein; metallochaperone, cytochrome C oxidase, metal binding protein; 1.80A {Saccharomyces cerevisiae} SCOP: c.47.1.10 PDB: 2b7j_A

Probab=84.50  E-value=2.5  Score=33.46  Aligned_cols=48  Identities=19%  Similarity=0.329  Sum_probs=36.8

Q ss_pred             HHHHHhcCCC-CC---------------ceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           33 KKVCTYYKLD-SI---------------PVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        33 ~~~~~~~~~~-~~---------------P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      ..+++.|++. ..               |.+.||++ +|.++..+.|..+++.+...|...+...
T Consensus       118 ~~~~~~~gv~~~~p~~~~~~~~~~~~~~~~~~liD~-~G~i~~~~~g~~~~~~~~~~i~~~l~~l  181 (200)
T 2b7k_A          118 KNACKKYRVYFSTPPNVKPGQDYLVDHSIFFYLMDP-EGQFVDALGRNYDEKTGVDKIVEHVKSY  181 (200)
T ss_dssp             HHHHHHTTC--------------CTTTCCCEEEECT-TSCEEEEECTTCCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHcCcEEeeccccCCCCCceeeecceEEEECC-CCcEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            4577778775 33               37899995 5999999999999999999998888764

>2k6v_A Putative cytochrome C oxidase assembly protein; thioredoxin fold, electron transfer protein, metal binding protein, electron transport; NMR {Thermus thermophilus}

Probab=84.39  E-value=0.83  Score=34.64  Aligned_cols=35  Identities=17%  Similarity=0.305  Sum_probs=29.0

Q ss_pred             CCCCceEEEEeCCCCceEEeeeCCC--ChHHHHHHHhhh
Q 025774           41 LDSIPVVLVVDPITGQKMRSWCGMV--QPESLLEDLVPF   77 (248)
Q Consensus        41 ~~~~P~l~ii~~~~g~~l~~~~G~~--~~e~l~~~L~~~   77 (248)
                      +..+|++.||+  +|.++.++.|..  +++++...|...
T Consensus       135 i~~~P~~~lid--~G~i~~~~~g~~~~~~~~l~~~l~~l  171 (172)
T 2k6v_A          135 VDHTATTFVVK--EGRLVLLYSPDKAEATDRVVADLQAL  171 (172)
T ss_dssp             EEECCCEEEEE--TTEEEEEECHHHHTCHHHHHHHHHHC
T ss_pred             EecCCEEEEEE--CCEEEEEECCCCCCCHHHHHHHHHHh
Confidence            35789999999  699999999988  888888877654

>1we0_A Alkyl hydroperoxide reductase C; peroxiredoxin, AHPC, oxidoreductase; 2.90A {Amphibacillus xylanus} SCOP: c.47.1.10

Probab=84.27  E-value=5.1  Score=30.94  Aligned_cols=60  Identities=12%  Similarity=0.133  Sum_probs=45.4

Q ss_pred             ceEEEEEecCChH-----------------------HHHHHHhcCCC------CCceEEEEeCCCCceEEeeeCCC----
Q 025774           19 NFIFWQVYDDTSE-----------------------GKKVCTYYKLD------SIPVVLVVDPITGQKMRSWCGMV----   65 (248)
Q Consensus        19 ~fV~w~~d~~~~e-----------------------g~~~~~~~~~~------~~P~l~ii~~~~g~~l~~~~G~~----   65 (248)
                      ++.+++.++++.+                       ...++..|++.      .+|+++||++ +|.++.++.|..    
T Consensus        65 ~v~vv~vs~d~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~v~~~~~g~~~P~~~lid~-~G~i~~~~~g~~~~~~  143 (187)
T 1we0_A           65 GVEVYSVSTDTHFVHKAWHENSPAVGSIEYIMIGDPSQTISRQFDVLNEETGLADRGTFIIDP-DGVIQAIEINADGIGR  143 (187)
T ss_dssp             TEEEEEEESSCHHHHHHHHHSCHHHHTCCSEEEECTTCHHHHHTTCEETTTTEECEEEEEECT-TSBEEEEEEECTTSCC
T ss_pred             CCEEEEEECCCHHHHHHHHHHhccccCCCceEEECCchHHHHHhCCCcCCCCceeeEEEEECC-CCeEEEEEecCCCCCC
Confidence            6777887776532                       23567788887      8999999995 599999888865    


Q ss_pred             ChHHHHHHHhhhhh
Q 025774           66 QPESLLEDLVPFMD   79 (248)
Q Consensus        66 ~~e~l~~~L~~~~~   79 (248)
                      ++++++..|.....
T Consensus       144 ~~~~l~~~l~~l~~  157 (187)
T 1we0_A          144 DASTLINKVKAAQY  157 (187)
T ss_dssp             CTTHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhh
Confidence            67888877776654

>2c0g_A ERP29 homolog, windbeutel protein; PDI-dbeta, PDI, protein disulfide isomerase, PIPE, dorsal-ventral patterning, chaperone, WIND mutants; 1.75A {Drosophila melanogaster} SCOP: a.71.1.1 c.47.1.7 PDB: 1ovn_A 2c0f_A 2c1y_A 2c0e_A

Probab=83.48  E-value=3.8  Score=34.18  Aligned_cols=58  Identities=17%  Similarity=0.201  Sum_probs=45.5

Q ss_pred             ceEEEEEecCC---hHHHHHHHhcCCC--CCceEEEEeCCCCc--eEEee--eCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDT---SEGKKVCTYYKLD--SIPVVLVVDPITGQ--KMRSW--CGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~---~eg~~~~~~~~~~--~~P~l~ii~~~~g~--~l~~~--~G~~~~e~l~~~L~~~~~   79 (248)
                      +++|..+|++.   .+...++..|++.  .||++.++-   |.  ....+  .|..+.+.|...|...+.
T Consensus        66 ~v~~akVD~d~~g~~~n~~la~~~~V~~~~~PTl~~F~---G~~~~~~~y~~~G~~~~~~L~~fi~~~~~  132 (248)
T 2c0g_A           66 DLLIATVGVKDYGELENKALGDRYKVDDKNFPSIFLFK---GNADEYVQLPSHVDVTLDNLKAFVSANTP  132 (248)
T ss_dssp             SEEEEEEEECSSTTCTTHHHHHHTTCCTTSCCEEEEES---SSSSSEEECCTTSCCCHHHHHHHHHHHSS
T ss_pred             CeEEEEEECCcccccccHHHHHHhCCCcCCCCeEEEEe---CCcCcceeecccCCCCHHHHHHHHHHhhc
Confidence            68999999875   2256799999999  999999884   55  25556  899999988777776654

>2ywm_A Glutaredoxin-like protein; redox protein, structural genomics, NPPSFA, national project protein structural and functional analyses; 2.30A {Aquifex aeolicus} PDB: 2ayt_A

Probab=82.71  E-value=4.6  Score=32.24  Aligned_cols=59  Identities=10%  Similarity=0.080  Sum_probs=44.7

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ..++.+...|.+.  ...++..|++..||++.++.  .|....++.|..+.+++...+...+.
T Consensus        57 ~~~v~~~~vd~~~--~~~l~~~~~v~~~Ptl~~~~--~~~~~~~~~G~~~~~~l~~~~~~~~~  115 (229)
T 2ywm_A           57 QDKIKLDIYSPFT--HKEETEKYGVDRVPTIVIEG--DKDYGIRYIGLPAGLEFTTLINGIFH  115 (229)
T ss_dssp             TTTEEEEEECTTT--CHHHHHHTTCCBSSEEEEES--SSCCCEEEESCCCTTHHHHHHHHHHH
T ss_pred             CCceEEEEecCcc--cHHHHHHcCCCcCcEEEEEC--CCcccceecCCccHHHHHHHHHHHHh
Confidence            4567888888754  46789999999999999984  35667778998888877666655543

>3us3_A Calsequestrin-1; calcium-binding protein; 1.74A {Oryctolagus cuniculus} PDB: 1a8y_A 3v1w_A* 3trq_A* 3trp_A* 3uom_A

Probab=81.83  E-value=4.5  Score=35.32  Aligned_cols=56  Identities=16%  Similarity=0.224  Sum_probs=45.4

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      ++.|..+|++..  ..++..|++..||++.++.  +|..+ ...|..+.+.++.-+...+.
T Consensus        69 ~v~~~~Vd~~~~--~~l~~~~~V~~~PTl~~f~--~G~~~-~y~G~~~~~~i~~~i~~~~~  124 (367)
T 3us3_A           69 GVGFGLVDSEKD--AAVAKKLGLTEEDSIYVFK--EDEVI-EYDGEFSADTLVEFLLDVLE  124 (367)
T ss_dssp             TEEEEEEETTTT--HHHHHHHTCCSTTEEEEEE--TTEEE-ECCSCCSHHHHHHHHHHHHS
T ss_pred             CceEEEEeCccc--HHHHHHcCCCcCceEEEEE--CCcEE-EeCCCCCHHHHHHHHHHhcC
Confidence            588888988753  4689999999999999985  47654 78899999998887776654

>3a2v_A Probable peroxiredoxin; thioredoxin peroxidase, hydrogen peroxide, antioxidant, oxidoreductase, redox-active center; 1.65A {Aeropyrum pernix} PDB: 1x0r_A 2zct_A 2nvl_A 2e2g_A 2cv4_A* 3a5w_A 2e2m_A 3a2x_A 3a2w_A

Probab=81.64  E-value=4.9  Score=33.47  Aligned_cols=60  Identities=13%  Similarity=0.046  Sum_probs=44.4

Q ss_pred             cceEEEEEecCChHH-------------------------HHHHHhcCCC-------CCceEEEEeCCCCceEEeeeCCC
Q 025774           18 TNFIFWQVYDDTSEG-------------------------KKVCTYYKLD-------SIPVVLVVDPITGQKMRSWCGMV   65 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg-------------------------~~~~~~~~~~-------~~P~l~ii~~~~g~~l~~~~G~~   65 (248)
                      .++.++++++++.+.                         ..++..|++.       .+|.++||++ +|.+...+.|..
T Consensus        66 ~gv~VI~VS~Ds~~~~~~w~~~~~~~~~~~i~fPil~D~~~~ia~~ygv~~~~~g~~~~p~~fIID~-dG~I~~~~~~~~  144 (249)
T 3a2v_A           66 LGVDLIGLSVDSVFSHIKWKEWIERHIGVRIPFPIIADPQGTVARRLGLLHAESATHTVRGVFIVDA-RGVIRTMLYYPM  144 (249)
T ss_dssp             TTEEEEEEESSCHHHHHHHHHHHHHHTCCCCCSCEEECTTSHHHHHHTCCCTTCSSSCCEEEEEECT-TSBEEEEEEECT
T ss_pred             CCcEEEEEECCCHHHHHHHHHHHHHhcCCCCceeEEECCchHHHHHhCCccccCCCcccceEEEECC-CCeEEEEEecCC
Confidence            478888888876541                         2477788886       8999999996 488888777754


Q ss_pred             ----ChHHHHHHHhhhh
Q 025774           66 ----QPESLLEDLVPFM   78 (248)
Q Consensus        66 ----~~e~l~~~L~~~~   78 (248)
                          +.++++..|....
T Consensus       145 ~~gr~~~Ellr~I~alq  161 (249)
T 3a2v_A          145 ELGRLVDEILRIVKALK  161 (249)
T ss_dssp             TBCCCHHHHHHHHHHHH
T ss_pred             cccchhHHHHHHHHHHH
Confidence                5678777766553

>2v1m_A Glutathione peroxidase; selenium, selenocysteine, oxidoreductase, lipid peroxidase, schistosoma detoxification pathway; 1.00A {Schistosoma mansoni} PDB: 2wgr_A

Probab=81.13  E-value=1.7  Score=32.67  Aligned_cols=38  Identities=16%  Similarity=0.326  Sum_probs=31.1

Q ss_pred             CCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           41 LDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        41 ~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +..+|.++||++ +|.++.++.|..+++++...|...+.
T Consensus       130 i~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~i~~ll~  167 (169)
T 2v1m_A          130 IKWNFSKFLVDR-QGQPVKRYSPTTAPYDIEGDIMELLE  167 (169)
T ss_dssp             CCSTTCEEEECT-TSCEEEEECTTSCGGGGHHHHHHHHH
T ss_pred             ccccceEEEECC-CCCEEEEcCCCCCHHHHHHHHHHHhc
Confidence            445689999995 69999999999999988888877664

>2h01_A 2-Cys peroxiredoxin; thioredoxin peroxidase, structural genomics, SGC, structural genomics consortium, oxidoreductase; 2.30A {Plasmodium yoelii} SCOP: c.47.1.10

Probab=80.80  E-value=4.3  Score=31.55  Aligned_cols=44  Identities=9%  Similarity=0.211  Sum_probs=33.6

Q ss_pred             HHHHhcCCC-----CCceEEEEeCCCCceEEeeeCCC----ChHHHHHHHhhhh
Q 025774           34 KVCTYYKLD-----SIPVVLVVDPITGQKMRSWCGMV----QPESLLEDLVPFM   78 (248)
Q Consensus        34 ~~~~~~~~~-----~~P~l~ii~~~~g~~l~~~~G~~----~~e~l~~~L~~~~   78 (248)
                      .++..|++.     .+|.++||++ +|.++....|..    +.++++..|....
T Consensus       106 ~~~~~~gv~~~~g~~~P~~~liD~-~G~i~~~~~g~~~~~~~~~~l~~~l~~l~  158 (192)
T 2h01_A          106 SIARSYDVLFNESVALRAFVLIDK-QGVVQHLLVNNLALGRSVDEILRLIDALQ  158 (192)
T ss_dssp             HHHHHTTCEETTTEECCEEEEECT-TSBEEEEEEGGGSSGGGHHHHHHHHHHHH
T ss_pred             HHHHHhCCcCcCCceeeEEEEEcC-CCEEEEEEeCCCCCCCCHHHHHHHHHHHh
Confidence            577889998     8999999995 589888887753    3567776666554

>2obi_A PHGPX, GPX-4, phospholipid hydroperoxide glutathione peroxidase (GPX4); human GPX4, selenoprotein, thioredoxin-fold, anti-oxidatve defense system; 1.55A {Homo sapiens}

Probab=80.80  E-value=1.2  Score=34.65  Aligned_cols=34  Identities=18%  Similarity=0.221  Sum_probs=26.8

Q ss_pred             CCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           42 DSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        42 ~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      ..+|.++||++ +|.++.++.|..+++++...|..
T Consensus       148 ~~~P~~~lid~-~G~i~~~~~g~~~~~~l~~~i~~  181 (183)
T 2obi_A          148 KWNFTKFLIDK-NGCVVKRYGPMEEPLVIEKDLPH  181 (183)
T ss_dssp             CSTTCEEEECT-TSCEEEEECTTSCTHHHHTTSGG
T ss_pred             cccceEEEECC-CCCEEEEeCCCCCHHHHHHHHHH
Confidence            44699999995 69999999999998887655543

>3evi_A Phosducin-like protein 2; alpha beta, 3-layer(ABA) sandwich, unknown function; 2.70A {Homo sapiens}

Probab=80.69  E-value=3.1  Score=30.32  Aligned_cols=40  Identities=18%  Similarity=0.350  Sum_probs=33.0

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV   65 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~   65 (248)
                      +..|...|++..     +..|++.+.|+++++  ++|..+.++.|..
T Consensus        54 ~v~f~kvd~d~~-----~~~~~v~~~PT~~~f--k~G~~v~~~~G~~   93 (118)
T 3evi_A           54 ETKFVKAIVNSC-----IQHYHDNCLPTIFVY--KNGQIEAKFIGII   93 (118)
T ss_dssp             TSEEEEEEGGGT-----STTCCGGGCSEEEEE--ETTEEEEEEESTT
T ss_pred             CCEEEEEEhHHh-----HHHCCCCCCCEEEEE--ECCEEEEEEeChh
Confidence            467788888653     588999999999998  4699999999965

>1uul_A Tryparedoxin peroxidase homologue; peroxiredoxin, oxidoreductase; 2.8A {Trypanosoma cruzi} SCOP: c.47.1.10

Probab=80.04  E-value=3.9  Score=32.24  Aligned_cols=44  Identities=11%  Similarity=0.142  Sum_probs=33.6

Q ss_pred             HHHHhcCCC------CCceEEEEeCCCCceEEeeeCCCC----hHHHHHHHhhhh
Q 025774           34 KVCTYYKLD------SIPVVLVVDPITGQKMRSWCGMVQ----PESLLEDLVPFM   78 (248)
Q Consensus        34 ~~~~~~~~~------~~P~l~ii~~~~g~~l~~~~G~~~----~e~l~~~L~~~~   78 (248)
                      .++..|++.      .+|.++||++ +|.++.++.|..+    .++++..|....
T Consensus       111 ~~~~~ygv~~~~~g~~~P~~~lid~-~G~i~~~~~g~~~~~~~~~ell~~l~~l~  164 (202)
T 1uul_A          111 CIMKSYGVLKEEDGVAYRGLFIIDP-KQNLRQITVNDLPVGRDVDEALRLVKAFQ  164 (202)
T ss_dssp             HHHHHHTCEETTTTEECEEEEEECT-TSBEEEEEEECTTBCCCHHHHHHHHHHHH
T ss_pred             HHHHHcCCccCCCCceeeEEEEECC-CCEEEEEEeCCCCCCCCHHHHHHHHHHhh
Confidence            567778888      8999999995 5898888777543    477777766554

---

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	248
d2cr5a1	96	d.15.1.2 (A:8-103) UBX domain-containing protein 6	4e-13
d1i42a_	89	d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId:	9e-13
d2dlxa1	147	c.47.1.24 (A:1-147) UBX domain-containing protein	7e-12
d1wj4a_	124	d.15.1.2 (A:) Hypothetical protein KIAA0794 {Human	5e-11
d1h8ca_	82	d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human	2e-09

>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 = 61.5 bits (149), Expect = 4e-13
 Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 4/87 (4%)

Query: 157 PILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTH 216
           P LPEEP      +  V +R P+GR ++R F ++   Q+L  +         +  +RL+ 
Sbjct: 3   PDLPEEPSETAEEVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVGYHKSL--YRLST 60

Query: 217 AIPGATKSLDYDSKLTFEDSGLANAMI 243
           + P   ++L+ +   + ED G+    +
Sbjct: 61  SFPR--RALEVEGGSSLEDIGITVDTV 85

>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 = 60.3 bits (146), Expect = 9e-13
 Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 3/77 (3%)

Query: 171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSK 230
             + +RL DG R+ + F  +  I  +  +            F L    P   K L  D  
Sbjct: 15  TNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPN--KELA-DEN 71

Query: 231 LTFEDSGLANAMISVTW 247
            T +++ L NA+I    
Sbjct: 72  QTLKEANLLNAVIVQRL 88

>d2dlxa1 c.47.1.24 (A:1-147) UBX domain-containing protein 7 {Human (Homo sapiens) [TaxId: 9606]} Length = 147

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: UAS domain
domain: UBX domain-containing protein 7
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 7e-12
 Identities = 38/100 (38%), Positives = 54/100 (54%), Gaps = 11/100 (11%)

Query: 1   MLNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRS 60
            LNRD W+NEAV   I  +FIFWQVY D+ EG++   +YKL   P V ++DP TGQK+  
Sbjct: 59  CLNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVE 118

Query: 61  WCGMVQPESLLEDLVPFMDGGPREQHAKVSHKRPRGSSTT 100
           W   +   S L+ +  F+            H +  G S++
Sbjct: 119 W-HQLDVSSFLDQVTGFLG----------EHGQLDGLSSS 147

>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 = 56.2 bits (135), Expect = 5e-11
 Identities = 23/112 (20%), Positives = 41/112 (36%), Gaps = 4/112 (3%)

Query: 130 ASGVSSSDTDVASTDKDEASATEKPAYPILPEEPKVDRSL-LCRVGVRLPDGRRMQRNFL 188
           +SG S + T+       ++   E P          +D +    ++ +R PDG+R Q    
Sbjct: 2   SSGSSGTATNHQGLPAVDSEILEMPPEKADGVVEGIDVNGPKAQLMLRYPDGKREQITLP 61

Query: 189 RTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN 240
               +  L    + Q +G   + F L    P    S       T +++GL  
Sbjct: 62  EQAKLLAL--VKHVQSKGYPNERFELLTNFPRRKLSHLDYDI-TLQEAGLCP 110

>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 = 51.0 bits (122), Expect = 2e-09
 Identities = 13/76 (17%), Positives = 33/76 (43%), Gaps = 4/76 (5%)

Query: 171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSK 230
            ++ +R P G  ++R FL ++ +Q+++ +  S  +G     ++L    P    +   D  
Sbjct: 6   SKLRIRTPSGEFLERRFLASNKLQIVFDFVAS--KGFPWDEYKLLSTFPRRDVTQL-DPN 62

Query: 231 LTFEDSGLA-NAMISV 245
            +  +  L     + +
Sbjct: 63  KSLLEVKLFPQETLFL 78

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	248
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	99.9
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	99.88
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	99.84
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	99.8
d2dlxa1	147	UBX domain-containing protein 7 {Human (Homo sapie	99.57
d1s3si_	50	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	98.91
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	97.55
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	97.34
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	97.27
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	97.26
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	97.25
d2fwha1	117	Thiol:disulfide interchange protein DsbD, C-termin	97.21
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	97.13
d1dbya_	107	Thioredoxin {Chlamydomonas reinhardtii [TaxId: 305	97.12
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	97.07
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	97.02
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	97.0
d1thxa_	108	Thioredoxin {Anabaena sp., pcc 7120 [TaxId: 1167]}	96.97
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	96.92
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	96.9
d1fb6a_	104	Thioredoxin {Spinach (Spinacia oleracea), thioredo	96.88
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	96.86
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	96.85
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	96.8
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	96.73
d1nw2a_	105	Thioredoxin {Alicyclobacillus acidocaldarius, form	96.71
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	96.65
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	96.63
d1z5ye1	136	Thioredoxin-like protein CcmG (CycY, DsbE) {Escher	96.63
d2trxa_	108	Thioredoxin {Escherichia coli [TaxId: 562]}	96.62
d1f9ma_	112	Thioredoxin {Spinach (Spinacia oleracea), thioredo	96.51
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	96.4
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	96.3
d2es7a1	119	Hydrogenase-1 operon protein HyaE {Salmonella typh	96.29
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	96.28
d1gh2a_	107	Thioredoxin-like protein, N-terminal domain {Human	96.22
d2hfda1	132	Hydrogenase-1 operon protein HyaE {Escherichia col	96.18
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	96.12
d1a8la2	107	Protein disulfide isomerase, PDI {Archaeon Pyrococ	96.11
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	96.07
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	95.96
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	95.86
d2ifqa1	105	Thioredoxin {Human (Homo sapiens) [TaxId: 9606]}	95.84
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	95.76
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	95.68
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	95.53
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	95.5
d1xfla_	114	Thioredoxin {Thale cress (Arabidopsis thaliana) [T	95.49
d1ep7a_	112	Thioredoxin {Chlamydomonas reinhardtii [TaxId: 305	95.46
d1r26a_	113	Thioredoxin {Trypanosoma brucei [TaxId: 5691]}	95.4
d1knga_	144	Thioredoxin-like protein CcmG (CycY, DsbE) {Bradyr	95.33
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	95.1
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	95.07
d2fy6a1	143	Peptide methionine sulfoxide reductase MsrA/MsrB,	94.88
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	94.79
d1xwaa_	111	Thioredoxin {Fruit fly (Drosophila melanogaster) [	94.6
d1jfua_	176	Membrane-anchored thioredoxin-like protein TlpA, s	94.59
d2b5xa1	143	thiol:disulfide oxidoreductase YkuV {Bacillus subt	94.33
d1st9a_	137	Thiol-disulfide oxidoreductase ResA {Bacillus subt	94.09
d1ti3a_	113	Thioredoxin {European aspen (Populus tremula), thi	94.05
d1syra_	103	Thioredoxin {Malarial parasite (Plasmodium falcipa	93.78
d1nhoa_	85	MTH807, thioredoxin/glutaredoxin-like protein {Arc	93.73
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	93.35
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	93.3
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	93.26
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	93.23
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	92.88
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	92.7
d1zmaa1	115	Bacterocin transport accessory protein Bta {Strept	92.33
d1hyua4	96	Alkyl hydroperoxide reductase subunit F (AhpF), N-	91.54
d1a8ya1	124	Calsequestrin {Rabbit (Oryctolagus cuniculus) [Tax	91.49
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	91.19
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	91.09
d1sena_	135	Thioredoxin-like protein p19, TLP19 {Human (Homo s	90.53
d1lu4a_	134	Soluble secreted antigen MPT53 {Mycobacterium tube	90.49
d1i5ga_	144	Tryparedoxin II {Crithidia fasciculata [TaxId: 565	89.91
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	89.48
d1fo5a_	85	MJ0307, thioredoxin/glutaredoxin-like protein {Arc	89.33
d1zzoa1	134	Lipoprotein DsbF {Mycobacterium tuberculosis [TaxI	89.19
d1o73a_	144	Tryparedoxin I {Trypanosoma brucei brucei [TaxId:	88.2
d1o8xa_	144	Tryparedoxin I {Crithidia fasciculata [TaxId: 5656	87.32
d2b5ea4	119	Protein disulfide isomerase, PDI {Baker's yeast (S	85.27
d1qgva_	137	spliceosomal protein U5-15Kd {Human (Homo sapiens)	84.52
d1wp0a1	160	Thioredoxin-like protein Sco1 (YpmQ), soluble doma	84.44
d1meka_	120	Protein disulfide isomerase, PDI {Human (Homo sapi	83.19
d2b7ka1	169	Thioredoxin-like protein Sco1 (YpmQ), soluble doma	82.38
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	80.2

>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=99.90  E-value=1.2e-23  Score=153.50  Aligned_cols=88  Identities=27%  Similarity=0.489  Sum_probs=77.6

Q ss_pred             CCCCCCCCCCCCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccc
Q 025774          156 YPILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFED  235 (248)
Q Consensus       156 ~~~l~~eP~~~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d  235 (248)
                      .+.||+||+.+.+++|+|+||||||++++|+|+.+++|++||+||.+.  ++....|.|+++||++.  +..|.++||+|
T Consensus         2 ~~~lp~EP~~~~~~~~~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~--~~~~~~f~l~~~~Pr~~--~~~d~~~TL~e   77 (96)
T d2cr5a1           2 VPDLPEEPSETAEEVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV--GYHKSLYRLSTSFPRRA--LEVEGGSSLED   77 (96)
T ss_dssp             CCCCCCCCCSSCSSEEEEEEECTTSCEEEEEEESSSBTHHHHHHHHHH--TCCTTTEEEECSSSCCB--CCCCSSCBHHH
T ss_pred             CCCCCCCCCCCCCCeEEEEEECCCCCEEEEEECCcccHHHHHHHHHHh--ccCcccceeecCCCcee--cCccCCCcHHH
Confidence            468999999888999999999999999999999999999999999987  45688999999999986  54578999999


Q ss_pred             cCCcCceE-EEEe
Q 025774          236 SGLANAMI-SVTW  247 (248)
Q Consensus       236 ~gl~~~~v-~v~~  247 (248)
                      +||.++++ +|.+
T Consensus        78 ~gl~p~~~L~v~~   90 (96)
T d2cr5a1          78 IGITVDTVLNVEE   90 (96)
T ss_dssp             HTCSSCEEEEEEE
T ss_pred             CCCCCCCEEEEec
Confidence            99997665 4543

>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=99.88  E-value=5.4e-23  Score=147.81  Aligned_cols=79  Identities=22%  Similarity=0.334  Sum_probs=71.7

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVT  246 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~  246 (248)
                      ++++|+|+||||||++++++|+.+++|++||+||.++..+....+|.|+++||++.  +. |.++||+|+||.|++|+|+
T Consensus        11 ~~p~t~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~~~~~~f~L~t~~Prr~--l~-d~~~TL~e~gL~~s~vl~k   87 (89)
T d1i42a_          11 AEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKE--LA-DENQTLKEANLLNAVIVQR   87 (89)
T ss_dssp             TSCCEEEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTTTSSCCEEEEETTTTEE--CC-CCSSCSGGGTTCCSEEEEE
T ss_pred             CCCcEEEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCccCCCCCEEEecCCCCcc--cC-CCcCcHHHCCCcCceEEEE
Confidence            35689999999999999999999999999999999875555678999999999986  64 7899999999999999999


Q ss_pred             eC
Q 025774          247 WE  248 (248)
Q Consensus       247 ~~  248 (248)
                      |.
T Consensus        88 ~t   89 (89)
T d1i42a_          88 LT   89 (89)
T ss_dssp             EC
T ss_pred             eC
Confidence            95

>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=99.84  E-value=5.4e-21  Score=135.19  Aligned_cols=77  Identities=17%  Similarity=0.385  Sum_probs=66.7

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCce-EEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAM-ISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~-v~v  245 (248)
                      .+++|+|+||||||++++|+|+.+++|++||+||.+.  ++.+.+|.|+++||++.++. .|.++||+|+||.|++ |+|
T Consensus         2 ~e~~~~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~--~~~~~~~~l~~~~Pr~~l~~-~d~~~TL~e~gL~p~~~L~v   78 (82)
T d1h8ca_           2 AEPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASK--GFPWDEYKLLSTFPRRDVTQ-LDPNKSLLEVKLFPQETLFL   78 (82)
T ss_dssp             CCCCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHH--TCCSSSEEEEETTTTEETTT-CCTTSBHHHHCCCSEEEEEE
T ss_pred             CCCcEEEEEECCCCCEEEEEECCCCcHHHHHHHHHhc--CCCCCceEEEecCccccccc-ccccCCHHHCCCCCCCEEEE
Confidence            4678999999999999999999999999999999986  55688999999999987443 4679999999998655 445


Q ss_pred             E
Q 025774          246 T  246 (248)
Q Consensus       246 ~  246 (248)
                      +
T Consensus        79 q   79 (82)
T d1h8ca_          79 E   79 (82)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.80  E-value=7.2e-20  Score=139.12  Aligned_cols=79  Identities=23%  Similarity=0.279  Sum_probs=67.3

Q ss_pred             CCCCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCce-
Q 025774          164 KVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAM-  242 (248)
Q Consensus       164 ~~~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~-  242 (248)
                      ...+.+.|+|+||||||++++|+|+.+++|++||+||.+.  ++...+|.|+++||++.+.. .|.++||+|+||+|++ 
T Consensus        37 ~d~~~p~~~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~--~~~~~~~~L~~~fPr~~l~~-~d~~~TL~e~gL~P~~~  113 (124)
T d1wj4a_          37 IDVNGPKAQLMLRYPDGKREQITLPEQAKLLALVKHVQSK--GYPNERFELLTNFPRRKLSH-LDYDITLQEAGLCPQET  113 (124)
T ss_dssp             CCCSSCEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHH--HCCTTTEEEECSSSCCEETS-SCSSSCTTTTTCCSSBC
T ss_pred             CCCCCCceEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc--ccCCcceEEeeccccccccc-ccccCcHHHcCCCCCCE
Confidence            3445678999999999999999999999999999999986  45688999999999997332 4789999999999655 


Q ss_pred             EEE
Q 025774          243 ISV  245 (248)
Q Consensus       243 v~v  245 (248)
                      |+|
T Consensus       114 L~v  116 (124)
T d1wj4a_         114 VFV  116 (124)
T ss_dssp             CEE
T ss_pred             EEE
Confidence            444

>d2dlxa1 c.47.1.24 (A:1-147) UBX domain-containing protein 7 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: UAS domain
domain: UBX domain-containing protein 7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3.4e-15  Score=116.21  Aligned_cols=79  Identities=44%  Similarity=0.881  Sum_probs=74.9

Q ss_pred             cccccCCCHHHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774            2 LNRDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus         2 ~~r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      |+|+||+|+.|+++++++||+|..++++++|..+++.|++..||+++||+|++|+.+..+ |.+++++|+..|..|++.+
T Consensus        60 m~~~v~~d~~V~~~l~~~fV~~~v~~~~~e~~~~~~~y~v~~~Pti~~idp~~ge~v~~~-~~~~~~~fl~~L~~fl~~~  138 (147)
T d2dlxa1          60 LNRDVWSNEAVKNIIREHFIFWQVYHDSEEGQRYIQFYKLGDFPYVSILDPRTGQKLVEW-HQLDVSSFLDQVTGFLGEH  138 (147)
T ss_dssp             HHHHTTTCHHHHHHHHHTEEEEEEESSSHHHHHHHHHHTCCSSSEEEEECTTTCCCCEEE-SSCCHHHHHHHHHHHHHHT
T ss_pred             HHHhccCCHHHHHHHhhheeEeeecccchhhhhhhhheecCceeEEEEEeCCCCeEeccc-CCCCHHHHHHHHHHHHhhC
Confidence            789999999999999999999999999999999999999999999999999999988666 5689999999999999976

>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=98.91  E-value=1.1e-10  Score=72.12  Aligned_cols=34  Identities=21%  Similarity=0.369  Sum_probs=11.6

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHH
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYC  200 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv  200 (248)
                      ..+++.|||||+||+|+..||+.+++|.+||.||
T Consensus        16 s~PtT~iQiRL~dG~R~v~rFN~~Htv~dir~fI   49 (50)
T d1s3si_          16 AEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFI   49 (50)
T ss_dssp             ----------------------CCCCHHHHHHHC
T ss_pred             CCCceEEEEEeCCCCEEEEEccCccCHHHHHHhh
Confidence            4568999999999999999999999999999997

>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=97.55  E-value=0.00034  Score=48.92  Aligned_cols=80  Identities=10%  Similarity=0.169  Sum_probs=61.5

Q ss_pred             CCCceEEEEEcCC---CceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEcc---CCCCccccCCCcCCCccccCCc-
Q 025774          167 RSLLCRVGVRLPD---GRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHA---IPGATKSLDYDSKLTFEDSGLA-  239 (248)
Q Consensus       167 ~~~~~~i~iRlp~---G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~---~Pr~~~~l~~d~~~tl~d~gl~-  239 (248)
                      ....++|.|+.|+   ++.+++++..+.||+.|-.-+... .+.+...-+|...   .|...-.+ +++++||.+.|+. 
T Consensus         6 s~~~iti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~-~gip~~~qrL~y~~~~~~~~~~~l-~~d~~tL~~YgI~d   83 (97)
T d1wjna_           6 SGQLLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRL-LKVPVSELLLSYESSKMPGREIEL-ENDLQPLQFYSVEN   83 (97)
T ss_dssp             SSCEEEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTT-TTCCTTTCEEEEECTTSCSCEEEC-CCSSSBSGGGTCCT
T ss_pred             CCCeEEEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHH-HCcChHHeEEEecCCCCCccccee-cCCCcCHhhccCCC
Confidence            3457899999875   788999999999999999999764 4667777788643   22221123 5789999999998 


Q ss_pred             CceEEEEeC
Q 025774          240 NAMISVTWE  248 (248)
Q Consensus       240 ~~~v~v~~~  248 (248)
                      ++.|+|.|.
T Consensus        84 g~~I~V~~~   92 (97)
T d1wjna_          84 GDCLLVRWS   92 (97)
T ss_dssp             TCEEEEECC
T ss_pred             CCEEEEEeC
Confidence            688899983

>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=97.34  E-value=0.00067  Score=47.70  Aligned_cols=83  Identities=12%  Similarity=0.097  Sum_probs=66.1

Q ss_pred             CCCCCCCCCCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccC
Q 025774          158 ILPEEPKVDRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSG  237 (248)
Q Consensus       158 ~l~~eP~~~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~g  237 (248)
                      .++|+...++...+.|.|+.-+|+.+.-....++||.+|-.=|.... +.++...+|+..  .+.  |  +++.||++.|
T Consensus        16 ~~~p~~~~~~~~~i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~-gip~~~qrLi~~--Gk~--L--~D~~tL~dyg   88 (100)
T d1uh6a_          16 SLVPRGSEGAATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQT-GTRWNKIVLKKW--YTI--F--KDHVSLGDYE   88 (100)
T ss_dssp             SSCCCCCSSCCCEEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHH-CCCGGGCEEEET--TEE--C--CSSCBHHHHT
T ss_pred             cccCCCCCCCCceEEEEEECCCCCEEEEEECCcChHHHHHHHHHHHH-CCCcceEEEEEE--eec--c--cCcCCHHHcC
Confidence            44556666667788999999999999999999999999999998764 667888889874  332  5  5689999999


Q ss_pred             Cc-CceEEEEe
Q 025774          238 LA-NAMISVTW  247 (248)
Q Consensus       238 l~-~~~v~v~~  247 (248)
                      +. +++|.+-|
T Consensus        89 I~~GstI~L~~   99 (100)
T d1uh6a_          89 IHDGMNLELYY   99 (100)
T ss_dssp             CCTTEEEEEEC
T ss_pred             CCCCCEEEEEE
Confidence            99 56666655

>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=97.27  E-value=0.0012  Score=47.63  Aligned_cols=70  Identities=17%  Similarity=0.164  Sum_probs=56.3

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhc-------CCCCCcCeEEEccCCCCccccCCCcCCCccccCCc
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQL-------EGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA  239 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~-------~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~  239 (248)
                      +++.+.|+|++.+|+.+.-.|..++||..|-.-|...+       .+.++...+|+..  .+.  |  +++.||+++++.
T Consensus        13 ~~~~i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~--Gk~--L--~D~~tL~~~~i~   86 (116)
T d1wgha_          13 PADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQ--GRF--L--HGNVTLGALKLP   86 (116)
T ss_dssp             CSSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEET--TEE--E--CSSCBTTTTTCC
T ss_pred             CCCeEEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEEC--CEE--e--cCCCCHHHcCCC
Confidence            35679999999999999999999999999999996543       2445788999774  443  5  568999999998


Q ss_pred             -Cce
Q 025774          240 -NAM  242 (248)
Q Consensus       240 -~~~  242 (248)
                       +++
T Consensus        87 ~g~~   90 (116)
T d1wgha_          87 FGKT   90 (116)
T ss_dssp             SSCE
T ss_pred             CCCE
Confidence             444

>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=97.26  E-value=0.0012  Score=43.61  Aligned_cols=69  Identities=22%  Similarity=0.226  Sum_probs=56.8

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ...|-||.++|+.+.-....++||.+|-.-+.... +.++...+|...  .+.  +  +.+.||++.|+. +++|.+
T Consensus         3 ~~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~-gi~~~~qrL~~~--gk~--L--~d~~tL~~y~I~~~sti~l   72 (76)
T d1z2ma2           3 PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLE-GVQDDLFWLTFE--GKP--L--EDQLPLGEYGLKPLSTVFM   72 (76)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHH-TCCGGGEEEEET--TEE--C--CTTSBGGGGTCCTTCEEEE
T ss_pred             CEEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHh-cCChhHeEEEEC--CeE--C--CCCCcHHHcCCCCCCEEEE
Confidence            57899999999999999999999999999998864 667888888775  332  5  458999999998 455544

>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=97.25  E-value=0.0012  Score=44.94  Aligned_cols=73  Identities=22%  Similarity=0.138  Sum_probs=59.4

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      .....|-||.++|+.+.-....+++|.+|-.-|... .+.++...+|+..  .+.  |  +++.||.+.|+. +++|.+.
T Consensus         5 s~~mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~-~gip~~~qrLi~~--Gk~--L--~d~~tL~~y~I~~~stl~l~   77 (87)
T d1wh3a_           5 SSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQ-QGLPKKQQQLEFQ--GQV--L--QDWLGLGIYGIQDSDTLILS   77 (87)
T ss_dssp             SSSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHH-TCCCTTTEEEEET--TEE--C--CSSSBHHHHTCCTTEEEEEE
T ss_pred             CCcEEEEEECCCCCEEEEEECCcCcHHHHHHHHHHH-HCcChHHeEEEee--ceE--c--CCCCcHHHcCCCCCCEEEEE
Confidence            456889999999999999999999999999999876 4667888999874  343  5  458999999998 5666554


Q ss_pred             e
Q 025774          247 W  247 (248)
Q Consensus       247 ~  247 (248)
                      +
T Consensus        78 ~   78 (87)
T d1wh3a_          78 K   78 (87)
T ss_dssp             E
T ss_pred             e
Confidence            3

>d2fwha1 c.47.1.1 (A:428-544) Thiol:disulfide interchange protein DsbD, C-terminal domain (DsbD-gamma) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thiol:disulfide interchange protein DsbD, C-terminal domain (DsbD-gamma)
species: Escherichia coli [TaxId: 562]

Probab=97.21  E-value=0.00046  Score=49.18  Aligned_cols=70  Identities=16%  Similarity=0.299  Sum_probs=54.3

Q ss_pred             ccCCCHHHHHHhhcceEEEEEec--CChHHHHHHHhcCCCCCceEEEEeCCCCceE--EeeeCCCChHHHHHHHhh
Q 025774            5 DTWANEAVSQTISTNFIFWQVYD--DTSEGKKVCTYYKLDSIPVVLVVDPITGQKM--RSWCGMVQPESLLEDLVP   76 (248)
Q Consensus         5 ~vl~~~~v~~~l~~~fV~w~~d~--~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l--~~~~G~~~~e~l~~~L~~   76 (248)
                      .++.++.+.+.++ +++++..++  +......++..|++..||++.++++ +|+.+  .++.|..++++|+..|+.
T Consensus        43 ~~~~~~~v~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~v~~~Pt~~~~~~-~G~~~~~~~~~G~~~~~~~~~~l~~  116 (117)
T d2fwha1          43 YTFSDPQVQKALA-DTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDG-QGQEHPQARVTGFMDAETFSAHLRD  116 (117)
T ss_dssp             HTTTSHHHHHHTT-TSEEEEEECTTCCHHHHHHHHHTTCCSSSEEEEECT-TSCBCGGGCBCSCCCHHHHHHHHHH
T ss_pred             hHHhHHHHHHhcc-ceEEEecccccchhHHHHHHhhhehhhceEEEEEeC-CCcEEecccccccCCHHHHHHHHhc
Confidence            4566777777665 566666665  4566778999999999999999986 47754  468899999999888763

>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=97.13  E-value=0.0016  Score=42.75  Aligned_cols=67  Identities=19%  Similarity=0.234  Sum_probs=54.7

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      .|.||.++|+.+.-....+++|.+|-.-+.... +.++..++|...  .+.  +  +++.||++.|+. +++|.+
T Consensus         2 ~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~-gi~~~~qrLi~~--Gk~--L--~d~~tL~~y~I~~~sti~l   69 (73)
T d1bt0a_           2 LIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKE-GIPPVQQRLIYA--GKQ--L--ADDKTAKDYNIEGGSVLHL   69 (73)
T ss_dssp             EEEEECTTSCEEEEECCTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTSBTGGGTCCTTCEEEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHh-CCChHHEEEEEC--CeE--c--CCCCcHHHcCCCCCCEEEE
Confidence            578999999999999999999999999998764 667888999764  443  5  458999999998 555543

>d1dbya_ c.47.1.1 (A:) Thioredoxin {Chlamydomonas reinhardtii [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Chlamydomonas reinhardtii [TaxId: 3055]

Probab=97.12  E-value=0.0012  Score=46.27  Aligned_cols=62  Identities=19%  Similarity=0.400  Sum_probs=50.7

Q ss_pred             HHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           14 QTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        14 ~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .-...++.+...|++..  ..++..|++.++|++.++.  +|..+.++.|..+.++|...|.++|+
T Consensus        46 ~~~~~~~~~~~vd~d~~--~~l~~~~~V~~~Pt~~~~~--~G~~v~~~~G~~~~~~l~~~i~~~L~  107 (107)
T d1dbya_          46 GEYKDKLKCVKLNTDES--PNVASEYGIRSIPTIMVFK--GGKKCETIIGAVPKATIVQTVEKYLN  107 (107)
T ss_dssp             HHTTTTCEEEEEETTTC--HHHHHHHTCCSSCEEEEES--SSSEEEEEESCCCHHHHHHHHHHHCC
T ss_pred             HhhcccceEEEEecccc--hhHHHHhcccceEEEEEEE--CCeEEEEEeCCCCHHHHHHHHHHhhC
Confidence            34445788888888643  4688999999999999994  69999999999999999888887753

>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=97.07  E-value=0.0013  Score=43.96  Aligned_cols=69  Identities=23%  Similarity=0.373  Sum_probs=56.7

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      .++|.||+.+|+.+.-....++||..|-.-|... .+.++...+|+..  .+.  +  +++.||.+.|+. +++|.+
T Consensus         3 e~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~-~~ip~~~qrLi~~--Gk~--L--~d~~tL~~y~I~~~sti~l   72 (80)
T d1ttna1           3 ECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAA-EGVEPGSQRWFFS--GRP--L--TDKMKFEELKIPKDYVVQV   72 (80)
T ss_dssp             SEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHT-TCCCSTTCEEEET--TEE--C--CTTSHHHHCCCSSSCEEEE
T ss_pred             eEEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHH-hCCCcccEEEEEC--ceE--c--CCCCcHHHcCCCCCCEEEE
Confidence            4789999999999999999999999999999876 4667888888764  343  5  458999999998 566554

>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=97.02  E-value=0.0027  Score=42.00  Aligned_cols=69  Identities=16%  Similarity=0.266  Sum_probs=55.1

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      .|.||..+|+.+.-....+++|.+|-.-|.... +.++...+|....=.+.  +  .++.||.+.|+.+ ++|.+
T Consensus         2 ~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~-gip~~~QrLi~~~~Gk~--L--~D~~tL~~y~i~~g~~i~l   71 (76)
T d1z2ma1           2 DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKI-GVHAFQQRLAVHPSGVA--L--QDRVPLASQGLGPGSTVLL   71 (76)
T ss_dssp             EEEEEESSSCEEEEECCSSCCHHHHHHHHHHHH-CCCGGGEEEEEETTCCB--C--CSSSCSGGGTCCTTCEEEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHh-ccCCccEEEEEcCCCee--c--cCCCcHHHcCCCCCCEEEE
Confidence            478999999999999999999999999998864 66778888875432332  5  4479999999984 55544

>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=97.00  E-value=0.0031  Score=44.19  Aligned_cols=68  Identities=21%  Similarity=0.276  Sum_probs=53.1

Q ss_pred             CCceEEEEEcCCCceE-EEeeCCCCchHHHHHHHHhhcC----CCC--CcCeEEEccCCCCccccCCCcCCCccccCCcC
Q 025774          168 SLLCRVGVRLPDGRRM-QRNFLRTDPIQLLWSYCYSQLE----GSE--MKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN  240 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~-~r~F~~~~~l~~l~~fv~~~~~----~~~--~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~  240 (248)
                      ++...|.||+.+|+.+ .-+|..++||..|-.-|...+.    +.+  +...+|+..  .+.  |  +++.||+|+++.+
T Consensus         5 ~~~i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~--Gk~--L--~D~~tL~dy~i~~   78 (101)
T d1se9a_           5 HNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISA--GKV--L--ENSKTVKDYRSPV   78 (101)
T ss_dssp             CCCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEET--TEE--C--CTTSBGGGGSCCT
T ss_pred             cceEEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEEC--CeE--e--cCCCCHHHcCCCC
Confidence            3468899999999987 5999999999999999987642    222  456888775  443  5  5689999999975


Q ss_pred             c
Q 025774          241 A  241 (248)
Q Consensus       241 ~  241 (248)
                      +
T Consensus        79 g   79 (101)
T d1se9a_          79 S   79 (101)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1thxa_ c.47.1.1 (A:) Thioredoxin {Anabaena sp., pcc 7120 [TaxId: 1167]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Anabaena sp., pcc 7120 [TaxId: 1167]

Probab=96.97  E-value=0.0018  Score=45.34  Aligned_cols=63  Identities=21%  Similarity=0.284  Sum_probs=50.5

Q ss_pred             HHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           12 VSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        12 v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      +..-+...+.+...|++.  ...++..|++..+|++.++.  +|+.+.++.|..+.++|...|.+.+
T Consensus        45 ~~~~~~~~~~~~~vd~d~--~~~l~~~~~I~~~Pt~~~~~--~g~~v~~~~G~~~~~~l~~~i~~~L  107 (108)
T d1thxa_          45 AANTYSDRLKVVKLEIDP--NPTTVKKYKVEGVPALRLVK--GEQILDSTEGVISKDKLLSFLDTHL  107 (108)
T ss_dssp             HHHHTTTTCEEEEEESTT--CHHHHHHTTCCSSSEEEEEE--TTEEEEEEESCCCHHHHHHHHHHHH
T ss_pred             HHHhcCCcceeceecccc--cHHHHHHhcccCCCEEEEEE--CCEEEEEEeCCCCHHHHHHHHHHhc
Confidence            334445568888888864  45688999999999999994  6899999999999999988777665

>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=96.92  E-value=0.0036  Score=41.01  Aligned_cols=70  Identities=17%  Similarity=0.265  Sum_probs=57.2

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      +.|-||..+|+.+.-.-..++||.+|-.-+.... +.++..++|...  .+.  +  +++.||++.|+. +++|.+-|
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~-~i~~~~q~Li~~--Gk~--L--~d~~tL~~y~I~~gstl~L~~   72 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQI-GTQPNKIVLQKG--GSV--L--KDHISLEDYEVHDQTNLELYY   72 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHH-CCTTTSEEEESS--SCE--E--CTTSBHHHHTCCTTEEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhh-cccccEEEEEEE--eEE--e--cccCcHHHcCCCCCCEEEEEE
Confidence            5788999999999999999999999999998865 667889999875  443  5  457899999999 45565544

>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=96.90  E-value=0.0028  Score=42.19  Aligned_cols=68  Identities=19%  Similarity=0.236  Sum_probs=55.5

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ..|-||+.+|+.+.-....+++|.+|-.-|.... +.++...+|+..  .+.  +  +++.||.++|+. +++|.+
T Consensus         3 M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~-gip~~~qrLi~~--Gk~--L--~d~~tL~~y~I~~~sti~l   71 (78)
T d2zeqa1           3 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQ-GVPADQLRVIFA--GKE--L--PNHLTVQNCDLEQQSIVHI   71 (78)
T ss_dssp             EEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHH-TCCGGGEEEEET--TEE--E--CTTCBGGGSSCCTTCEEEE
T ss_pred             eEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHH-CcChhHeEEEEe--eeE--c--CCCCCHHHcCCCCCCEEEE
Confidence            4689999999999999999999999999998764 667778888764  443  6  458999999998 466654

>d1fb6a_ c.47.1.1 (A:) Thioredoxin {Spinach (Spinacia oleracea), thioredoxin M [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Spinach (Spinacia oleracea), thioredoxin M [TaxId: 3562]

Probab=96.88  E-value=0.0022  Score=44.47  Aligned_cols=61  Identities=23%  Similarity=0.435  Sum_probs=47.7

Q ss_pred             HHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           13 SQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        13 ~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      .+-...++.+...+.+.  ...++..|++..+|++.++  .+|+.+.++.|..++++|...|.+.
T Consensus        43 ~~~~~~~~~~~~v~~d~--~~~l~~~~~V~~~Pt~~~~--~~G~~v~~~~G~~~~~~l~~~i~~~  103 (104)
T d1fb6a_          43 AKEYSGKIAVYKLNTDE--APGIATQYNIRSIPTVLFF--KNGERKESIIGAVPKSTLTDSIEKY  103 (104)
T ss_dssp             HHHTTTTCEEEEEETTT--CHHHHHHTTCCSSSEEEEE--ETTEEEEEEEECCCHHHHHHHHHHH
T ss_pred             HHhhcCccceeEEeccc--chhhhhhcceeeeeEEEEE--EcCeEEEEEeCCCCHHHHHHHHHHh
Confidence            33444567777777754  4468999999999998888  4699999999999999987777654

>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=96.86  E-value=0.0043  Score=42.71  Aligned_cols=69  Identities=12%  Similarity=0.156  Sum_probs=54.2

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcC--CCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLE--GSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~--~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      .|-||..+|+.+.-....++||..|-.-+.....  +.++...+|+..  .+.  |  +++.||++.|+. +++|.+.
T Consensus         2 ~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~--Gk~--L--~d~~tL~~y~I~~~s~i~lv   73 (95)
T d1uela_           2 QVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYA--GKI--L--NDDTALKEYKIDEKNFVVVM   73 (95)
T ss_dssp             EEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEET--TEE--C--CTTSBGGGGTCCSSSEEEEE
T ss_pred             EEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEEC--CeE--c--cCCCcHHHcCCCCCCEEEEE
Confidence            5789999999999999999999999999987542  345678898775  443  5  447899999998 5666543

>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=96.85  E-value=0.0028  Score=42.71  Aligned_cols=72  Identities=18%  Similarity=0.214  Sum_probs=56.9

Q ss_pred             CCCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEE
Q 025774          166 DRSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMIS  244 (248)
Q Consensus       166 ~~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~  244 (248)
                      +.+.+++|.|+.++|+ ..-....+++|.+|-.-|.... +.++...+|+..  .+.  +  +++.||+++|+. +++|.
T Consensus         3 ~~~~~i~I~Vkt~~~~-~~~~V~~~~tV~~lK~~i~~~~-gi~~~~qrL~~~--Gk~--L--~D~~tL~~y~i~~gsti~   74 (84)
T d1yqba1           3 GSPHLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRF-KAHPDQLVLIFA--GKI--L--KDPDSLAQCGVRDGLTVH   74 (84)
T ss_dssp             CCTTEEEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHH-TCCGGGEEEEET--TEE--C--CTTSBHHHHTCCTTCEEE
T ss_pred             CCCCEEEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHH-CcCchhEEEEEe--eee--c--cccCcHHHcCCCCCCEEE
Confidence            4567899999999875 5677889999999999998764 667888999864  443  5  457899999998 56664


Q ss_pred             E
Q 025774          245 V  245 (248)
Q Consensus       245 v  245 (248)
                      +
T Consensus        75 l   75 (84)
T d1yqba1          75 L   75 (84)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=96.80  E-value=0.011  Score=41.23  Aligned_cols=72  Identities=15%  Similarity=0.224  Sum_probs=56.2

Q ss_pred             CCCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          167 RSLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       167 ~~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      .+..++|.|+.++|+ ..-....+++|.+|-.-|.... +.+....+|+..  .+.  |  +++.||.++|+. +++|.+
T Consensus        29 ~~~~i~V~Vk~~~~~-~~i~V~~~~tV~~LK~~I~~~~-gi~~~~qrLi~~--Gk~--L--~D~~tL~~~~I~~g~~I~l  100 (103)
T d1j8ca_          29 EPKIIKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRF-KSQTDQLVLIFA--GKI--L--KDQDTLIQHGIHDGLTVHL  100 (103)
T ss_dssp             CCCCEEEEEECSSCE-EEEEECTTCCHHHHHHHHHHHH-CSCSSSEEEEET--TEE--E--STTSCGGGTTCSSSEEEEE
T ss_pred             CCCeEEEEEECCCcc-EEEEECCCChHHHHHHHHHHHH-CcCHHHeeeeee--eec--c--cCCCcHHHcCCCCCCEEEE
Confidence            455789999999886 5668899999999999998864 667888999864  443  5  347899999999 455554


Q ss_pred             E
Q 025774          246 T  246 (248)
Q Consensus       246 ~  246 (248)
                      .
T Consensus       101 v  101 (103)
T d1j8ca_         101 V  101 (103)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=96.73  E-value=0.005  Score=40.53  Aligned_cols=67  Identities=18%  Similarity=0.239  Sum_probs=54.2

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +|-||..+|+.+.-....+++|.+|-.-+.... +.++...+|+..  .+.  +  +++.||++.|+. +++|.+
T Consensus         2 qI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~-gi~~~~qrL~~~--Gk~--L--~d~~tL~~y~i~~~s~I~L   69 (76)
T d1ogwa_           2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKE-GIPPDQQRLIFA--GKQ--L--EDGRTLSDYNIQKESTLHL   69 (76)
T ss_dssp             EEEEEETTSCEEEEECCTTSBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTSBGGGGTCCTTCEEEE
T ss_pred             EEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhc-CCChHHEEeEEC--CeE--c--CCCCCHHHcCCCCCCEEEE
Confidence            688999999999999999999999999998764 667888888774  342  5  457899999998 455543

>d1nw2a_ c.47.1.1 (A:) Thioredoxin {Alicyclobacillus acidocaldarius, formerly Bacillus acidocaldarius [TaxId: 405212]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Alicyclobacillus acidocaldarius, formerly Bacillus acidocaldarius [TaxId: 405212]

Probab=96.71  E-value=0.003  Score=43.89  Aligned_cols=61  Identities=15%  Similarity=0.289  Sum_probs=48.7

Q ss_pred             HHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           14 QTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        14 ~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      .-..+++.|...|++..  ..++..|++.++|++.++.  +|..+.++.|..+.++|...|...+
T Consensus        44 ~~~~~~~~~~~vd~~~~--~~~~~~~~V~~~Pt~~~~~--~G~~~~~~~G~~~~~~l~~~i~~~L  104 (105)
T d1nw2a_          44 EAHADKVTVAKLNVDEN--PETTSQFGIMSIPTLILFK--GGEPVKQLIGYQPKEQLEAQLADVL  104 (105)
T ss_dssp             HHHTTTCEEEEEETTTC--HHHHHHTTCCBSSEEEEEE--TTEEEEEEESCCCHHHHHHHTTTTC
T ss_pred             hhcCCceEEEEEECCCC--cccHHHCCcceeeEEEEEE--CCEEEEEEECCCCHHHHHHHHHHHh
Confidence            33445788888888654  4668999999999999984  6999999999999999877666554

>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=96.65  E-value=0.0047  Score=40.82  Aligned_cols=70  Identities=10%  Similarity=0.156  Sum_probs=54.8

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcC--CCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLE--GSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~--~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      ..+|.||..+|+.+.-....+++|.+|-.-+.....  ..++...+|...  ++.  |  ++++||.+.|+. ++.|++
T Consensus         2 ~~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~--Gk~--L--~D~~tL~~y~I~~~s~i~~   74 (77)
T d1oqya4           2 AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYA--GKI--L--SDDVPIRDYRIDEKNFVVV   74 (77)
T ss_dssp             CCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESS--SSE--E--CSSSBTTTTCCCTTSCEEE
T ss_pred             cEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEEC--CcC--c--cCCCcHHHcCCCCCCEEEE
Confidence            357999999999999999999999999998876532  245677888764  553  6  458999999999 555544

>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=96.63  E-value=0.0048  Score=43.05  Aligned_cols=71  Identities=20%  Similarity=0.145  Sum_probs=57.1

Q ss_pred             CCceEEEEEcCC----CceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-Cce
Q 025774          168 SLLCRVGVRLPD----GRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAM  242 (248)
Q Consensus       168 ~~~~~i~iRlp~----G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~  242 (248)
                      .+.++|+|++|.    |+.+.-....++||.+|-.-|...+ +.++...+|+..  .+.  |  +.+.||.+.|+. ++.
T Consensus        13 tg~ati~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~-gi~~~~qkLi~~--Gk~--L--~d~~tL~~~gI~~~s~   85 (100)
T d1wjua_          13 TGIATIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETF-GLQENYIKIVIN--KKQ--L--QLGKTLEEQGVAHNVK   85 (100)
T ss_dssp             CCEEEEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHT-TCCSTTCEEEET--TEE--C--CTTSBHHHHTCCSSEE
T ss_pred             cceEEEEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHH-CCCCeeEEEEEc--ccC--c--CCCcCHHHcCCCCCCE
Confidence            467889999974    8889999999999999999998865 667888999875  443  5  458999999998 455


Q ss_pred             EEE
Q 025774          243 ISV  245 (248)
Q Consensus       243 v~v  245 (248)
                      |+|
T Consensus        86 i~v   88 (100)
T d1wjua_          86 AMV   88 (100)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            544

>d1z5ye1 c.47.1.10 (E:49-184) Thioredoxin-like protein CcmG (CycY, DsbE) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Thioredoxin-like protein CcmG (CycY, DsbE)
species: Escherichia coli [TaxId: 562]

Probab=96.63  E-value=0.0034  Score=45.66  Aligned_cols=47  Identities=15%  Similarity=0.213  Sum_probs=41.3

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      .++..|++..+|+.+||++ +|.++.++.|.++.+++...|...++++
T Consensus        85 ~~~~~~~v~~~P~~~liD~-~G~i~~~~~G~~~~~~l~~~i~~ll~kl  131 (136)
T d1z5ye1          85 MLGLDLGVYGAPETFLIDG-NGIIRYRHAGDLNPRVWEEEIKPLWEKY  131 (136)
T ss_dssp             HHHHHHTCCSBSEEEEECT-TSCEEEEEESCCCHHHHHHHTHHHHHHH
T ss_pred             hHHHhcccCCcceEEEEcC-CCEEEEEEEcCCCHHHHHHHHHHHHHHH
Confidence            4677889999999999995 5999999999999999988888888764

>d2trxa_ c.47.1.1 (A:) Thioredoxin {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Escherichia coli [TaxId: 562]

Probab=96.62  E-value=0.0049  Score=42.94  Aligned_cols=61  Identities=16%  Similarity=0.223  Sum_probs=49.0

Q ss_pred             HHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           14 QTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        14 ~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      .....++.+...|++..  ..++..|++.++|++.++.  .|+.+.++.|..++++|...|.+.|
T Consensus        47 ~~~~~~~~~~~vd~d~~--~~l~~~~~v~~~PT~~~~~--~G~~v~~~~G~~~~~~l~~~i~~~L  107 (108)
T d2trxa_          47 DEYQGKLTVAKLNIDQN--PGTAPKYGIRGIPTLLLFK--NGEVAATKVGALSKGQLKEFLDANL  107 (108)
T ss_dssp             HHTTTTEEEEEEETTTC--TTHHHHTTCCSSSEEEEEE--TTEEEEEEESCCCHHHHHHHHHHHH
T ss_pred             HHhhcceeeeeccccch--hhHHHHhCCCcEEEEEEEE--CCEEEEEEeCCCCHHHHHHHHHHhc
Confidence            34455788888888644  4688999999999988884  6999999999999999877776554

>d1f9ma_ c.47.1.1 (A:) Thioredoxin {Spinach (Spinacia oleracea), thioredoxin F [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Spinach (Spinacia oleracea), thioredoxin F [TaxId: 3562]

Probab=96.51  E-value=0.0042  Score=43.98  Aligned_cols=64  Identities=14%  Similarity=0.219  Sum_probs=48.6

Q ss_pred             HHHHHHhh--cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           10 EAVSQTIS--TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        10 ~~v~~~l~--~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +.+.++-+  .+.+|...|++. +...++..|++.++|+++++  .+|..+.++.|. .++++++.|...
T Consensus        45 p~~~~l~~~~~~v~~~~vd~~~-~~~~l~~~~~V~~~Pt~~~~--k~G~~v~~~~G~-~~~~l~e~i~~~  110 (112)
T d1f9ma_          45 PKYEKLAEEYLDVIFLKLDCNQ-ENKTLAKELGIRVVPTFKIL--KENSVVGEVTGA-KYDKLLEAIQAA  110 (112)
T ss_dssp             HHHHHHHHHCTTSEEEEEECSS-TTHHHHHHHCCSSSSEEEEE--ETTEEEEEEESS-CHHHHHHHHHHH
T ss_pred             HHHhhhccccccceeecccccc-cchhhHhheeeccCCEEEEE--ECCEEEEEEeCC-CHHHHHHHHHHc
Confidence            34444444  367888888753 34568899999999999998  479999999996 778887777654

>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=96.40  E-value=0.012  Score=38.38  Aligned_cols=67  Identities=12%  Similarity=0.129  Sum_probs=52.4

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEE
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      .+|.|+.+++ ++.-....++||.+|-.-+.... |.++...+|+..  .+.  +  +++.||.++|+. +++|.+
T Consensus         2 i~I~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~-gip~~~qrLi~~--Gk~--L--~D~~tL~~~~I~~g~~i~l   69 (73)
T d2bwfa1           2 LNIHIKSGQD-KWEVNVAPESTVLQFKEAINKAN-GIPVANQRLIYS--GKI--L--KDDQTVESYHIQDGHSVHL   69 (73)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTSBTGGGTCCTTCEEEE
T ss_pred             EEEEEEeCCe-EEEEEECCCChHHHHHHHHHHHH-CcChHHeEEEEC--CeE--c--cCCCcHHHCCCCCCCEEEE
Confidence            5788888654 57888999999999999998864 677888999864  443  5  457899999998 555544

>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=96.30  E-value=0.0041  Score=40.71  Aligned_cols=66  Identities=12%  Similarity=0.067  Sum_probs=54.1

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMIS  244 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~  244 (248)
                      .|.||..+|+.+.-....++||.+|-.-+.... +.++...+|+..  .+.  |  +++.||.|.|+.+++|.
T Consensus         2 ~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~-gip~~~qrLi~~--Gk~--L--~d~~tL~dy~i~~~ti~   67 (73)
T d1wx9a1           2 EVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASV-SIPSEKQRLIYQ--GRV--L--QDDKKLQEYNVGGKVIH   67 (73)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHHH-CCCTTTCCCEET--TEE--C--CSSSBHHHHTCTTEEEB
T ss_pred             EEEEEcCCCCEEEEEECCCChHHHHHHHHHHHh-CCChHHEEEEEC--CeE--c--cCCCCHHHhCCCCCEEE
Confidence            688999999999999999999999999998864 667778888764  342  5  45899999999776664

>d2es7a1 c.47.1.20 (A:7-125) Hydrogenase-1 operon protein HyaE {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: HyaE-like
domain: Hydrogenase-1 operon protein HyaE
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.29  E-value=0.0062  Score=43.67  Aligned_cols=57  Identities=14%  Similarity=0.211  Sum_probs=44.0

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +|.+-..|.  .....+++.|++..+|++.++  .+|+.+.++.|..+.++++..+...+|
T Consensus        63 ~~~~~~Vd~--d~~~~l~~~~~V~~~Pt~~~~--~~G~~v~~~~G~~~~~~l~~~i~~lLd  119 (119)
T d2es7a1          63 DWQVAVADL--EQSEAIGDRFNVRRFPATLVF--TDGKLRGALSGIHPWAELLTLMRSIVD  119 (119)
T ss_dssp             CCEEEEECH--HHHHHHHHTTTCCSSSEEEEE--SCC----CEESCCCHHHHHHHHHHHHC
T ss_pred             ceEEEEEEC--CCCHHHHHhcCcCcceEEEEE--EcCeEEEEeeCCCCHHHHHHHHHHHhC
Confidence            466666665  455679999999999999998  469999999999999999999988765

>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=96.28  E-value=0.01  Score=39.08  Aligned_cols=69  Identities=17%  Similarity=0.235  Sum_probs=54.6

Q ss_pred             ceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          170 LCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       170 ~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      .++|.|+-+||+.+..+-..+.+++.|.+...... +.+...++|+.  -.+.  +  +.+.|++++|+.. .+|-|
T Consensus         2 ~I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~-~~~~~~~~f~f--dG~~--l--~~~~T~~~l~~edgD~Idv   71 (77)
T d2uyzb1           2 YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQ-GVPMNSLRFLF--EGQR--I--ADNHTPKELGMEEEDVIEV   71 (77)
T ss_dssp             EEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHH-TCCGGGEEEEE--TTEE--C--CTTCCHHHHTCCTTEEEEE
T ss_pred             EEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHh-CCChhHEEEEE--CCEE--C--CCCCCHHHcCCCCCCEEEE
Confidence            57899999999999988899999999999876654 45678888874  3543  5  5678999999994 54433

>d1gh2a_ c.47.1.1 (A:) Thioredoxin-like protein, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin-like protein, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.22  E-value=0.0099  Score=41.57  Aligned_cols=64  Identities=13%  Similarity=0.202  Sum_probs=49.5

Q ss_pred             HHHHHhhc--ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           11 AVSQTIST--NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        11 ~v~~~l~~--~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .+.++-++  +..|...|++.  ...++..|++.++|++.++  ++|..+.++.| .+++.|...|.++|+
T Consensus        42 ~~~~la~~~~~~~f~~vd~d~--~~~l~~~~~v~~~Pt~~~~--~~G~~v~~~~G-~~~~~l~~~i~k~le  107 (107)
T d1gh2a_          42 AFSSMSNKYPQAVFLEVDVHQ--CQGTAATNNISATPTFQFF--RNKVRIDQYQG-ADAVGLEEKIKQHLE  107 (107)
T ss_dssp             HHHHHHHHCTTSEEEEEETTT--SHHHHHHTTCCSSSEEEEE--ETTEEEEEEES-SCHHHHHHHHHHHHC
T ss_pred             hhhcccccccccccccccccc--chhhhhhcCceeceEEEEE--ECCEEEEEEeC-CCHHHHHHHHHHhhC
Confidence            34444443  57888888864  4567899999999999888  57999999999 488888888877764

>d2hfda1 c.47.1.20 (A:1-132) Hydrogenase-1 operon protein HyaE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: HyaE-like
domain: Hydrogenase-1 operon protein HyaE
species: Escherichia coli [TaxId: 562]

Probab=96.18  E-value=0.011  Score=43.25  Aligned_cols=57  Identities=11%  Similarity=0.098  Sum_probs=47.8

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      |.+-..|+  .+-..+++.|++..+|++.++  ++|+.+.++.|..+.++++..|...++.
T Consensus        70 ~~~a~Vd~--d~~~~la~~~~V~~~PT~~~~--~~G~~v~~~~G~~~~~~l~~~i~~ll~~  126 (132)
T d2hfda1          70 WQVAIADL--EQSEAIGDRFGVFRFPATLVF--TGGNYRGVLNGIHPWAELINLMRGLVEP  126 (132)
T ss_dssp             EEEEEECH--HHHHHHHHHHTCCSCCEEEEE--ETTEEEEEECCCSCHHHHHHHHHHHHSC
T ss_pred             ceeEEEEe--cCCHHHHHhhccCcceeEEEE--EcCcEeeeecCCCCHHHHHHHHHHHhCc
Confidence            44445554  455689999999999999998  5699999999999999999999988874

>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=96.12  E-value=0.022  Score=40.31  Aligned_cols=71  Identities=11%  Similarity=0.193  Sum_probs=55.0

Q ss_pred             ceEEEEEcC---CCceEEEeeCC-CCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEE
Q 025774          170 LCRVGVRLP---DGRRMQRNFLR-TDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMIS  244 (248)
Q Consensus       170 ~~~i~iRlp---~G~r~~r~F~~-~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~  244 (248)
                      .++|+|++|   ||+.+.-.... ++||.+|-.-|... .+.+....+|+..  .+.  +  .++.||.+.|+. +++|.
T Consensus        27 ~~ti~V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~-~gip~~~QrLi~~--Gk~--L--~D~~tL~~ynI~~gsti~   99 (111)
T d1we6a_          27 PATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGE-IQIPANKQKLSGK--AGF--L--KDNMSLAHYNVGAGEILT   99 (111)
T ss_dssp             CEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHH-TTCCTTTSEEECS--SSB--C--CTTSBTTTTTCSSSCEEE
T ss_pred             CEEEEEEcccCCCCeEEEEEecCCccHHHHHHHHHHHH-HCCCccceEEEEe--eEE--c--cccCCHHHcCCCCCCEEE
Confidence            356777764   69999999975 99999999999876 4667888999764  443  5  457899999998 56666


Q ss_pred             EEe
Q 025774          245 VTW  247 (248)
Q Consensus       245 v~~  247 (248)
                      +.+
T Consensus       100 L~l  102 (111)
T d1we6a_         100 LSL  102 (111)
T ss_dssp             EEC
T ss_pred             EEe
Confidence            654

>d1a8la2 c.47.1.2 (A:120-226) Protein disulfide isomerase, PDI {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: PDI-like
domain: Protein disulfide isomerase, PDI
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.11  E-value=0.0069  Score=41.97  Aligned_cols=56  Identities=16%  Similarity=0.254  Sum_probs=45.0

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      ++.+...|.  .+...++..|++.++|++.+.  .+|..+.++.|..+.+.|.+.|..+|
T Consensus        51 ~v~~~~id~--~~~~~l~~~~~V~~vPTi~i~--~~G~~~~~~~G~~~~~~~~~~i~~al  106 (107)
T d1a8la2          51 KILGDMVEA--IEYPEWADQYNVMAVPKIVIQ--VNGEDRVEFEGAYPEKMFLEKLLSAL  106 (107)
T ss_dssp             CEEEEEEEG--GGCHHHHHHTTCCSSCEEEEE--ETTEEEEEEESCCCHHHHHHHHHHHH
T ss_pred             cEEEEEecc--ccccccccccccccceEEEEE--eCCeEEEEEECCCCHHHHHHHHHHhh
Confidence            355555665  455578999999999998654  46999999999999999999988775

>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=96.07  E-value=0.012  Score=39.40  Aligned_cols=70  Identities=16%  Similarity=0.215  Sum_probs=53.7

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +..++|.|+.++|+ ..-.+..+++|.+|-.-+.... +.++...+|+..  .+.  |  .++.||+++|+.+ ++|.+
T Consensus         8 ~~~i~v~Vk~~~~~-~~i~v~~~~tV~~lK~~I~~~~-~v~~~~qrL~f~--Gk~--L--~d~~tL~~~gI~~gs~I~l   78 (83)
T d1wx8a1           8 SRIIRVSVKTPQDC-HEFFLAENSNVRRFKKQISKYL-HCNADRLVLIFT--GKI--L--RDQDILSQRGILDGSTVHV   78 (83)
T ss_dssp             SCEEEEEEECSSSE-EEEEEETTCCHHHHHHHHHHHT-CSCTTTBCCEET--TEE--C--CTTSCHHHHTCCTTEEEEC
T ss_pred             CCeEEEEEEcCCCc-EEEEECCCChHHHHHHHHHHHh-CCChhHEEEEEE--hhc--c--ccCCcHHHcCCCCCCEEEE
Confidence            45799999998875 5778889999999999998764 667778888753  343  5  3467999999985 55543

>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=95.96  E-value=0.019  Score=39.43  Aligned_cols=69  Identities=17%  Similarity=0.170  Sum_probs=53.3

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      ....+|.||+.||+.+.-.-..++||.+|-.-+..    .++...+|+..  .+.  | .|+.+||.++|+.+ ++|.+
T Consensus         5 ~s~m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~~----~~~~~qrLi~~--Gk~--L-~dd~~tL~~y~i~~g~~v~l   74 (95)
T d1wiaa_           5 SSGINVRLKFLNDTEELAVARPEDTVGTLKSKYFP----GQESQMKLIYQ--GRL--L-QDPARTLSSLNITNNCVIHC   74 (95)
T ss_dssp             CCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSS----STTTTCEEEET--TEE--C-CCSSCBTTTTTCCTTEEEEE
T ss_pred             CCcEEEEEEcCCCCEEEEEECCcCcHHHHHHHHhc----CCcceeEEEEC--CEE--c-ccCCCCHHHcCCCCCCEEEE
Confidence            45789999999999999999999999999876643    24667888753  443  5 36689999999984 55544

>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=95.86  E-value=0.026  Score=36.96  Aligned_cols=69  Identities=22%  Similarity=0.173  Sum_probs=52.6

Q ss_pred             EEEEEcCCCc-eEEE-eeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEEe
Q 025774          172 RVGVRLPDGR-RMQR-NFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVTW  247 (248)
Q Consensus       172 ~i~iRlp~G~-r~~r-~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~~  247 (248)
                      +|.||..+|+ .+.- .-..+++|.+|-..|.... |.++...+|+..  .+.  +  +++.||.+.|+. +++|.+.+
T Consensus         2 ~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~-gip~~~qrLi~~--Gk~--L--~D~~tL~~y~I~~~sti~lv~   73 (76)
T d2faza1           2 WIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELF-HVEPGLQRLFYR--GKQ--M--EDGHTLFDYEVRLNDTIQLLV   73 (76)
T ss_dssp             EEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHH-CCCGGGEEEEET--TEE--C--CTTCBTTTTTCCTTCEEEEEE
T ss_pred             EEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHH-CcChHHeEEEEe--eEe--c--cCCCcHHHcCCCCCCEEEEEE
Confidence            5889999996 4443 5789999999999998764 667888888764  443  5  457999999998 56665543

>d2ifqa1 c.47.1.1 (A:1-105) Thioredoxin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.84  E-value=0.02  Score=39.50  Aligned_cols=54  Identities=24%  Similarity=0.377  Sum_probs=43.0

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +++|...|++.  ...++..|++.++|++.++  ++|..+.++.|. ++++|...|.++
T Consensus        51 ~~~~~~vd~d~--~~~~~~~~~V~~~Pt~~~~--~~G~~v~~~~G~-~~~~l~~~i~~~  104 (105)
T d2ifqa1          51 NVIFLEVDVDD--CQDVASECEVKCMPTFQFF--KKGQKVGEFSGA-NKEKLEATINEL  104 (105)
T ss_dssp             TSEEEEEETTT--CHHHHHHTTCCBSSEEEEE--ETTEEEEEEESC-CHHHHHHHHHHH
T ss_pred             cceeeeccccc--CHhHHHHcCceEEEEEEEE--ECCEEEEEEeCC-CHHHHHHHHHhh
Confidence            57777788764  4467899999999999998  479999999995 778777666654

>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=95.76  E-value=0.025  Score=38.71  Aligned_cols=69  Identities=13%  Similarity=0.037  Sum_probs=53.6

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      ...+.|.|++ +|+.+.-.+..++||.+|-.-|... .+.++...+|+  |.. .  +  .++.||.++|+.+ +.|++
T Consensus        15 ~~~i~v~V~~-~~k~~~i~v~~~~TV~~LK~~I~~~-tgvp~~~q~Li--~~g-~--l--~D~~tL~~~~I~~gs~i~l   84 (95)
T d1v86a_          15 KELVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSI-TGLPPAMQKVM--YKG-L--V--PEDKTLREIKVTSGAKIMV   84 (95)
T ss_dssp             CCCEEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHH-HCSCSTTCCCB--SSS-B--C--CSSSBHHHHCCCTTEEEEE
T ss_pred             ccEEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHH-hCCChhHEEEE--ecc-c--c--cCCCcHHHCCCCCCCEEEE
Confidence            4578888886 8889999999999999999999875 46667777786  433 2  4  4478999999994 55544

>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=95.68  E-value=0.041  Score=36.12  Aligned_cols=69  Identities=19%  Similarity=0.253  Sum_probs=51.9

Q ss_pred             CceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          169 LLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       169 ~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      ..++|+++- +|+.+.-+-..+++++.|.+.+.... +.+...++|+..  .+.  +  +.+.|++++|+.. ++|-+
T Consensus         3 ~~I~ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~-~i~~~~~~l~f~--G~~--l--~~~~T~~~~~i~dgd~I~v   72 (79)
T d1euvb_           3 THINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQ-GKEMDSLRFLYD--GIR--I--QADQTPEDLDMEDNDIIEA   72 (79)
T ss_dssp             SEEEEEEES-SSCEEEEEEETTSCTHHHHHHHHHHT-TCCGGGEEEEET--TEE--C--CTTCCTTTTTCCTTEEEEE
T ss_pred             cEEEEEECC-CCeEEEEEECCCCcHHHHHHHHHHHh-CCChHhEEEEEC--CEE--e--CCCCCHHHCCCCCCCEEEE
Confidence            356777775 67788888899999999999887764 556778888754  443  5  6688999999985 55443

>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=95.53  E-value=0.056  Score=34.89  Aligned_cols=70  Identities=17%  Similarity=0.211  Sum_probs=55.5

Q ss_pred             eEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCceEEEEe
Q 025774          171 CRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAMISVTW  247 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~v~v~~  247 (248)
                      ++|.++-.+|+.+..+-..+.+++.|++...... +.++..++|+.  -...  +  +.+.|.+++|+...-++-+|
T Consensus         2 I~lkv~~~~g~~v~f~vk~~t~l~kl~~~y~~~~-~~~~~~~~f~f--dG~~--i--~~~~Tp~~l~med~D~Idv~   71 (72)
T d1wm3a_           2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQ-GLSMRQIRFRF--DGQP--I--NETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHH-TCCTTTCEEEE--TTEE--C--CTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHh-CCCccceEEEE--CCEE--c--CCCCCHHHcCCCCCCEEEEE
Confidence            6789999999999999999999999999766654 44567777764  3443  4  56789999999977777666

>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=95.50  E-value=0.049  Score=35.56  Aligned_cols=68  Identities=22%  Similarity=0.270  Sum_probs=51.8

Q ss_pred             EEEEEcCCCce-EEE-eeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRR-MQR-NFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r-~~r-~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +|.||..+|++ ++- .-..++||.+|-.-+.... |.+....+|...  .+.  +  +.+.||.+.|+. +++|.+.
T Consensus         2 ~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~-gip~~~qrLi~~--Gk~--L--~d~~tL~~y~I~~~s~i~lv   72 (76)
T d1wy8a1           2 WIQVRTIDGSKTCTIEDVSRKATIEELRERVWALF-DVRPECQRLFYR--GKQ--L--ENGYTLFDYDVGLNDIIQLL   72 (76)
T ss_dssp             EEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHS-CCCTTTEEEEET--TEE--C--CSSSBHHHHTCCTTCEEEEE
T ss_pred             EEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHH-CCCchhcEEEEE--eeE--e--cCCCCHHHcCCCCCCEEEEE
Confidence            58899999963 443 5689999999999998764 677888999774  342  5  558999999998 4555543

>d1xfla_ c.47.1.1 (A:) Thioredoxin {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=95.49  E-value=0.031  Score=39.15  Aligned_cols=54  Identities=19%  Similarity=0.389  Sum_probs=41.7

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      +++|...|.+.  ...++..|++..+|++.++  .+|+.+.++.|. ++++|...|.+.
T Consensus        59 ~~~~~~vd~~~--~~~l~~~~~V~~~Pt~~~~--~~G~~v~~~~G~-~~~~l~~~i~k~  112 (114)
T d1xfla_          59 NVLFLKVDTDE--LKSVASDWAIQAMPTFMFL--KEGKILDKVVGA-KKDELQSTIAKH  112 (114)
T ss_dssp             SEEEEEEETTT--SHHHHHHTTCCSSSEEEEE--ETTEEEEEEESC-CHHHHHHHHHHH
T ss_pred             ccceeEEEeee--ceeeccccceeeeEEEEEE--ECCEEEEEEeCc-CHHHHHHHHHHh
Confidence            57777777654  4567899999999998888  579999999995 777776665544

>d1ep7a_ c.47.1.1 (A:) Thioredoxin {Chlamydomonas reinhardtii [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Chlamydomonas reinhardtii [TaxId: 3055]

Probab=95.46  E-value=0.033  Score=38.94  Aligned_cols=57  Identities=21%  Similarity=0.296  Sum_probs=42.9

Q ss_pred             HHHHHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHH
Q 025774           11 AVSQTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLE   72 (248)
Q Consensus        11 ~v~~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~   72 (248)
                      .+..-+..++.|...|++..  ..++..|++..+|++.++.  +|+.+.++.| .+.++|.+
T Consensus        48 ~l~~~~~~~v~~~~vd~d~~--~~l~~~~~v~~~Pt~~~~~--~G~~v~~~~G-~~~~~l~~  104 (112)
T d1ep7a_          48 TLSNDYAGKVIFLKVDVDAV--AAVAEAAGITAMPTFHVYK--DGVKADDLVG-ASQDKLKA  104 (112)
T ss_dssp             HHHHHTTTTSEEEEEETTTT--HHHHHHHTCCBSSEEEEEE--TTEEEEEEES-CCHHHHHH
T ss_pred             hhhhcccceEEEEEeecccc--ccccccccccCCCEEEEEE--CCEEEEEEeC-cCHHHHHH
Confidence            34444445688999998643  5788999999999988874  6999999999 46666533

>d1r26a_ c.47.1.1 (A:) Thioredoxin {Trypanosoma brucei [TaxId: 5691]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Trypanosoma brucei [TaxId: 5691]

Probab=95.40  E-value=0.047  Score=38.25  Aligned_cols=56  Identities=16%  Similarity=0.328  Sum_probs=45.8

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      +..|...|++.  ...++..|++.++|++.++  .+|..+.++.|. +++.+...|.+++.
T Consensus        57 ~v~~~~vd~d~--~~~l~~~~~V~~~Pt~~~~--~~G~~v~~~~G~-~~~~l~~~l~~~ik  112 (113)
T d1r26a_          57 TVKFAKVDADN--NSEIVSKCRVLQLPTFIIA--RSGKMLGHVIGA-NPGMLRQKLRDIIK  112 (113)
T ss_dssp             TSEEEEEETTT--CHHHHHHTTCCSSSEEEEE--ETTEEEEEEESS-CHHHHHHHHHHHHH
T ss_pred             ccccccccccc--chhhHHHccccCCCEEEEE--ECCEEEEEEeCC-CHHHHHHHHHHHhc
Confidence            66777788754  3468999999999999888  469999999995 68888888888764

>d1knga_ c.47.1.10 (A:) Thioredoxin-like protein CcmG (CycY, DsbE) {Bradyrhizobium japonicum [TaxId: 375]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Thioredoxin-like protein CcmG (CycY, DsbE)
species: Bradyrhizobium japonicum [TaxId: 375]

Probab=95.33  E-value=0.014  Score=42.59  Aligned_cols=46  Identities=22%  Similarity=0.412  Sum_probs=39.6

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhc
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDG   80 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~   80 (248)
                      .++..|++..+|+.+||++ .|.++.+..|.++.+++.+.|...++.
T Consensus        97 ~~~~~~~v~~~P~~~liD~-~G~i~~~~~G~~~~~~l~~~i~~~l~k  142 (144)
T d1knga_          97 RASIEWGVYGVPETFVVGR-EGTIVYKLVGPITPDNLRSVLLPQMEK  142 (144)
T ss_dssp             HHHHHTTCCSSCEEEEECT-TSBEEEEEESCCCHHHHHHTHHHHHHH
T ss_pred             hhhhhcCccccceEEEEcC-CCeEEEEEeCCCCHHHHHHHHHHHHHH
Confidence            5788899999999999995 599999999999999988877776653

>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=95.10  E-value=0.077  Score=35.45  Aligned_cols=60  Identities=17%  Similarity=0.201  Sum_probs=47.5

Q ss_pred             CCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcC-ceEEE
Q 025774          179 DGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLAN-AMISV  245 (248)
Q Consensus       179 ~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~-~~v~v  245 (248)
                      +|+.+.-....+++|.+|-.-|... .+.++....|...  .+.  +  +++.||++.|+.+ ++|.+
T Consensus        20 ~G~~~~l~v~~~~tV~~lK~~I~~~-~~ip~~~q~Li~~--Gk~--L--~D~~tL~dY~I~~gsti~l   80 (86)
T d1zkha1          20 NGQVLVFTLPLTDQVSVIKVKIHEA-TGMPAGKQKLQYE--GIF--I--KDSNSLAYYNMANGAVIHL   80 (86)
T ss_dssp             SSCEEEEEECTTSBHHHHHHHHHHH-TCCCTTTEEEEET--TEE--E--CTTSBHHHHTCCTTEEEEE
T ss_pred             CCeEEEEEECCCChHHHHHHHHHhh-hcCChHHEEEEeC--CcC--c--CCCCCHHHcCCCCCCEEEE
Confidence            6888888999999999999999886 4667888888764  332  5  4588999999985 55544

>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=95.07  E-value=0.024  Score=38.97  Aligned_cols=71  Identities=13%  Similarity=0.129  Sum_probs=55.4

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      ....+|.|+..+|+...-....+++|.+|-.-|... .+.++...+|+.  ..+.  +. |  .||.++|+. +.+|++.
T Consensus         5 s~~~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~-~gvp~~~QkLi~--~Gk~--L~-d--~tL~~~gi~~g~~i~lv   76 (96)
T d1wgga_           5 SSGYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFAL-TGVQPARQKVMV--KGGT--LK-D--DDWGNIKMKNGMTVLMM   76 (96)
T ss_dssp             CCEEEEEEEETTEEEEEEEEESSSCHHHHHHHHHHH-TCCCTTTSCCEE--TTEE--CC-S--SCCCSCCCCSSCEEECC
T ss_pred             CCceEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhh-cCccceeeEEee--cCcc--cC-C--CcHHHCCCCCCCEEEEE
Confidence            457889999999987788899999999999999875 466778888864  4553  63 3  389999998 5666653

>d2fy6a1 c.47.1.10 (A:33-175) Peptide methionine sulfoxide reductase MsrA/MsrB, N-terminal domain {Neisseria meningitidis serogroup A [TaxId: 65699]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Peptide methionine sulfoxide reductase MsrA/MsrB, N-terminal domain
species: Neisseria meningitidis serogroup A [TaxId: 65699]

Probab=94.88  E-value=0.026  Score=40.80  Aligned_cols=43  Identities=12%  Similarity=0.126  Sum_probs=36.9

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      .++..|++..+|+++||+ .+|.++.+..|.++.+++...|...
T Consensus        97 ~~~~~~~v~~~P~~~liD-~~G~i~~~~~G~~~~~~~~~~l~~~  139 (143)
T d2fy6a1          97 TIAQSLNISVYPSWALIG-KDGDVQRIVKGSINEAQALALIRDP  139 (143)
T ss_dssp             HHHHHTTCCSSSEEEEEC-TTSCEEEEEESCCCHHHHHHHHHCT
T ss_pred             HHHHHcCCCccCEEEEEC-CCCEEEEEEECCCCHHHHHHHHHHH
Confidence            578899999999999999 4699999999999998887666543

>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=94.79  E-value=0.046  Score=36.82  Aligned_cols=72  Identities=14%  Similarity=0.102  Sum_probs=52.6

Q ss_pred             CCceEEEEEcCCCceEEE-eeCCCCchHHHHHHHHhhcCCCCCcCeEEEcc-CCCCccccCCCcCCCccccCCc-CceEE
Q 025774          168 SLLCRVGVRLPDGRRMQR-NFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHA-IPGATKSLDYDSKLTFEDSGLA-NAMIS  244 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r-~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~-~Pr~~~~l~~d~~~tl~d~gl~-~~~v~  244 (248)
                      ....+|.|++.++ ++.- ....+++|.+|-.-|... .+.++...+|+.. |=.+  .+  +++.||.++|+. +++|+
T Consensus         5 s~~~~i~Vk~~~~-~~~i~~v~~~~tV~~LK~~i~~~-t~vp~~~QkLi~~~~~Gk--~L--~D~~tL~~~~i~~g~~i~   78 (90)
T d1v5ta_           5 SSGLPIIVKWGGQ-EYSVTTLSEDDTVLDLKQFLKTL-TGVLPERQKLLGLKVKGK--PA--ENDVKLGALKLKPNTKIM   78 (90)
T ss_dssp             CCSCCEEEEETTE-EEEECSCCSSSBHHHHHHHHHHH-TCCCTTTCEEESCEETTE--EC--CTTSBHHHHTCCTTEEEE
T ss_pred             CCcEEEEEEECCe-EEEEEEeCCCCcHHHHHHHHHHH-HcCCHHHhhhhhhccCCc--CC--CCcCcHHHcCCCCCCEEE
Confidence            4567899998554 4544 689999999999999875 4677888999753 2223  24  457899999999 45555


Q ss_pred             E
Q 025774          245 V  245 (248)
Q Consensus       245 v  245 (248)
                      +
T Consensus        79 l   79 (90)
T d1v5ta_          79 M   79 (90)
T ss_dssp             E
T ss_pred             E
Confidence            4

>d1xwaa_ c.47.1.1 (A:) Thioredoxin {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=94.60  E-value=0.11  Score=35.94  Aligned_cols=52  Identities=19%  Similarity=0.407  Sum_probs=38.8

Q ss_pred             hcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHH
Q 025774           17 STNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLED   73 (248)
Q Consensus        17 ~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~   73 (248)
                      .+.+.++..+.+..  ..+++.|++..+|++.++  .+|+.+.++.|. .++++.+.
T Consensus        55 ~~~~~~~~i~~d~~--~~l~~~~~V~~~Pt~~~~--~~G~~v~~~~G~-~~~~l~~~  106 (111)
T d1xwaa_          55 ADNVVVLKVDVDEC--EDIAMEYNISSMPTFVFL--KNGVKVEEFAGA-NAKRLEDV  106 (111)
T ss_dssp             TTTEEEEEEETTTC--HHHHHHTTCCSSSEEEEE--ETTEEEEEEESC-CHHHHHHH
T ss_pred             ccceEEEEEEeecC--cchhhcCCCccccEEEEE--ECCEEEEEEeCC-CHHHHHHH
Confidence            34577777777643  458899999999999888  469999999996 55555433

>d1jfua_ c.47.1.10 (A:) Membrane-anchored thioredoxin-like protein TlpA, soluble domain {Bradyrhizobium japonicum [TaxId: 375]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Membrane-anchored thioredoxin-like protein TlpA, soluble domain
species: Bradyrhizobium japonicum [TaxId: 375]

Probab=94.59  E-value=0.049  Score=40.96  Aligned_cols=67  Identities=13%  Similarity=0.109  Sum_probs=44.9

Q ss_pred             HHHHHHhhc-ceE--EEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCC--ChHHHHHHHhhh
Q 025774           10 EAVSQTIST-NFI--FWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMV--QPESLLEDLVPF   77 (248)
Q Consensus        10 ~~v~~~l~~-~fV--~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~--~~e~l~~~L~~~   77 (248)
                      +.+.+|+++ ++-  .+-.|....-+..+...|++..+|+.+||+ .+|.++.++.|.+  +.++++..|...
T Consensus       103 ~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~v~~~P~~~lID-~~G~I~~~~~G~~~~~~~e~~~~l~al  174 (176)
T d1jfua_         103 EKPKTFLKEANLTRLGYFNDQKAKVFQDLKAIGRALGMPTSVLVD-PQGCEIATIAGPAEWASEDALKLIRAA  174 (176)
T ss_dssp             THHHHHHHHTTCCTTCCEECTTCHHHHHHHTTTCCSSSSEEEEEC-TTSBEEEEEESCCCTTSHHHHHHHHHH
T ss_pred             hhhhhhHhhhCCcceeeeecchhHHHHHHhhhccCCCCCeEEEEc-CCCEEEEEEECCCCCChHHHHHHHHHh
Confidence            456666664 221  122233344556677788899999999999 5699999999976  446777766654

>d2b5xa1 c.47.1.10 (A:1-143) thiol:disulfide oxidoreductase YkuV {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: thiol:disulfide oxidoreductase YkuV
species: Bacillus subtilis [TaxId: 1423]

Probab=94.33  E-value=0.041  Score=39.92  Aligned_cols=42  Identities=19%  Similarity=0.184  Sum_probs=35.1

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      .++..|++..+|+++||++ +|.++.+..|..+.+.+...|.+
T Consensus       101 ~~~~~~~v~~~P~~~~id~-~G~i~~~~~G~~~~~~l~~~l~~  142 (143)
T d2b5xa1         101 ALTDAFENEYVPAYYVFDK-TGQLRHFQAGGSGMKMLEKRVNR  142 (143)
T ss_dssp             HHHHHTCCCCSSEEEEECT-TCBEEEEEESCSTTHHHHHHHHH
T ss_pred             chHHHcCCCcCCEEEEECC-CCEEEEEEECCCCHHHHHHHHHh
Confidence            4677899999999999995 59999999999888887766643

>d1st9a_ c.47.1.10 (A:) Thiol-disulfide oxidoreductase ResA {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Thiol-disulfide oxidoreductase ResA
species: Bacillus subtilis [TaxId: 1423]

Probab=94.09  E-value=0.044  Score=39.33  Aligned_cols=36  Identities=17%  Similarity=0.505  Sum_probs=31.3

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHH
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESL   70 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l   70 (248)
                      .++..|++..+|++.||++ +|.++.++.|.++.+.+
T Consensus        93 ~~~~~~~v~~~P~~~liD~-~G~i~~~~~G~~~~~~~  128 (137)
T d1st9a_          93 QVLDAYDVSPLPTTFLINP-EGKVVKVVTGTMTESMI  128 (137)
T ss_dssp             HHHHHTTCCSSCEEEEECT-TSEEEEEEESCCCHHHH
T ss_pred             hhhhhhhccccceEEEECC-CCEEEEEEECCCCHHHH
Confidence            5778889999999999995 59999999999987665

>d1ti3a_ c.47.1.1 (A:) Thioredoxin {European aspen (Populus tremula), thioredoxin H [TaxId: 113636]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: European aspen (Populus tremula), thioredoxin H [TaxId: 113636]

Probab=94.05  E-value=0.094  Score=36.41  Aligned_cols=53  Identities=19%  Similarity=0.327  Sum_probs=40.9

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      ++.|...|++.  ...++..|++..+|++.++.  +|+.+.++.| .++++|...|.+
T Consensus        57 ~~~~~~vd~d~--~~~l~~~~~I~~~Pt~~~~k--~G~~v~~~~G-~~~~~l~~~i~k  109 (113)
T d1ti3a_          57 NVTFLKVDVDE--LKAVAEEWNVEAMPTFIFLK--DGKLVDKTVG-ADKDGLPTLVAK  109 (113)
T ss_dssp             SEEEEEEETTT--CHHHHHHHHCSSTTEEEEEE--TTEEEEEEEC-CCTTHHHHHHHH
T ss_pred             CceEEeeeeec--cccccccCeecccceEEEEE--CCEEEEEEcC-CCHHHHHHHHHH
Confidence            67777777753  45688999999999999884  7999999999 477766554443

>d1syra_ c.47.1.1 (A:) Thioredoxin {Malarial parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin
species: Malarial parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=93.78  E-value=0.16  Score=34.45  Aligned_cols=62  Identities=19%  Similarity=0.252  Sum_probs=43.2

Q ss_pred             HHHHHhhc--ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           11 AVSQTIST--NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        11 ~v~~~l~~--~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      .+.++.++  +.+|...|++  +...++..|++..+|++.++  ++|..+.++.|. +.++    |.+++++|
T Consensus        39 ~~~~l~~~~~~~~~~~vd~d--~~~~~~~~~~V~~~Pt~i~~--k~G~~v~~~~G~-~~~~----l~~~i~k~  102 (103)
T d1syra_          39 FYEECSKTYTKMVFIKVDVD--EVSEVTEKENITSMPTFKVY--KNGSSVDTLLGA-NDSA----LKQLIEKY  102 (103)
T ss_dssp             HHHHHHHHCTTSEEEEEETT--TTHHHHHHTTCCSSSEEEEE--ETTEEEEEEESC-CHHH----HHHHHHTT
T ss_pred             cchhhhhcccceEEEeeccc--cCcceeeeeeeecceEEEEE--ECCEEEEEEeCc-CHHH----HHHHHHhh
Confidence            34444443  5667677775  33468899999999998888  469999999995 5554    45555543

>d1nhoa_ c.47.1.1 (A:) MTH807, thioredoxin/glutaredoxin-like protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: MTH807, thioredoxin/glutaredoxin-like protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=93.73  E-value=0.05  Score=35.87  Aligned_cols=57  Identities=16%  Similarity=0.232  Sum_probs=42.2

Q ss_pred             HHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhh
Q 025774           14 QTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFM   78 (248)
Q Consensus        14 ~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~   78 (248)
                      +-.+.++.+...|++  +...++..|++.++|++.+ .   |.  .+..|..+++.|.+.|.+.+
T Consensus        28 ~~~~~~v~~~~vd~d--~~~~l~~~~~V~~~Pt~~~-~---~~--~~~~G~~~~~~l~~~i~~~l   84 (85)
T d1nhoa_          28 KEFGDKIDVEKIDIM--VDREKAIEYGLMAVPAIAI-N---GV--VRFVGAPSREELFEAINDEM   84 (85)
T ss_dssp             HHHCSSCCEEEECTT--TCGGGGGGTCSSCSSEEEE-T---TT--EEEECSSCCHHHHHHHHHHC
T ss_pred             ccccccccccccccc--cchhhHHhcCceEeCEEEE-C---Cc--EEEEcCCCHHHHHHHHHHhh
Confidence            333456778777775  4556899999999999754 3   33  24679999999988887765

>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=93.35  E-value=0.23  Score=33.67  Aligned_cols=76  Identities=14%  Similarity=0.035  Sum_probs=54.9

Q ss_pred             CCceEEEEEcC-CCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEc-cCCCCc-cccCCCcCCCccccCCcC-ceE
Q 025774          168 SLLCRVGVRLP-DGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTH-AIPGAT-KSLDYDSKLTFEDSGLAN-AMI  243 (248)
Q Consensus       168 ~~~~~i~iRlp-~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~-~~Pr~~-~~l~~d~~~tl~d~gl~~-~~v  243 (248)
                      ...+.|-|.-+ ++....|||..+.||..|-.-+... .|.++..-+|.. .-+.+. ..+ .+++++|.+.|+.+ ..|
T Consensus         5 ss~v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~-tGip~~~qrL~~~~~~~~~~~~l-~~d~~~L~~y~i~dg~~i   82 (95)
T d1v6ea_           5 SSGVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELV-VGSPASCMELELYGADDKFYSKL-DQEDALLGSYPVDDGCRI   82 (95)
T ss_dssp             CCCEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHH-TCSCTTTCBCEEECSSSCEEEEC-CCSSSBTTSSSCCTTCEE
T ss_pred             CCcEEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHH-hCcCchhEEEEEeCCCCceeecc-cCCcCCHHHCCCCCCCEE
Confidence            34678889986 6667999999999999999999875 566677777654 211111 123 47799999999984 555


Q ss_pred             EE
Q 025774          244 SV  245 (248)
Q Consensus       244 ~v  245 (248)
                      .|
T Consensus        83 hl   84 (95)
T d1v6ea_          83 HV   84 (95)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>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=93.30  E-value=0.39  Score=32.00  Aligned_cols=77  Identities=12%  Similarity=0.083  Sum_probs=53.3

Q ss_pred             CceEEEEEcC-CCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCc-cccCCCcCCCccccCCc-CceEEE
Q 025774          169 LLCRVGVRLP-DGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGAT-KSLDYDSKLTFEDSGLA-NAMISV  245 (248)
Q Consensus       169 ~~~~i~iRlp-~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~-~~l~~d~~~tl~d~gl~-~~~v~v  245 (248)
                      +.+.|.|... .+..+.+||..+.||..|-.-+.... |.++..-+|..--.... .....+.++||.+.|+. +..|.|
T Consensus         3 ~~~~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~-Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihv   81 (90)
T d1t0ya_           3 EVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVV-GTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHA   81 (90)
T ss_dssp             CEEEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHH-CCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEE
T ss_pred             cEEEEEEEECCCccEEEEecCCCCCHHHHHHHHHHHH-CCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEE
Confidence            3567777763 35568999999999999999998754 66777777754211110 01224779999999998 455655


Q ss_pred             E
Q 025774          246 T  246 (248)
Q Consensus       246 ~  246 (248)
                      +
T Consensus        82 v   82 (90)
T d1t0ya_          82 V   82 (90)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=93.26  E-value=0.31  Score=32.76  Aligned_cols=66  Identities=17%  Similarity=0.012  Sum_probs=51.0

Q ss_pred             CCceEEEEEcCCCce--EEEeeCCCCchHHHHHHHHhhcC-CCCCcCeEEEccCCCCccccCCCcCCCccccCCc
Q 025774          168 SLLCRVGVRLPDGRR--MQRNFLRTDPIQLLWSYCYSQLE-GSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA  239 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r--~~r~F~~~~~l~~l~~fv~~~~~-~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~  239 (248)
                      ...++|.|+.|+++.  +.-....++||..|-+-|...+. ..++...+|+..  .+.  |  .++.||.|++..
T Consensus         5 s~~i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~--Gk~--L--~D~~~L~d~~~~   73 (93)
T d1wgda_           5 SSGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYS--GKL--L--LDHQCLRDLLPK   73 (93)
T ss_dssp             SCCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEET--TEE--C--CSSSCHHHHSCS
T ss_pred             CCcEEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEEC--CeE--c--cCCCCHHHhCcc
Confidence            346899999999876  55555789999999999988753 345788999875  342  5  568999999765

>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=93.23  E-value=0.089  Score=36.52  Aligned_cols=73  Identities=21%  Similarity=0.192  Sum_probs=54.5

Q ss_pred             CCceEEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCC--------------CCCcCeEEEccCCCCccccCCCcCCCc
Q 025774          168 SLLCRVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEG--------------SEMKPFRLTHAIPGATKSLDYDSKLTF  233 (248)
Q Consensus       168 ~~~~~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~--------------~~~~~f~L~~~~Pr~~~~l~~d~~~tl  233 (248)
                      +...+|.|+..||+.+.-.-..++||.+|-.-|.....-              +.+..|.|+..  .+.  |. |.+.||
T Consensus         5 ss~M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~--G~~--L~-d~~~tL   79 (105)
T d1v2ya_           5 SSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSA--GEK--LT-EDRKKL   79 (105)
T ss_dssp             CCSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESS--SCE--EC-CSSSBH
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEEC--CEE--Cc-ccCCCH
Confidence            456789999999999999999999999999998775310              01345778764  333  53 667899


Q ss_pred             cccCCc-CceEEE
Q 025774          234 EDSGLA-NAMISV  245 (248)
Q Consensus       234 ~d~gl~-~~~v~v  245 (248)
                      .+.|+. +++|.+
T Consensus        80 ~~~gI~~g~~l~l   92 (105)
T d1v2ya_          80 RDYGIRNRDEVSF   92 (105)
T ss_dssp             HHHTCCSSEEEEE
T ss_pred             HHcCCCCCCEEEE
Confidence            999998 566644

>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=92.88  E-value=0.33  Score=31.68  Aligned_cols=68  Identities=13%  Similarity=0.102  Sum_probs=50.0

Q ss_pred             eEEEEEcCCCceEEEee-----CCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEE
Q 025774          171 CRVGVRLPDGRRMQRNF-----LRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMIS  244 (248)
Q Consensus       171 ~~i~iRlp~G~r~~r~F-----~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~  244 (248)
                      .+|.|.. +|.+..-.+     +.++||.+|-.-+... .+.++....|...  .+.  + .+.+.||.++|+. ++.|+
T Consensus         2 i~i~V~~-~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~-tgvp~~~QkL~~~--G~~--L-~~d~~tL~~~gi~~g~~i~   74 (81)
T d1wxva1           2 LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEV-IGVPQSFQKLIFK--GKS--L-KEMETPLSALGIQDGCRVM   74 (81)
T ss_dssp             EEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHH-TCCCTTTCEEEET--TEE--E-CCSSSBHHHHTCCSSEEEE
T ss_pred             EEEEEEE-CCeeEEEEEecCCCCCccHHHHHHHHHHHH-HCcCHHHEEeeec--CeE--e-CcCCCChHHCCCCCCCEEE
Confidence            3566655 455666677     4688999999999886 4677888999753  443  5 3678999999998 56665


Q ss_pred             E
Q 025774          245 V  245 (248)
Q Consensus       245 v  245 (248)
                      +
T Consensus        75 l   75 (81)
T d1wxva1          75 L   75 (81)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=92.70  E-value=0.24  Score=34.02  Aligned_cols=65  Identities=12%  Similarity=0.111  Sum_probs=49.9

Q ss_pred             EcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          176 RLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       176 Rlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      |=-+|..+.-.-..+++|.+|-..|.... +.+....+|+.+  .+.  |. |.++||+++|+. ++.|++.
T Consensus        17 ~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~-gip~~~Q~Li~~--Gk~--L~-dd~~tL~~~gI~~g~~i~l~   82 (102)
T d1v5oa_          17 RDLTEVTFSLQVNPDFELSNFRVLCELES-GVPAEEAQIVYM--EQL--LT-DDHCSLGSYGLKDGDMVVLL   82 (102)
T ss_dssp             CCCCCCEEEEEECTTCBHHHHHHHHHHHT-CCCGGGBCEEET--TEE--EC-CSSSBHHHHTCCTTEEEEEC
T ss_pred             cCCCCCEEEEEECCcccHHHHHHHHHHHh-CCCcceEEEEeC--CeE--ee-cccCCHHHcCCCCCCEEEEE
Confidence            33458888888899999999999998764 667888888764  443  63 567899999998 5555553

>d1zmaa1 c.47.1.1 (A:1-115) Bacterocin transport accessory protein Bta {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Bacterocin transport accessory protein Bta
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=92.33  E-value=0.18  Score=34.97  Aligned_cols=41  Identities=10%  Similarity=0.150  Sum_probs=34.6

Q ss_pred             HHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHH
Q 025774           31 EGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLED   73 (248)
Q Consensus        31 eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~   73 (248)
                      +...++..|++.++|+++++.  +|..+.++.|..+.+++..-
T Consensus        72 ~~~~~~~~~~V~~~PTli~~~--~gk~~~~~~G~~~~~el~~f  112 (115)
T d1zmaa1          72 DLQAFRSRYGIPTVPGFVHIT--DGQINVRCDSSMSAQEIKDF  112 (115)
T ss_dssp             HHHHHHHHHTCCSSCEEEEEE--TTEEEEECCTTCCHHHHHHH
T ss_pred             cccccccccccccccEEEEEE--CCEEEEEEcCCCCHHHHHHH
Confidence            345789999999999999884  68899999999999888543

>d1hyua4 c.47.1.2 (A:103-198) Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: PDI-like
domain: Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=91.54  E-value=0.47  Score=31.69  Aligned_cols=50  Identities=14%  Similarity=0.159  Sum_probs=38.2

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLV   75 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~   75 (248)
                      .++-+...|.+.  -..++..|++.++|++++    +|+.+  ..|..+.++|+..|.
T Consensus        45 ~~i~~~~vd~~~--~~~l~~~~~I~~vPt~~~----ng~~~--~~G~~~~~~l~~~le   94 (96)
T d1hyua4          45 PRIKHTAIDGGT--FQNEITERNVMGVPAVFV----NGKEF--GQGRMTLTEIVAKVD   94 (96)
T ss_dssp             TTEEEEEEETTT--CHHHHHHTTCCSSSEEEE----TTEEE--EESCCCHHHHHHHHC
T ss_pred             CceEEEEEeccc--chHHHhhcccccccEEEE----CCEEE--EecCCCHHHHHHHHh
Confidence            367777777754  357889999999999854    57765  569999999988764

>d1a8ya1 c.47.1.3 (A:3-126) Calsequestrin {Rabbit (Oryctolagus cuniculus) [TaxId: 9986]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Calsequestrin
domain: Calsequestrin
species: Rabbit (Oryctolagus cuniculus) [TaxId: 9986]

Probab=91.49  E-value=0.53  Score=32.78  Aligned_cols=56  Identities=16%  Similarity=0.226  Sum_probs=44.5

Q ss_pred             ceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhh
Q 025774           19 NFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMD   79 (248)
Q Consensus        19 ~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~   79 (248)
                      .+.|-.+|.+...  .++..|++..||+|.++.  +|..+ ...|..+.+.|+.-|...++
T Consensus        67 ~v~~a~Vd~~~~~--~l~~~~~I~~yPTi~~f~--~g~~~-~y~G~r~~~~l~~fi~~~l~  122 (124)
T d1a8ya1          67 GVGFGLVDSEKDA--AVAKKLGLTEEDSIYVFK--EDEVI-EYDGEFSADTLVEFLLDVLE  122 (124)
T ss_dssp             TEEEEEEETTTSH--HHHHTTTCCSTTCEEEEE--SSSEE-ECCSCCSHHHHHHHHHHHHS
T ss_pred             CeEEEEEEeeccc--chhhccccccCCcEEEec--cCccE-EeeCCCCHHHHHHHHHHhcC
Confidence            4777788876443  578999999999998885  46654 58899999999888887765

>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=91.19  E-value=0.38  Score=31.21  Aligned_cols=63  Identities=19%  Similarity=0.229  Sum_probs=52.4

Q ss_pred             EEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCcCce
Q 025774          173 VGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLANAM  242 (248)
Q Consensus       173 i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~~~~  242 (248)
                      |-|=.|||.|.+-+...+.++.+|.+=+-.+. ++++..|.|...  ++  .+  |.+..+-=.||.|.+
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~-~~~~~~~~Lkh~--~k--~l--dLsl~~R~sgLpnna   65 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQ-DFNPSEYDLKFQ--RT--VL--DLSLQWRFANLPNNA   65 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHT-TCCGGGCEEEET--TE--EE--SSSCBHHHHCCCSSC
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHh-CCChhHceeeeC--CE--Ec--CccceeeecCCCCCC
Confidence            56678999999999999999999999876664 678999999885  33  25  889999999999654

>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=91.09  E-value=0.54  Score=31.56  Aligned_cols=72  Identities=18%  Similarity=0.153  Sum_probs=46.1

Q ss_pred             eEEEEEcCCCc-eEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEcc----CCCC-----ccccCCCcCCCccccCCcC
Q 025774          171 CRVGVRLPDGR-RMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHA----IPGA-----TKSLDYDSKLTFEDSGLAN  240 (248)
Q Consensus       171 ~~i~iRlp~G~-r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~----~Pr~-----~~~l~~d~~~tl~d~gl~~  240 (248)
                      +-||||.-||. |++-- +.+.||.+|-.-++..+. .+...-.|.++    .++.     .+....|...+|..+|+.+
T Consensus         1 ~iiRiRsrdG~eRv~v~-~~~~Tl~~LK~~Ie~~L~-VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~h   78 (94)
T d1wf9a1           1 TMLRVRSRDGLERVSVD-GPHITVSQLKTLIQDQLQ-IPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAH   78 (94)
T ss_dssp             EEEEEECSSCEEEEEEC-CTTSBHHHHHHHHHHHSC-CCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCT
T ss_pred             CeEEEEecCCceEEEec-CCCCcHHHHHHHHHHHhC-CCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccC
Confidence            35899999997 44431 346799999999999873 34444444332    0110     1222347789999999986


Q ss_pred             ceEE
Q 025774          241 AMIS  244 (248)
Q Consensus       241 ~~v~  244 (248)
                      ++++
T Consensus        79 Gsiv   82 (94)
T d1wf9a1          79 GSMV   82 (94)
T ss_dssp             TCEE
T ss_pred             ceEE
Confidence            6554

>d1sena_ c.47.1.1 (A:) Thioredoxin-like protein p19, TLP19 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: Thioredoxin-like protein p19, TLP19
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.53  E-value=0.06  Score=38.57  Aligned_cols=74  Identities=18%  Similarity=0.213  Sum_probs=50.9

Q ss_pred             cccCCCHHHHHHhhcceEEEEEecCChHHHHHHH-hcCCCCCceEEEEeCCCCceEEeeeC----------CCChHHHHH
Q 025774            4 RDTWANEAVSQTISTNFIFWQVYDDTSEGKKVCT-YYKLDSIPVVLVVDPITGQKMRSWCG----------MVQPESLLE   72 (248)
Q Consensus         4 r~vl~~~~v~~~l~~~fV~w~~d~~~~eg~~~~~-~~~~~~~P~l~ii~~~~g~~l~~~~G----------~~~~e~l~~   72 (248)
                      ..++.++.+.. ++.+||+...|.+....  .+. .+....+|++++++|. |..+..+.|          ..+.+.++.
T Consensus        45 ~~~~~~~~~~~-~~~~fv~v~vd~~~~~~--~~~~~~~~~~~Pt~~~~d~~-G~~~~~~~g~~~~~~~~~~~~~~~~~~~  120 (135)
T d1sena_          45 PKFAESTEISE-LSHNFVMVNLEDEEEPK--DEDFSPDGGYIPRILFLDPS-GKVHPEIINENGNPSYKYFYVSAEQVVQ  120 (135)
T ss_dssp             HHHHTCHHHHH-HHTTSEEEEEEGGGSCS--CGGGCTTCSCSSEEEEECTT-SCBCTTCCCTTSCTTSTTCCCSHHHHHH
T ss_pred             hhhhhhHHHHH-hcCCcEEEeCCCCcCHH--HHHHHhhcccceeEEEECCC-CeEEEEecCCCCCcchhccCCCHHHHHH
Confidence            34667778877 56899999998764322  122 2344568999999974 777666665          346788888


Q ss_pred             HHhhhhhcC
Q 025774           73 DLVPFMDGG   81 (248)
Q Consensus        73 ~L~~~~~~~   81 (248)
                      .+..+++..
T Consensus       121 ~~~~a~~~~  129 (135)
T d1sena_         121 GMKEAQERL  129 (135)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            888777653

>d1lu4a_ c.47.1.10 (A:) Soluble secreted antigen MPT53 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Soluble secreted antigen MPT53
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=90.49  E-value=0.19  Score=35.73  Aligned_cols=42  Identities=10%  Similarity=0.189  Sum_probs=33.3

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCce--EEeeeCCCChHHHHHHHhh
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQK--MRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~--l~~~~G~~~~e~l~~~L~~   76 (248)
                      .++..|++..+|+++||++ .|.+  +....|..+.+++..+|..
T Consensus        90 ~~~~~~~v~~~P~~~lid~-~G~i~~v~~~~g~~~~~~l~~~l~~  133 (134)
T d1lu4a_          90 VIWARYNVPWQPAFVFYRA-DGTSTFVNNPTAAMSQDELSGRVAA  133 (134)
T ss_dssp             HHHHHTTCCSSSEEEEECT-TSCEEEECCSSSCCCHHHHHHHHHH
T ss_pred             HHHHHcCCCcCCEEEEEeC-CCeEEEEeccCCCCCHHHHHHHHHc
Confidence            4788899999999999995 4765  3445677899999888764

>d1i5ga_ c.47.1.10 (A:) Tryparedoxin II {Crithidia fasciculata [TaxId: 5656]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Tryparedoxin II
species: Crithidia fasciculata [TaxId: 5656]

Probab=89.91  E-value=0.22  Score=36.09  Aligned_cols=26  Identities=23%  Similarity=0.387  Sum_probs=22.3

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEE
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMR   59 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~   59 (248)
                      .++..|++..+|+++||++.+|.++.
T Consensus        99 ~l~~~y~v~~iPt~~lid~~~G~vi~  124 (144)
T d1i5ga_          99 FLTTGFDVKSIPTLVGVEADSGNIIT  124 (144)
T ss_dssp             HHHHHTTCCSSSEEEEEETTTCCEEE
T ss_pred             HHHHHCCCCCcCEEEEEeCCCCEEEe
Confidence            57889999999999999987788754

>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=89.48  E-value=0.96  Score=30.42  Aligned_cols=68  Identities=18%  Similarity=0.209  Sum_probs=46.4

Q ss_pred             EEEEEcCCCceEEEeeCCCCchHHHHHHHHhhcCC-C-CCcCeEEEccCCCCccccCCCcCCCccccCCc-CceEEEE
Q 025774          172 RVGVRLPDGRRMQRNFLRTDPIQLLWSYCYSQLEG-S-EMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA-NAMISVT  246 (248)
Q Consensus       172 ~i~iRlp~G~r~~r~F~~~~~l~~l~~fv~~~~~~-~-~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~-~~~v~v~  246 (248)
                      +..|++|+++.-. .=..+.+|..|-+.+...+.. . ++..++|+..  .+.  +  +++.||.+.|+. +++|.++
T Consensus        20 k~~i~~p~~~~~~-~~~~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~--Gk~--L--~D~~tL~~y~I~~gstihLV   90 (94)
T d1x1ma1          20 KSILQLPETELGE-YSLGGYSISFLKQLIAGKLQESVPDPELIDLIYC--GRK--L--KDDQTLDFYGIQPGSTVHVL   90 (94)
T ss_dssp             CEEECCCCCSSCS-SCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEET--TEE--C--CTTCBHHHHTCCTTCEEEEE
T ss_pred             cceEECCCCccCc-cCCCccCHHHHHHHHHHHcccCCCChhheEEEEC--CeE--E--CCCccHHHcCCCCCCEEEEE
Confidence            4677888754211 124578999999999877542 1 3577888764  443  5  568999999998 5666543

>d1fo5a_ c.47.1.1 (A:) MJ0307, thioredoxin/glutaredoxin-like protein {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Thioltransferase
domain: MJ0307, thioredoxin/glutaredoxin-like protein
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=89.33  E-value=0.11  Score=33.90  Aligned_cols=52  Identities=12%  Similarity=0.141  Sum_probs=36.6

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPF   77 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~   77 (248)
                      ....+...+.+.  ...+++.|++.++|++.+ . .+|    .+.|..+.++|.+.|.+.
T Consensus        33 ~~~~~~~~~~d~--~~~la~~~~V~~~Pt~~i-~-~~g----~~~G~~~~~~l~~~i~~~   84 (85)
T d1fo5a_          33 DAVEVEYINVME--NPQKAMEYGIMAVPTIVI-N-GDV----EFIGAPTKEALVEAIKKR   84 (85)
T ss_dssp             SSEEEEEEESSS--SCCTTTSTTTCCSSEEEE-T-TEE----ECCSSSSSHHHHHHHHHH
T ss_pred             cccccccccccc--cccccccCCceEeeEEEE-E-CCc----EEECCCCHHHHHHHHHhc
Confidence            456666666643  345789999999999754 3 234    356988999988777654

>d1zzoa1 c.47.1.10 (A:45-178) Lipoprotein DsbF {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Lipoprotein DsbF
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=89.19  E-value=0.44  Score=33.42  Aligned_cols=41  Identities=20%  Similarity=0.331  Sum_probs=33.2

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhh
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~   76 (248)
                      .++..|++..+|+++||++ .|.+ ..+.|..+.+++...|..
T Consensus        92 ~~~~~~~v~~~P~~~iiD~-~G~i-~~~~g~~~~~~l~~~i~~  132 (134)
T d1zzoa1          92 SVWANFGVTQQPAYAFVDP-HGNV-DVVRGRMSQDELTRRVTA  132 (134)
T ss_dssp             HHHHHTTCCSSSEEEEECT-TCCE-EEEESCCCHHHHHHHHHH
T ss_pred             hHHHhcCCCccCeEEEECC-CCeE-EEEECCCCHHHHHHHHHh
Confidence            6788899999999999995 4775 447899999988777654

>d1o73a_ c.47.1.10 (A:) Tryparedoxin I {Trypanosoma brucei brucei [TaxId: 5702]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Tryparedoxin I
species: Trypanosoma brucei brucei [TaxId: 5702]

Probab=88.20  E-value=0.27  Score=35.29  Aligned_cols=27  Identities=19%  Similarity=0.466  Sum_probs=22.9

Q ss_pred             HHHHhcCCCCCceEEEEeCCCCceEEe
Q 025774           34 KVCTYYKLDSIPVVLVVDPITGQKMRS   60 (248)
Q Consensus        34 ~~~~~~~~~~~P~l~ii~~~~g~~l~~   60 (248)
                      .+++.|++..+|+++||++.+|.++..
T Consensus        99 ~l~~~y~v~~~Pt~~lID~~~G~Ii~~  125 (144)
T d1o73a_          99 ELGKTFGVESIPTLITINADTGAIIGT  125 (144)
T ss_dssp             HHHHHHTCCSSSEEEEEETTTCCEEES
T ss_pred             HHHHHcCCCcCCEEEEEECCCCEEEee
Confidence            577889999999999999877877653

>d1o8xa_ c.47.1.10 (A:) Tryparedoxin I {Crithidia fasciculata [TaxId: 5656]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Tryparedoxin I
species: Crithidia fasciculata [TaxId: 5656]

Probab=87.32  E-value=0.36  Score=34.36  Aligned_cols=28  Identities=25%  Similarity=0.477  Sum_probs=23.6

Q ss_pred             HHHHHHhcCCCCCceEEEEeCCCCceEE
Q 025774           32 GKKVCTYYKLDSIPVVLVVDPITGQKMR   59 (248)
Q Consensus        32 g~~~~~~~~~~~~P~l~ii~~~~g~~l~   59 (248)
                      ...+++.|++..+|++.||++.+|.++.
T Consensus        95 ~~~l~~~y~v~~~Pt~~liD~~~G~Vi~  122 (144)
T d1o8xa_          95 VQKLSKHFNVESIPTLIGVDADSGDVVT  122 (144)
T ss_dssp             HHHHHHHTTCCSSSEEEEEETTTCCEEE
T ss_pred             hhhHHHHcCCCcCCEEEEEeCCCCEEEE
Confidence            4578999999999999999987777653

>d2b5ea4 c.47.1.2 (A:23-141) Protein disulfide isomerase, PDI {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: PDI-like
domain: Protein disulfide isomerase, PDI
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.27  E-value=2.3  Score=28.99  Aligned_cols=55  Identities=11%  Similarity=0.218  Sum_probs=39.5

Q ss_pred             cceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceE--EeeeCCCChHHHHHHHhh
Q 025774           18 TNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKM--RSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        18 ~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l--~~~~G~~~~e~l~~~L~~   76 (248)
                      .++.|-..|++.  ...++..|++..||++.++  .+|...  ....|..+.++|+.-|.+
T Consensus        59 ~~v~~~~vd~~~--~~~l~~~~~v~~~Pti~~f--~~g~~~~~~~y~g~~~~~~l~~fi~k  115 (119)
T d2b5ea4          59 KNITLAQIDCTE--NQDLCMEHNIPGFPSLKIF--KNSDVNNSIDYEGPRTAEAIVQFMIK  115 (119)
T ss_dssp             TTCEEEEEETTT--CHHHHHHTTCCSSSEEEEE--ETTCTTCEEECCSCCSHHHHHHHHHH
T ss_pred             cceeeeeeeccc--hHHHHHHhccccCCeEEEE--ECCEEeeeEEecCCCCHHHHHHHHHH
Confidence            356666778764  3478999999999999888  346543  335688898888765554

>d1qgva_ c.47.1.8 (A:) spliceosomal protein U5-15Kd {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: spliceosomal protein U5-15Kd
domain: spliceosomal protein U5-15Kd
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.52  E-value=1.3  Score=31.72  Aligned_cols=62  Identities=6%  Similarity=0.031  Sum_probs=43.0

Q ss_pred             HHhhcceEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCceEEeee---------CCC-ChHHHHHHHhhhhh
Q 025774           14 QTISTNFIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQKMRSWC---------GMV-QPESLLEDLVPFMD   79 (248)
Q Consensus        14 ~~l~~~fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~l~~~~---------G~~-~~e~l~~~L~~~~~   79 (248)
                      +-+.+.++|..+|++...  .+++.|++.++|++.+.-  +|..+..-.         |.+ +.++|+..+.....
T Consensus        49 ~~~~~~v~~~~VDvd~~~--~la~~~~I~~~PT~~~f~--~g~~i~~~~g~~~~~k~~~~l~~~~~~i~~ie~i~~  120 (137)
T d1qgva_          49 EKVKNFAVIYLVDITEVP--DFNKMYELYDPCTVMFFF--RNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYR  120 (137)
T ss_dssp             HHHTTTEEEEEEETTTCC--TTTTSSCSCSSCEEEEEE--TTEEEEEECC------CCSCCSCHHHHHHHHHHHHH
T ss_pred             HHhhccceEEEeeccccc--hhhhhcCeeeEEEEEEEe--CCcEEEEEecCCCcceeeeehhhhHHHHHHHHHHHH
Confidence            334456889899996543  588999999999999984  477554333         333 66777777665544

>d1wp0a1 c.47.1.10 (A:138-297) Thioredoxin-like protein Sco1 (YpmQ), soluble domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Thioredoxin-like protein Sco1 (YpmQ), soluble domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.44  E-value=1.3  Score=31.29  Aligned_cols=37  Identities=8%  Similarity=0.183  Sum_probs=31.2

Q ss_pred             CceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           44 IPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        44 ~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      .+.++||+| .|.++..+.+..+++++...|.+.|..|
T Consensus       124 ~~~~~LId~-~G~i~~~~~~~~~~~~i~~~I~~~lk~~  160 (160)
T d1wp0a1         124 TIIMYLIGP-DGEFLDYFGQNKRKGEIAASIATHMRPY  160 (160)
T ss_dssp             CCEEEEECT-TSCEEEEEETTCCHHHHHHHHHHHHTTC
T ss_pred             cceEEEECC-CCcEEEEECCCCCHHHHHHHHHHHHhcC
Confidence            468899997 5999999988889999999998887654

>d1meka_ c.47.1.2 (A:) Protein disulfide isomerase, PDI {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: PDI-like
domain: Protein disulfide isomerase, PDI
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.19  E-value=0.55  Score=32.27  Aligned_cols=53  Identities=9%  Similarity=0.196  Sum_probs=36.1

Q ss_pred             eEEEEEecCChHHHHHHHhcCCCCCceEEEEeCCCCce--EEeeeCCCChHHHHHHHhh
Q 025774           20 FIFWQVYDDTSEGKKVCTYYKLDSIPVVLVVDPITGQK--MRSWCGMVQPESLLEDLVP   76 (248)
Q Consensus        20 fV~w~~d~~~~eg~~~~~~~~~~~~P~l~ii~~~~g~~--l~~~~G~~~~e~l~~~L~~   76 (248)
                      +++..+|.+..  ..++..|++..||++.++.  .|..  .....|..+.++|+.-|.+
T Consensus        60 v~~~~vd~~~~--~~l~~~~~i~~~Pt~~~~~--~G~~~~~~~~~g~~~~~~l~~fi~~  114 (120)
T d1meka_          60 IRLAKVDATEE--SDLAQQYGVRGYPTIKFFR--NGDTASPKEYTAGREADDIVNWLKK  114 (120)
T ss_dssp             CBCEEEETTTC--CSSHHHHTCCSSSEEEEEE--SSCSSSCEECCCCSSHHHHHHHHHT
T ss_pred             eeeeccccccc--hhHHHHhCCccCCeEEEEE--CCeEeeeEEecCCCCHHHHHHHHHH
Confidence            55566666432  3567789999999998885  3543  3457788888887555544

>d2b7ka1 c.47.1.10 (A:111-279) Thioredoxin-like protein Sco1 (YpmQ), soluble domain {Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: Glutathione peroxidase-like
domain: Thioredoxin-like protein Sco1 (YpmQ), soluble domain
species: Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.38  E-value=0.81  Score=32.43  Aligned_cols=40  Identities=15%  Similarity=0.226  Sum_probs=32.2

Q ss_pred             CCCCceEEEEeCCCCceEEeeeCCCChHHHHHHHhhhhhcC
Q 025774           41 LDSIPVVLVVDPITGQKMRSWCGMVQPESLLEDLVPFMDGG   81 (248)
Q Consensus        41 ~~~~P~l~ii~~~~g~~l~~~~G~~~~e~l~~~L~~~~~~~   81 (248)
                      +.+.|.++||+| .|.++.++.+..+++.+..+|.+.+...
T Consensus       127 i~h~~~~fLID~-~G~vv~~~~~~~~~~~~~~~I~e~ik~l  166 (169)
T d2b7ka1         127 VDHSIFFYLMDP-EGQFVDALGRNYDEKTGVDKIVEHVKSY  166 (169)
T ss_dssp             TTTCCCEEEECT-TSCEEEEECTTCCTTHHHHHHHHHHHHC
T ss_pred             eeccceEEEECC-CCeEEEEECCCCCHHHHHHHHHHHHHHH
Confidence            556799999996 5999999999899988777777666543

>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=80.20  E-value=4.4  Score=27.38  Aligned_cols=52  Identities=13%  Similarity=0.070  Sum_probs=41.2

Q ss_pred             ceEEEeeCCCCchHHHHHHHHhhcCCCCCcCeEEEccCCCCccccCCCcCCCccccCCc
Q 025774          181 RRMQRNFLRTDPIQLLWSYCYSQLEGSEMKPFRLTHAIPGATKSLDYDSKLTFEDSGLA  239 (248)
Q Consensus       181 ~r~~r~F~~~~~l~~l~~fv~~~~~~~~~~~f~L~~~~Pr~~~~l~~d~~~tl~d~gl~  239 (248)
                      +.+.-....+++|.+|-..|... .|.+....+|+..  ++.  |  ++++||.|.|+.
T Consensus        11 ~Ti~l~v~~~~TV~~lK~~I~~~-~gip~~~QrLi~~--Gk~--L--~D~~TL~dYgI~   62 (103)
T d2c9wb1          11 TTIFTDAKESSTVFELKRIVEGI-LKRPPDEQRLYKD--DQL--L--DDGKTLGECGFT   62 (103)
T ss_dssp             EEEEEEECTTSBHHHHHHHHHHH-HCCCGGGEEEEET--TEE--C--CTTSBHHHHTCC
T ss_pred             EEEEEEeCCCCcHHHHHHHHHHH-hCCCcccEEEEEC--CEE--c--CCCCCHHHcCCC
Confidence            35666778999999999999885 4667888999775  443  5  568999999995